The Human BioMolecular Atlas Program (HuBMAP)
The Human BioMolecular Atlas Program (HuBMAP)
Program Publications
Publications Search by Program
Search Result
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date | PubMedLink |
|---|---|---|---|---|---|---|
| Spatially Resolved Panoramic in vivo CRISPR Screen via Perturb-DBiT. | Fan R, Baysoy A, Tian X, Zhang F, Renauer P, Bai Z, Shi H, Zhang D, Li H, Tao B, Yang M, Enninful A, Gao F, Wang G, Zhang W, Tran T, Patterson N, Sheng J, Bao S, Dong C, Xin S, Chen B, Zhong M, Rankin S, Guy C, Wang Y, Connelly J, Pruett-Miller S, Wang D, Xu M, Gerstein M, Chi H, Chen S | Research square | 40386382 | Res Sq | 2025 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/40386382 |
| Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping. | Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R | Research square | 35378748 | Res Sq | 2022 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/35378748 |
| Spatial profiling of chromatin accessibility in mouse and human tissues. | Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R | Nature | 35978191 | Nature | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35978191 |
| Spatial multi-omics sequencing for fixed tissue via DBiT-seq. | Su G, Qin X, Enninful A, Bai Z, Deng Y, Liu Y, Fan R | STAR protocols | 34027489 | STAR Protoc | 2021 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/34027489 |
| High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq. | Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Nam J, Gao F, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R | Nature biotechnology | 36823353 | Nat Biotechnol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36823353 |
| Exploring endothelial cell environments across organs in spatially resolved omics data. | Jain Y, Jepson J, Chen R, Maier E, Herr BW 2nd, Puig-Barbe A, Quardokus EM, Qaurooni D, Yapp C, Ewing SL, Enninful A, Farzad N, Bueckle A, Easter QT, Matuck B, Zhu C, Monte EM, Purkerson JM, Jehrio M, Misra RS, Fan R, Ginty F, Karunamurthy A, Fan J, Campbell-Thompson M, Pryhuber GS, Byrd KM, Hickey JW, Börner K | bioRxiv : the preprint server for biology | 41040203 | bioRxiv | 2025 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/41040203 |
| Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping. | Zhang D, Rubio Rodríguez-Kirby LA, Lin Y, Song M, Wang L, Wang L, Kanatani S, Jimenez-Beristain T, Dang Y, Zhong M, Kukanja P, Wang S, Chen XL, Gao F, Wang D, Xu H, Lou X, Liu Y, Chen J, Sestan N, Uhlén P, Kriegstein A, Zhao H, Castelo-Branco G, Fan R | bioRxiv : the preprint server for biology | 39091821 | bioRxiv | 2024 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/39091821 |
| Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping. | Fan R, Zhang D, Rodríguez-Kirby L, Lin Y, Song M, Wang L, Wang L, Kanatani S, Jimenez-Beristain T, Dang Y, Zhong M, Kukanja P, Wang S, Chen X, Gao F, Wang D, Xu H, Lou X, Liu Y, Chen J, Sestan N, Uhlen P, Kriegstein AR, Zhao H, Castelo-Branco G | Research square | 39184075 | Res Sq | 2024 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/39184075 |
| Spatial dynamics of brain development and neuroinflammation. | Zhang D, Rubio Rodríguez-Kirby LA, Lin Y, Wang W, Song M, Wang L, Wang L, Kanatani S, Jimenez-Beristain T, Dang Y, Zhong M, Kukanja P, Bao S, Wang S, Chen XL, Gao F, Wang D, Xu H, Ma C, Lou X, Liu Y, Chen J, Sestan N, Uhlén P, Kriegstein A, Zhao H, Castelo-Branco G, Fan R | Nature | 41193846 | Nature | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/41193846 |
| Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus. | Enninful A, Zhang Z, Klymyshyn D, Zong H, Bai Z, Farzad N, Su G, Baysoy A, Nam J, Yang M, Lu Y, Zhang NR, Braubach O, Xu ML, Ma Z, Fan R | bioRxiv : the preprint server for biology | 39605581 | bioRxiv | 2024 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/39605581 |
| Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. | Deng Y, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Castelo-Branco G, Fan R | Science (New York, N.Y.) | 35143307 | Science | 2022 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/35143307 |
| The technological landscape and applications of single-cell multi-omics. | Baysoy A, Bai Z, Satija R, Fan R | Nature reviews. Molecular cell biology | 37280296 | Nat Rev Mol Cell Biol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37280296 |
| Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. | Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R | bioRxiv : the preprint server for biology | 38370833 | bioRxiv | 2024 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/38370833 |
| Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. | Farzad N, Enninful A, Bao S, Zhang D, Deng Y, Fan R | Nature protocols | 38943021 | Nat Protoc | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38943021 |
| Spatial epigenome-transcriptome co-profiling of mammalian tissues. | Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R | Nature | 36922587 | Nature | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36922587 |
| Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus. | Enninful A, Zhang Z, Klymyshyn D, Zong H, Bai Z, Farzad N, Su G, Baysoy A, Nam J, Yang M, Lu Y, Zhang NR, Braubach O, Xu ML, Ma Z, Fan R | Research square | 39711562 | Res Sq | 2024 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/39711562 |
| Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT. | Baysoy A, Tian X, Zhang F, Renauer P, Bai Z, Shi H, Li H, Tao B, Yang M, Enninful A, Gao F, Wang G, Zhang W, Tran T, Patterson NH, Bao S, Dong C, Xin S, Zhong M, Rankin S, Guy C, Wang Y, Connelly JP, Pruett-Miller SM, Chi H, Chen S, Fan R | bioRxiv : the preprint server for biology | 39605490 | bioRxiv | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39605490 |
| Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus. | Enninful A, Zhang Z, Klymyshyn D, Ingalls M, Yang M, Zong H, Bai Z, Farzad N, Su G, Baysoy A, Nam J, Lu Y, Bao S, Deng S, Zhang NR, Braubach O, Xu ML, Ma Z, Fan R | Nature methods | 41540123 | Nat Methods | 2026 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/41540123 |
| High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. | Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R | Cell | 33188776 | Cell | 2020 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/33188776 |
| Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. | Bai Z, Zhang D, Gao Y, Tao B, Zhang D, Bao S, Enninful A, Wang Y, Li H, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R | Cell | 39353436 | Cell | 2024 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/39353436 |
| A Novel Targeted Long-read Sequencing Approach Boosts Transcriptomic Profiling. | Tian X, Fan R | Genomics, proteomics & bioinformatics | 39724297 | Genomics Proteomics Bioinformatics | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39724297 |
| Spatially resolved m(6)A profiling using m(6)A-ARTR-DBiT. | Xiao Y, Bai Z, Zou Z, Ye C, Tao B, Zheng Z, Chen YM, Zou Z, Jiang L, Zhao L, Fan Y, Gao Y, Fan R, He C | Nature methods | 42265211 | Nat Methods | 2026 Jul | https://www.ncbi.nlm.nih.gov/pubmed/42265211 |
| Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT. | Baysoy A, Tian X, Renauer P, Zhang F, Bai Z, Shi H, Yang M, Zhang D, Liu M, Li H, Tao B, Enninful A, Lu Y, Gao F, Wang G, Zhang W, Tran T, Patterson NH, Sheng J, Bao S, Dong C, Xin S, Chen B, Zhong M, Rankin S, Guy C, Wang Y, Connelly JP, Pruett-Miller SM, Wang D, Xu M, Gerstein MB, Chi H, Chen S, Fan R | Nature biotechnology | 42277225 | Nat Biotechnol | 2026 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/42277225 |
| Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. | Ramos EK, Tsai CF, Jia Y, Cao Y, Manu M, Taftaf R, Hoffmann AD, El-Shennawy L, Gritsenko MA, Adorno-Cruz V, Schuster EJ, Scholten D, Patel D, Liu X, Patel P, Wray B, Zhang Y, Zhang S, Moore RJ, Mathews JV, Schipma MJ, Liu T, Tokars VL, Cristofanilli M, Shi T, Shen Y, Dashzeveg NK, Liu H | eLife | 36193887 | Elife | 2022 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/36193887 |
| A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics. | Tsai CF, Wang YT, Hsu CC, Kitata RB, Chu RK, Velickovic M, Zhao R, Williams SM, Chrisler WB, Jorgensen ML, Moore RJ, Zhu Y, Rodland KD, Smith RD, Wasserfall CH, Shi T, Liu T | Communications biology | 36653408 | Commun Biol | 2023 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/36653408 |
| Robust collection and processing for label-free single voxel proteomics. | Kitata RB, Velickovic M, Xu Z, Zhao R, Scholten D, Chu RK, Orton DJ, Chrisler WB, Mathews JV, Piehowski PD, Liu T, Smith RD, Liu H, Wasserfall CH, Tsai CF, Shi T | bioRxiv : the preprint server for biology | 37645907 | bioRxiv | 2023 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/37645907 |
| Integrated antibody language model accelerates IgG screening and design for broad-spectrum antiviral therapy. | Almubarak HF, Tan W, Hoffmann AD, Sun Y, Wei J, El-Shennawy L, Squires JR, Dashzeveg NK, Simonton B, Jia Y, Iyer R, Xu Y, Nicolaescu V, Elli D, Randall GC, Schipma MJ, Swaminathan S, Ison MG, Liu H, Fang D, Shen Y | iScience | 41126882 | iScience | 2025 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/41126882 |
| Double-positive T cells form heterotypic clusters with circulating tumor cells to foster cancer metastasis. | Scholten D, El-Shennawy L, Jia Y, Zhang Y, Hyun E, Reduzzi C, Hoffmann AD, Almubarak HF, Tong F, Dashzeveg NK, Sun Y, Squires JR, Lu J, Platanias LC, Wasserfall CH, Gradishar WJ, Cristofanilli M, Fang D, Liu H | The Journal of clinical investigation | 40955669 | J Clin Invest | 2025 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/40955669 |
| Succinate drives gut inflammation by promoting FOXP3 degradation through a molecular switch. | Wang H, Hu D, Cheng Y, Gao Q, Liu K, Mani NL, Tang AY, Iyer R, Gao B, Sun L, Zhou Q, Yu Q, Weinberg SE, Zhang X, Cong Y, Dulai PS, Zhang Y, Liu Z, Fang D | Nature immunology | 40457062 | Nat Immunol | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40457062 |
| Ubiquitin-specific peptidase 22 controls integrin-dependent cancer cell stemness and metastasis. | Liu K, Gao Q, Jia Y, Wei J, Chaudhuri SM, Wang S, Tang A, Mani NL, Iyer R, Cheng Y, Gao B, Lu W, Sun Z, Zhang B, Liu H, Fang D | iScience | 39246448 | iScience | 2024 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/39246448 |
| Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer. | Min S, Kwantwi-Barima P, Attah IK, Fillmore TL, Gaffrey MJ, Kitata RB, Ibrahim YM, Shi T | Analytical chemistry | 41926161 | Anal Chem | 2026 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/41926161 |
| Computational ranking identifies Plexin-B2 in circulating tumor cell clustering with monocytes in breast cancer metastasis. | Schuster E, Dashzeveg NK, Tong F, Jia Y, El-Shennawy L, Zhang T, Hoffman AD, Kitata RB, Kibria G, Zhang Y, Squires JR, Zheng C, Ramos E, Taftaf R, Scholten D, Almubarak HF, Adorno-Cruz V, Sullivan DP, Reduzzi C, Minor AC, Purev-Ochir W, Spahija S, Xu R, Siziopikou KP, Platanias LC, Shah A, Muller WA, Gradishar WJ, Cristofanilli M, Tsai CF, Shi T, Liu H | Nature communications | 40818975 | Nat Commun | 2025 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/40818975 |
| Dynamic Glycoprotein Hyposialylation Promotes Chemotherapy Evasion and Metastatic Seeding of Quiescent Circulating Tumor Cell Clusters in Breast Cancer. | Dashzeveg NK, Jia Y, Zhang Y, Gerratana L, Patel P, Shajahan A, Dandar T, Ramos EK, Almubarak HF, Adorno-Cruz V, Taftaf R, Schuster EJ, Scholten D, Sokolowski MT, Reduzzi C, El-Shennawy L, Hoffmann AD, Manai M, Zhang Q, D'Amico P, Azadi P, Colley KJ, Platanias LC, Shah AN, Gradishar WJ, Cristofanilli M, Muller WA, Cobb BA, Liu H | Cancer discovery | 37272843 | Cancer Discov | 2023 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/37272843 |
| Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). | Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, HuBMAP Consortium, Börner K, Snyder MP | Nature cell biology | 37468756 | Nat Cell Biol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37468756 |
| Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells. | Martin K, Zhang T, Lin TT, Habowski AN, Zhao R, Tsai CF, Chrisler WB, Sontag RL, Orton DJ, Lu YJ, Rodland KD, Yang B, Liu T, Smith RD, Qian WJ, Waterman ML, Wiley HS, Shi T | Journal of proteome research | 34351778 | J Proteome Res | 2021 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/34351778 |
| Ductal Carcinoma In Situ of Breast: From Molecular Etiology to Therapeutic Management. | Hophan SL, Odnokoz O, Liu H, Luo Y, Khan S, Gradishar W, Zhou Z, Badve S, Torres MA, Wan Y | Endocrinology | 35245349 | Endocrinology | 2022 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/35245349 |
| Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics. | Tsai CF, Zhang P, Scholten D, Martin K, Wang YT, Zhao R, Chrisler WB, Patel DB, Dou M, Jia Y, Reduzzi C, Liu X, Moore RJ, Burnum-Johnson KE, Lin MH, Hsu CC, Jacobs JM, Kagan J, Srivastava S, Rodland KD, Steven Wiley H, Qian WJ, Smith RD, Zhu Y, Cristofanilli M, Liu T, Liu H, Shi T | Communications biology | 33649493 | Commun Biol | 2021 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/33649493 |
| Robust collection and processing for label-free single voxel proteomics. | Kitata RB, Velickovic M, Xu Z, Zhao R, Scholten D, Chu RK, Orton DJ, Chrisler WB, Zhang T, Mathews JV, Bumgarner BM, Gursel DB, Moore RJ, Piehowski PD, Liu T, Smith RD, Liu H, Wasserfall CH, Tsai CF, Shi T | Nature communications | 39805815 | Nat Commun | 2025 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/39805815 |
| Robust Surfactant-Assisted One-Pot Sample Preparation for Label-Free Single-Cell and Nanoscale Proteomics. | Xu Z, Zou R, Horn NC, Kitata RB, Shi T | Methods in molecular biology (Clifton, N.J.) | 38907149 | Methods Mol Biol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38907149 |
| Mass spectrometry-based targeted proteomics for analysis of protein mutations. | Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T | Mass spectrometry reviews | 34719806 | Mass Spectrom Rev | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34719806 |
| Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells. | Martin K, Zhang T, Zhang P, Chrisler WB, Thomas FL, Liu F, Liu T, Qian WJ, Smith RD, Shi T | Journal of visualized experiments : JoVE | 33226031 | J Vis Exp | 2020 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/33226031 |
| Ubiquitin-specific peptidase 22 controls integrin-dependent cancer cell stemness and metastasis. | Liu K, Gao Q, Jia Y, Wei J, Chaudhuri S, Wang S, Tang A, Mani N, Iyer R, Cheng Y, Gao B, Lu W, Sun Z, Liu H, Fang D | Research square | 37398311 | Res Sq | 2023 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/37398311 |
| USP22 drives tumor immune evasion and checkpoint blockade resistance through EZH2-mediated epigenetic silencing of MHC-I. | Liu K, Iyer R, Li Y, Zhu J, Cai Z, Wei J, Cheng Y, Tang AY, Wang H, Gao Q, Mani NL, Marx N, Gao B, Watterson DM, Khan SA, Gradishar WJ, Liu H, Fang D | The Journal of clinical investigation | 41252204 | J Clin Invest | 2026 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/41252204 |
| Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications. | Stockwell BR | Cell | 35803244 | Cell | 2022 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/35803244 |
| Multiomics Imaging Using High-Energy Water Gas Cluster Ion Beam Secondary Ion Mass Spectrometry [(H(2)O)(n)-GCIB-SIMS] of Frozen-Hydrated Cells and Tissue. | Tian H, Sheraz Née Rabbani S, Vickerman JC, Winograd N | Analytical chemistry | 34038090 | Anal Chem | 2021 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/34038090 |
| Multimodal mass spectrometry imaging identifies cell-type-specific metabolic and lipidomic variation in the mammalian liver. | Tian H, Rajbhandari P, Tarolli J, Decker AM, Neelakantan TV, Angerer T, Zandkarimi F, Remotti H, Frache G, Winograd N, Stockwell BR | Developmental cell | 38359832 | Dev Cell | 2024 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/38359832 |
| Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging. | Quardokus EM, Saunders DC, McDonough E, Hickey JW, Werlein C, Surrette C, Rajbhandari P, Casals AM, Tian H, Lowery L, Neumann EK, Björklund F, Neelakantan TV, Croteau J, Wiblin AE, Fisher J, Livengood AJ, Dowell KG, Silverstein JC, Spraggins JM, Pryhuber GS, Deutsch G, Ginty F, Nolan GP, Melov S, Jonigk D, Caldwell MA, Vlachos IS, Muller W, Gehlenborg N, Stockwell BR, Lundberg E, Snyder MP, Germain RN, Camarillo JM, Kelleher NL, Börner K, Radtke AJ | Nature methods | 37468619 | Nat Methods | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37468619 |
| Successive High-Resolution (H(2)O)(n)-GCIB and C(60)-SIMS Imaging Integrates Multi-Omics in Different Cell Types in Breast Cancer Tissue. | Tian H, Sparvero LJ, Anthonymuthu TS, Sun WY, Amoscato AA, He RR, Bayır H, Kagan VE, Winograd N | Analytical chemistry | 34075742 | Anal Chem | 2021 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/34075742 |
| Machine Learning Classifies Ferroptosis and Apoptosis Cell Death Modalities with TfR1 Immunostaining. | Jin J, Schorpp K, Samaga D, Unger K, Hadian K, Stockwell BR | ACS chemical biology | 35230809 | ACS Chem Biol | 2022 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/35230809 |
| Spatial pharmacology using mass spectrometry imaging. | Rajbhandari P, Neelakantan TV, Hosny N, Stockwell BR | Trends in pharmacological sciences | 38103980 | Trends Pharmacol Sci | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38103980 |
| Anatomical structures, cell types and biomarkers of the Human Reference Atlas. | Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW 2nd, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G | Nature cell biology | 34750582 | Nat Cell Biol | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34750582 |
| Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models. | Tang X, Luo Y, Yuan D, Calandrelli R, Malhi NK, Sriram K, Miao Y, Lou CH, Tsark W, Tapia A, Chen AT, Zhang G, Roeth D, Kalkum M, Wang ZV, Chien S, Natarajan R, Cooke JP, Zhong S, Chen ZB | The Journal of clinical investigation | 36512424 | J Clin Invest | 2023 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/36512424 |
| Single-cell multiplex chromatin and RNA interactions in ageing human brain. | Wen X, Luo Z, Zhao W, Calandrelli R, Nguyen TC, Wan X, Charles Richard JL, Zhong S | Nature | 38538789 | Nature | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38538789 |
| Genome-wide mapping of RNA-protein associations through sequencing. | Qi Z, Xue S, Chen J, Zhao W, Johnson K, Wen X, Charles Richard JL, Lin P, Zhong S | Nature biotechnology | 40925998 | Nat Biotechnol | 2026 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40925998 |
| Genome-Wide Mapping of RNA-Protein Associations via Sequencing. | Qi Z, Xue S, Chen J, Zhao W, Johnson K, Wen X, Richard JLC, Zhong S | bioRxiv : the preprint server for biology | 39282297 | bioRxiv | 2024 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/39282297 |
| PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. | Chen X, Calandrelli R, Girardini J, Yan Z, Tan Z, Xu X, Hiniker A, Zhong S | Cell metabolism | 35508105 | Cell Metab | 2022 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/35508105 |
| Modeling blood-brain barrier formation and cerebral cavernous malformations in human PSC-derived organoids. | Dao L, You Z, Lu L, Xu T, Sarkar AK, Zhu H, Liu M, Calandrelli R, Yoshida G, Lin P, Miao Y, Mierke S, Kalva S, Zhu H, Gu M, Vadivelu S, Zhong S, Huang LF, Guo Z | Cell stem cell | 38754427 | Cell Stem Cell | 2024 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/38754427 |
| Single-cell multiplex chromatin and RNA interactions in aging human brain. | Wen X, Luo Z, Zhao W, Calandrelli R, Nguyen TC, Wan X, Richard JLC, Zhong S | bioRxiv : the preprint server for biology | 37425846 | bioRxiv | 2024 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/37425846 |
| Transcriptional regulation by PHGDH drives amyloid pathology in Alzheimer's disease. | Chen J, Hadi F, Wen X, Zhao W, Xu M, Xue S, Lin P, Calandrelli R, Richard JLC, Song Z, Li J, Amani A, Liu Y, Chen X, Zhong S | Cell | 40273909 | Cell | 2025 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/40273909 |
| Spatial top-down proteomics for the functional characterization of human kidney. | Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Veličković M, Williams SM, Moore RJ, Bramer LM, Veličković D, Zhu Y, Zhou M, Paša-Tolić L | Clinical proteomics | 40045235 | Clin Proteomics | 2025 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/40045235 |
| Spatial Proteomics towards cellular Resolution. | Kwon Y, Fulcher JM, Paša-Tolić L, Qian WJ | Expert review of proteomics | 39710940 | Expert Rev Proteomics | 2024 Dec 25 | https://www.ncbi.nlm.nih.gov/pubmed/39710940 |
| Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting. | Fulcher JM, Markillie LM, Mitchell HD, Williams SM, Engbrecht KM, Degnan DJ, Bramer LM, Moore RJ, Chrisler WB, Cantlon-Bruce J, Bagnoli JW, Qian WJ, Seth A, Paša-Tolić L, Zhu Y | Nature communications | 39638780 | Nat Commun | 2024 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/39638780 |
| Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection. | Zemaitis KJ, Veličković D, Kew W, Fort KL, Reinhardt-Szyba M, Pamreddy A, Ding Y, Kaushik D, Sharma K, Makarov AA, Zhou M, Paša-Tolić L | Analytical chemistry | 36067026 | Anal Chem | 2022 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/36067026 |
| Top-down proteomics. | Roberts DS, Loo JA, Tsybin YO, Liu X, Wu S, Chamot-Rooke J, Agar JN, Paša-Tolić L, Smith LM, Ge Y | Nature reviews. Methods primers | 39006170 | Nat Rev Methods Primers | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39006170 |
| 193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI. | Zemaitis KJ, Zhou M, Kew W, Paša-Tolić L | Journal of the American Society for Mass Spectrometry | 36622763 | J Am Soc Mass Spectrom | 2023 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/36622763 |
| Properties, Origin, and Consistency of Truncated Proteoforms Across Top-Down Proteomic Studies. | Kaulich PT, Fulcher JM, Tholey A | Molecular & cellular proteomics : MCP | 41237901 | Mol Cell Proteomics | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41237901 |
| Challenges in Spatial Metabolomics and Proteomics for Functional Tissue Unit and Single-Cell Resolution. | Zemaitis KJ, Paša-Tolić L | Seminars in nephrology | 40263091 | Semin Nephrol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40263091 |
| IsoMatchMS: Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra. | Degnan DJ, Zemaitis KJ, Lewis LA, McCue LA, Bramer LM, Fulcher JM, Veličković D, Paša-Tolić L, Zhou M | Journal of the American Society for Mass Spectrometry | 37523489 | J Am Soc Mass Spectrom | 2023 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/37523489 |
| Advances in mass spectrometry-enabled multiomics at single-cell resolution. | Kumar R, Zemaitis KJ, Fulcher JM, Paša-Tolić L | Current opinion in biotechnology | 38432187 | Curr Opin Biotechnol | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38432187 |
| Spatial top-down proteomics for the functional characterization of human kidney. | Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Veličković M, Williams SM, Moore RJ, Bramer LM, Veličković D, Zhu Y, Zhou M, Paša-Tolić L | bioRxiv : the preprint server for biology | 38405958 | bioRxiv | 2024 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/38405958 |
| Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform. | Liao YC, Fulcher JM, Degnan DJ, Williams SM, Bramer LM, Veličković D, Zemaitis KJ, Veličković M, Sontag RL, Moore RJ, Paša-Tolić L, Zhu Y, Zhou M | Molecular & cellular proteomics : MCP | 36603806 | Mol Cell Proteomics | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36603806 |
| Advances in Proximity Ligation in situ Hybridization (PLISH). | Nagendran M, Andruska AM, Harbury PB, Desai TJ | Bio-protocol | 33659462 | Bio Protoc | 2020 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/33659462 |
| KRAS(G12D) drives lepidic adenocarcinoma through stem-cell reprogramming. | Juul NH, Yoon JK, Martinez MC, Rishi N, Kazadaeva YI, Morri M, Neff NF, Trope WL, Shrager JB, Sinha R, Desai TJ | Nature | 37468622 | Nature | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37468622 |
| Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. | Salahudeen AA, Choi SS, Rustagi A, Zhu J, van Unen V, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ | Nature | 33238290 | Nature | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33238290 |
| Advances in spatial transcriptomic data analysis. | Dries R, Chen J, Del Rossi N, Khan MM, Sistig A, Yuan GC | Genome research | 34599004 | Genome Res | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34599004 |
| Giotto: a toolbox for integrative analysis and visualization of spatial expression data. | Dries R, Zhu Q, Dong R, Eng CL, Li H, Liu K, Fu Y, Zhao T, Sarkar A, Bao F, George RE, Pierson N, Cai L, Yuan GC | Genome biology | 33685491 | Genome Biol | 2021 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/33685491 |
| Analyzing Spatial Transcriptomics Data Using Giotto. | Del Rossi N, Chen JG, Yuan GC, Dries R | Current protocols | 35384407 | Curr Protoc | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35384407 |
| Community-wide hackathons to identify central themes in single-cell multi-omics. | Lê Cao KA, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Righelli D, Singh A, Sodicoff JS, Stein-O'Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan GC, Culhane AC, Fertig E | Genome biology | 34353350 | Genome Biol | 2021 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/34353350 |
| Signal amplification by cyclic extension enables high-sensitivity single-cell mass cytometry. | Lun XK, Sheng K, Yu X, Lam CY, Gowri G, Serrata M, Zhai Y, Su H, Luan J, Kim Y, Ingber DE, Jackson HW, Yaffe MB, Yin P | Nature biotechnology | 39075149 | Nat Biotechnol | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39075149 |
| Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels. | Hong F, Kishi JY, Delgado RN, Jeong J, Saka SK, Su H, Cepko CL, Yin P | Nature methods | 38151595 | Nat Methods | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38151595 |
| Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. | Kishi JY, Liu N, West ER, Sheng K, Jordanides JJ, Serrata M, Cepko CL, Saka SK, Yin P | Nature methods | 36216958 | Nat Methods | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36216958 |
| Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. | Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK | Nature methods | 34811556 | Nat Methods | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34811556 |
| Application of Delta T1 maps for quantitative and objective assessment of extent of resection and survival prediction in glioblastoma. | Laing BR, Prah MA, Best BJ, Krucoff MO, Mueller WM, Schmainda KM | Neurosurgery practice | 38919518 | Neurosurg Pract | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38919518 |
| Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution. | Piehowski PD, Zhu Y, Bramer LM, Stratton KG, Zhao R, Orton DJ, Moore RJ, Yuan J, Mitchell HD, Gao Y, Webb-Robertson BM, Dey SK, Kelly RT, Burnum-Johnson KE | Nature communications | 31911630 | Nat Commun | 2020 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/31911630 |
| Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation. | Schachner LF, Soye BD, Ro S, Kenney GE, Ives AN, Su T, Goo YA, Jewett MC, Rosenzweig AC, Kelleher NL | ACS chemical biology | 35951581 | ACS Chem Biol | 2022 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/35951581 |
| Spatial Segmentation of Mass Spectrometry Imaging Data by Combining Multivariate Clustering and Univariate Thresholding. | Hu H, Yin R, Brown HM, Laskin J | Analytical chemistry | 33570915 | Anal Chem | 2021 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/33570915 |
| Hardware and software solutions for implementing nanospray desorption electrospray ionization (nano-DESI) sources on commercial mass spectrometers. | Jiang LX, Hilger RT, Laskin J | Journal of mass spectrometry : JMS | 38866597 | J Mass Spectrom | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38866597 |
| Quantitative Mass Spectrometry Imaging of Intact Proteins in Tissues. | Iqfath M, Swansiger AK, Yang M, Miller L, Moore AM, Hernly E, Bai Y, Zhang ZY, Prell JS, Laskin J | Analytical chemistry | 41538409 | Anal Chem | 2026 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/41538409 |
| High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry. | Yin R, Burnum-Johnson KE, Sun X, Dey SK, Laskin J | Nature protocols | 31723300 | Nat Protoc | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31723300 |
| Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. | Yang M, Unsihuay D, Hu H, Nguele Meke F, Qu Z, Zhang ZY, Laskin J | Analytical chemistry | 36917636 | Anal Chem | 2023 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/36917636 |
| Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. | Yang M, Hu H, Su P, Thomas PM, Camarillo JM, Greer JB, Early BP, Fellers RT, Kelleher NL, Laskin J | Angewandte Chemie (International ed. in English) | 35446460 | Angew Chem Int Ed Engl | 2022 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/35446460 |
| Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment. | Veličković M, Fillmore TL, Attah IK, Posso C, Pino JC, Zhao R, Williams SM, Veličković D, Jacobs JM, Burnum-Johnson KE, Zhu Y, Piehowski PD | Analytical chemistry | 39089681 | Anal Chem | 2024 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/39089681 |
| MSIGen: An Open-Source Python Package for Processing and Visualizing Mass Spectrometry Imaging Data. | Hernly E, Hu H, Laskin J | Journal of the American Society for Mass Spectrometry | 39221961 | J Am Soc Mass Spectrom | 2024 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/39221961 |
| Proteome Landscapes of Human Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma. | Yi X, Zhu J, Liu W, Peng L, Lu C, Sun P, Huang L, Nie X, Huang S, Guo T, Zhu Y | Molecular & cellular proteomics : MCP | 37353004 | Mol Cell Proteomics | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37353004 |
| High-Throughput Mass Spectrometry Imaging of Biological Systems: Current Approaches and Future Directions. | Jiang LX, Yang M, Wali SN, Laskin J | Trends in analytical chemistry : TRAC | 37206615 | Trends Analyt Chem | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37206615 |
| Nanospray Desorption Electrospray Ionization (Nano-DESI) Mass Spectrometry Imaging with High Ion Mobility Resolution. | Jiang LX, Hernly E, Hu H, Hilger RT, Neuweger H, Yang M, Laskin J | Journal of the American Society for Mass Spectrometry | 37463098 | J Am Soc Mass Spectrom | 2023 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/37463098 |
| A monolithic microfluidic probe for ambient mass spectrometry imaging of biological tissues. | Jiang LX, Polack M, Li X, Yang M, Belder D, Laskin J | Lab on a chip | 37782224 | Lab Chip | 2023 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/37782224 |
| High-Throughput Nano-DESI Mass Spectrometry Imaging of Biological Tissues Using an Integrated Microfluidic Probe. | Li X, Hu H, Yin R, Li Y, Sun X, Dey SK, Laskin J | Analytical chemistry | 35770488 | Anal Chem | 2022 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/35770488 |
| New Views of Old Proteins: Clarifying the Enigmatic Proteome. | Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL | Molecular & cellular proteomics : MCP | 35654359 | Mol Cell Proteomics | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35654359 |
| An Integrated Microfluidic Probe for Mass Spectrometry Imaging of Biological Samples*. | Li X, Yin R, Hu H, Li Y, Sun X, Dey SK, Laskin J | Angewandte Chemie (International ed. in English) | 32743957 | Angew Chem Int Ed Engl | 2020 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/32743957 |
| Quantitative Mass Spectrometry Imaging of Biological Systems. | Unsihuay D, Mesa Sanchez D, Laskin J | Annual review of physical chemistry | 33441032 | Annu Rev Phys Chem | 2021 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/33441032 |
| Isomer-Selective Mass Spectrometry Imaging Using Nanospray Desorption Electrospray Ionization (Nano-DESI). | Amer S, Jiang LX, Iqfath M, Weigand MR, Laskin J | Accounts of chemical research | 41058124 | Acc Chem Res | 2025 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/41058124 |
| Self-supervised clustering of mass spectrometry imaging data using contrastive learning. | Hu H, Bindu JP, Laskin J | Chemical science | 35059155 | Chem Sci | 2021 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/35059155 |
| Deep Learning Approach for Dynamic Sparse Sampling for High-Throughput Mass Spectrometry Imaging. | Helminiak D, Hu H, Laskin J, Ye DH | IS&T International Symposium on Electronic Imaging | 34722959 | IS&T Int Symp Electron Imaging | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34722959 |
| Deep Learning Approach for Dynamic Sampling for Multichannel Mass Spectrometry Imaging. | Helminiak D, Hu H, Laskin J, Hye Ye D | IEEE transactions on computational imaging | 37251286 | IEEE Trans Comput Imaging | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37251286 |
| Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence. | Gosline SJC, Veličković M, Pino JC, Day LZ, Attah IK, Swensen AC, Danna V, Posso C, Rodland KD, Chen J, Matthews CE, Campbell-Thompson M, Laskin J, Burnum-Johnson K, Zhu Y, Piehowski PD | Molecular & cellular proteomics : MCP | 37328065 | Mol Cell Proteomics | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37328065 |
| High-resolution integrated microfluidic probe for mass spectrometry imaging of biological tissues. | Li X, Hu H, Laskin J | Analytica chimica acta | 37827646 | Anal Chim Acta | 2023 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/37827646 |
| Emerging Computational Methods in Mass Spectrometry Imaging. | Hu H, Laskin J | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 36253139 | Adv Sci (Weinh) | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36253139 |
| High-Throughput Mass Spectrometry Imaging with Dynamic Sparse Sampling. | Hu H, Helminiak D, Yang M, Unsihuay D, Hilger RT, Ye DH, Laskin J | ACS measurement science au | 36281292 | ACS Meas Sci Au | 2022 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/36281292 |
| Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. | Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL | Science advances | 35947651 | Sci Adv | 2022 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/35947651 |
| Automated imaging and identification of proteoforms directly from ovarian cancer tissue. | McGee JP, Su P, Durbin KR, Hollas MAR, Bateman NW, Maxwell GL, Conrads TP, Fellers RT, Melani RD, Camarillo JM, Kafader JO, Kelleher NL | Nature communications | 37838706 | Nat Commun | 2023 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/37838706 |
| The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells. | Melani RD, Gerbasi VR, Anderson LC, Sikora JW, Toby TK, Hutton JE, Butcher DS, Negrão F, Seckler HS, Srzentić K, Fornelli L, Camarillo JM, LeDuc RD, Cesnik AJ, Lundberg E, Greer JB, Fellers RT, Robey MT, DeHart CJ, Forte E, Hendrickson CL, Abbatiello SE, Thomas PM, Kokaji AI, Levitsky J, Kelleher NL | Science (New York, N.Y.) | 35084980 | Science | 2022 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/35084980 |
| Single Cell Analysis of Proteoforms. | Su P, Hollas MAR, Butun FA, Kanchustambham VL, Rubakhin S, Ramani N, Greer JB, Early BP, Fellers RT, Caldwell MA, Sweedler JV, Kafader JO, Kelleher NL | Journal of proteome research | 38497708 | J Proteome Res | 2024 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/38497708 |
| Author Correction: Automated imaging and identification of proteoforms directly from ovarian cancer tissue. | McGee JP, Su P, Durbin KR, Hollas MAR, Bateman NW, Maxwell GL, Conrads TP, Fellers RT, Melani RD, Camarillo JM, Kafader JO, Kelleher NL | Nature communications | 38040721 | Nat Commun | 2023 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/38040721 |
| Parsing 20 Years of Public Data by AI Maps Trends in Proteomics and Forecasts Technology. | Green JJ, Grimm C, Fristo A, Byrum J, Kelleher NL | Journal of proteome research | 38096378 | J Proteome Res | 2024 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/38096378 |
| The emerging landscape of single-molecule protein sequencing technologies. | Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C | Nature methods | 34099939 | Nat Methods | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34099939 |
| Mapping the Proteoform Landscape of Five Human Tissues. | Drown BS, Jooß K, Melani RD, Lloyd-Jones C, Camarillo JM, Kelleher NL | Journal of proteome research | 35413190 | J Proteome Res | 2022 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/35413190 |
| Proteoform profiling of endogenous single cells from rat hippocampus at scale. | Su P, Hollas MAR, Pla I, Rubakhin S, Butun FA, Greer JB, Early BP, Fellers RT, Caldwell MA, Sweedler JV, Kafader JO, Kelleher NL | Nature biotechnology | 40374954 | Nat Biotechnol | 2026 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40374954 |
| Wavelength Dependence of Intact Protein Extraction Using Femtosecond Laser Ablation. | Wainwright AAC, Madhoun K, Su P, Janisse SE, Besaw JE, Grewal HS, Ernst OP, Kafader JO, Kelleher NL, Miller RJD | The journal of physical chemistry letters | 40833879 | J Phys Chem Lett | 2025 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/40833879 |
| Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? | Plubell DL, Käll L, Webb-Robertson BJ, Bramer LM, Ives A, Kelleher NL, Smith LM, Montine TJ, Wu CC, MacCoss MJ | Journal of proteome research | 35220718 | J Proteome Res | 2022 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/35220718 |
| Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. | LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, Kelleher NL, Thomas PM, Vizcaíno JA | Journal of proteome research | 35290070 | J Proteome Res | 2022 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/35290070 |
| Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. | Zhou XX, Bracken CJ, Zhang K, Zhou J, Mou Y, Wang L, Cheng Y, Leung KK, Wells JA | Journal of the American Chemical Society | 32924468 | J Am Chem Soc | 2020 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/32924468 |
| Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. | Gerbasi VR, Melani RD, Abbatiello SE, Belford MW, Huguet R, McGee JP, Dayhoff D, Thomas PM, Kelleher NL | Analytical chemistry | 33844503 | Anal Chem | 2021 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/33844503 |
| New Interface for Faster Proteoform Analysis: Immunoprecipitation Coupled with SampleStream-Mass Spectrometry. | Santos Seckler HD, Park HM, Lloyd-Jones CM, Melani RD, Camarillo JM, Wilkins JT, Compton PD, Kelleher NL | Journal of the American Society for Mass Spectrometry | 34043341 | J Am Soc Mass Spectrom | 2021 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/34043341 |
| Immune monitoring using mass cytometry and related high-dimensional imaging approaches. | Hartmann FJ, Bendall SC | Nature reviews. Rheumatology | 31892734 | Nat Rev Rheumatol | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31892734 |
| High-Parameter Immune Profiling with CyTOF. | Sahaf B, Rahman A, Maecker HT, Bendall SC | Methods in molecular biology (Clifton, N.J.) | 31502160 | Methods Mol Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/31502160 |
| Terminal deoxynucleotidyl transferase and CD84 identify human multi-potent lymphoid progenitors. | Kim Y, Calderon AA, Favaro P, Glass DR, Tsai AG, Ho D, Borges L, Greenleaf WJ, Bendall SC | Nature communications | 39003273 | Nat Commun | 2024 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/39003273 |
| Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition in metastatic TNBC. | Greenwald NF, Nederlof I, Sowers C, Ding DY, Park S, Kong A, Houlahan KE, Varra SR, de Graaf M, Geurts V, Liu CC, Ranek JS, Voorwerk L, de Maaker M, Kagel A, McCaffrey E, Khan A, Yeh CY, Fullaway CC, Khair Z, Simon BG, Bai Y, Piyadasa H, Risom T, Delmastro A, Hartmann FJ, Mangiante L, Sotomayor-Vivas C, Bendall SC, Schumacher TN, Ma Z, Bosse M, van de Vijver MJ, Tibshirani R, Horlings HM, Curtis C, Kok M, Angelo M | Nature cancer | 41708895 | Nat Cancer | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41708895 |
| Multiplexed single-cell morphometry for hematopathology diagnostics. | Tsai AG, Glass DR, Juntilla M, Hartmann FJ, Oak JS, Fernandez-Pol S, Ohgami RS, Bendall SC | Nature medicine | 32161403 | Nat Med | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32161403 |
| An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. | Glass DR, Tsai AG, Oliveria JP, Hartmann FJ, Kimmey SC, Calderon AA, Borges L, Glass MC, Wagar LE, Davis MM, Bendall SC | Immunity | 32668225 | Immunity | 2020 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/32668225 |
| Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. | Risom T, Glass DR, Averbukh I, Liu CC, Baranski A, Kagel A, McCaffrey EF, Greenwald NF, Rivero-Gutiérrez B, Strand SH, Varma S, Kong A, Keren L, Srivastava S, Zhu C, Khair Z, Veis DJ, Deschryver K, Vennam S, Maley C, Hwang ES, Marks JR, Bendall SC, Colditz GA, West RB, Angelo M | Cell | 35063072 | Cell | 2022 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/35063072 |
| Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. | Greenwald NF, Miller G, Moen E, Kong A, Kagel A, Dougherty T, Fullaway CC, McIntosh BJ, Leow KX, Schwartz MS, Pavelchek C, Cui S, Camplisson I, Bar-Tal O, Singh J, Fong M, Chaudhry G, Abraham Z, Moseley J, Warshawsky S, Soon E, Greenbaum S, Risom T, Hollmann T, Bendall SC, Keren L, Graf W, Angelo M, Van Valen D | Nature biotechnology | 34795433 | Nat Biotechnol | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34795433 |
| Automated classification of cellular expression in multiplexed imaging data with Nimbus. | Rumberger JL, Greenwald NF, Ranek JS, Boonrat P, Walker C, Franzen J, Varra SR, Kong A, Sowers C, Liu CC, Averbukh I, Piyadasa H, Vanguri R, Nederlof I, Wang XJ, Van Valen D, Kok M, Bendall SC, Hollmann TJ, Kainmueller D, Angelo M | Nature methods | 41062826 | Nat Methods | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/41062826 |
| Gestationally dependent immune organization at the maternal-fetal interface. | Moore AR, Vivanco Gonzalez N, Plummer KA, Mitchel OR, Kaur H, Rivera M, Collica B, Goldston M, Filiz F, Angelo M, Palmer TD, Bendall SC | Cell reports | 36384130 | Cell Rep | 2022 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/36384130 |
| The automated computational workflow QUICHE reveals structural definitions of antitumor responses in triple-negative breast cancer. | Ranek JS, Greenwald NF, Goldston M, Camacho Fullaway C, Sowers C, Kong A, Mouron S, Quintela-Fandino M, West RB, Bendall SC, Angelo M | Nature cancer | 41708893 | Nat Cancer | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41708893 |
| Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets. | Glass MC, Glass DR, Oliveria JP, Mbiribindi B, Esquivel CO, Krams SM, Bendall SC, Martinez OM | Cell reports | 35443184 | Cell Rep | 2022 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/35443184 |
| Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts. | Baskar R, Kimmey SC, Bendall SC | Trends in cell biology | 35181197 | Trends Cell Biol | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35181197 |
| Reproducible, high-dimensional imaging in archival human tissue by multiplexed ion beam imaging by time-of-flight (MIBI-TOF). | Liu CC, Bosse M, Kong A, Kagel A, Kinders R, Hewitt SM, Varma S, van de Rijn M, Nowak SH, Bendall SC, Angelo M | Laboratory investigation; a journal of technical methods and pathology | 35351966 | Lab Invest | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35351966 |
| Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. | Baskar R, Chen AF, Favaro P, Reynolds W, Mueller F, Borges L, Jiang S, Park HS, Kool ET, Greenleaf WJ, Bendall SC | Cell reports methods | 35463156 | Cell Rep Methods | 2022 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/35463156 |
| Single-cell metabolic profiling of human cytotoxic T cells. | Hartmann FJ, Mrdjen D, McCaffrey E, Glass DR, Greenwald NF, Bharadwaj A, Khair Z, Verberk SGS, Baranski A, Baskar R, Graf W, Van Valen D, Van den Bossche J, Angelo M, Bendall SC | Nature biotechnology | 32868913 | Nat Biotechnol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32868913 |
| Single-cell spatial proteomic imaging for human neuropathology. | Vijayaragavan K, Cannon BJ, Tebaykin D, Bossé M, Baranski A, Oliveria JP, Bukhari SA, Mrdjen D, Corces MR, McCaffrey EF, Greenwald NF, Sigal Y, Marquez D, Khair Z, Bruce T, Goldston M, Bharadwaj A, Montine KS, Angelo RM, Montine TJ, Bendall SC | Acta neuropathologica communications | 36333818 | Acta Neuropathol Commun | 2022 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/36333818 |
| An atlas of healthy and injured cell states and niches in the human kidney. | Lake BB, Menon R, Winfree S, Hu Q, Melo Ferreira R, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, Eddy S, Zhang B, Wu Y, Salamon D, Williams JC, Wang X, Balderrama KS, Hoover PJ, Murray E, Marshall JL, Noel T, Vijayan A, Hartman A, Chen F, Waikar SS, Rosas SE, Wilson FP, Palevsky PM, Kiryluk K, Sedor JR, Toto RD, Parikh CR, Kim EH, Satija R, Greka A, Macosko EZ, Kharchenko PV, Gaut JP, Hodgin JB, KPMP Consortium, Eadon MT, Dagher PC, El-Achkar TM, Zhang K, Kretzler M, Jain S | Nature | 37468583 | Nature | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37468583 |
| The expanding vistas of spatial transcriptomics. | Tian L, Chen F, Macosko EZ | Nature biotechnology | 36192637 | Nat Biotechnol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36192637 |
| Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. | Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, Welch J, Chen LM, Chen F, Macosko EZ | Science (New York, N.Y.) | 30923225 | Science | 2019 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/30923225 |
| Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. | Zhao T, Chiang ZD, Morriss JW, LaFave LM, Murray EM, Del Priore I, Meli K, Lareau CA, Nadaf NM, Li J, Earl AS, Macosko EZ, Jacks T, Buenrostro JD, Chen F | Nature | 34912115 | Nature | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34912115 |
| Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. | Kobayashi-Kirschvink KJ, Comiter CS, Gaddam S, Joren T, Grody EI, Ounadjela JR, Zhang K, Ge B, Kang JW, Xavier RJ, So PTC, Biancalani T, Shu J, Regev A | Nature biotechnology | 38200118 | Nat Biotechnol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38200118 |
| Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. | Russell AJC, Weir JA, Nadaf NM, Shabet M, Kumar V, Kambhampati S, Raichur R, Marrero GJ, Liu S, Balderrama KS, Vanderburg CR, Shanmugam V, Tian L, Iorgulescu JB, Yoon CH, Wu CJ, Macosko EZ, Chen F | Nature | 38093010 | Nature | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38093010 |
| Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. | Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA, Pryhuber GJ, Misra RS, Purkerson JM, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber GM, Jain Y, Qaurooni D, Kong Y, HRA Team, Bueckle A, Herr BW 2nd | Nature methods | 40082611 | Nat Methods | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40082611 |
| 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging. | Ghose S, Ju Y, McDonough E, Ho J, Karunamurthy A, Chadwick C, Cho S, Rose R, Corwin A, Surrette C, Martinez J, Williams E, Sood A, Al-Kofahi Y, Falo LD Jr, Börner K, Ginty F | Communications biology | 37468758 | Commun Biol | 2023 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/37468758 |
| The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. | HuBMAP Consortium | Nature | 31597973 | Nature | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31597973 |
| Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures. | Salahudeen AA, Choi SS, Rustagi A, Zhu J, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, van Unen V, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ | bioRxiv : the preprint server for biology | 32743583 | bioRxiv | 2020 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/32743583 |
| Integrated spatial genomics reveals global architecture of single nuclei. | Takei Y, Yun J, Zheng S, Ollikainen N, Pierson N, White J, Shah S, Thomassie J, Suo S, Eng CL, Guttman M, Yuan GC, Cai L | Nature | 33505024 | Nature | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33505024 |
| Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. | Zhu Q, Shah S, Dries R, Cai L, Yuan GC | Nature biotechnology | 30371680 | Nat Biotechnol | 2018 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/30371680 |
| Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L | Nature | 30911168 | Nature | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30911168 |
| SpatialDWLS: accurate deconvolution of spatial transcriptomic data. | Dong R, Yuan GC | Genome biology | 33971932 | Genome Biol | 2021 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/33971932 |
| Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. | Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P | Nature biotechnology | 31427819 | Nat Biotechnol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31427819 |
| Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. | Wang Y, Liu X, Zeng Y, Saka SK, Xie W, Goldaracena I, Kohman RE, Yin P, Church GM | Nucleic acids research | 38966983 | Nucleic Acids Res | 2024 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/38966983 |
| SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. | Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P | Nature methods | 31110282 | Nat Methods | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31110282 |
| A Pilot Study of Urine Proteomics in COVID-19-Associated Acute Kidney Injury. | Ye Y, Swensen AC, Wang Y, Kaushal M, Salamon D, Knoten A, Nicora CD, Marks L, Gaut JP, Vijayan A, Orton DJ, Mudd PA, Parikh CR, Qian WJ, O'Halloran JA, Piehowski PD, Jain S | Kidney international reports | 34642644 | Kidney Int Rep | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34642644 |
| Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. | Favaro P, Glass DR, Borges L, Baskar R, Reynolds W, Ho D, Bruce T, Tebaykin D, Scanlon VM, Shestopalov I, Bendall SC | bioRxiv : the preprint server for biology | 37693547 | bioRxiv | 2023 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/37693547 |
| Spatial proteomics reveals human microglial states shaped by anatomy and neuropathology. | Mrdjen D, Amouzgar M, Cannon B, Liu C, Spence A, McCaffrey E, Bharadwaj A, Tebaykin D, Bukhari S, Hartmann FJ, Kagel A, Vijayaragavan K, Oliveria JP, Yakabi K, Serrano GE, Corrada MM, Kawas CH, Camacho C, Bosse M, Tibshirani R, Beach TG, Angelo M, Montine T, Bendall SC | Research square | 37398389 | Res Sq | 2023 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/37398389 |
| Systems biology approaches to unravel lymphocyte subsets and function. | Kim Y, Greenleaf WJ, Bendall SC | Current opinion in immunology | 37028221 | Curr Opin Immunol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37028221 |
| Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming. | Favaro P, Glass DR, Borges L, Baskar R, Lam A, Reynolds W, Ho D, Bruce T, Tebaykin D, Koehnke T, Scanlon VM, Shestopalov I, Bendall SC | Cell reports | 40577131 | Cell Rep | 2025 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/40577131 |
| A deep single cell mass cytometry approach to capture canonical and noncanonical cell cycle states. | Amouzgar M, Favaro P, Ho D, Bruce T, Bendall SC | bioRxiv : the preprint server for biology | 40672327 | bioRxiv | 2025 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/40672327 |
| A deep single cell mass cytometry approach to capture canonical and noncanonical cell cycle states. | Amouzgar M, Favaro P, Ho D, Bruce T, Bendall SC | Nature communications | 41044455 | Nat Commun | 2025 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/41044455 |
| Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope using the Tile/SED/Array Interface. | Piyadasa H, Oberlton B, Kong A, Camacho Fullaway C, Reddy Varra S, Sowers C, Tsai AG | Journal of visualized experiments : JoVE | 37782085 | J Vis Exp | 2023 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/37782085 |
| Spatial proteomics of Alzheimer's disease-specific human microglial states. | Mrdjen D, Cannon BJ, Amouzgar M, Kim Y, Liu C, Vijayaragavan K, Camacho C, Spence A, McCaffrey EF, Bharadwaj A, Tebaykin D, Bukhari S, Bosse M, Hartmann FJ, Kagel A, Oliveria JP, Yakabi K, Serrano GE, Corrada MM, Kawas CH, Tibshirani R, Beach TG, Corces MR, Greenleaf W, Angelo RM, Montine T, Bendall SC | Nature immunology | 40696045 | Nat Immunol | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40696045 |
| Multi-omic landscape of human gliomas from diagnosis to treatment and recurrence. | Piyadasa H, Oberlton B, Ribi M, Leow K, Ranek JS, Averbukh I, Amouzgar M, Liu CC, Franchina DG, Greenwald NF, McCaffrey EF, Kumar R, Ferrian S, Tsai AG, Filiz F, Fullaway CC, Bosse M, Varra SR, Kong A, Sowers C, Gephart MH, Nuñez-Perez P, Yang E, Travers M, Schachter MJ, Liang S, Santi MR, Bucktrout S, Gherardini PF, Connolly J, Cole K, Barish ME, Brown CE, Oldridge DA, Drake RR, Phillips JJ, Okada H, Prins R, Bendall SC, Angelo M | Cancer cell | 41386224 | Cancer Cell | 2026 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/41386224 |
| A spatially resolved timeline of the human maternal-fetal interface. | Greenbaum S, Averbukh I, Soon E, Rizzuto G, Baranski A, Greenwald NF, Kagel A, Bosse M, Jaswa EG, Khair Z, Kwok S, Warshawsky S, Piyadasa H, Goldston M, Spence A, Miller G, Schwartz M, Graf W, Van Valen D, Winn VD, Hollmann T, Keren L, van de Rijn M, Angelo M | Nature | 37468587 | Nature | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37468587 |
| A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography. | Duong TE, Diep D, Conklin KY, Bui I, Purkerson JM, Boone E, Olness J, Patel S, Peng B, Kern C, Zhao Z, Misra RS, Huyck HL, Verheyden JM, Borok Z, Zhang Y, Scheuermann RH, Zhu Q, Deutsch G, Hagood J, Sun X, Zhang K, Pryhuber GS | bioRxiv : the preprint server for biology | 40475598 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/40475598 |
| Precision-Cut Lung Slices: Emerging Tools for Preclinical and Translational Lung Research: An Official American Thoracic Society Workshop Report. | Lehmann M, Krishnan R, Sucre J, Kulkarni HS, Pineda RH, Anderson C, Banovich NE, Behrsing HP, Dean CH, Haak A, Gosens R, Kaminski N, Zagorska A, Koziol-White C, Metcalf JP, Kim YH, Loebel C, Neptune E, Noel A, Raghu G, Sewald K, Sharma A, Suki B, Sperling A, Tatler A, Turner S, Rosas IO, Van Ry P, Wille T, Randell SH, Pryhuber G, Rojas M, Bourke J, Königshoff M | American journal of respiratory cell and molecular biology | 39499861 | Am J Respir Cell Mol Biol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39499861 |
| LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. | Gaddis N, Fortriede J, Guo M, Bardes EE, Kouril M, Tabar S, Burns K, Ardini-Poleske ME, Loos S, Schnell D, Jin K, Iyer B, Du Y, Huo BX, Bhattacharjee A, Korte J, Munshi R, Smith V, Herbst A, Kitzmiller JA, Clair GC, Carson JP, Adkins J, Morrisey EE, Pryhuber GS, Misra R, Whitsett JA, Sun X, Heathorn T, Paten B, Prasath VBS, Xu Y, Tickle T, Aronow BJ, Salomonis N | American journal of respiratory cell and molecular biology | 36413377 | Am J Respir Cell Mol Biol | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36413377 |
| Super-Resolution Stimulated Raman Scattering Microscopy with Graphical User Interface-Supported A-PoD. | Jang H, Li Y, Wu S, Shi L | Current protocols | 38270527 | Curr Protoc | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38270527 |
| Influence of the irradiated pulmonary microenvironment on macrophage and T cell dynamics. | Groves AM, Misra R, Clair G, Hernady E, Olson H, Orton D, Finkelstein J, Marples B, Johnston CJ | Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology | 36813173 | Radiother Oncol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36813173 |
| Discovery of optimal cell type classification marker genes from single cell RNA sequencing data. | Liu A, Peng B, Pankajam AV, Duong TE, Pryhuber G, Scheuermann RH, Zhang Y | bioRxiv : the preprint server for biology | 38712147 | bioRxiv | 2024 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/38712147 |
| Discovery of optimal cell type classification marker genes from single cell RNA sequencing data. | Liu A, Peng B, Pankajam AV, Duong TE, Pryhuber G, Scheuermann RH, Zhang Y | BMC methods | 40893796 | BMC Methods | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/40893796 |
| Sorted-cell proteomics reveals an AT1-associated epithelial cornification phenotype and suggests endothelial redox imbalance in human bronchopulmonary dysplasia. | Ushakumary MG, Chrisler WB, Bandyopadhyay G, Huyck H, Gorman BL, Beishembieva N, Pitonzo A, Lai ZJ, Fillmore TL, Attah IK, Deutsch G, Purkerson JM, Dylag AM, Misra RS, Carson JP, Adkins JN, Pryhuber GS, Clair GC | American journal of physiology. Lung cellular and molecular physiology | 40960949 | Am J Physiol Lung Cell Mol Physiol | 2025 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/40960949 |
| Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. | Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network | Nature medicine | 33654293 | Nat Med | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33654293 |
| Integrating N -glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung. | Veličković D, Purkerson J, Bhotika H, Huyck H, Clair G, Pryhuber GS, Anderton C | bioRxiv : the preprint server for biology | 39416038 | bioRxiv | 2024 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/39416038 |
| Metabolic nanoscopy enhanced by experimental and computational approaches. | Jang H, Wu S, Li Y, Li Z, Shi L | Npj imaging | 39677560 | Npj Imaging | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39677560 |
| Multi-molecular hyperspectral PRM-SRS microscopy. | Zhang W, Li Y, Fung AA, Li Z, Jang H, Zha H, Chen X, Gao F, Wu JY, Sheng H, Yao J, Skowronska-Krawczyk D, Jain S, Shi L | Nature communications | 38383552 | Nat Commun | 2024 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/38383552 |
| The evolving pathophysiology of bronchopulmonary dysplasia. | Ambalavanan N, Deutsch G, Pryhuber G, Travers CP, Willis KA | Physiological reviews | 40880213 | Physiol Rev | 2026 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/40880213 |
| Piecing together the alveolar-capillary unit: arterial-venous capillary polarization. | Majka SM, Niethamer TK, Caporarello N, Thorndyke HF, Clair G, West JD, Karmouty-Quintana H, Alvira CM | American journal of physiology. Lung cellular and molecular physiology | 42227649 | Am J Physiol Lung Cell Mol Physiol | 2026 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/42227649 |
| Integrating N-glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung. | Veličković D, Purkerson J, Bhotika H, Huyck H, Clair G, Pryhuber GS, Anderton C | Molecular omics | 40392055 | Mol Omics | 2025 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/40392055 |
| FUSION: a web-based application for in-depth exploration of multi-omics data with brightfield histology. | Border SP, Ferreira RM, Lucarelli N, Kumar SKC, Paul AS, Manthey D, Barisoni L, Levites Strekalova YA, Ray J, Cheng YH, Rosenberg AZ, Tomaszewski JE, Mimar S, Hodgin JB, Hickey JW, Wei B, Ginty F, Karunamurthy A, Wang J, Raina M, Pryhuber GS, Purkerson J, HuBMAP consortium, El-Achkar TM, Jain S, Eadon MT, Sarder P | Nature communications | 40998789 | Nat Commun | 2025 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/40998789 |
| An integrated cell atlas of the lung in health and disease. | Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, Lung Biological Network Consortium, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ | Nature medicine | 37291214 | Nat Med | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37291214 |
| Early cancer detection by SERS spectroscopy and machine learning. | Shi L, Li Y, Li Z | Light, science & applications | 37714845 | Light Sci Appl | 2023 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/37714845 |
| Far-red chemigenetic biosensors for multi-dimensional and super-resolved kinase activity imaging. | Frei MS, Sanchez SA, Liu L, Schneider F, Wang Z, Hakozaki H, Li Y, Lyons AC, Rohm TV, Olefsky JM, Shi L, Schöneberg J, Fraser SE, Mehta S, Wang Y, Zhang J | bioRxiv : the preprint server for biology | 38370804 | bioRxiv | 2024 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/38370804 |
| Multimodal imaging of metabolic activities for distinguishing subtypes of breast cancer. | Li Z, Nguyen C, Jang H, Hoang D, Min S, Ackerstaff E, Koutcher JA, Shi L | Biomedical optics express | 38021123 | Biomed Opt Express | 2023 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/38021123 |
| Sorted-Cell Proteomics Reveals an AT1-Associated Epithelial Cornification Phenotype and Suggests Endothelial Redox Imbalance in Human Bronchopulmonary Dysplasia. | Ushakumary MG, Chrisler WB, Bandyopadhyay G, Huyck H, Gorman BL, Beishembieva N, Pitonza A, Lai ZJ, Fillmore TL, Attah IK, Dylag AM, Misra R, Carson JP, Adkins JN, Pryhuber GS, Clair G | bioRxiv : the preprint server for biology | 40166356 | bioRxiv | 2025 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/40166356 |
| Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. | Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA, Pryhuber G, Misra RS, Purkerson J, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber G, Jain Y, Qaurooni D, Kong Y, HRA Team, Bueckle A, Herr BW 2nd | bioRxiv : the preprint server for biology | 38826261 | bioRxiv | 2024 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/38826261 |
| Cell Population-resolved Multiomics Atlas of the Developing Lung. | Ushakumary MG, Feng S, Bandyopadhyay G, Olson H, Weitz KK, Huyck HL, Poole C, Purkerson JM, Bhattacharya S, Ljungberg MC, Mariani TJ, Deutsch GH, Misra RS, Carson JP, Adkins JN, Pryhuber GS, Clair G | American journal of respiratory cell and molecular biology | 39447176 | Am J Respir Cell Mol Biol | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39447176 |
| Multimodal Imaging Unveils the Impact of Nanotopography on Cellular Metabolic Activities. | Li Z, Sarikhani E, Prayotamornkul S, Meganathan DP, Jahed Z, Shi L | Chemical & biomedical imaging | 39735831 | Chem Biomed Imaging | 2024 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/39735831 |
| Imaging Cellular Metabolic Rewiring with SuMMIT-SRS. | Li Y, Li Z, Li Y, Rhine K, Ranamukhaarachchi S, Qin S, Jang H, Villazon J, Bai Z, Fraley SI, Yeo GW, Fan R, Shi L | bioRxiv : the preprint server for biology | 41279865 | bioRxiv | 2025 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/41279865 |
| Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids. | Bagheri P, Hoang K, Kuo CY, Trivedi H, Jang H, Shi L | Journal of visualized experiments : JoVE | 37246865 | J Vis Exp | 2023 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/37246865 |
| Editorial: Global excellence in inflammatory diseases: North America 2021. | Kusner LL, Misra RS, Lucas R | Frontiers in immunology | 37483602 | Front Immunol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37483602 |
| Super-resolution SRS microscopy with A-PoD. | Jang H, Li Y, Fung AA, Bagheri P, Hoang K, Skowronska-Krawczyk D, Chen X, Wu JY, Bintu B, Shi L | Nature methods | 36797410 | Nat Methods | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36797410 |
| An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue. | Lukowski JK, Olson H, Velickovic M, Wang J, Kyle JE, Kim YM, Williams SM, Zhu Y, Huyck HL, McGraw MD, Poole C, Rogers L, Misra R, Alexandrov T, Ansong C, Pryhuber GS, Clair G, Adkins JN, Carson JP, Anderton CR | Frontiers in molecular biosciences | 36465564 | Front Mol Biosci | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36465564 |
| A multimodal imaging approach for imaging the metabolic changes resulting from bronchopulmonary dysplasia. | Gorman BL, Li Z, Deutsch G, Huyck HL, Beishembieva N, Olson H, Villazon J, Yu P, Pryhuber GS, Clair G, Shi L, Anderton CR | bioRxiv : the preprint server for biology | 40667045 | bioRxiv | 2025 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/40667045 |
| Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring. | Yu W, Biyik-Sit R, Uzun Y, Chen CH, Thadi A, Sussman JH, Pang M, Wu CY, Grossmann LD, Gao P, Wu DW, Yousey A, Zhang M, Turn CS, Zhang Z, Bandyopadhyay S, Huang J, Patel T, Chen C, Martinez D, Surrey LF, Hogarty MD, Bernt K, Zhang NR, Maris JM, Tan K | Nature genetics | 40229600 | Nat Genet | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40229600 |
| Bone marrow adipogenic lineage precursors are the major regulator of bone resorption in adult mice. | Lu J, He Q, Wang H, Yao L, Duffy M, Guo H, Braun C, Zhou Y, Liang Q, Lin Y, Bandyopadhyay S, Tan K, Choi Y, Liu XS, Qin L | Bone research | 40102423 | Bone Res | 2025 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/40102423 |
| Genetics-nutrition interactions control diurnal enhancer-promoter dynamics and liver lipid metabolism. | Zhou D, Chen Y, Liu P, Zhu K, Holder-Haynes J, Lloyd SJ, La CM, Astapova II, Choa S, Xiong Y, Bae H, Aguilar M, Yang H, An YA, Sun Z, Herman MA, Gao X, Pei L, Jang C, Rabinowitz JD, Mattar SG, Zhang Y, Guan D | Cell metabolism | 40858101 | Cell Metab | 2025 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/40858101 |
| In vivo imaging of reactive oxygen species after myocardial ischemia-reperfusion injury: a large animal multimodal imaging and transcriptomic study. | Swago S, Camillo C, Awad M, Gallagher E, Thompson EW, Castillero E, Peng T, Pei L, Cheng Z, Tsourkas A, Gorman R, Ferrari VA, McManus M, Mach RH, Karp JS, Tschabrunn C, Ferrari G, Witschey WR, Bravo PE | bioRxiv : the preprint server for biology | 41415408 | bioRxiv | 2025 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/41415408 |
| N-Orbit: towards a universal model and metric for comparing tissue microenvironments. | Xiong B, Hu Y, Tan K | Nature communications | 42173891 | Nat Commun | 2026 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/42173891 |
| A multiomic atlas identifies a treatment-resistant, bone marrow progenitor-like cell population in T cell acute lymphoblastic leukemia. | Xu J, Chen C, Sussman JH, Yoshimura S, Vincent T, Pölönen P, Hu J, Bandyopadhyay S, Elghawy O, Yu W, Tumulty J, Chen CH, Li EY, Diorio C, Shraim R, Newman H, Uppuluri L, Li A, Chen GM, Wu DW, Ding YY, Xu JA, Karanfilovski D, Lim T, Hsu M, Thadi A, Ahn KJ, Wu CY, Peng J, Sun Y, Wang A, Mehta R, Frank D, Meyer L, Loh ML, Raetz EA, Chen Z, Wood BL, Devidas M, Dunsmore KP, Winter SS, Chang TC, Wu G, Pounds SB, Zhang NR, Carroll W, Hunger SP, Bernt K, Yang JJ, Mullighan CG, Tan K, Teachey DT | Nature cancer | 39587259 | Nat Cancer | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39587259 |
| Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging. | Bandyopadhyay S, Duffy M, Ahn KJ, Pang M, Smith D, Duncan G, Sussman J, Zhang I, Huang J, Lin Y, Xiong B, Imtiaz T, Chen CH, Thadi A, Chen C, Xu J, Reichart M, Pillai V, Snaith O, Oldridge D, Bhattacharyya S, Maillard I, Carroll M, Nelson C, Qin L, Tan K | bioRxiv : the preprint server for biology | 38559168 | bioRxiv | 2024 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/38559168 |
| CelloType: A Unified Model for Segmentation and Classification of Tissue Images. | Pang M, Roy TK, Wu X, Tan K | bioRxiv : the preprint server for biology | 39345491 | bioRxiv | 2024 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/39345491 |
| Bone marrow adipogenic lineage precursors are the major regulator of bone resorption in adult mice. | Qin L, Lu J, He Q, Wang H, Yao L, Duffy M, Guo H, Braun C, Lin Y, Zhou Y, Liang Q, Bandyopadhyay S, Tan K, Choi Y, Liu S | Research square | 39257979 | Res Sq | 2024 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/39257979 |
| STAT1-mediated interferon signatures are associated with preclinical JAK inhibitor sensitivity in T-ALL. | Xu J, Sussman JH, Yang A, Yoshimura S, Hu J, Chen C, Vincent T, Bandyopadhyay S, Li EY, Lim T, Elghawy O, Barsouk A, Karanfilovski D, Wald SL, Chen GM, Wu D, Newman H, Li A, Sun Y, Chen CH, Bernt K, Wood BL, Winter SS, Dunsmore KP, Raetz E, Devidas M, Pounds S, Loh M, Hunger SP, Chiang MY, Diorio C, Di Giacomo D, Pölönen P, Mullighan CG, Yang JJ, Tan K, Teachey DT | Blood | 40101143 | Blood | 2025 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/40101143 |
| Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes. | Hu Y, Rong J, Xu Y, Xie R, Peng J, Gao L, Tan K | Nature methods | 38191930 | Nat Methods | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38191930 |
| Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging. | Bandyopadhyay S, Duffy MP, Ahn KJ, Sussman JH, Pang M, Smith D, Duncan G, Zhang I, Huang J, Lin Y, Xiong B, Imtiaz T, Chen CH, Thadi A, Chen C, Xu J, Reichart M, Martinez Z, Diorio C, Chen C, Pillai V, Snaith O, Oldridge D, Bhattacharyya S, Maillard I, Carroll M, Nelson C, Qin L, Tan K | Cell | 38714197 | Cell | 2024 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/38714197 |
| Comprehensive Multiomic Analysis Reveals Metabolic Reprogramming Underlying Human Fontan-Associated Liver Disease. | Sule R, Hu P, Shoffler C, Petucci C, Wilkins BJ, Rychik J, Pei L | Journal of the American Heart Association | 40055870 | J Am Heart Assoc | 2025 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/40055870 |
| Partial restoration of mitochondrial dysfunction by AAV-Ant1 protects from dilated cardiomyopathy in Ant1(-/-) plus mtDNA mutant mice. | Angelin A, Keller K, Lu P, Guarnieri JW, Widjaja GA, Sule R, Janssen K, Olali A, Cen Z, Carosi V, Beauplan M, Murdock DG, Potluri P, Pei L, Wallace DC | Nature communications | 41398158 | Nat Commun | 2025 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/41398158 |
| Single-cell multiomics guided mechanistic understanding of Fontan-associated liver disease. | Hu P, Rychik J, Zhao J, Bai H, Bauer A, Yu W, Rand EB, Dodds KM, Goldberg DJ, Tan K, Wilkins BJ, Pei L | Science translational medicine | 38657025 | Sci Transl Med | 2024 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/38657025 |
| A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma. | Sussman JH, Oldridge DA, Yu W, Chen CH, Zellmer AM, Rong J, Parvaresh-Rizi A, Thadi A, Xu J, Bandyopadhyay S, Sun Y, Wu D, Emerson Hunter C, Brosius S, Ahn KJ, Baxter AE, Koptyra MP, Vanguri RS, McGrory S, Resnick AC, Storm PB, Amankulor NM, Santi M, Viaene AN, Zhang N, Raedt T, Cole K, Tan K | bioRxiv : the preprint server for biology | 38496580 | bioRxiv | 2024 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/38496580 |
| Single-cell panleukemia signatures of HSPC-like blasts predict drug response and clinical outcome. | Chen C, Xu J, Sussman JH, Vincent T, Tumulty JS, Yoshimura S, Alikarami F, Yu W, Ding YY, Chen CH, Li EY, Yang A, Qin X, Bandyopadhyay S, Peng J, Pölönen P, Newman H, Wood BL, Hu J, Shraim R, Hughes AD, Diorio C, Uppuluri L, Shi G, Ryan T, Fuller T, Loh ML, Raetz EA, Hunger SP, Pounds SB, Mullighan CG, Frank D, Yang JJ, Bernt KM, Teachey DT, Tan K | Blood | 40089994 | Blood | 2025 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/40089994 |
| CelloType: a unified model for segmentation and classification of tissue images. | Pang M, Roy TK, Wu X, Tan K | Nature methods | 39578628 | Nat Methods | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39578628 |
| Segmentation quality assessment by automated detection of erroneous surface regions in medical images. | Zaman FA, Zhang L, Zhang H, Sonka M, Wu X | Computers in biology and medicine | 37591161 | Comput Biol Med | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37591161 |
| Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia. | Tan K, Xu J, Chen C, Vincent T, Pölönen P, Hu J, Yoshimura S, Yu W, Sussman J, Chen CH, Li E, Diorio C, Shraim R, Newman H, Uppuluri L, Li A, Chen G, Bandyopadhyay S, Wu D, Ding YY, Xu J, Lim T, Hsu M, Thadi A, Ahn KJ, Wu CY, Peng J, Sun Y, Wang A, Mehta R, Frank D, Meyer L, Loh M, Raetz E, Chen Z, Wood B, Devidas M, Dunsmore K, Winter S, Chang TC, Wu G, Pounds S, Zhang N, Carroll W, Hunger S, Bernt K, Yang J, Mullighan C, Teachey D | Research square | 37961674 | Res Sq | 2023 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/37961674 |
| Query-driven generative AI synthesizes multi-modal spatial omics from histology. | Pang M, Roy TK, Wu X, Tan K | bioRxiv : the preprint server for biology | 41415434 | bioRxiv | 2025 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/41415434 |
| HSPC-like blasts in acute lymphoblastic leukemia: biology and therapeutic opportunities. | Xu J, Kennedy VA, Ma C, Sussman JH, Bandyopadhyay S, Chen C, Teachey DT, Tan K | Trends in cancer | 41436318 | Trends Cancer | 2026 Apr | https://www.ncbi.nlm.nih.gov/pubmed/41436318 |
| Cellular neighborhoods in cancer. | Ma L, Xiong B, Liu M, Tan K | Nature cancer | 41545713 | Nat Cancer | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41545713 |
| Lymphatic Microsurgical Preventative Healing Approach for the Primary Prevention of Lymphedema: A 4-Year Follow-Up. | Friedman R, Johnson AR, Brunelle CL, Chang DW, Coriddi M, Dayan JH, Mehrara BJ, Skoracki R, Taghian AG, Singhal D | Plastic and reconstructive surgery | 38266142 | Plast Reconstr Surg | 2024 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/38266142 |
| Non-Linear Lymphatic Anatomy in Breast Cancer Patients Prior to Axillary Lymph Node Dissection: A Risk Factor For Lymphedema Development. | Kinney JR, Friedman R, Kim E, Tillotson E, Shillue K, Lee BT, Singhal D | Journal of mammary gland biology and neoplasia | 37480365 | J Mammary Gland Biol Neoplasia | 2023 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/37480365 |
| Quantifying radiation in the axillary bed at the site of lymphedema surgical prevention. | Friedman R, Spiegel DY, Kinney J, Willcox J, Recht A, Singhal D | Breast cancer research and treatment | 37382815 | Breast Cancer Res Treat | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37382815 |
| Immediate lymphatic reconstruction: Lessons learned over eight years. | Friedman R, Ismail Aly MA, Fanning JE, Pardo JA, Johnson AR, Lee BT, James T, Singhal D | Journal of plastic, reconstructive & aesthetic surgery : JPRAS | 38729046 | J Plast Reconstr Aesthet Surg | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38729046 |
| Collateralization of the upper extremity lymphatic system after axillary lymph node dissection. | Fanning JE, Chung DKV, Reynolds HM, Jayathungage Don TD, Suami H, Donohoe KJ, Singhal D | Journal of surgical oncology | 39315466 | J Surg Oncol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39315466 |
| Changes on noncontrast magnetic resonance imaging following lymphatic surgery for upper extremity secondary lymphedema. | Babapour S, Lee C, Kim E, Kinney JR, Fanning J, Singhal D, Tsai LL | Journal of vascular surgery. Venous and lymphatic disorders | 39117036 | J Vasc Surg Venous Lymphat Disord | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39117036 |
| snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives. | Wang T, Roach MJ, Harvey K, Morlanes JE, Kiedik B, Al-Eryani G, Greenwald A, Kalavros N, Dezem FS, Ma Y, Pita-Juarez YH, Wise K, Degletagne C, Elz A, Hadadianpour A, Johanneson J, Pakiam F, Ryu H, Newell EW, Tonon L, Kohlway A, Drennon T, Abousoud J, Stott R, Lund P, Durruthy J, Vallejo AF, Li W, Salomon R, Kaczorowski D, Warren J, Butler LM, O'Toole S, Plummer J, Vlachos IS, Lundeberg J, Swarbrick A, Martelotto LG | Communications biology | 39414943 | Commun Biol | 2024 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/39414943 |
| Piezo1 regulates meningeal lymphatic vessel drainage and alleviates excessive CSF accumulation. | Choi D, Park E, Choi J, Lu R, Yu JS, Kim C, Zhao L, Yu J, Nakashima B, Lee S, Singhal D, Scallan JP, Zhou B, Koh CJ, Lee E, Hong YK | Nature neuroscience | 38528202 | Nat Neurosci | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38528202 |
| Surgical Treatment of Lymphedema at LE&RN Comprehensive Centers of Excellence. | Fanning JE, Friedman R, Shillue K, Fleishman A, Repicci W, Donohoe K, Singhal D | Journal of reconstructive microsurgery | 40054489 | J Reconstr Microsurg | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/40054489 |
| The deltopectoral lymph node: a potential protective biomarker for breast cancer-related lymphedema. | Fanning JE, Chen A, Thomson S, Tillotson E, Fleishman A, Parker JA, Donohoe K, Singhal D | Breast cancer research and treatment | 40563073 | Breast Cancer Res Treat | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40563073 |
| Edematous Dermal Thickening on Magnetic Resonance Imaging as a Biomarker for Lymphatic Surgical Outcomes. | Kinney JR, Babapour S, Kim E, Friedman R, Singhal D, Lee BT, Tsai LL | Medicina (Kaunas, Lithuania) | 37629659 | Medicina (Kaunas) | 2023 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/37629659 |
| Discussion: Commercial Insurance Rates and Coding for Lymphedema Procedures: The Current State of Confusion and Need for Consensus. | Friedman R, Lee BT, Chatterjee A, Singhal D | Plastic and reconstructive surgery | 38127452 | Plast Reconstr Surg | 2024 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/38127452 |
| Mapping the Anatomy of the Human Lymphatic System. | Bustos VP, Wang R, Pardo J, Boppana A, Weber G, Itkin M, Singhal D | Journal of reconstructive microsurgery | 38547908 | J Reconstr Microsurg | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38547908 |
| FixNCut: A Practical Guide to Sample Preservation by Reversible Fixation for Single Cell Assays. | Wang S, Jiménez-Gracia L, De Amaral AA, Vlachos IS, Plummer J, Heyn H, Martelotto LG | Bio-protocol | 39315321 | Bio Protoc | 2024 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/39315321 |
| Epitrochlear and Humeral Lymph Nodes: A Biomarker for Deep Lymphatic Function and Implications for Breast Cancer-Related Lymphedema Risk. | Fanning JE, Chen A, Thomson S, Tillotson E, Fleishman A, Parker JA, Donohoe K, Singhal D | Journal of surgical oncology | 40552796 | J Surg Oncol | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40552796 |
| A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. | Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Gregory M, He S, Patrick M, Rane T, Wardhani A, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF Jr, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LT, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov YV, Jiang ZG, Vlachos IS | Genome biology | 40087773 | Genome Biol | 2025 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/40087773 |
| Bringing to Light the Invisible Lymphatic Anatomy of the Upper Extremity: Report From the 2024 Harvard Radcliffe Institute Accelerator Workshop. | Fanning JE, Tsai LL, Amore MA, Crescenzi R, De Paepe KN, Donohoe KJ, Maki JH, Padera TP, Pieper CC, Reynolds HM, Suami H, Singhal D | Annals of surgery | 40767571 | Ann Surg | 2026 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/40767571 |
| Key refinements to a large animal model for measurement of real-time lymphatic transport. | Fanning JE, Bustos V, Jang P, Ser J, Kim E, Kinney J, Yamashita A, Choi HS, Singhal D | BMC medical imaging | 41402756 | BMC Med Imaging | 2025 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/41402756 |
| Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). | Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, HuBMAP Consortium, Börner K, Snyder MP | Nature cell biology | 38429479 | Nat Cell Biol | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38429479 |
| Patterns of forearm lymphatic drainage to the epitrochlear lymph nodes in 1400 cutaneous melanoma patients. | Fanning JE, Singhal D, Reynolds HM, Don TDJ, Donohoe KJ, Suami H, Chung DKV | Journal of surgical oncology | 39138920 | J Surg Oncol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39138920 |
| Surgical management of lymphedema: Does a microsurgeon's bias exist? | Friedman R, Ismail Aly ME, Singhal D | Microsurgery | 37339916 | Microsurgery | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37339916 |
| Noncontrast Ultra-High-Frequency Ultrasound for Preoperative Lymphovenous Mapping in Patients Undergoing Lymphaticovenous Anastomosis Surgery for Extremity Lymphedema. | Kim C, Lee C, Queiros I, Mercado N, Fanning JE, Weinstein J, Singhal D, Tsai LL | AJR. American journal of roentgenology | 39440799 | AJR Am J Roentgenol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39440799 |
| Major anatomic variations of the lateral upper arm lymphatic pathway in a healthy female population. | Fanning JE, Givant M, Chen A, Thomson S, Tillotson E, Fleishman A, Donohoe K, Singhal D | Breast cancer (Tokyo, Japan) | 40665199 | Breast Cancer | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40665199 |
| Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. | Uzun Y, Wu H, Tan K | Genome research | 33219054 | Genome Res | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33219054 |
| CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data. | Hu Y, Peng T, Gao L, Tan K | Science advances | 33853780 | Sci Adv | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33853780 |
| Supervised classification enables rapid annotation of cell atlases. | Pliner HA, Shendure J, Trapnell C | Nature methods | 31501545 | Nat Methods | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31501545 |
| The single-cell transcriptional landscape of mammalian organogenesis. | Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J | Nature | 30787437 | Nature | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30787437 |
| Nuclear oligo hashing improves differential analysis of single-cell RNA-seq. | Kim HJ, Booth G, Saunders L, Srivatsan S, McFaline-Figueroa JL, Trapnell C | Nature communications | 35562344 | Nat Commun | 2022 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/35562344 |
| Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. | Aman AJ, Saunders LM, Carr AA, Srivatasan S, Eberhard C, Carrington B, Watkins-Chow D, Pavan WJ, Trapnell C, Parichy DM | eLife | 37695017 | Elife | 2023 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/37695017 |
| A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. | McFaline-Figueroa JL, Hill AJ, Qiu X, Jackson D, Shendure J, Trapnell C | Nature genetics | 31477929 | Nat Genet | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31477929 |
| Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart. | Read DF, Booth GT, Daza RM, Jackson DL, Gladden RG, Srivatsan SR, Ewing B, Franks JM, Spurrell CH, Gomes AR, O'Day D, Gogate AA, Martin BK, Larson H, Pfleger C, Starita L, Lin Y, Shendure J, Lin S, Trapnell C | Communications biology | 39187646 | Commun Biol | 2024 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/39187646 |
| Embryo-scale, single-cell spatial transcriptomics. | Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C | Science (New York, N.Y.) | 34210887 | Science | 2021 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/34210887 |
| Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation. | Menon R, Bomback AS, Lake BB, Stutzke C, Grewenow SM, Menez S, D'Agati VD, Jain S, Kidney Precision Medicine Project | Kidney international | 35339536 | Kidney Int | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35339536 |
| A tool for federated training of segmentation models on whole slide images. | Lutnick B, Manthey D, Becker JU, Zuckerman JE, Rodrigues L, Jen KY, Sarder P | Journal of pathology informatics | 35910077 | J Pathol Inform | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35910077 |
| A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology. | Lutnick B, Manthey D, Becker JU, Ginley B, Moos K, Zuckerman JE, Rodrigues L, Gallan AJ, Barisoni L, Alpers CE, Wang XX, Myakala K, Jones BA, Levi M, Kopp JB, Yoshida T, Zee J, Han SS, Jain S, Rosenberg AZ, Jen KY, Sarder P, Kidney Precision Medicine Project | Communications medicine | 35996627 | Commun Med (Lond) | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35996627 |
| A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys. | Lake BB, Chen S, Hoshi M, Plongthongkum N, Salamon D, Knoten A, Vijayan A, Venkatesh R, Kim EH, Gao D, Gaut J, Zhang K, Jain S | Nature communications | 31249312 | Nat Commun | 2019 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/31249312 |
| Spatially Aware Transformer Networks for Contextual Prediction of Diabetic Nephropathy Progression from Whole Slide Images. | Shickel B, Lucarelli N, Rao AS, Yun D, Moon KC, Han SS, Sarder P | medRxiv : the preprint server for health sciences | 36865174 | medRxiv | 2023 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/36865174 |
| Gene panel selection for targeted spatial transcriptomics. | Zhang Y, Petukhov V, Biederstedt E, Que R, Zhang K, Kharchenko PV | bioRxiv : the preprint server for biology | 36993340 | bioRxiv | 2023 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/36993340 |
| Automated Tubular Morphometric Visualization for Whole Kidney Biopsy. | Kavthekar N, Ginley B, Border S, Lucarelli N, Jen KY, Sarder P | Proceedings of SPIE--the International Society for Optical Engineering | 37817876 | Proc SPIE Int Soc Opt Eng | 2022 Feb-Mar | https://www.ncbi.nlm.nih.gov/pubmed/37817876 |
| Integrating image analysis with single cell RNA-seq data to study podocyte-specific changes in diabetic kidney disease. | Govind D, Meamardoost S, Yacoub R, Gunawan R, Tomaszewski JE, Sarder P | Proceedings of SPIE--the International Society for Optical Engineering | 37817877 | Proc SPIE Int Soc Opt Eng | 2022 Feb-Mar | https://www.ncbi.nlm.nih.gov/pubmed/37817877 |
| Label-free multimodal optical biopsy reveals biomolecular and morphological features of diabetic kidney tissue in 2D and 3D. | Fung AA, Li Z, Boote C, Markov P, Gaut JP, Jain S, Shi L | Nature communications | 40374604 | Nat Commun | 2025 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/40374604 |
| High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. | Chen S, Lake BB, Zhang K | Nature biotechnology | 31611697 | Nat Biotechnol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31611697 |
| Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. | Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer C, Yuan Y, Zhang Y, Song J, Knoten A, Lake BB, Gaut JP, Keene D, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K | bioRxiv : the preprint server for biology | 37645998 | bioRxiv | 2023 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/37645998 |
| HistoLens: A generalizable tool for increasing accessibility and interpretability of quantitative analyses in digital pathology. | Border SP, Ginley B, Tomaszewski JE, Sarder P | Proceedings of SPIE--the International Society for Optical Engineering | 37817875 | Proc SPIE Int Soc Opt Eng | 2022 Feb-Mar | https://www.ncbi.nlm.nih.gov/pubmed/37817875 |
| Label-Free Optical Biopsy Reveals Biomolecular and Morphological Features of Diabetic Kidney Tissue in 2D and 3D. | Fung AA, Li Z, Boote C, Markov P, Jain S, Shi L | bioRxiv : the preprint server for biology | 39553929 | bioRxiv | 2024 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/39553929 |
| Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu Y, Zhang K | Nature reviews. Nephrology | 32221477 | Nat Rev Nephrol | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32221477 |
| A census of the lung: CellCards from LungMAP. | Sun X, Perl AK, Li R, Bell SM, Sajti E, Kalinichenko VV, Kalin TV, Misra RS, Deshmukh H, Clair G, Kyle J, Crotty Alexander LE, Masso-Silva JA, Kitzmiller JA, Wikenheiser-Brokamp KA, Deutsch G, Guo M, Du Y, Morley MP, Valdez MJ, Yu HV, Jin K, Bardes EE, Zepp JA, Neithamer T, Basil MC, Zacharias WJ, Verheyden J, Young R, Bandyopadhyay G, Lin S, Ansong C, Adkins J, Salomonis N, Aronow BJ, Xu Y, Pryhuber G, Whitsett J, Morrisey EE, NHLBI LungMAP Consortium | Developmental cell | 34936882 | Dev Cell | 2022 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/34936882 |
| A single-cell regulatory map of postnatal lung alveologenesis in humans and mice. | Duong TE, Wu Y, Sos BC, Dong W, Limaye S, Rivier LH, Myers G, Hagood JS, Zhang K | Cell genomics | 35434692 | Cell Genom | 2022 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/35434692 |
| Histo-Fetch - On-the-Fly Processing of Gigapixel Whole Slide Images Simplifies and Speeds Neural Network Training. | Lutnick B, Murali LK, Ginley B, Rosenberg AZ, Sarder P | Journal of pathology informatics | 35136674 | J Pathol Inform | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35136674 |
| Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2). | Plongthongkum N, Diep D, Chen S, Lake BB, Zhang K | Nature protocols | 34650278 | Nat Protoc | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34650278 |
| A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project. | El-Achkar TM, Eadon MT, Menon R, Lake BB, Sigdel TK, Alexandrov T, Parikh S, Zhang G, Dobi D, Dunn KW, Otto EA, Anderton CR, Carson JM, Luo J, Park C, Hamidi H, Zhou J, Hoover P, Schroeder A, Joanes M, Azeloglu EU, Sealfon R, Winfree S, Steck B, He Y, D'Agati V, Iyengar R, Troyanskaya OG, Barisoni L, Gaut J, Zhang K, Laszik Z, Rovin BH, Dagher PC, Sharma K, Sarwal MM, Hodgin JB, Alpers CE, Kretzler M, Jain S | Physiological genomics | 33197228 | Physiol Genomics | 2021 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/33197228 |
| Mapping human tissues with highly multiplexed RNA in situ hybridization. | Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer CR, Yuan Y, Zhang Y, Li X, Song J, Knoten A, Lake BB, Gaut JP, Keene CD, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K | Nature communications | 38509069 | Nat Commun | 2024 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/38509069 |
| Gene panel selection for targeted spatial transcriptomics. | Zhang Y, Petukhov V, Biederstedt E, Que R, Zhang K, Kharchenko PV | Genome biology | 38273415 | Genome Biol | 2024 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/38273415 |
| Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas. | Herr BW 2nd, Hardi J, Quardokus EM, Bueckle A, Chen L, Wang F, Caron AR, Osumi-Sutherland D, Musen MA, Börner K | Scientific data | 36973309 | Sci Data | 2023 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/36973309 |
| A reference tissue atlas for the human kidney. | Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU, Kidney Precision Medicine Project | Science advances | 35675394 | Sci Adv | 2022 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/35675394 |
| A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. | Canela VH, Bowen WS, Ferreira RM, Syed F, Lingeman JE, Sabo AR, Barwinska D, Winfree S, Lake BB, Cheng YH, Gaut JP, Ferkowicz M, LaFavers KA, Zhang K, Coe FL, Worcester E, Kidney Precision Medicine Project, Jain S, Eadon MT, Williams JC Jr, El-Achkar TM | Nature communications | 37468493 | Nat Commun | 2023 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/37468493 |
| Tissue registration and exploration user interfaces in support of a human reference atlas. | Börner K, Bueckle A, Herr BW 2nd, Cross LE, Quardokus EM, Record EG, Ju Y, Silverstein JC, Browne KM, Jain S, Wasserfall CH, Jorgensen ML, Spraggins JM, Patterson NH, Weber GM | Communications biology | 36513738 | Commun Biol | 2022 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/36513738 |
| A cloud-based tool for federated segmentation of whole slide images. | Lutnick B, Manthey D, Becker JU, Zuckerman JE, Rodrigues L, Jen KY, Sarder P | Proceedings of SPIE--the International Society for Optical Engineering | 37817879 | Proc SPIE Int Soc Opt Eng | 2022 Feb-Mar | https://www.ncbi.nlm.nih.gov/pubmed/37817879 |
| Spatially organized inflammatory myeloid-CD8(+) T cell aggregates linked to Merkel-cell Polyomavirus driven Reorganization of the Tumor Microenvironment. | Haist M, Matusiak M, Tan Y, Zimmer S, Stege H, Kempchen TN, Mitschke S, Chu P, Weidenthaler-Barth B, Barlow GL, Rogall F, Gonzalez AD, Baertsch MA, Albertini S, Gariglio M, Borgogna C, Goltsev Y, Grabbe S, Hickey JW, Nolan GP | bioRxiv : the preprint server for biology | 40501860 | bioRxiv | 2025 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/40501860 |
| Integration of spatial and single-cell data across modalities with weak linkage. | Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z | bioRxiv : the preprint server for biology | 36711792 | bioRxiv | 2023 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/36711792 |
| Comparative Evaluation of Antibody-Oligonucleotide Conjugation Strategies for Multiplexed Imaging Applications. | Caraccio C, van de Klashorst J, Cherkas S, Ancel S, Kempchen TN, Vazquez G, Goltsev Y, Wang YX, Nolan GP, Hickey JW | Laboratory investigation; a journal of technical methods and pathology | 41270905 | Lab Invest | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41270905 |
| SPACEc: a streamlined, interactive Python workflow for multiplexed image processing and analysis. | Tan Y, Kempchen TN, Becker M, Haist M, Feyaerts D, Liu J, Toma M, Xiao Y, Su G, Rech AJ, Hölzel M, Fan R, Hickey JW, Nolan GP | Nature communications | 41309581 | Nat Commun | 2025 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/41309581 |
| Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases. | Ober-Reynolds B, Wang C, Ko JM, Rios EJ, Aasi SZ, Davis MM, Oro AE, Greenleaf WJ | Nature genetics | 37500727 | Nat Genet | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37500727 |
| Achieving Inclusive Healthcare through Integrating Education and Research with AI and Personalized Curricula. | Bahmani A, Cha K, Alavi A, Dixit A, Ross A, Park R, Goncalves F, Ma S, Saxman P, Nair R, Akhavan-Sarraf R, Zhou X, Wang M, Contrepois K, Li-Pook-Than J, Monte E, Florez Rodriguez DJ, Lai J, Babu M, Tondar A, Schüssler-Fiorenza Rose SM, Akbari I, Zhang X, Yegnashankaran K, Yracheta J, Dale K, Miller AD, Edmiston S, McGhee EM, Nebeker C, Wu JC, Kundaje A, Snyder M | medRxiv : the preprint server for health sciences | 39211867 | medRxiv | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/39211867 |
| Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers. | Sundaram L, Kumar A, Zatzman M, Salcedo A, Ravindra N, Shams S, Louie BH, Bagdatli ST, Myers MA, Sarmashghi S, Choi HY, Choi WY, Yost KE, Zhao Y, Granja JM, Hinoue T, Hayes DN, Cherniack A, Felau I, Choudhry H, Zenklusen JC, Farh KK, McPherson A, Curtis C, Laird PW, Cancer Genome Atlas Analysis Network‡, Demchok JA, Yang L, Tarnuzzer R, Caesar-Johnson SJ, Wang Z, Doane AS, Khurana E, Castro MAA, Lazar AJ, Broom BM, Weinstein JN, Akbani R, Kumar SV, Raphael BJ, Wong CK, Stuart JM, Safavi R, Benz CC, Johnson BK, Kyi C, Shen H, Corces MR, Chang HY, Greenleaf WJ | Science (New York, N.Y.) | 39236169 | Science | 2024 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/39236169 |
| Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data. | Hickey JW, Tan Y, Nolan GP, Goltsev Y | Frontiers in immunology | 34484237 | Front Immunol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34484237 |
| Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. | Andreasson JOL, Gotrik MR, Wu MJ, Wayment-Steele HK, Kladwang W, Portela F, Wellington-Oguri R, Eterna Participants, Das R, Greenleaf WJ | Proceedings of the National Academy of Sciences of the United States of America | 35471911 | Proc Natl Acad Sci U S A | 2022 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/35471911 |
| Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. | Jain Y, Godwin LL, Joshi S, Mandarapu S, Le T, Lindskog C, Lundberg E, Börner K | bioRxiv : the preprint server for biology | 36711953 | bioRxiv | 2023 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/36711953 |
| Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. | Kennedy-Darling J, Bhate SS, Hickey JW, Black S, Barlow GL, Vazquez G, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP | European journal of immunology | 33548142 | Eur J Immunol | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33548142 |
| Predicting drug outcome of population via clinical knowledge graph. | Brbić M, Yasunaga M, Agarwal P, Leskovec J | medRxiv : the preprint server for health sciences | 38496488 | medRxiv | 2024 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/38496488 |
| Human mobility networks reveal increased segregation in large cities. | Nilforoshan H, Looi W, Pierson E, Villanueva B, Fishman N, Chen Y, Sholar J, Redbird B, Grusky D, Leskovec J | Nature | 38030732 | Nature | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38030732 |
| Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. | Jain Y, Godwin LL, Joshi S, Mandarapu S, Le T, Lindskog C, Lundberg E, Börner K | Nature communications | 37537179 | Nat Commun | 2023 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/37537179 |
| Segmentation of human functional tissue units in support of a Human Reference Atlas. | Jain Y, Godwin LL, Ju Y, Sood N, Quardokus EM, Bueckle A, Longacre T, Horning A, Lin Y, Esplin ED, Hickey JW, Snyder MP, Patterson NH, Spraggins JM, Börner K | Communications biology | 37468557 | Commun Biol | 2023 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/37468557 |
| Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy. | Hickey JW, Agmon E, Horowitz N, Tan TK, Lamore M, Sunwoo JB, Covert MW, Nolan GP | Cell systems | 38636457 | Cell Syst | 2024 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/38636457 |
| Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. | Becker WR, Nevins SA, Chen DC, Chiu R, Horning AM, Guha TK, Laquindanum R, Mills M, Chaib H, Ladabaum U, Longacre T, Shen J, Esplin ED, Kundaje A, Ford JM, Curtis C, Snyder MP, Greenleaf WJ | Nature genetics | 35726067 | Nat Genet | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35726067 |
| Spatial epitope barcoding reveals clonal tumor patch behaviors. | Rovira-Clavé X, Drainas AP, Jiang S, Bai Y, Baron M, Zhu B, Dallas AE, Lee MC, Chu TP, Holzem A, Ayyagari R, Bhattacharya D, McCaffrey EF, Greenwald NF, Markovic M, Coles GL, Angelo M, Bassik MC, Sage J, Nolan GP | Cancer cell | 36240778 | Cancer Cell | 2022 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/36240778 |
| Annotation of spatially resolved single-cell data with STELLAR. | Brbić M, Cao K, Hickey JW, Tan Y, Snyder MP, Nolan GP, Leskovec J | Nature methods | 36280720 | Nat Methods | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36280720 |
| Multicellular modules as clinical diagnostic and therapeutic targets. | Baertsch MA, Nolan GP, Hickey JW | Trends in cancer | 34872889 | Trends Cancer | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34872889 |
| Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging. | Phillips D, Schürch CM, Khodadoust MS, Kim YH, Nolan GP, Jiang S | Frontiers in immunology | 34093591 | Front Immunol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34093591 |
| Integration of spatial and single-cell data across modalities with weakly linked features. | Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z | Nature biotechnology | 37679544 | Nat Biotechnol | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37679544 |
| High-Dimensional Spatiotemporal Single-Cell and 3D Atlas of the Bone Marrow Microenvironment during Leukemic Progression. | Li L, Rottmann I, Ivison G, Wei H, Schroeder JC, Dunkel G, Goltsev Y, Nolan GP, Mayer AT, Saeed BR, Weigelin B, Schürch CM | bioRxiv : the preprint server for biology | 41256395 | bioRxiv | 2025 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/41256395 |
| Organization of the human intestine at single-cell resolution. | Hickey JW, Becker WR, Nevins SA, Horning A, Perez AE, Zhu C, Zhu B, Wei B, Chiu R, Chen DC, Cotter DL, Esplin ED, Weimer AK, Caraccio C, Venkataraaman V, Schürch CM, Black S, Brbić M, Cao K, Chen S, Zhang W, Monte E, Zhang NR, Ma Z, Leskovec J, Zhang Z, Lin S, Longacre T, Plevritis SK, Lin Y, Nolan GP, Greenleaf WJ, Snyder M | Nature | 37468586 | Nature | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37468586 |
| Quantitative characterization of tissue states using multiomics and ecological spatial analysis. | Ding DY, Tang Z, Zhu B, Ren H, Shalek AK, Tibshirani R, Nolan GP | Nature genetics | 40169791 | Nat Genet | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40169791 |
| Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN. | Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J | bioRxiv : the preprint server for biology | 36778387 | bioRxiv | 2023 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/36778387 |
| Landscape of coordinated immune responses to H1N1 challenge in humans. | Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, Hensley SE, Idoyaga J, Aghaeepour N, Kim K, Nolan GP, McIlwain DR | The Journal of clinical investigation | 33044226 | J Clin Invest | 2020 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/33044226 |
| Artificial intelligence foundation for therapeutic science. | Huang K, Fu T, Gao W, Zhao Y, Roohani Y, Leskovec J, Coley CW, Xiao C, Sun J, Zitnik M | Nature chemical biology | 36131149 | Nat Chem Biol | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36131149 |
| CODEX multiplexed tissue imaging with DNA-conjugated antibodies. | Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP | Nature protocols | 34215862 | Nat Protoc | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34215862 |
| Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. | Alseekh S, Aharoni A, Brotman Y, Contrepois K, D'Auria J, Ewald J, C Ewald J, Fraser PD, Giavalisco P, Hall RD, Heinemann M, Link H, Luo J, Neumann S, Nielsen J, Perez de Souza L, Saito K, Sauer U, Schroeder FC, Schuster S, Siuzdak G, Skirycz A, Sumner LW, Snyder MP, Tang H, Tohge T, Wang Y, Wen W, Wu S, Xu G, Zamboni N, Fernie AR | Nature methods | 34239102 | Nat Methods | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34239102 |
| Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma. | Phillips D, Matusiak M, Gutierrez BR, Bhate SS, Barlow GL, Jiang S, Demeter J, Smythe KS, Pierce RH, Fling SP, Ramchurren N, Cheever MA, Goltsev Y, West RB, Khodadoust MS, Kim YH, Schürch CM, Nolan GP | Nature communications | 34795254 | Nat Commun | 2021 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/34795254 |
| Cross-Laboratory Standardization of Preclinical Lipidomics Using Differential Mobility Spectrometry and Multiple Reaction Monitoring. | Ghorasaini M, Mohammed Y, Adamski J, Bettcher L, Bowden JA, Cabruja M, Contrepois K, Ellenberger M, Gajera B, Haid M, Hornburg D, Hunter C, Jones CM, Klein T, Mayboroda O, Mirzaian M, Moaddel R, Ferrucci L, Lovett J, Nazir K, Pearson M, Ubhi BK, Raftery D, Riols F, Sayers R, Sijbrands EJG, Snyder MP, Su B, Velagapudi V, Williams KJ, de Rijke YB, Giera M | Analytical chemistry | 34859676 | Anal Chem | 2021 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/34859676 |
| Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. | Schürch CM, Bhate SS, Barlow GL, Phillips DJ, Noti L, Zlobec I, Chu P, Black S, Demeter J, McIlwain DR, Kinoshita S, Samusik N, Goltsev Y, Nolan GP | Cell | 32763154 | Cell | 2020 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/32763154 |
| Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. | Ji AL, Rubin AJ, Thrane K, Jiang S, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA | Cell | 32579974 | Cell | 2020 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/32579974 |
| Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy. | Hickey JW, Agmon E, Horowitz N, Lamore M, Sunwoo J, Covert M, Nolan GP | bioRxiv : the preprint server for biology | 38106218 | bioRxiv | 2023 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/38106218 |
| In-depth triacylglycerol profiling using MS(3) Q-Trap mass spectrometry. | Cabruja M, Priotti J, Domizi P, Papsdorf K, Kroetz DL, Brunet A, Contrepois K, Snyder MP | Analytica chimica acta | 34625255 | Anal Chim Acta | 2021 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/34625255 |
| NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. | Chen AF, Parks B, Kathiria AS, Ober-Reynolds B, Goronzy JJ, Greenleaf WJ | Nature methods | 35501385 | Nat Methods | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35501385 |
| A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. | Keyes TJ, Domizi P, Lo YC, Nolan GP, Davis KL | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 32602650 | Cytometry A | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32602650 |
| Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. | Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J | Nature methods | 38366243 | Nat Methods | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38366243 |
| Potential and risks of artificial intelligence models: Common in medicine practice and special in pediatric urology. | Wen Y, Di H | Journal of pediatric urology | 37355343 | J Pediatr Urol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37355343 |
| Foundation models for generalist medical artificial intelligence. | Moor M, Banerjee O, Abad ZSH, Krumholz HM, Leskovec J, Topol EJ, Rajpurkar P | Nature | 37045921 | Nature | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37045921 |
| Single-cell spatial mapping reveals alteration of tissue microenvironment during early colorectal cancer. | Guha TK, Esplin ED, Horning AM, Chiu R, Paul K, Weimer AK, Becker WR, Laquindanum R, Mills MA, Esplin DG, Shen J, Monte E, White S, Karathanos TV, Cotter D, Bi J, Ladabaum U, Longacre TA, Curtis C, Ford JM, Greenleaf WJ, Snyder MP | bioRxiv : the preprint server for biology | 39605357 | bioRxiv | 2025 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/39605357 |
| Predicting transcriptional outcomes of novel multigene perturbations with GEARS. | Roohani Y, Huang K, Leskovec J | Nature biotechnology | 37592036 | Nat Biotechnol | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37592036 |
| T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response. | Hickey JW, Haist M, Horowitz N, Caraccio C, Tan Y, Rech AJ, Baertsch MA, Rovira-Clavé X, Zhu B, Vazquez G, Barlow G, Agmon E, Goltsev Y, Sunwoo JB, Covert M, Nolan GP | Cell reports | 38085642 | Cell Rep | 2023 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/38085642 |
| A Multicompartmental Diffusion Model for Improved Assessment of Whole-Body Diffusion-weighted Imaging Data and Evaluation of Prostate Cancer Bone Metastases. | Conlin CC, Feng CH, Digma LA, Rodríguez-Soto AE, Kuperman JM, Rakow-Penner R, Karow DS, White NS, Seibert TM, Hahn ME, Dale AM | Radiology. Imaging cancer | 36705559 | Radiol Imaging Cancer | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36705559 |
| Classification system of human ovarian follicle morphology: recommendations of the National Institute of Child Health and Human Development - sponsored ovarian nomenclature workshop. | Yano Maher JC, Zelinski MB, Oktay KH, Duncan FE, Segars JH, Lujan ME, Lou H, Yun BH, Hanfling SN, Schwartz LE, Laronda MM, Halvorson LM, O'Neill KE, Gomez-Lobo V | Fertility and sterility | 39549739 | Fertil Steril | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39549739 |
| Anatomic nomenclature and 3-dimensional regional model of the human ovary: call for a new paradigm. | O'Neill KE, Maher JY, Laronda MM, Duncan FE, LeDuc RD, Lujan ME, Oktay KH, Pouch AM, Segars JH, Tsui EL, Zelinski MB, Halvorson LM, Gomez-Lobo V | American journal of obstetrics and gynecology | 36191605 | Am J Obstet Gynecol | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36191605 |
| Systematic Sampling of the Female Reproductive System for Molecular Characterization. | Fisher SA, Grijalva M, Guo R, Johnston SA, Laurent LC, Nguyen H, Renz J, Rosario JG, Rudich S, Gregory BD, Kim J, O'Neill K | Current protocols | 37584588 | Curr Protoc | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37584588 |
| Creating a common language for the subanatomy of the ovary. | Tsui EL, O'Neill KE, LeDuc RD, Shikanov A, Gomez-Lobo V, Laronda MM | Biology of reproduction | 36308436 | Biol Reprod | 2023 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/36308436 |
| Open-source graphical user interface for the creation of synthetic skeletons for medical image analysis. | Herz C, Vergnet N, Tian S, Aly AH, Jolley MA, Tran N, Arenas G, Lasso A, Schwartz N, O'Neill KE, Yushkevich PA, Pouch AM | Journal of medical imaging (Bellingham, Wash.) | 38751729 | J Med Imaging (Bellingham) | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38751729 |
| X-CRISP: Domain-Adaptable and Interpretable CRISPR Repair Outcome Prediction. | Seale C, Gonçalves JP | bioRxiv : the preprint server for biology | 39974883 | bioRxiv | 2025 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/39974883 |
| Consensus tissue domain detection in spatial omics data using multiplex image labeling with regional morphology (MILWRM). | Kaur H, Heiser CN, McKinley ET, Ventura-Antunes L, Harris CR, Roland JT, Farrow MA, Selden HJ, Pingry EL, Moore JF, Ehrlich LIR, Shrubsole MJ, Spraggins JM, Coffey RJ, Lau KS, Vandekar SN | Communications biology | 39478141 | Commun Biol | 2024 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/39478141 |
| Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. | McMillen JC, Fincher JA, Klein DR, Spraggins JM, Caprioli RM | Journal of mass spectrometry : JMS | 33241625 | J Mass Spectrom | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33241625 |
| Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. | Sharman K, Patterson NH, Weiss A, Neumann EK, Guiberson ER, Ryan DJ, Gutierrez DB, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM | Journal of proteome research | 35849531 | J Proteome Res | 2023 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/35849531 |
| RIPK3-mediated inflammation is a conserved β cell response to ER stress. | Yang B, Maddison LA, Zaborska KE, Dai C, Yin L, Tang Z, Zang L, Jacobson DA, Powers AC, Chen W | Science advances | 33355143 | Sci Adv | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33355143 |
| MALDI IMS-Derived Molecular Contour Maps: Augmenting Histology Whole-Slide Images. | Sharman K, Patterson NH, Migas LG, Neumann EK, Allen J, Gibson-Corley KN, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM | Journal of the American Society for Mass Spectrometry | 37061946 | J Am Soc Mass Spectrom | 2023 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/37061946 |
| Advances in Imaging Mass Spectrometry for Biomedical and Clinical Research. | Djambazova KV, van Ardenne JM, Spraggins JM | Trends in analytical chemistry : TRAC | 38045023 | Trends Analyt Chem | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38045023 |
| CT CONTRAST PHASE IDENTIFICATION BY PREDICTING THE TEMPORAL ANGLE USING CIRCULAR REGRESSION. | Su D, Van Schaik KD, Remedios LW, Li T, Maldonado F, Sandler KL, Dawant BM, Landman BA | Proceedings. IEEE International Symposium on Biomedical Imaging | 40822980 | Proc IEEE Int Symp Biomed Imaging | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40822980 |
| Exocrine Pancreas in Type 1 and Type 2 Diabetes: Different Patterns of Fibrosis, Metaplasia, Angiopathy, and Adiposity. | Wright JJ, Eskaros A, Windon A, Bottino R, Jenkins R, Bradley AM, Aramandla R, Philips S, Kang H, Saunders DC, Brissova M, Powers AC | Diabetes | 37881846 | Diabetes | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/37881846 |
| ELISL: early-late integrated synthetic lethality prediction in cancer. | Tepeli YI, Seale C, Gonçalves JP | Bioinformatics (Oxford, England) | 38113447 | Bioinformatics | 2024 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/38113447 |
| Human Pseudoislet System for Synchronous Assessment of Fluorescent Biosensor Dynamics and Hormone Secretory Profiles. | Richardson TM, Pettway YD, Walker JT, Nelson HA, Ishahak M, Poffenberger G, Aramandla R, Reihsmann C, Agarwal A, Powers AC, Brissova M | Journal of visualized experiments : JoVE | 37982512 | J Vis Exp | 2023 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/37982512 |
| Blind Polarization Demultiplexing of Shaped QAM Signals Assisted by Temporal Correlations. | Bajaj V, Van de Plas R, Wahls S | Journal of lightwave technology : a joint IEEE/OSA publication | 38586243 | J Lightwave Technol | 2024 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/38586243 |
| Unmixing of Imaging Mass Spectrometry Measurements Using Microscopy-Informed Constraints. | Moens RAR, Patterson NH, Migas LG, Esselman-Lawrence AB, Moser FA, Spraggins JM, Van de Plas R | bioRxiv : the preprint server for biology | 41279206 | bioRxiv | 2025 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/41279206 |
| Calibrating CT Slice Location and Body Part in Body Part Regression. | Su D, Li T, Zuo L, Tang Y, Dawant BM, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 41459000 | Proc SPIE Int Soc Opt Eng | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41459000 |
| Insertion Network for Image Sequence Correspondence Building. | Su D, Hong W, Dawant BM, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 42181987 | Proc SPIE Int Soc Opt Eng | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/42181987 |
| Signal Strength Aware Latent Spaces Reveal Molecularly Distinct Substructures within Human Kidney Tissue. | Delacour PL, Migas LG, Farrow MA, Yang H, Fogo AB, Spraggins JM, Van de Plas R | bioRxiv : the preprint server for biology | 41648449 | bioRxiv | 2026 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/41648449 |
| Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High-Resolution Imaging Mass Spectrometry. | Anderson DMG, Messinger JD, Patterson NH, Rivera ES, Kotnala A, Spraggins JM, Caprioli RM, Curcio CA, Schey KL | Journal of the American Society for Mass Spectrometry | 32628476 | J Am Soc Mass Spectrom | 2020 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/32628476 |
| RAP-NET: COARSE-TO-FINE MULTI-ORGAN SEGMENTATION WITH SINGLE RANDOM ANATOMICAL PRIOR. | Lee HH, Tang Y, Bao S, Abramson RG, Huo Y, Landman BA | Proceedings. IEEE International Symposium on Biomedical Imaging | 34667487 | Proc IEEE Int Symp Biomed Imaging | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34667487 |
| Spatially Resolved Proteomic Analysis of the Lens Extracellular Diffusion Barrier. | Wang Z, Cantrell LS, Schey KL | Investigative ophthalmology & visual science | 34554179 | Invest Ophthalmol Vis Sci | 2021 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/34554179 |
| Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program. | Shapira SN, Naji A, Atkinson MA, Powers AC, Kaestner KH | Cell metabolism | 36206763 | Cell Metab | 2022 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/36206763 |
| Body Part Regression With Self-Supervision. | Tang Y, Gao R, Han S, Chen Y, Gao D, Nath V, Bermudez C, Savona MR, Bao S, Lyu I, Huo Y, Landman BA | IEEE transactions on medical imaging | 33560981 | IEEE Trans Med Imaging | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33560981 |
| Human pancreatic capillaries and nerve fibers persist in type 1 diabetes despite beta cell loss. | Richardson TM, Saunders DC, Haliyur R, Shrestha S, Cartailler JP, Reinert RB, Petronglo J, Bottino R, Aramandla R, Bradley AM, Jenkins R, Phillips S, Kang H, Human Pancreas Analysis Program, Caicedo A, Powers AC, Brissova M | American journal of physiology. Endocrinology and metabolism | 36696598 | Am J Physiol Endocrinol Metab | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36696598 |
| Thermal Denaturation of Fresh Frozen Tissue Enhances Mass Spectrometry Detection of Peptides. | Kruse ARS, Judd AM, Gutierrez DB, Allen JL, Dufresne M, Farrow MA, Powers AC, Norris JL, Caprioli RM, Spraggins JM | Analytical chemistry | 39392310 | Anal Chem | 2024 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/39392310 |
| In situ molecular profiles of glomerular cells by integrated imaging mass spectrometry and multiplexed immunofluorescence microscopy. | Esselman AB, Moser FA, Tideman LEM, Migas LG, Djambazova KV, Colley ME, Pingry EL, Patterson NH, Farrow MA, Yang H, Fogo AB, de Caestecker M, Van de Plas R, Spraggins JM | Kidney international | 39571907 | Kidney Int | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39571907 |
| Characterizing Low-cost Registration for Photographic Images to Computed Tomography. | Kim ME, Lee HH, Ramadass K, Gao C, Van Schaik K, Tkaczyk E, Spraggins J, Moyer DC, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 39220622 | Proc SPIE Int Soc Opt Eng | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39220622 |
| MALDI TIMS IMS Reveals Ganglioside Molecular Diversity within Murine S. aureus Kidney Tissue Abscesses. | Djambazova KV, Gibson-Corley KN, Freiberg JA, Caprioli RM, Skaar EP, Spraggins JM | Journal of the American Society for Mass Spectrometry | 39052897 | J Am Soc Mass Spectrom | 2024 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/39052897 |
| Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. | Kruse ARS, Spraggins JM | Frontiers in physiology | 35222094 | Front Physiol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35222094 |
| Mutant GNAS drives a pyloric metaplasia with tumor suppressive glycans in intraductal papillary mucinous neoplasia. | Quoc-Huy Trinh V, Ankenbauer KE, Torbit SM, Taranto CP, Liu J, Batardiere M, Kumar B, Maurer HC, Revetta F, Chen Z, Kruse ARS, Judd AM, Copeland C, Wong J, Ben-Levy O, Jarvis B, Brown M, Brown JW, Das K, Makino Y, Spraggins JM, Lau KS, Azadi P, Maitra A, Tan MCB, DelGiorno KE | Cell reports | 41370125 | Cell Rep | 2025 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/41370125 |
| Spatial Dependence and Heterogeneity in Molecular Imaging: Moran Quadrant Maps Enable Advanced Spatial-Statistical Analysis. | Tideman LEM, Moser FA, Migas LG, Spathies J, Djambazova KV, Marshall CR, Schrag MS, Skaar EP, Spraggins JM, Van de Plas R | bioRxiv : the preprint server for biology | 41279631 | bioRxiv | 2025 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/41279631 |
| Robust Body Composition Analysis by Generating 3D CT Volumes from Limited 2D Slices. | Zuo L, Yu X, Su D, Xu K, Krishnan AR, Liu Y, Bao S, Maldonado F, Ferrucci L, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 41451396 | Proc SPIE Int Soc Opt Eng | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41451396 |
| Tissue Mass Spectrometry: How Solid Is Our Future? | Unsihuay D, Phipps WS, Paulovich AG, Chapman JR, Ducret A, Eberlin LS, Spraggins JM, Goodwin RJA | Clinical chemistry | 37293883 | Clin Chem | 2023 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/37293883 |
| Lysolipids are prominent in subretinal drusenoid deposits, a high-risk phenotype in age-related macular degeneration. | Anderson DMG, Kotnala A, Migas LG, Patterson NH, Tideman L, Cao D, Adhikari B, Messinger JD, Ach T, Tortorella S, Van de Plas R, Curcio CA, Schey KL | Frontiers in ophthalmology | 38186747 | Front Ophthalmol (Lausanne) | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38186747 |
| Genetic risk converges on regulatory networks mediating early type 2 diabetes. | Walker JT, Saunders DC, Rai V, Chen HH, Orchard P, Dai C, Pettway YD, Hopkirk AL, Reihsmann CV, Tao Y, Fan S, Shrestha S, Varshney A, Petty LE, Wright JJ, Ventresca C, Agarwala S, Aramandla R, Poffenberger G, Jenkins R, Mei S, Hart NJ, Phillips S, Kang H, Greiner DL, Shultz LD, Bottino R, Liu J, Below JE, HPAP Consortium, Parker SCJ, Powers AC, Brissova M | Nature | 38049589 | Nature | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38049589 |
| X-CRISP: domain-adaptable and interpretable CRISPR repair outcome prediction. | Seale C, Gonçalves JP | Bioinformatics advances | 40677735 | Bioinform Adv | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40677735 |
| Advanced Dimensionality Reduction for Imaging Mass Spectrometry of Human Eye Tissue through Low-Rank Modeling with Sparse and Dense Residuals. | Moens RAR, Migas LG, Anderson DMG, Messinger JD, Ovchinnikova OS, Caprioli RM, Curcio CA, Schey KL, Spraggins JM, Van de Plas R | Analytical chemistry | 41081442 | Anal Chem | 2025 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/41081442 |
| Ex Vivo OCT-Based Multimodal Imaging of Human Donor Eyes for Research into Age-Related Macular Degeneration. | Messinger JD, Brinkmann M, Kimble JA, Berlin A, Freund KB, Grossman GH, Ach T, Curcio CA | Journal of visualized experiments : JoVE | 37306417 | J Vis Exp | 2023 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/37306417 |
| α-Cyano-4-hydroxycinnamic Acid and Tri-Potassium Citrate Salt Pre-Coated Silicon Nanopost Array Provides Enhanced Lipid Detection for High Spatial Resolution MALDI Imaging Mass Spectrometry. | Dufresne M, Fincher JA, Patterson NH, Schey KL, Norris JL, Caprioli RM, Spraggins JM | Analytical chemistry | 34449196 | Anal Chem | 2021 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/34449196 |
| Acceleration of age-induced proteolysis in the guinea pig lens nucleus by in vivo exposure to hyperbaric oxygen: A mass spectrometry analysis. | Giblin FJ, Anderson DMG, Han J, Rose KL, Wang Z, Schey KL | Experimental eye research | 34233175 | Exp Eye Res | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34233175 |
| Imaging Mass Spectrometry of Isotopically Resolved Intact Proteins on a Trapped Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometer. | Klein DR, Rivera ES, Caprioli RM, Spraggins JM | Analytical chemistry | 38517028 | Anal Chem | 2024 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/38517028 |
| Integrative Spatial Omics for Systems-Level Mapping of Pathological Niches. | Kruse ARS, Lardenoije R, Migas LG, Scott CF, Marshall C, Malek MC, Eskaros A, Pham T, Aamodt K, Colley M, Ventura-Antunes L, Farrow MA, Van de Plas R, Goncalves J, Schrag M, Powers AC, Spraggins JM | bioRxiv : the preprint server for biology | 41000710 | bioRxiv | 2025 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/41000710 |
| Scaling up 3D Kernels with Bayesian Frequency Re-parameterization for Medical Image Segmentation. | Lee HH, Liu Q, Bao S, Yang Q, Yu X, Cai LY, Li TZ, Huo Y, Koutsoukos X, Landman BA | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 41458213 | Med Image Comput Comput Assist Interv | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/41458213 |
| Automated biomarker candidate discovery in imaging mass spectrometry data through spatially localized Shapley additive explanations. | Tideman LEM, Migas LG, Djambazova KV, Patterson NH, Caprioli RM, Spraggins JM, Van de Plas R | Analytica chimica acta | 34482894 | Anal Chim Acta | 2021 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/34482894 |
| Localization of the lens intermediate filament switch by imaging mass spectrometry. | Wang Z, Ryan DJ, Schey KL | Experimental eye research | 32682822 | Exp Eye Res | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32682822 |
| Changes to Zonular Tension Alters the Subcellular Distribution of AQP5 in Regions of Influx and Efflux of Water in the Rat Lens. | Petrova RS, Bavana N, Zhao R, Schey KL, Donaldson PJ | Investigative ophthalmology & visual science | 32945844 | Invest Ophthalmol Vis Sci | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32945844 |
| Overcoming selection bias in synthetic lethality prediction. | Seale C, Tepeli Y, Gonçalves JP | Bioinformatics (Oxford, England) | 35876858 | Bioinformatics | 2022 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/35876858 |
| MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis. | Seale C, Barazas M, van Schendel R, Tijsterman M, Gonçalves JP | bioRxiv : the preprint server for biology | 39975194 | bioRxiv | 2025 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/39975194 |
| Super-resolution multi-contrast unbiased eye atlases with deep probabilistic refinement. | Lee HH, Saunders AM, Kim ME, Remedios SW, Remedios LW, Tang Y, Yang Q, Yu X, Bao S, Cho C, Mawn LA, Rex TS, Schey KL, Dewey BE, Spraggins JM, Prince JL, Huo Y, Landman BA | Journal of medical imaging (Bellingham, Wash.) | 39554509 | J Med Imaging (Bellingham) | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39554509 |
| MUSICiAn: genome-wide identification of genes involved in DNA repair via control-free mutational spectra analysis. | Seale C, Barazas M, van Schendel R, Tijsterman M, Gonçalves JP | NAR genomics and bioinformatics | 41524026 | NAR Genom Bioinform | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41524026 |
| CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations. | Luo X, Huang Y, Zeng H, Tao Y, Bao X, Feng F, Hopkirk AL, Pham T, Bate TSR, Saunders DC, Orchard P, Robertson C, Shrestha S, Spraggins JM, Cartailler JP, Parker SCJ, Brissova M, Liu J | Nucleic acids research | 41335468 | Nucleic Acids Res | 2025 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/41335468 |
| Enhancing Hierarchical Transformers for Whole Brain Segmentation with Intracranial Measurements Integration. | Yu X, Tang Y, Yang Q, Lee HH, Bao S, Huo Y, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 39220623 | Proc SPIE Int Soc Opt Eng | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39220623 |
| Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web. | Manz T, Gold I, Patterson NH, McCallum C, Keller MS, Herr BW 2nd, Börner K, Spraggins JM, Gehlenborg N | Nature methods | 35545714 | Nat Methods | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35545714 |
| Supervised Deep Generation of High-Resolution Arterial Phase Computed Tomography Kidney Substructure Atlas. | Lee HH, Tang Y, Bao S, Yang Q, Xu X, Fogo AB, Harris R, de Caestecker MP, Spraggins JM, Heinrich M, Huo Y, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 36303577 | Proc SPIE Int Soc Opt Eng | 2022 Feb-Mar | https://www.ncbi.nlm.nih.gov/pubmed/36303577 |
| Aminated cinnamic acid analogs as dual polarity matrices for high spatial resolution MALDI imaging mass spectrometry. | Dufresne M, Migas LG, Djambazova KV, Colley ME, Van de Plas R, Spraggins JM | Analytica chimica acta | 40825634 | Anal Chim Acta | 2025 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/40825634 |
| High-Specificity and Sensitivity Imaging of Neutral Lipids Using Salt-Enhanced MALDI TIMS. | Molloy KR, Dufresne M, Colley ME, Migas LG, Van de Plas R, Spraggins JM | Journal of the American Society for Mass Spectrometry | 40906615 | J Am Soc Mass Spectrom | 2025 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/40906615 |
| Virtual staining of label-free tissue in imaging mass spectrometry. | Zhang Y, Huang L, Pillar N, Li Y, Li Y, Migas LG, Van de Plas R, Spraggins JM, Ozcan A | Science advances | 40749063 | Sci Adv | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40749063 |
| A Streamlined Workflow for Microscopy-Driven MALDI Imaging Mass Spectrometry Data Collection. | Esselman AB, Ward MS, Marshall CR, Pingry EL, Dufresne M, Farrow MA, Schrag M, Spraggins JM | Journal of the American Society for Mass Spectrometry | 39510845 | J Am Soc Mass Spectrom | 2024 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/39510845 |
| Multi-contrast computed tomography healthy kidney atlas. | Lee HH, Tang Y, Xu K, Bao S, Fogo AB, Harris R, de Caestecker MP, Heinrich M, Spraggins JM, Huo Y, Landman BA | Computers in biology and medicine | 35533459 | Comput Biol Med | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35533459 |
| Validation of an organ mapping antibody panel for cyclical immunofluorescence microscopy on normal human kidneys. | Brewer M, Migas LG, Clouthier KA, Allen JL, Anderson DM, Pingry E, Farrow M, Quardokus EM, Spraggins JM, Van de Plas R, de Caestecker MP | American journal of physiology. Renal physiology | 38721662 | Am J Physiol Renal Physiol | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38721662 |
| The intestinal microbiota impacts nutritional immunity and resistance to Acinetobacter baumannii pneumonia. | Green ER, Negretti NM, Brunner TH, Shealy NG, Moser FA, Drury SL, Traina KA, Reyes Ruiz VM, Yang TS, Lehmann CJ, Byndloss MX, van de Plas R, Zackular JP, Light SH, Sucre JMS, Skaar EP | Proceedings of the National Academy of Sciences of the United States of America | 42012958 | Proc Natl Acad Sci U S A | 2026 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/42012958 |
| Prospective on Imaging Mass Spectrometry in Clinical Diagnostics. | Moore JL, Patterson NH, Norris JL, Caprioli RM | Molecular & cellular proteomics : MCP | 37209813 | Mol Cell Proteomics | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37209813 |
| Preserving full spectrum information in imaging mass spectrometry data reduction. | Moens RAR, Migas LG, Van Ardenne JM, Skaar EP, Spraggins JM, Van de Plas R | Bioinformatics (Oxford, England) | 40341809 | Bioinformatics | 2025 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/40341809 |
| Integration of spatial multiplexed protein imaging and transcriptomics in the human kidney tracks the regenerative potential timeline of proximal tubules. | Asghari M, Sabo AR, Barwinska D, Ferreira RM, Ferkowicz M, Bowen WS, Cheng YH, Gisch DL, Gulbronson C, Phillips CL, Kelly KJ, Sutton TA, Williams JC, Vazquez M, O'Toole J, Palevsky P, Rosas SE, Waikar SS, Kiryluk K, Parikh C, Hodgins J, Sarder P, De Boer IH, Himmelfarb J, Kretzler M, Kidney Precision Medicine Project, Jain S, Eadon MT, Winfree S, El-Achkar TM, Dagher PC | bioRxiv : the preprint server for biology | 39677736 | bioRxiv | 2024 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/39677736 |
| FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology. | Border S, Ferreira RM, Lucarelli N, Manthey D, Kumar S, Paul A, Mimar S, Naglah A, Cheng YH, Barisoni L, Ray J, Strekalova Y, Rosenberg AZ, Tomaszewski JE, Hodgin JB, HuBMAP consortium, El-Achkar TM, Jain S, Eadon MT, Sarder P | bioRxiv : the preprint server for biology | 39026885 | bioRxiv | 2024 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/39026885 |
| Protein N -Glycans in Healthy and Sclerotic Glomeruli in Diabetic Kidney Disease. | Veličković D, Shapiro JP, Parikh SV, Rovin B, Toto RD, Vazquez MA, Poggio ED, O'Toole JF, Sedor JR, Alexandrov T, Jain S, Bitzer M, Hodgin J, Veličković M, Sharma K, Anderton CR, Kidney Precision Medicine Project | Journal of the American Society of Nephrology : JASN | 38771634 | J Am Soc Nephrol | 2024 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/38771634 |
| Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney. | Lake BB, Melo Ferreira R, Hansen J, Menon R, Basta J, Thiessen Philbrook H, Reinert S, Fallegger R, Lagwankar AK, Chen X, Maity S, Djambazova KV, Gorman BL, Lucarelli N, Gisch DL, Schmidt IM, Nair V, Alakwaa F, Kefaloyianni E, Zhang B, Knoten AL, Kaushal M, Otto EA, Farrow MA, Diep D, Velickovic D, Sabo AR, Cole E, Tamayo I, Tanevski J, Conklin KY, Sealfon RSG, He Y, Brennan M, Robbins L, Cheng YH, Bitzer M, Surapaneni A, Menez S, Kharchenko PV, Alpers CE, Balis UGJ, Barisoni L, de Boer IH, Demeke D, Fogo AB, Henderson JM, Herlitz L, Moeckel GW, Randhawa PS, Rosenberg AZ, Schaub JA, Setty S, Brosius FC, Caramori ML, Coca SG, Figenshau RS, Kim EH, Kiryluk K, Lash JP, Miller RT, O'Toole JF, Palevsky PM, Rhee EP, Ricardo AC, Rosas SE, Roy-Chaudhury P, Sarwal MM, Sedor JR, Toto RD, Turkmen A, Waikar SS, Williams JC, Wilson FP, Woodle ES, Macosko EZ, Saez-Rodriguez J, Dagher PC, Grams ME, Bjornstad P, El-Achkar TM, Troyanskaya OG, Bonevich N, Sarder P, Kumar S, Anderton CR, Spraggins JM, Sharma K, Rauchman M, Himmelfarb J, Gaut JP, Precision Medicine Project K, Zhang K, Iyengar R, Kretzler M, Hodgin JB, Parikh CR, Eadon MT, Jain S | bioRxiv : the preprint server for biology | 41040183 | bioRxiv | 2025 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/41040183 |
| Spatial Atlas Creation at the Single Cell Level: Unveiling the Human Kidney Metaverse. | Dagher PC, Eadon MT, El-Achkar TM | Clinical journal of the American Society of Nephrology : CJASN | 41066188 | Clin J Am Soc Nephrol | 2026 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/41066188 |
| Shared multicellular injury programs of acute and chronic kidney disease enable mechanistic patient stratification. | Fallegger R, Gomez-Ochoa SA, Boys C, Flores ROR, Tanevski J, Pashos E, Feliers D, Piper M, Schaub JA, Zhou Z, Mao W, Chen X, Sealfon RSG, Menon R, Nair V, Eddy S, Alakwaa FM, Pyle L, Choi YJ, Bjornstad P, Alpers CE, Bitzer M, Bomback AS, Caramori ML, Demeke D, Fogo AB, Herlitz LC, Kiryluk K, Lash JP, Murugan R, O'Toole JF, Palevsky PM, Parikh CR, Rosas SE, Rosenberg AZ, Sedor JR, Vazquez MA, Waikar SS, Wilson FP, Hodgin JB, Barisoni L, Himmelfarb J, Jain S, Ju W, Troyanskaya OG, Kretzler M, Eadon MT, Saez-Rodriguez J | medRxiv : the preprint server for health sciences | 41822697 | medRxiv | 2026 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/41822697 |
| Three dimensional multiscalar neurovascular nephron connectivity map of the human kidney across the lifespan. | McLaughlin L, Zhang B, Sharma S, Knoten AL, Kaushal M, Purkerson JM, Huyck HL, Pryhuber GS, Gaut JP, Jain S | Nature communications | 40461472 | Nat Commun | 2025 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/40461472 |
| Summer Research Internship Curriculum to Promote Self-Efficacy, Researcher Identity, and Peer-to-Peer Learning: Retrospective Cohort Study. | Levites Strekalova YA, Liu-Galvin R, Border S, Midence S, Khan M, VanZanten M, Tomaszewski J, Jain S, Sarder P | JMIR formative research | 39899006 | JMIR Form Res | 2025 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/39899006 |
| The chromatin landscape of healthy and injured cell types in the human kidney. | Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Stout L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, De Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Winfree S, Jefferson N, Türkmen A, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S, Kidney Precision Medicine Project (KPMP), Jain S, Rauchman M, Eadon MT | Nature communications | 38199997 | Nat Commun | 2024 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/38199997 |
| Spatial transcriptomics in health and disease. | Jain S, Eadon MT | Nature reviews. Nephrology | 38719971 | Nat Rev Nephrol | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38719971 |
| Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury. | Ghag R, Kaushal M, Nwanne G, Knoten A, Kiryluk K, Rosenberg A, Menez S, Bagnasco SM, Sperati CJ, Atta MG, Gaut JP, Williams JC, El-Achkar TM, Arend LJ, Parikh CR, Jain S | bioRxiv : the preprint server for biology | 37986991 | bioRxiv | 2023 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/37986991 |
| Integration of spatial protein imaging and transcriptomics in the human kidney tracks the regenerative potential of proximal tubules. | Asghari M, Sabo AR, Barwinska D, Melo Ferreira R, Ferkowicz MJ, Bowen WS, Cheng YH, Gisch DL, Gulbronson C, Phillips CL, Kelly KJ, Sutton TA, Williams JC, Vazquez M, O'Toole J, Palevsky P, Rosas SE, Waikar SS, Kiryluk K, Parikh C, Hodgin JB, Sarder P, De Boer IH, Himmelfarb J, Kretzler M, Kidney Precision Medicine Project, Jain S, Eadon MT, Winfree S, El-Achkar TM, Dagher PC | Science advances | 40815665 | Sci Adv | 2025 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/40815665 |
| Cancer Cell Line Classification Using Raman Spectroscopy of Cancer-Derived Exosomes and Machine Learning. | Villazon J, Dela Cruz N, Shi L | Analytical chemistry | 40145503 | Anal Chem | 2025 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/40145503 |
| A MEF2C transcription factor network regulates proliferation of glomerular endothelial cells in diabetic kidney disease. | Ferreira RM, Gisch DL, Phillips CL, Cheng YH, Asthana M, Lake BB, Bowen WS, Fang F, Asghari M, Sabo A, Barwinska D, Ferkowicz MJ, Toto RD, Sedor JR, Rosas SE, Bjornstad P, Hodgin JB, Alpers CE, Sarder P, Himmelfarb J, Schaub JA, Nair V, Winfree S, Sutton TA, Kelly KJ, Kidney Precision Medicine Project, Kretzler M, Jain S, El-Achkar TM, Dagher PC, Eadon MT | bioRxiv : the preprint server for biology | 39803522 | bioRxiv | 2024 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/39803522 |
| Dimension-agnostic and granularity-based spatially variable gene identification using BSP. | Wang J, Li J, Kramer ST, Su L, Chang Y, Xu C, Eadon MT, Kiryluk K, Ma Q, Xu D | Nature communications | 37963892 | Nat Commun | 2023 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/37963892 |
| Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. | Lucarelli N, Ginley B, Zee J, Mimar S, Paul AS, Jain S, Han SS, Rodrigues L, Ozrazgat-Baslanti T, Wong ML, Nadkarni G, Clapp WL, Jen KY, Sarder P | Kidney360 | 37966063 | Kidney360 | 2023 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/37966063 |
| Role of Artificial Intelligence in Kidney Pathology: Promises and Pitfalls. | Goodman K, Sarullo K, Swamidass SJ, Gaut JP, Jain S | Kidney360 | 39254464 | Kidney360 | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/39254464 |
| A cross-species single-cell epigenome kidney atlas identifies epithelial cells as a driver of epigenetic aging. | Jeong H, Lake BB, Diep D, Li X, Yan Q, Gisch DL, Reinert S, Eadon MT, Gaut JP, Jain S, Zhang K | bioRxiv : the preprint server for biology | 41648348 | bioRxiv | 2026 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/41648348 |
| Hypoxia inducible factor network reflects kidney disease progression in diabetes and sodium-glucose co-transporters inhibition. | Nair V, Minakawa A, Smith C, Berthier CC, Hartman J, Menon R, Fermin D, Otto EA, Gisch DL, Eadon MT, Jain S, Choi YJ, Pyle L, Eichinger F, Alakwaa FM, Rose MP, Subramanian L, El Saghir J, Beamish JA, Hodgin JB, Brosius FC, Bjornstad P, Nelson PJ, Harder JL, Werner T, Kretzler M, Schaub JA | Signal transduction and targeted therapy | 42009641 | Signal Transduct Target Ther | 2026 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/42009641 |
| Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan. | McLaughlin L, Zhang B, Sharma S, Knoten AL, Kaushal M, Purkerson JM, Huyck H, Pryhuber GS, Gaut JP, Jain S | bioRxiv : the preprint server for biology | 39211059 | bioRxiv | 2024 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/39211059 |
| Conundrums of choice of 'normal' kidney tissue for single cell studies. | Jain S | Current opinion in nephrology and hypertension | 36811638 | Curr Opin Nephrol Hypertens | 2023 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/36811638 |
| Computational Pathology Fusing Spatial Technologies. | Border S, Lucarelli N, Eadon MT, El-Achkar TM, Jain S, Sarder P | Clinical journal of the American Society of Nephrology : CJASN | 36913267 | Clin J Am Soc Nephrol | 2023 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/36913267 |
| Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine. | He YO, Barisoni L, Rosenberg AZ, Robinson P, Diehl AD, Chen Y, Phuong J, Hansen J, Herr Ii BW, Börner K, Schaub J, Bonevich N, Arnous G, Boddapati S, Zheng J, Alakwaa F, Sardar P, Duncan WD, Liang C, Valerius MT, Jain S, Iyengar R, Himmelfarb J, Kretzler M, Kidney Precision Medicine Project | AMIA ... Annual Symposium proceedings. AMIA Symposium | 40417545 | AMIA Annu Symp Proc | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/40417545 |
| Multimodal Optical Imaging Platform for Studying Cellular Metabolism. | Villazon J, Li Z, Fan A, Shi L | Journal of visualized experiments : JoVE | 40549710 | J Vis Exp | 2025 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/40549710 |
| Navigating the kidney organoid: insights into assessment and enhancement of nephron function. | Tabibzadeh N, Satlin LM, Jain S, Morizane R | American journal of physiology. Renal physiology | 37767571 | Am J Physiol Renal Physiol | 2023 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/37767571 |
| NetTracer3D Enables User-Friendly Analysis of Diverse Microscopic and Medical 3D Datasets. | Mclaughlin L, Curic M, Sharma S, Villazon J, Salamon RJ, Yamaguch M, Sequeira-Lopez MLS, Kennedy PR, Lyons RC, Shi L, Gomez RA, Jain S | bioRxiv : the preprint server for biology | 41929015 | bioRxiv | 2026 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/41929015 |
| A MEF2C transcription factor network regulates proliferation of glomerular endothelial cells in diabetic kidney disease. | Melo Ferreira R, Gisch DL, Phillips CL, Cheng YH, Lucarelli N, Yennapureddy S, Asthana M, Lake BB, Bowen WS, Fang F, Asghari M, Sabo A, Barwinska D, Ferkowicz MJ, Toto RD, Sedor JR, Rosas SE, Bjornstad P, Hodgin JB, Alpers CE, Sarder P, Himmelfarb J, Schaub JA, Nair V, Winfree S, Sutton TA, Kelly KJ, Kidney Precision Medicine Project, Kretzler M, Jain S, El-Achkar TM, Dagher PC, Eadon MT | Kidney international | 42055320 | Kidney Int | 2026 Jul | https://www.ncbi.nlm.nih.gov/pubmed/42055320 |
| Hanging drop sample preparation improves sensitivity of spatial proteomics. | Kwon Y, Piehowski PD, Zhao R, Sontag RL, Moore RJ, Burnum-Johnson KE, Smith RD, Qian WJ, Kelly RT, Zhu Y | Lab on a chip | 35838077 | Lab Chip | 2022 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/35838077 |
| Pancreas Optical Clearing and 3-D Microscopy in Health and Diabetes. | Campbell-Thompson M, Tang SC | Frontiers in endocrinology | 33981285 | Front Endocrinol (Lausanne) | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33981285 |
| Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. | Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y | bioRxiv : the preprint server for biology | 38496682 | bioRxiv | 2024 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/38496682 |
| Islet sympathetic innervation and islet neuropathology in patients with type 1 diabetes. | Campbell-Thompson M, Butterworth EA, Boatwright JL, Nair MA, Nasif LH, Nasif K, Revell AY, Riva A, Mathews CE, Gerling IC, Schatz DA, Atkinson MA | Scientific reports | 33753784 | Sci Rep | 2021 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/33753784 |
| Integrated Physiology of the Exocrine and Endocrine Compartments in Pancreatic Diseases: Workshop Proceedings. | Mastracci TL, Apte M, Amundadottir LT, Alvarsson A, Artandi S, Bellin MD, Bernal-Mizrachi E, Caicedo A, Campbell-Thompson M, Cruz-Monserrate Z, El Ouaamari A, Gaulton KJ, Geisz A, Goodarzi MO, Hara M, Hull-Meichle RL, Kleger A, Klein AP, Kopp JL, Kulkarni RN, Muzumdar MD, Naren AP, Oakes SA, Olesen SS, Phelps EA, Powers AC, Stabler CL, Tirkes T, Whitcomb DC, Yadav D, Yong J, Zaghloul NA, Pandol SJ, Sander M | Diabetes | 36940317 | Diabetes | 2023 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/36940317 |
| Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements. | Sarkar S, Zheng X, Clair GC, Kwon YM, You Y, Swensen AC, Webb-Robertson BM, Nakayasu ES, Qian WJ, Metz TO | Trends in molecular medicine | 39152082 | Trends Mol Med | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39152082 |
| Proteome-Scale Tissue Mapping Using Mass Spectrometry Based on Label-Free and Multiplexed Workflows. | Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y | Molecular & cellular proteomics : MCP | 39307423 | Mol Cell Proteomics | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39307423 |
| Increased inflammation as well as decreased endoplasmic reticulum stress and translation differentiate pancreatic islets from donors with pre-symptomatic stage 1 type 1 diabetes and non-diabetic donors. | Swensen AC, Piehowski PD, Chen J, Chan XY, Kelly SS, Petyuk VA, Moore RJ, Nasif L, Butterworth EA, Atkinson MA, Kulkarni RN, Campbell-Thompson M, Mathews CE, Qian WJ | Diabetologia | 40457096 | Diabetologia | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40457096 |
| Deep learning-powered quantification of endocrine cells and CD3(+) T cells in the natural history of type 1 diabetes. | Kang S, Maya N, Morillo M, Outar M, Posgai AL, Lamb DG, Campbell-Thompson M, Kim S | Diabetologia | 42096070 | Diabetologia | 2026 Aug | https://www.ncbi.nlm.nih.gov/pubmed/42096070 |
| Increased Inflammation as well as Decreased Endoplasmic Reticulum Stress and Translation Differentiate Pancreatic Islets of Pre-symptomatic Stage 1 Type 1 Diabetes and Non-diabetic Cases. | Swensen AC, Piehowski PD, Chen J, Chan XY, Kelly SS, Petyuk VA, Moore RJ, Nasif L, Butterworth EA, Atkinson MA, Kulkarni RN, Campbell-Thompson M, Mathews CE, Qian WJ | bioRxiv : the preprint server for biology | 39345556 | bioRxiv | 2024 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/39345556 |
| Multiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry. | Prentice BM, McMillen JC, Caprioli RM | International journal of mass spectrometry | 30906202 | Int J Mass Spectrom | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30906202 |
| Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. | Prentice BM, Hart NJ, Phillips N, Haliyur R, Judd A, Armandala R, Spraggins JM, Lowe CL, Boyd KL, Stein RW, Wright CV, Norris JL, Powers AC, Brissova M, Caprioli RM | Diabetologia | 30955045 | Diabetologia | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30955045 |
| Staphylococcus aureus exhibits heterogeneous siderophore production within the vertebrate host. | Perry WJ, Spraggins JM, Sheldon JR, Grunenwald CM, Heinrichs DE, Cassat JE, Skaar EP, Caprioli RM | Proceedings of the National Academy of Sciences of the United States of America | 31611408 | Proc Natl Acad Sci U S A | 2019 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/31611408 |
| Phase identification for dynamic CT enhancements with generative adversarial network. | Tang Y, Gao R, Lee HH, Chen Y, Gao D, Bermudez C, Bao S, Huo Y, Savoie BV, Landman BA | Medical physics | 33410167 | Med Phys | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33410167 |
| The Importance of Clinical Tissue Imaging. | Spraggins JM, Schwamborn K, Heeren RMA, Eberlin LS | Clinical mass spectrometry (Del Mar, Calif.) | 32483555 | Clin Mass Spectrom | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32483555 |
| Renal Cortex, Medulla and Pelvicaliceal System Segmentation on Arterial Phase CT Images with Random Patch-based Networks. | Tang Y, Gao R, Lee HH, Xu Z, Savoie BV, Bao S, Huo Y, Fogo AB, Harris R, de Caestecker MP, Spraggins J, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 34531632 | Proc SPIE Int Soc Opt Eng | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34531632 |
| Highly multiplexed immunofluorescence of the human kidney using co-detection by indexing. | Neumann EK, Patterson NH, Rivera ES, Allen JL, Brewer M, deCaestecker MP, Caprioli RM, Fogo AB, Spraggins JM | Kidney international | 34619231 | Kidney Int | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34619231 |
| Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. | Islam M, Chen B, Spraggins JM, Kelly RT, Lau KS | Gastroenterology | 32417404 | Gastroenterology | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32417404 |
| Protein identification strategies in MALDI imaging mass spectrometry: a brief review. | Ryan DJ, Spraggins JM, Caprioli RM | Current opinion in chemical biology | 30476689 | Curr Opin Chem Biol | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30476689 |
| Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. | Verbeeck N, Caprioli RM, Van de Plas R | Mass spectrometry reviews | 31602691 | Mass Spectrom Rev | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/31602691 |
| Construction of a Multi-Phase Contrast Computed Tomography Kidney Atlas. | Lee HH, Tang Y, Xu K, Bao S, Fogo AB, Harris R, de Caestecker MP, Heinrich M, Spraggins JM, Huo Y, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 34354322 | Proc SPIE Int Soc Opt Eng | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34354322 |
| UNesT: Local spatial representation learning with hierarchical transformer for efficient medical segmentation. | Yu X, Yang Q, Zhou Y, Cai LY, Gao R, Lee HH, Li T, Bao S, Xu Z, Lasko TA, Abramson RG, Zhang Z, Huo Y, Landman BA, Tang Y | Medical image analysis | 37725868 | Med Image Anal | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37725868 |
| Vitessce: integrative visualization of multimodal and spatially resolved single-cell data. | Keller MS, Gold I, McCallum C, Manz T, Kharchenko PV, Gehlenborg N | Nature methods | 39333268 | Nat Methods | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39333268 |
| Permanent defects in renal medullary structure and function after reversal of urinary obstruction. | Vanichapol T, Gonzalez A, Delgado R, Brewer M, Clouthier KA, Menshikh AA, Snyder WE, Rahman T, Sander V, Yang H, Davidson AJ, de Caestecker MP | JCI insight | 39847447 | JCI Insight | 2025 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/39847447 |
| Discovering New Lipidomic Features Using Cell Type Specific Fluorophore Expression to Provide Spatial and Biological Specificity in a Multimodal Workflow with MALDI Imaging Mass Spectrometry. | Jones MA, Cho SH, Patterson NH, Van de Plas R, Spraggins JM, Boothby MR, Caprioli RM | Analytical chemistry | 32298091 | Anal Chem | 2020 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/32298091 |
| Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. | Rivera ES, Djambazova KV, Neumann EK, Caprioli RM, Spraggins JM | Journal of mass spectrometry : JMS | 32955134 | J Mass Spectrom | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32955134 |
| Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. | Neumann EK, Djambazova KV, Caprioli RM, Spraggins JM | Journal of the American Society for Mass Spectrometry | 32886506 | J Am Soc Mass Spectrom | 2020 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/32886506 |
| Protocol for multimodal analysis of human kidney tissue by imaging mass spectrometry and CODEX multiplexed immunofluorescence. | Neumann EK, Patterson NH, Allen JL, Migas LG, Yang H, Brewer M, Anderson DM, Harvey J, Gutierrez DB, Harris RC, deCaestecker MP, Fogo AB, Van de Plas R, Caprioli RM, Spraggins JM | STAR protocols | 34430920 | STAR Protoc | 2021 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/34430920 |
| A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. | Judd AM, Gutierrez DB, Moore JL, Patterson NH, Yang J, Romer CE, Norris JL, Caprioli RM | Journal of mass spectrometry : JMS | 31254303 | J Mass Spectrom | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31254303 |
| High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry. | Spraggins JM, Djambazova KV, Rivera ES, Migas LG, Neumann EK, Fuetterer A, Suetering J, Goedecke N, Ly A, Van de Plas R, Caprioli RM | Analytical chemistry | 31593446 | Anal Chem | 2019 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/31593446 |
| Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments. | Richardson LT, Neumann EK, Caprioli RM, Spraggins JM, Solouki T | Analytical chemistry | 35344335 | Anal Chem | 2022 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/35344335 |
| Unsupervised Registration Refinement for Generating Unbiased Eye Atlas. | Lee HH, Tang Y, Bao S, Yang Q, Xu X, Schey KL, Spraggins JM, Huo Y, Landman BA | Proceedings of SPIE--the International Society for Optical Engineering | 37465097 | Proc SPIE Int Soc Opt Eng | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37465097 |
| MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies. | Ryan DJ, Patterson NH, Putnam NE, Wilde AD, Weiss A, Perry WJ, Cassat JE, Skaar EP, Caprioli RM, Spraggins JM | Analytical chemistry | 31149808 | Anal Chem | 2019 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/31149808 |
| Integrated molecular imaging technologies for investigation of metals in biological systems: A brief review. | Perry WJ, Weiss A, Van de Plas R, Spraggins JM, Caprioli RM, Skaar EP | Current opinion in chemical biology | 32087551 | Curr Opin Chem Biol | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32087551 |
| Two Specific Sulfatide Species Are Dysregulated during Renal Development in a Mouse Model of Alport Syndrome. | Gessel MM, Spraggins JM, Voziyan PA, Abrahamson DR, Caprioli RM, Hudson BG | Lipids | 31197846 | Lipids | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31197846 |
| Uncovering matrix effects on lipid analyses in MALDI imaging mass spectrometry experiments. | Perry WJ, Patterson NH, Prentice BM, Neumann EK, Caprioli RM, Spraggins JM | Journal of mass spectrometry : JMS | 31860760 | J Mass Spectrom | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31860760 |
| CDKL5: a promising new therapeutic target for acute kidney injury? | de Caestecker M | American journal of physiology. Renal physiology | 33073588 | Am J Physiol Renal Physiol | 2020 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/33073588 |
| Semantic-Aware Contrastive Learning for Multi-Object Medical Image Segmentation. | Lee HH, Tang Y, Yang Q, Yu X, Cai LY, Remedios LW, Bao S, Landman BA, Huo Y | IEEE journal of biomedical and health informatics | 37310834 | IEEE J Biomed Health Inform | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37310834 |
| Regenerative Versus Nonregenerative Repair of the Renal Medulla After Reversal of Ureteral Obstruction. | Gonzalez A, Delgado R, de Caestecker MP | Seminars in nephrology | 40850858 | Semin Nephrol | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40850858 |
| qMAP enabled microanatomical mapping of human skin aging. | Han KS, Sander IB, Kumer J, Resnick E, Booth C, Cheng G, Im Y, Starich B, Kiemen AL, Phillip JM, Reddy S, Joshu CE, Sunshine JC, Walston JD, Wirtz D, Wu PH | bioRxiv : the preprint server for biology | 39005293 | bioRxiv | 2024 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/39005293 |
| E-Cadherin Induces Serine Synthesis to Support Progression and Metastasis of Breast Cancer. | Lee G, Wong C, Cho A, West JJ, Crawford AJ, Russo GC, Si BR, Kim J, Hoffner L, Jang C, Jung M, Leone RD, Konstantopoulos K, Ewald AJ, Wirtz D, Jeong S | Cancer research | 38959339 | Cancer Res | 2024 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/38959339 |
| MLL1 regulates cytokine-driven cell migration and metastasis. | Nair PR, Danilova L, Gómez-de-Mariscal E, Kim D, Fan R, Muñoz-Barrutia A, Fertig EJ, Wirtz D | Science advances | 38478601 | Sci Adv | 2024 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/38478601 |
| Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces. | Deshpande A, Loth M, Sidiropoulos DN, Zhang S, Yuan L, Bell ATF, Zhu Q, Ho WJ, Santa-Maria C, Gilkes DM, Williams SR, Uytingco CR, Chew J, Hartnett A, Bent ZW, Favorov AV, Popel AS, Yarchoan M, Kiemen A, Wu PH, Fujikura K, Wirtz D, Wood LD, Zheng L, Jaffee EM, Anders RA, Danilova L, Stein-O'Brien G, Kagohara LT, Fertig EJ | Cell systems | 37080163 | Cell Syst | 2023 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/37080163 |
| Engineering self-propelled tumor-infiltrating CAR T cells using synthetic velocity receptors. | Johnston AC, Alicea GM, Lee CC, Patel PV, Hanna EA, Vaz E, Forjaz A, Wan Z, Nair PR, Lim Y, Chen T, Du W, Kim D, Nichakawade TD, Rebecca VW, Bonifant CL, Fan R, Kiemen AL, Wu PH, Wirtz D | bioRxiv : the preprint server for biology | 38168186 | bioRxiv | 2024 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/38168186 |
| Senescent cell heterogeneity and responses to senolytic treatment are related to cell cycle status during senescence induction. | Neri F, Zheng S, Watson MA, Desprez PY, Gerencser AA, Campisi J, Wirtz D, Wu PH, Schilling B | Aging | 40778874 | Aging (Albany NY) | 2025 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/40778874 |
| Selecting the optimal cell migration assay: fundamentals and practical guidelines. | Du W, Nair PR, Forjaz A, Phillip JM, Wu PH, Wirtz D | Nature methods | 41413344 | Nat Methods | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41413344 |
| Hyper-migratory CAR T cells alleviate ovarian cancer metastatic burden and improve prognosis. | Nair PR, Hanna E, Joshi S, Duarte-Alvarado V, Bonifant CL, Wirtz D | bioRxiv : the preprint server for biology | 41256709 | bioRxiv | 2025 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/41256709 |
| Deep learning identification of stiffness markers in breast cancer. | Sneider A, Kiemen A, Kim JH, Wu PH, Habibi M, White M, Phillip JM, Gu L, Wirtz D | Biomaterials | 35537336 | Biomaterials | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35537336 |
| Cell Trafficking at the Intersection of the Tumor-Immune Compartments. | Du W, Nair P, Johnston A, Wu PH, Wirtz D | Annual review of biomedical engineering | 35385679 | Annu Rev Biomed Eng | 2022 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/35385679 |
| Three-dimensional assessments are necessary to determine the true, spatially-resolved composition of tissues. | Forjaz A, Vaz E, Romero VM, Joshi S, Braxton AM, Jiang AC, Fujikura K, Cornish T, Hong SM, Hruban RH, Wu PH, Wood LD, Kiemen AL, Wirtz D | bioRxiv : the preprint server for biology | 38106231 | bioRxiv | 2024 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/38106231 |
| Combined assembloid modeling and 3D whole-organ mapping captures the microanatomy and function of the human fallopian tube. | Crawford AJ, Forjaz A, Bons J, Bhorkar I, Roy T, Schell D, Queiroga V, Ren K, Kramer D, Huang W, Russo GC, Lee MH, Wu PH, Shih IM, Wang TL, Atkinson MA, Schilling B, Kiemen AL, Wirtz D | Science advances | 39331707 | Sci Adv | 2024 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/39331707 |
| Mechano-induced homotypic patterned domain formation by monocytes. | Wirtz D, Du W, Zhu J, Wu Y, Kiemen A, Wan Z, Hanna E, Sun S | Research square | 37790337 | Res Sq | 2023 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/37790337 |
| PanIN or IPMN? Redefining Lesion Size in 3 Dimensions. | Kiemen AL, Dequiedt L, Shen Y, Zhu Y, Matos-Romero V, Forjaz A, Campbell K, Dhana W, Cornish T, Braxton AM, Wu PH, Fishman EK, Wood LD, Wirtz D, Hruban RH | The American journal of surgical pathology | 38764379 | Am J Surg Pathol | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38764379 |
| InterpolAI: deep learning-based optical flow interpolation and restoration of biomedical images for improved 3D tissue mapping. | Joshi S, Forjaz A, Han KS, Shen Y, Queiroga V, Selaru FA, Gérard M, Xenes D, Matelsky J, Wester B, Barrutia AM, Kiemen AL, Wu PH, Wirtz D | Nature methods | 40437217 | Nat Methods | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40437217 |
| Methods to analyze cell migration data: fundamentals and practical guidelines. | Wu PH, Phillip JM, Du W, Forjaz A, Nair PR, Wirtz D | Nature methods | 41413346 | Nat Methods | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41413346 |
| NLTD 2.0: A Nonlinear Framework for Robust and Customizable Color Deconvolution in Histopathology. | Selaru F, Phillip JM, Wirtz D, Wu PH | bioRxiv : the preprint server for biology | 41256483 | bioRxiv | 2025 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/41256483 |
| Small Extracellular Vesicles Promote Stiffness-mediated Metastasis. | Sneider A, Liu Y, Starich B, Du W, Nair PR, Marar C, Faqih N, Ciotti GE, Kim JH, Krishnan S, Ibrahim S, Igboko M, Locke A, Lewis DM, Hong H, Karl MN, Vij R, Russo GC, Gómez-de-Mariscal E, Habibi M, Muñoz-Barrutia A, Gu L, Eisinger-Mathason TSK, Wirtz D | Cancer research communications | 38630893 | Cancer Res Commun | 2024 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/38630893 |
| Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping. | Joshi S, Forjaz A, Han KS, Shen Y, Queiroga V, Xenes D, Matelsk J, Wester B, Barrutia AM, Kiemen AL, Wu PH, Wirtz D | bioRxiv : the preprint server for biology | 38496512 | bioRxiv | 2024 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/38496512 |
| Power-law growth models explain incidences and sizes of pancreatic cancer precursor lesions and confirm spatial genomic findings. | Kiemen AL, Wu PH, Braxton AM, Cornish TC, Hruban RH, Wood LD, Wirtz D, Zwicker D | Science advances | 39058773 | Sci Adv | 2024 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/39058773 |
| Local, Sustained, and Targeted Co-Delivery of MEK Inhibitor and Doxorubicin Inhibits Tumor Progression in E-Cadherin-Positive Breast Cancer. | Kuhn PM, Russo GC, Crawford AJ, Venkatraman A, Yang N, Starich BA, Schneiderman Z, Wu PH, Vo T, Wirtz D, Kokkoli E | Pharmaceutics | 39204325 | Pharmaceutics | 2024 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/39204325 |
| HuBMAPR: an R Client for the HuBMAP Data Portal. | Hou C, Ghazanfar S, Marini F, Morgan M, Hicks SC | bioRxiv : the preprint server for biology | 39386647 | bioRxiv | 2024 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/39386647 |
| HuBMAPR: an R client for the HuBMAP data portal. | Hou C, Ghazanfar S, Marini F, Morgan M, Hicks SC | Bioinformatics advances | 40212885 | Bioinform Adv | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40212885 |
| Spatial proteomics and transcriptomics reveal early immune cell organization in pancreatic intraepithelial neoplasia. | Lyman MR, Mitchell JT, Raghavan S, Kagohara LT, Huff AL, Haldar SD, Shin SM, Guinn S, Barrett B, Longway G, Hernandez A, Coyne EM, Yuan X, Andaloori L, Lai J, Liu YZ, Karchin R, Gupta A, Kiemen AL, Forjaz A, Wirtz D, Wu PH, Deshpande A, Lee JW, Armstrong TD, Azad NS, Zimmerman JW, Wood LD, Anders RA, Thompson ED, Jaffee EM, Fertig EJ, Ho WJ, Zaidi N | JCI insight | 40569674 | JCI Insight | 2025 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/40569674 |
| Tumor proliferation and invasion are intrinsically coupled and unraveled through tunable spheroid and physics-based models. | Crawford AJ, Gomez-Cruz C, Russo GC, Huang W, Bhorkar I, Roy T, Muñoz-Barrutia A, Wirtz D, Garcia-Gonzalez D | Acta biomaterialia | 38160858 | Acta Biomater | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38160858 |
| Three-dimensional reconstruction of fetal rhesus macaque kidneys at single-cell resolution reveals complex inter-relation of structures. | Dequiedt L, Forjaz A, Lo JO, McCarty O, Wu PH, Rosenberg A, Wirtz D, Kiemen A | bioRxiv : the preprint server for biology | 38106004 | bioRxiv | 2024 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/38106004 |
| Mechano-induced patterned domain formation by monocytes. | Du W, Zhu J, Wu Y, Liu H, Kiemen AL, Wan Z, Hanna EA, Zhang H, Sun SX, Wirtz D | Nature materials | 41193876 | Nat Mater | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41193876 |
| vSPACE: exploring virtual spatial representation of articular chondrocytes at the single-cell level. | Zhang C, Wang H, Chung Y, Hong SH, Olmer M, Swahn H, Lotz M, Maye P, Rowe D, Shin DG | Bioinformatics (Oxford, England) | 39363499 | Bioinformatics | 2024 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/39363499 |
| vSPACE: Exploring Virtual Spatial Representation of Articular Chondrocytes at the Single-Cell Level. | Zhang C, Wang H, Hong SH, Olmer M, Swahn H, Lotz MK, Maye P, Rowe D, Shin DG | bioRxiv : the preprint server for biology | 38370845 | bioRxiv | 2024 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/38370845 |
| rPAC: Route based pathway analysis for cohorts of gene expression data sets. | Joshi P, Basso B, Wang H, Hong SH, Giardina C, Shin DG | Methods (San Diego, Calif.) | 34628030 | Methods | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34628030 |
| Senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus. | Swahn H, Li K, Duffy T, Olmer M, D'Lima DD, Mondala TS, Natarajan P, Head SR, Lotz MK | Annals of the rheumatic diseases | 36564153 | Ann Rheum Dis | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36564153 |
| Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. | Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Haddad EK, IMPACC Network, Reed EF, Kraft M, McComsey GA, Metcalf JP, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar WL, Maecker HT, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Sekaly RP, Ehrlich LI, Fourati S, Peters B, Kleinstein SH, Guan L | The Journal of clinical investigation | 38690733 | J Clin Invest | 2024 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/38690733 |
| Chronic Viral Reactivation and Associated Host Immune Response and Clinical Outcomes in Acute COVID-19 and Post-Acute Sequelae of COVID-19. | Maguire C, Chen J, Rouphael N, Pickering H, Phan HV, Glascock A, Chu V, Dandekar R, Corry D, Kheradmand F, Baden LR, Selaky R, McComsey GA, Haddad EK, Cairns CB, Pulendran B, Fernandez-Sesma A, Simon V, Metcalf JP, Higuita NIA, Messer WB, David MM, Nadeau KC, Kraft M, Bime C, Schaenman J, Erle D, Calfee CS, Atkinson MA, Brackenridge SC, Ehrlich LIR, Montgomery RR, Shaw AC, Hough CL, Geng LN, Hafler DA, Augustine AD, Becker PM, Peters B, Ozonoff A, Kim-Schulze SH, Krammer F, Bosinger S, Eckalbar W, Altman MC, Wilson M, Guan L, Kleinstein SH, IMPACC Network, Smolen KK, Reed EF, Levy O, Maecker H, Hunt P, Steen H, Diray-Arce J, Langelier CR, Melamed E | bioRxiv : the preprint server for biology | 39605478 | bioRxiv | 2024 Nov 16 | https://www.ncbi.nlm.nih.gov/pubmed/39605478 |
| Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study. | IMPACC Manuscript Writing Team, IMPACC Network Steering Committee | Science immunology | 34376480 | Sci Immunol | 2021 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/34376480 |
| Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. | Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LIR, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N, IMPACC study group members | EBioMedicine | 35952496 | EBioMedicine | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35952496 |
| Identification of a multi-omics factor predictive of long COVID in the IMPACC study. | Gabernet G, Maciuch J, Gygi JP, Moore JF, Hoch A, Syphurs C, Chu T, Jayavelu ND, Corry DB, Kheradmand F, Baden LR, Sekaly RP, McComsey GA, Haddad EK, Cairns CB, Rouphael N, Fernandez-Sesma A, Simon V, Metcalf JP, Agudelo Higuita NI, Hough CL, Messer WB, Davis MM, Nadeau KC, Pulendran B, Kraft M, Bime C, Reed EF, Schaenman J, Erle DJ, Calfee CS, Atkinson MA, Brackenridge SC, Melamed E, Shaw AC, Hafler DA, Ozonoff A, Bosinger SE, Eckalbar W, Maecker HT, Kim-Schulze S, Steen H, Krammer F, Westendorf K, IMPACC Network, Peters B, Fourati S, Altman MC, Levy O, Smolen KK, Montgomery RR, Diray-Arce J, Kleinstein SH, Guan L, Ehrlich LIR | bioRxiv : the preprint server for biology | 39990442 | bioRxiv | 2025 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/39990442 |
| Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors. | Jayavelu ND, Samaha H, Wimalasena ST, Hoch A, Gygi JP, Gabernet G, Ozonoff A, Liu S, Milliren CE, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Schaenman J, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Sesma AF, Simon V, Krammer F, Kraft M, Bime C, Calfee CS, Erle DJ, Langelier CR, IMPACC Network, Guan L, Maecker HT, Peters B, Kleinstein SH, Reed EF, Diray-Arce J, Rouphael N, Altman MC | medRxiv : the preprint server for health sciences | 39990570 | medRxiv | 2025 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/39990570 |
| geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq. | Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R, Marioni JC | Genome biology | 34872616 | Genome Biol | 2021 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/34872616 |
| Editorial: Footprints of Immune Cells in the Type 1 Diabetic Pancreas. | Brusko TM, Mallone R, Rodriguez-Calvo T | Frontiers in endocrinology | 34721308 | Front Endocrinol (Lausanne) | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34721308 |
| Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. | Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, IMPACC Network, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH | Cell reports. Medicine | 37327781 | Cell Rep Med | 2023 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/37327781 |
| MICBG406A polymorphism reduces risk of mechanical ventilation and death during viral acute lung injury. | Pickering H, Alipanah-Lechner N, Chen E, Duchen D, Maecker HT, Kim-Schulze S, Montgomery RR, Cotsapas C, Steen H, Krammer F, Langelier CR, Levy O, Baden LR, Melamed E, Ehrlich LI, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, Kraft M, Bime C, Erle DJ, Schaenmann J, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Altman MC, Bosinger S, Eckalbar W, IMPACC Network, Calfee CS, Aguilar OA, Reed EF, Greenland JR, Calabrese DR | JCI insight | 40608426 | JCI Insight | 2025 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/40608426 |
| IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. | Haslund-Gourley BS, Woloszczuk K, Hou J, Connors J, Cusimano G, Bell M, Taramangalam B, Fourati S, Mege N, Bernui M, Altman MC, Krammer F, van Bakel H, IMPACC Network, Maecker HT, Rouphael N, Diray-Arce J, Wigdahl B, Kutzler MA, Cairns CB, Haddad EK, Comunale MA | Nature communications | 38195739 | Nat Commun | 2024 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/38195739 |
| Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors. | Doni Jayavelu N, Samaha H, Wimalasena ST, Hoch A, Gygi JP, Gabernet G, Ozonoff A, Liu S, Milliren CE, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Schaenman J, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuit NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Fernandez Sesma A, Simon V, Krammer F, Kraft M, Bime C, Calfee CS, Erle DJ, Langelier CR, IMPACC Network, Guan L, Maecker HT, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Altman MC | Communications medicine | 41484172 | Commun Med (Lond) | 2026 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/41484172 |
| Protocol for processing and analyzing multiplexed images improves lymphatic cell identification and spatial architecture in human tissue. | Smith JA, Bloss DT, Williams MD, Posgai AL, Brusko TM, Atkinson MA, Wasserfall CH, Brusko MA | STAR protocols | 40714562 | STAR Protoc | 2025 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/40714562 |
| Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients. | Pickering H, Schaenman J, Phan HV, Maguire C, Tsitsiklis A, Rouphael N, Higuita NIA, Atkinson MA, Brakenridge S, Fung M, Messer W, IMPACC Network, Salehi-Rad R, Altman MC, Becker PM, Bosinger SE, Eckalbar W, Hoch A, Doni Jayavelu N, Kim-Schulze S, Jenkins M, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Diray-Arce J, Shaw A, Baden L, Levy O, Reed EF, Langelier CR | Nature communications | 39794319 | Nat Commun | 2025 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/39794319 |
| Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19. | Glascock A, Maguire C, Phan HV, Lydon EC, Schaenman J, Calfee CS, Melamed E, Greenland J, Corry DB, Kheradmand F, Baden LR, Sekaly R, McComsey GA, Haddad EK, Cairns CB, Geng LN, Pulendran B, Fernandez-Sesma A, Simon V, Metcalf JP, Agudelo Higuita NI, Messer WB, Davis MM, Nadeau KC, Kraft M, Bime C, Erle DJ, Atkinson MA, Brakenridge SC, Ehrlich LIR, Montgomery RR, Shaw AC, Hough CL, Hafler DA, Augustine AD, Becker PM, Peters B, Ozonoff A, Hoch A, Kim-Schulze S, Krammer F, Bosinger S, Eckalbar W, Altman MC, Wilson M, Guan L, Maecker H, Steen H, IMPACC Network, Diray-Arce J, Rouphael N, Kleinstein SH, Jayavelu ND, Reed EF, Levy O, Chu VT, Langelier CR | Nature microbiology | 41840216 | Nat Microbiol | 2026 Apr | https://www.ncbi.nlm.nih.gov/pubmed/41840216 |
| Incidence Trends of New-Onset Diabetes in Children and Adolescents Before and During the COVID-19 Pandemic: Findings From Florida. | Guo Y, Bian J, Chen A, Wang F, Posgai AL, Schatz DA, Shenkman EA, Atkinson MA | Diabetes | 36094294 | Diabetes | 2022 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/36094294 |
| Characterizing cell-type spatial relationships across length scales in spatially resolved omics data. | Dos Santos Peixoto R, Miller BF, Brusko MA, Aihara G, Atta L, Anant M, Atkinson MA, Brusko TM, Wasserfall CH, Fan J | bioRxiv : the preprint server for biology | 39314450 | bioRxiv | 2024 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/39314450 |
| Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology. | Van Phan H, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, Van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns C, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, IMPACC Network, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR | medRxiv : the preprint server for health sciences | 38405760 | medRxiv | 2024 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/38405760 |
| Longitudinal plasma proteomic analysis of 1117 hospitalized patients with COVID-19 identifies features associated with severity and outcomes. | Viode A, Smolen KK, van Zalm P, Stevenson D, Jha M, Parker K, IMPACC Network‡, Levy O, Steen JA, Steen H | Science advances | 38787940 | Sci Adv | 2024 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/38787940 |
| High-affinity CD16A polymorphism associated with reduced risk ofsevere COVID-19. | Qualls AE, Tsao T, Lui I, Lim SA, Su Y, Chen E, Duchen D, Maecker HT, Kim-Schulze S, Montgomery RR, Krammer F, Langelier CR, Levy O, Baden LR, Melamed E, Ehrlich LI, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez-Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Schaenmann J, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, IMPACC Network, Goldman JD, Calabrese DR, Heath JR, Wells JA, Reed EF, Lanier LL, Pickering H, Aguilar OA | JCI insight | 40402577 | JCI Insight | 2025 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/40402577 |
| A multiomics recovery factor predicts long COVID in the IMPACC study. | Gabernet G, Maciuch J, Gygi JP, Moore JF, Hoch A, Syphurs C, Chu T, Doni Jayavelu N, Corry DB, Kheradmand F, Baden LR, Sekaly RP, McComsey GA, Haddad EK, Cairns CB, Rouphael N, Fernandez-Sesma A, Simon V, Metcalf JP, Agudelo Higuita NI, Hough CL, Messer WB, Davis MM, Nadeau KC, Pulendran B, Kraft M, Bime C, Reed EF, Schaenman J, Erle DJ, Calfee CS, Atkinson MA, Brakenridge SC, Melamed E, Shaw AC, Hafler DA, Augustine AD, Becker PM, Ozonoff A, Bosinger SE, Eckalbar W, Maecker HT, Kim-Schulze S, Steen H, Krammer F, Westendorf K, IMPACC Network, Peters B, Fourati S, Altman MC, Levy O, Smolen KK, Montgomery RR, Diray-Arce J, Kleinstein SH, Guan L, Ehrlich LI | The Journal of clinical investigation | 40924481 | J Clin Invest | 2025 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/40924481 |
| A Parallelization Strategy for the Time Efficient Analysis of Thousands of LC/MS Runs in High-Performance Computing Environment. | van Zalm P, Viodé A, Smolen K, Fatou B, Hayati AN, Schlaffner CN, Levy O, Steen J, Steen H | Journal of proteome research | 36201825 | J Proteome Res | 2022 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/36201825 |
| Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study. | Hou J, Haslund-Gourley B, Diray-Arce J, Hoch A, Rouphael N, Becker PM, Augustine AD, Ozonoff A, Guan L, Kleinstein SH, Peters B, Reed E, Altman M, Langelier CR, Maecker H, Kim S, Montgomery RR, Krammer F, Wilson M, Eckalbar W, Bosinger SE, Levy O, Steen H, Rosen LB, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Schaenman J, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuita NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Impacc Network, Robinson LF, Cairns CB, Haddad EK, Comunale MA | Frontiers in medicine | 40687705 | Front Med (Lausanne) | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40687705 |
| Limited extent and consequences of pancreatic SARS-CoV-2 infection. | van der Heide V, Jangra S, Cohen P, Rathnasinghe R, Aslam S, Aydillo T, Geanon D, Handler D, Kelley G, Lee B, Rahman A, Dawson T, Qi J, D'Souza D, Kim-Schulze S, Panzer JK, Caicedo A, Kusmartseva I, Posgai AL, Atkinson MA, Albrecht RA, García-Sastre A, Rosenberg BR, Schotsaert M, Homann D | Cell reports | 35247306 | Cell Rep | 2022 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/35247306 |
| A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics. | Viode A, van Zalm P, Smolen KK, Fatou B, Stevenson D, Jha M, Levy O, Steen J, Steen H, IMPACC Network | Science advances | 36989362 | Sci Adv | 2023 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/36989362 |
| IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. | Haslund-Gourley B, Woloszcuk K, Hou J, Connors J, Cusimano G, Bell M, Taramangalam B, Fourati S, Mege N, Bernui M, Altman M, Krammer F, van Bakel H, Maecker H, Wigdahl B, Cairns C, Haddad E, Comunale M | Research square | 37398192 | Res Sq | 2023 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/37398192 |
| Minimalistic Transcriptomic Signatures Permit Accurate Early Prediction of COVID-19 Mortality. | Narendra R, Lydon EC, Van Phan H, Spottiswoode N, Neyton LP, Diray-Arce J, IMPACC Network, COMET Consortium, EARLI Consortium, Becker PM, Kim-Schulze S, Hoch A, Pickering H, van Zalm P, Cairns CB, Altman MC, Augustine AD, Bosinger S, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Carillo SA, Erle D, Hendrickson CM, Krummel MF, Matthay MA, Woodruff P, Haddad EK, Calfee CS, Langelier CR | medRxiv : the preprint server for health sciences | 40475132 | medRxiv | 2025 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/40475132 |
| Empiric Azithromycin in COVID-19 Impacts the Respiratory Microbiome and Antimicrobial Resistome without Anti-inflammatory Benefit. | Langelier C, Glascock A, Maguire C, Van Phan H, Lydon E, Calfee C, Corry D, Kheradmand F, Baden L, Sekaly RP, McComsey G, Haddad E, Cairns C, Pulendran B, Fernandez-Sesma A, Simon V, Metcalf J, Higuita N, Messer W, Davis M, Nadeau KC, Kraft M, Bime C, Schaenman J, Erle D, Atkinson M, Ehrlich LIR, Melamed E, Montgomery R, Shaw A, Hough C, Geng L, Hoch A, Hafler D, Augustine A, Becker P, Peters B, Ozonoff A, Kim-Schulze S, Krammer F, Bosinger S, Eckalbar W, Altman M, Wilson M, Guan L, Maecker H, Steen H, Diray-Arce J, Rouphael N, Kleinstein S, Reed E, Levy O, Chu V | Research square | 40585204 | Res Sq | 2025 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/40585204 |
| Characterizing cell-type spatial relationships across length scales in spatially resolved omics data. | Dos Santos Peixoto R, Miller BF, Brusko MA, Aihara G, Atta L, Anant M, Atkinson MA, Brusko TM, Wasserfall CH, Fan J | Nature communications | 39753600 | Nat Commun | 2025 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/39753600 |
| Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients. | Langelier C, Pickering H, Schaenman J, Phan H, Maguire C, Tsitsiklis A, Rouphael N, Higuita N, Atkinson M, Breckenridge S, Fung M, Messer W, IMPACC Network, Salehi-Rad R, Altman M, Becker P, Bosinger S, Eckalbar W, Hoch A, Jayavelu N, Kim-Schulze S, Jenkins M, Kleinstein S, Krammer F, Maecker H, Ozonoff A, Diray-Arce J, Shaw A, Baden L, Levy O, Reed E | Research square | 38196658 | Res Sq | 2023 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/38196658 |
| Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. | Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, IMPACC Network, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N | Nature communications | 38172101 | Nat Commun | 2024 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/38172101 |
| Type 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort. | Jayavelu ND, Qi J, Milliren CE, Ozonoff A, Liu S, Levy O, Baden LR, Melamed E, McComsey GA, Cairns CB, Schaenman J, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuita NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Sesma AF, Simon V, Krammer F, Bime C, Calfee CS, Bosinger SE, Eckalbar W, Steen H, Maecker HT, IMPACC Network, Augustine AD, Diray-Arce J, Haddad EK, Sekaly RP, Kraft M, Woodruff PG, Erle DJ, Ehrlich LIR, Montgomery RR, Becker PM, Altman MC, Fourati S | The journal of allergy and clinical immunology. Global | 40709330 | J Allergy Clin Immunol Glob | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40709330 |
| Evaluating COVID-19 severity prediction and immune dynamics with NULISAseq: Insights from the IMPACC study. | Abe K, Holmes TH, Nguyen TT, IMPACC Network, Kim-Schulze S, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuita NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez-Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Schaenman J, Reed EF, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Maecker HT | Journal of immunology (Baltimore, Md. : 1950) | 41166719 | J Immunol | 2025 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/41166719 |
| Minimalistic transcriptomic signatures permit accurate early prediction of COVID-19 mortality. | Narendra R, Lydon EC, Phan HV, Spottiswoode N, Neyton LP, Diray-Arce J, IMPACC Network, COMET Consortium, EARLI Consortium, Becker PM, Kim-Schulze S, Hoch A, Pickering H, van Zalm P, Cairns CB, Altman MC, Augustine AD, Bosinger S, Eckalbar W, Guan L, Doni Jayavelu N, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Haller SC, Erle D, Hendrickson CM, Krummel MF, Matthay MA, Woodruff P, Haddad EK, Calfee CS, Langelier CR | JCI insight | 41212055 | JCI Insight | 2025 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/41212055 |
| Circulating endothelial signatures correlate with worse outcomes in COVID-19, respiratory failure and ARDS. | Costa Monteiro AC, Pickering H, Sarma A, Taylor CS, Jenkins MM, Hsu FM, Nadel B, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Fernandez-Sesma A, Simon V, Krammer F, Kraft M, Bime C, Calfee CS, Erle DJ, Bosinger S, Eckalbar W, Maecker H, Rahman A, Guan L, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, IMPACC Network, CAFPINT Site investigators of the PALISI Network, Agus M, Kulkarni H, Schaenmann JM, Salehi-Rad R, Matthay MA, Reed EF, Sapru A | Critical care (London, England) | 41088445 | Crit Care | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/41088445 |
| Polygenic prediction of preeclampsia and gestational hypertension. | Honigberg MC, Truong B, Khan RR, Xiao B, Bhatta L, Vy HMT, Guerrero RF, Schuermans A, Selvaraj MS, Patel AP, Koyama S, Cho SMJ, Vellarikkal SK, Trinder M, Urbut SM, Gray KJ, Brumpton BM, Patil S, Zöllner S, Antopia MC, Saxena R, Nadkarni GN, Do R, Yan Q, Pe'er I, Verma SS, Gupta RM, Haas DM, Martin HC, van Heel DA, Laisk T, Natarajan P | Nature medicine | 37248299 | Nat Med | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37248299 |
| Integrative analysis of single-cell transcriptomics and genetic associations identify cell states associated with vascular disease. | Pepin ME, Schwartzman WE, Fang S, Vellarikkal SK, Atri DS, Reddy A, Xu Q, Hamel AR, Billaud M, Segrè AV, Gupta RM | Atherosclerosis | 40120433 | Atherosclerosis | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40120433 |
| Missing Regulation Between Genetic Association and Transcriptional Abundance for Hypercholesterolemia Genes. | Hakim A, Connally NJ, Schnitzler GR, Cho MH, Jiang ZG, Sunyaev SR, Gupta RM | Genes | 39858631 | Genes (Basel) | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39858631 |
| REECAP: Contrastive learning of retinal aging reveals genetic loci linking morphology to eye disease. | Shilova L, Sens D, Aliyeva A, Chaudhary S, Xu Q, Salin E, Schiefelbein J, Asani B, Amarie OV, Schneltzer E, Segrè AV, Schnabel JA, Cai N, Eskofier BM, Casale FP | medRxiv : the preprint server for health sciences | 41332846 | medRxiv | 2025 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/41332846 |
| Common Coronary Artery Disease Risk Variants in Endothelial Regulatory Elements Modulate Tetraspanin 14 Expression and Notch Signaling. | Lee-Kim VS, Schnitzler GR, Fang S, Mardani-Kamali N, Cai XS, Cui R, Barry AE, Zandavi M, Yoo HJ, Kant S, Mahajan R, Rao SSP, Aiden EL, Engreitz JM, Gupta RM | Arteriosclerosis, thrombosis, and vascular biology | 42021732 | Arterioscler Thromb Vasc Biol | 2026 Jun | https://www.ncbi.nlm.nih.gov/pubmed/42021732 |
| The Role of Endothelial Cells in Atherosclerosis: Insights from Genetic Association Studies. | Pepin ME, Gupta RM | The American journal of pathology | 37827214 | Am J Pathol | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37827214 |
| Multiomic Analysis and CRISPR Perturbation Screens Identify Endothelial Cell Programs and Novel Therapeutic Targets for Coronary Artery Disease. | Gupta RM, Schnitzler GR, Fang S, Lee-Kim VS, Barry A | Arteriosclerosis, thrombosis, and vascular biology | 36994731 | Arterioscler Thromb Vasc Biol | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36994731 |
| Endothelial cell-related genetic variants identify LDL cholesterol-sensitive individuals who derive greater benefit from aggressive lipid lowering. | Marston NA, Kamanu FK, Melloni GEM, Schnitzler G, Hakim A, Ma RX, Kang H, Chasman DI, Giugliano RP, Ellinor PT, Ridker PM, Engreitz JM, Sabatine MS, Ruff CT, Gupta RM | Nature medicine | 40011692 | Nat Med | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/40011692 |
| Convergence of coronary artery disease genes onto endothelial cell programs. | Schnitzler GR, Kang H, Fang S, Angom RS, Lee-Kim VS, Ma XR, Zhou R, Zeng T, Guo K, Taylor MS, Vellarikkal SK, Barry AE, Sias-Garcia O, Bloemendal A, Munson G, Guckelberger P, Nguyen TH, Bergman DT, Hinshaw S, Cheng N, Cleary B, Aragam K, Lander ES, Finucane HK, Mukhopadhyay D, Gupta RM, Engreitz JM | Nature | 38326615 | Nature | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38326615 |
| Decoding Vascular Cell Diversity: Single-Cell Approaches to Mechanisms of Vascular Disease. | Schwartzman WE, Jiang J, Rao JS, Schnitzler G, Maurya M, Widdup L, Pepin ME, Kang H, Zheng C, Gupta RM | Circulation research | 41481684 | Circ Res | 2026 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/41481684 |
| Characteristics of p.Gln368Ter Myocilin Variant and Influence of Polygenic Risk on Glaucoma Penetrance in the UK Biobank. | Zebardast N, Sekimitsu S, Wang J, Elze T, Gharahkhani P, Cole BS, Lin MM, Segrè AV, Wiggs JL, International Glaucoma Genetics Consortium | Ophthalmology | 33713785 | Ophthalmology | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/33713785 |
| MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. | Shao X, Gomez CD, Kapoor N, Considine JM, Grams C, Gao YT, Naba A | Nucleic acids research | 36399478 | Nucleic Acids Res | 2023 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/36399478 |
| Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives. | Naba A | Molecular & cellular proteomics : MCP | 36918099 | Mol Cell Proteomics | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36918099 |
| Mechanisms of assembly and remodelling of the extracellular matrix. | Naba A | Nature reviews. Molecular cell biology | 39223427 | Nat Rev Mol Cell Biol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39223427 |
| MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface. | Samarasinghe KW, Kotlyar M, Vallet SD, Hayes C, Naba A, Jurisica I, Lisacek F, Ricard-Blum S | Nucleic acids research | 39558161 | Nucleic Acids Res | 2025 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/39558161 |
| Blood proteomics: insights from public data. | Larrea-Sebal A, Dai C, Brenes AJ, Korff K, Neely BA, Geyer PE, Dagley LF, Unwin RD, Naba A, MacCoss MJ, Guo T, Deutsch EW, Martin C, Schwenk JM, Perez-Riverol Y | Genome biology | 41821120 | Genome Biol | 2026 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/41821120 |
| Time-lapse tryptic digestion: a proteomic approach to improve sequence coverage of extracellular matrix proteins. | Lee F, Shao X, Considine JM, Gao YT, Naba A | bioRxiv : the preprint server for biology | 40196545 | bioRxiv | 2025 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/40196545 |
| MatriCom: a scRNA-Seq data mining tool to infer ECM-ECM and cell-ECM communication systems. | Lamba R, Paguntalan AM, Petrov PB, Naba A, Izzi V | bioRxiv : the preprint server for biology | 39763937 | bioRxiv | 2024 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/39763937 |
| Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms. | Petrov PB, Considine JM, Izzi V, Naba A | Journal of cell science | 37555624 | J Cell Sci | 2023 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/37555624 |
| A guide to building the matrisome interactome: from computational predictions to experimental validation. | Leverton L, Bains AK, Isa I, Ricard-Blum S, Naba A | The FEBS journal | 41261523 | FEBS J | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41261523 |
| The Gene Ontology knowledgebase in 2026. | Gene Ontology Consortium | Nucleic acids research | 41413728 | Nucleic Acids Res | 2026 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/41413728 |
| Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. | Petrov PB, Considine JM, Izzi V, Naba A | bioRxiv : the preprint server for biology | 37131773 | bioRxiv | 2023 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/37131773 |
| MatriCom, a single-cell RNA-sequencing data mining tool to infer cell-extracellular matrix interactions. | Lamba R, Paguntalan AM, Petrov PB, Naba A, Izzi V | Journal of cell science | 40501363 | J Cell Sci | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40501363 |
| Proteomic insights into the extracellular matrix: a focus on proteoforms and their implications in health and disease. | Bains AK, Naba A | Expert review of proteomics | 39512072 | Expert Rev Proteomics | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39512072 |
| Primary human ovarian interstitial cells contribute to murine follicle growth through follicle-interstitial paracrine crosstalk. | Tsui EL, Saunders DC, Lu L, Kennedy T, Lee S, Filip SK, Faull PA, Hunter N, Rowell EE, Gao R, Laronda MM | Research square | 41041526 | Res Sq | 2025 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/41041526 |
| Establishing the baseline: understanding follicle activation morphometrics in multiple mammalian species†. | Kubo H, McCauley CJ, Zelinski MB, Laronda MM | Biology of reproduction | 40121544 | Biol Reprod | 2025 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/40121544 |
| Ovarian tissue cryopreservation in pediatric patients with malignancy involving the ovary. | Bak MJ, Farje D, Tsui EL, Lautz TB, Laronda MM, Rowell EE | Fertility and sterility | 38838804 | Fertil Steril | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38838804 |
| Heterogeneity of ovarian matrisome hydrogels elucidates factors that may influence follicle growth in vitro. | McDowell HB, Henning NF, Laronda MM | Reproduction (Cambridge, England) | 38888996 | Reproduction | 2024 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/38888996 |
| Digital analysis of ovarian tissue: generating a standardized method of follicle analysis†. | McDowell H, Vieco-Martí I, VanZanten M, Pant S, Kubo H, Saunders DC, Laronda MM, Granados-Aparici S | Biology of reproduction | 39903671 | Biol Reprod | 2025 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/39903671 |
| Engineering strategies and challenges in building the follicular microenvironment for a bioprosthetic ovary. | Saunders DC, Laronda MM | Best practice & research. Clinical obstetrics & gynaecology | 40763416 | Best Pract Res Clin Obstet Gynaecol | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40763416 |
| Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. | Taylor DJ, Eizenga JM, Li Q, Das A, Jenike KM, Kenny EE, Miga KH, Monlong J, McCoy RC, Paten B, Schatz MC | Annual review of genomics and human genetics | 38663087 | Annu Rev Genomics Hum Genet | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38663087 |
| Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation. | Billingsley KJ, Meredith M, Daida K, Jerez PA, Negi S, Malik L, Genner RM, Moller A, Zheng X, Gibson SB, Mastoras M, Baker B, Kouam C, Paquette K, Jarreau P, Makarious MB, Moore A, Hong S, Vitale D, Shah S, Monlong J, Pantazis CB, Asri M, Shafin K, Carnevali P, Marenco S, Auluck P, Mandal A, Miga KH, Rhie A, Reed X, Ding J, Cookson MR, Nalls M, Singleton A, Miller DE, Chaisson M, Timp W, Gibbs JR, Phillippy AM, Kolmogorov M, Jain M, Sedlazeck FJ, Paten B, Blauwendraat C | bioRxiv : the preprint server for biology | 39764002 | bioRxiv | 2024 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/39764002 |
| DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies. | Park J, Cook DE, Chang PC, Kolesnikov A, Brambrink L, Mier JC, Gardner J, McNulty B, Sacco S, Keskus A, Bryant A, Ahmad T, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Yoo B, Pushel I, Lansdon LA, Bi C, Walter A, Gibson M, Pastinen T, Farooqi MS, Robine N, Miga KH, Carroll A, Kolmogorov M, Paten B, Shafin K | bioRxiv : the preprint server for biology | 39229187 | bioRxiv | 2024 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/39229187 |
| Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. | Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B | Nature methods | 37710018 | Nat Methods | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37710018 |
| Phased nanopore assembly with Shasta and modular graph phasing with GFAse. | Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga J, Juul S, McKenzie S, Simmonds SE, Park J, Asri M, Koren S, Eichler E, Axel R, Martin B, Carnevali P, Miga K, Paten B | bioRxiv : the preprint server for biology | 36865218 | bioRxiv | 2023 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/36865218 |
| CytoSpatio: Learning cell type spatial relationships using multirange, multitype point process models. | Chen H, Zhang Y, Murphy RF | PLoS computational biology | 40839662 | PLoS Comput Biol | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40839662 |
| Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic. | Park J, Cook DE, Chang PC, Kolesnikov A, Brambrink L, Mier JC, Gardner J, McNulty B, Sacco S, Keskus AG, Bryant A, Ahmad T, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Yoo B, Pushel I, Lansdon LA, Bi C, Walter A, Gibson M, Pastinen T, Reiman R, Mankame S, Ranallo-Benavidez TR, Brown C, Robine N, Barthel FP, Farooqi MS, Miga KH, Carroll A, Kolmogorov M, Paten B, Shafin K | Nature biotechnology | 41102444 | Nat Biotechnol | 2025 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/41102444 |
| A draft human pangenome reference. | Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B | Nature | 37165242 | Nature | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37165242 |
| Genetic regulation of TERT splicing affects cancer risk by altering cellular longevity and replicative potential. | Florez-Vargas O, Ho M, Hogshead MH, Papenberg BW, Lee CH, Forsythe K, Jones K, Luo W, Teshome K, Blauwendraat C, Billingsley KJ, Kolmogorov M, Meredith M, Paten B, Chari R, Zhang C, Schneekloth JS, Machiela MJ, Chanock SJ, Gadalla SM, Savage SA, Mbulaiteye SM, Prokunina-Olsson L | Nature communications | 39956830 | Nat Commun | 2025 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/39956830 |
| Personalized pangenome references. | Sirén J, Eskandar P, Ungaro MT, Hickey G, Eizenga JM, Novak AM, Chang X, Chang PC, Kolmogorov M, Carroll A, Monlong J, Paten B | Nature methods | 39261641 | Nat Methods | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39261641 |
| Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing. | Keskus AG, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Bi C, Walter A, Gibson M, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M | Nature biotechnology | 40185952 | Nat Biotechnol | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/40185952 |
| The UCSC Genome Browser database: 2025 update. | Perez G, Barber GP, Benet-Pages A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Raney BJ, Speir ML, van Baren MJ, Vaske CJ, Haussler D, Kent WJ, Haeussler M | Nucleic acids research | 39460617 | Nucleic Acids Res | 2025 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/39460617 |
| SPRM: spatial process and relationship modeling for multiplexed images. | Zhang T, Chen H, Lee YJ, Ruffalo M, Murphy RF | Bioinformatics advances | 41695258 | Bioinform Adv | 2026 | https://www.ncbi.nlm.nih.gov/pubmed/41695258 |
| Pangenome graph construction from genome alignments with Minigraph-Cactus. | Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B | Nature biotechnology | 37165083 | Nat Biotechnol | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37165083 |
| Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. | Negi S, Stenton SL, Berger SI, Canigiula P, McNulty B, Violich I, Gardner J, Hillaker T, O'Rourke SM, O'Leary MC, Carbonell E, Austin-Tse C, Lemire G, Serrano J, Mangilog B, VanNoy G, Kolmogorov M, Vilain E, O'Donnell-Luria A, Délot E, Miga KH, Monlong J, Paten B | American journal of human genetics | 39862869 | Am J Hum Genet | 2025 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/39862869 |
| Expanding the coverage of spatial proteomics: a machine learning approach. | Sun H, Li J, Murphy RF | Bioinformatics (Oxford, England) | 38310340 | Bioinformatics | 2024 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/38310340 |
| Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. | Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M | medRxiv : the preprint server for health sciences | 38585974 | medRxiv | 2024 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/38585974 |
| Phased nanopore assembly with Shasta and modular graph phasing with GFAse. | Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen HE, McNulty B, Porubsky D, Montague TG, Lucas JK, Condon C, Eizenga JM, Juul S, McKenzie SK, Simmonds SE, Park J, Asri M, Koren S, Eichler EE, Axel R, Martin B, Carnevali P, Miga KH, Paten B | Genome research | 38627094 | Genome Res | 2024 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/38627094 |
| 3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation. | Chen H, Murphy RF | bioRxiv : the preprint server for biology | 38559093 | bioRxiv | 2024 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/38559093 |
| Flexible and robust cell type annotation for highly multiplexed tissue images. | Sun H, Yu S, Casals AM, Bäckström A, Lu Y, Lindskog C, Ruffalo M, Lundberg E, Murphy RF | bioRxiv : the preprint server for biology | 39345395 | bioRxiv | 2024 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/39345395 |
| Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. | Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PA, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, North American Brain Expression Consortium (NABEC), Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B | bioRxiv : the preprint server for biology | 36711673 | bioRxiv | 2023 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/36711673 |
| CytoSpatio: Learning cell type spatial relationships using multirange, multitype point process models. | Chen H, Murphy RF | bioRxiv : the preprint server for biology | 39553984 | bioRxiv | 2024 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/39553984 |
| Genetic regulation of TERT splicing contributes to reduced or elevated cancer risk by altering cellular longevity and replicative potential. | Florez-Vargas O, Ho M, Hogshead M, Lee CH, Papenberg BW, Forsythe K, Jones K, Luo W, Teshome K, Blauwendraat C, Billingsley KJ, Kolmogorov M, Meredith M, Paten B, Chari R, Zhang C, Schneekloth JS, Machiela MJ, Chanock SJ, Gadalla S, Savage SA, Mbulaiteye SM, Prokunina-Olsson L | medRxiv : the preprint server for health sciences | 39802763 | medRxiv | 2024 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/39802763 |
| Local read haplotagging enables accurate long-read small variant calling. | Kolesnikov A, Cook D, Nattestad M, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K | bioRxiv : the preprint server for biology | 37745389 | bioRxiv | 2023 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/37745389 |
| Personalized Pangenome References. | Sirén J, Eskandar P, Ungaro MT, Hickey G, Eizenga JM, Novak AM, Chang X, Chang PC, Kolmogorov M, Carroll A, Monlong J, Paten B | bioRxiv : the preprint server for biology | 38168361 | bioRxiv | 2023 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/38168361 |
| Flexible and robust cell-type annotation for highly multiplexed tissue images. | Sun H, Yu S, Casals AM, Bäckström A, Lu Y, Lindskog C, Ruffalo M, Lundberg E, Murphy RF | Cell systems | 40925369 | Cell Syst | 2025 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/40925369 |
| Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. | Missarova A, Dann E, Rosen L, Satija R, Marioni J | Genome biology | 39026254 | Genome Biol | 2024 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/39026254 |
| Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens. | Jiang L, Dalgarno C, Papalexi E, Mascio I, Wessels HH, Yun H, Iremadze N, Lithwick-Yanai G, Lipson D, Satija R | Nature cell biology | 40011560 | Nat Cell Biol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/40011560 |
| Evidence of off-target probe binding affecting 10x Genomics Xenium gene panels compromise accuracy of spatial transcriptomic profiling. | Hallinan C, Ji HJ, Tsou E, Salzberg SL, Fan J | eLife | 42065925 | Elife | 2026 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/42065925 |
| Multimodal characterization of antigen-specific CD8 (+) T cells across SARS-CoV-2 vaccination and infection. | Zhang B, Upadhyay R, Hao Y, Samanovic MI, Herati RS, Blair J, Axelrad J, Mulligan MJ, Littman DR, Satija R | bioRxiv : the preprint server for biology | 36747786 | bioRxiv | 2023 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/36747786 |
| SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. | Aihara G, Clifton K, Chen M, Li Z, Atta L, Miller BF, Satija R, Hickey JW, Fan J | Bioinformatics (Oxford, England) | 38902953 | Bioinformatics | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38902953 |
| A panoramic view of cell population dynamics in mammalian aging. | Zhang Z, Schaefer C, Jiang W, Lu Z, Lee J, Sziraki A, Abdulraouf A, Wick B, Haeussler M, Li Z, Molla G, Satija R, Zhou W, Cao J | Science (New York, N.Y.) | 39607904 | Science | 2025 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/39607904 |
| Dictionary learning for integrative, multimodal and scalable single-cell analysis. | Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R | Nature biotechnology | 37231261 | Nat Biotechnol | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37231261 |
| Multiplexed single-cell characterization of alternative polyadenylation regulators. | Kowalski MH, Wessels HH, Linder J, Dalgarno C, Mascio I, Choudhary S, Hartman A, Hao Y, Kundaje A, Satija R | Cell | 38925112 | Cell | 2024 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/38925112 |
| Multimodal single-cell datasets characterize antigen-specific CD8(+) T cells across SARS-CoV-2 vaccination and infection. | Zhang B, Upadhyay R, Hao Y, Samanovic MI, Herati RS, Blair JD, Axelrad J, Mulligan MJ, Littman DR, Satija R | Nature immunology | 37735591 | Nat Immunol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37735591 |
| The future of rapid and automated single-cell data analysis using reference mapping. | Lotfollahi M, Yuhan Hao, Theis FJ, Satija R | Cell | 38729109 | Cell | 2024 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/38729109 |
| A Panoramic View of Cell Population Dynamics in Mammalian Aging. | Zhang Z, Schaefer C, Jiang W, Lu Z, Lee J, Sziraki A, Abdulraouf A, Wick B, Haeussler M, Li Z, Molla G, Satija R, Zhou W, Cao J | bioRxiv : the preprint server for biology | 38496474 | bioRxiv | 2024 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/38496474 |
| CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators. | Kowalski MH, Wessels HH, Linder J, Choudhary S, Hartman A, Hao Y, Mascio I, Dalgarno C, Kundaje A, Satija R | bioRxiv : the preprint server for biology | 36798324 | bioRxiv | 2023 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/36798324 |
| Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph. | Bueckle A, Herr BW 2nd, Hardi J, Quardokus EM, Musen MA, Börner K | Scientific data | 40592888 | Sci Data | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40592888 |
| The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data. | Ahooyi TM, Stear B, Simmons JA, Metzger VT, Kumar P, Evangelista JE, Clarke DJB, Xie Z, Kim H, Jenkins SL, Maurya MR, Ramachandran S, Fahy E, Gillespie TH, Imam FT, Kokash N, Roth ME, Fullem R, Jevtic D, Mihajlovic A, Tiemeyer M, Bakker C, Schroeder AJ, Markowski J, Nedzel J, Hill DD, Terry J, Nemarich C, Boline J, Park PJ, Ardlie KG, Vora J, Mazumder R, Ranzinger R, de Bono B, Subramaniam S, Grethe JS, Yang JJ, Lambert CG, Resnick A, Milosavljevic A, Ma'ayan A, Silverstein JC, Taylor DM | bioRxiv : the preprint server for biology | 40832351 | bioRxiv | 2025 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/40832351 |
| Constructing and Using Cell Type Populations of the Human Reference Atlas. | Bueckle A, Herr BW 2nd, Chen L, Bolin D, Qaurooni D, Ginda M, Jain Y, Puig-Barbe A, Ardlie K, Wang F, Börner K | bioRxiv : the preprint server for biology | 40894635 | bioRxiv | 2025 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/40894635 |
| An open source knowledge graph ecosystem for the life sciences. | Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, Mungall CJ, Cavalleri E, Fontana T, Valentini G, Mesiti M, Gillenwater LA, Santangelo B, Vasilevsky NA, Hoehndorf R, Bennett TD, Ryan PB, Hripcsak G, Kahn MG, Bada M, Baumgartner WA Jr, Hunter LE | Scientific data | 38605048 | Sci Data | 2024 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/38605048 |
| Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph for Linked Open Data. | Bueckle A, Herr BW 2nd, Hardi J, Quardokus EM, Musen MA, Börner K | bioRxiv : the preprint server for biology | 39764040 | bioRxiv | 2025 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/39764040 |
| Modeling community standards for metadata as templates makes data FAIR. | Musen MA, O'Connor MJ, Schultes E, Martínez-Romero M, Hardi J, Graybeal J | Scientific data | 36371407 | Sci Data | 2022 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/36371407 |
| Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets. | O'Connor MJ, Hardi J, Martínez-Romero M, Somasundaram S, Honick B, Fisher SA, Pillai A, Musen MA | Scientific data | 39952970 | Sci Data | 2025 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/39952970 |
| Generalized cell phenotyping for spatial proteomics with language-informed vision models. | Wang XJ, Dilip R, Iqbal AR, Bussi Y, Brown C, Pradhan E, Jain Y, Yu K, Li S, Abt M, Börner K, Keren L, Yue Y, Barnowski R, Van Valen D | bioRxiv : the preprint server for biology | 39605651 | bioRxiv | 2025 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/39605651 |
| Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data. | Stear BJ, Mohseni Ahooyi T, Simmons JA, Kollar C, Hartman L, Beigel K, Lahiri A, Vasisht S, Callahan TJ, Nemarich CM, Silverstein JC, Taylor DM | Scientific data | 39695169 | Sci Data | 2024 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/39695169 |
| Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data. | Morth E, Sidak K, Maliga Z, Moller T, Gehlenborg N, Sorger P, Pfister H, Beyer J, Kruger R | IEEE transactions on visualization and computer graphics | 39255170 | IEEE Trans Vis Comput Graph | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39255170 |
| scCausalVI disentangles single-cell perturbation responses with causality-aware generative model. | An S, Cho JW, Cao K, Xiong J, Hemberg M, Wan L | Cell systems | 41197632 | Cell Syst | 2025 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/41197632 |
| The State of Single-Cell Atlas Data Visualization in the Biological Literature. | Keller MS, Morth E, Smits TC, Warchol S, Guo G, Wang Q, Krueger R, Pfister H, Gehlenborg N | IEEE computer graphics and applications | 40577289 | IEEE Comput Graph Appl | 2025 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/40577289 |
| Interactive visualization of kidney micro-compartmental segmentations and associated pathomics on whole slide images. | Keller MS, Lucarelli N, Chen Y, Border S, Janowczyk A, Himmelfarb J, Kretzler M, Hodgin J, Barisoni L, Demeke D, Herlitz L, Moeckel G, Rosenberg AZ, Ding Y, Kidney Precision Medicine Project and HuBMAP Consortium, Sarder P, Gehlenborg N | ArXiv | 41281218 | ArXiv | 2025 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/41281218 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support. | Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Casas Moreno X, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Küpcü Yoldaş A, Kyoda K, le Tournoulx de la Villegeorges A, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR | Histochemistry and cell biology | 37428210 | Histochem Cell Biol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37428210 |
| A General Framework for Comparing Embedding Visualizations Across Class-Label Hierarchies. | Manz T, Lekschas F, Greene E, Finak G, Gehlenborg N | IEEE transactions on visualization and computer graphics | 39255153 | IEEE Trans Vis Comput Graph | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39255153 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support. | Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Moreno XC, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Yoldaş AK, Kyoda K, de la Villegeorges ALT, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR | bioRxiv : the preprint server for biology | 36865282 | bioRxiv | 2023 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/36865282 |
| Can LLMs Bridge Domain and Visualization? A Case Study on High-Dimension Data Visualization in Single-Cell Transcriptomics. | Wang Q, Liu X, Gehlenborg N | IEEE transactions on visualization and computer graphics | 41269823 | IEEE Trans Vis Comput Graph | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41269823 |
| Polyphony: an Interactive Transfer Learning Framework for Single-Cell Data Analysis. | Cheng F, Keller MS, Qu H, Gehlenborg N, Wang Q | IEEE transactions on visualization and computer graphics | 36155452 | IEEE Trans Vis Comput Graph | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36155452 |
| Host response during unresolved urinary tract infection alters female mammary tissue homeostasis through collagen deposition and TIMP1. | Henry S, Lewis SM, Cyrill SL, Callaway MK, Chatterjee D, Hanasoge Somasundara AV, Jones G, He XY, Caligiuri G, Ciccone MF, Diaz IA, Biswas AA, Hernandez E, Ha T, Wilkinson JE, Egeblad M, Tuveson DA, Dos Santos CO | Nature communications | 38627380 | Nat Commun | 2024 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/38627380 |
| CellSAM: A Foundation Model for Cell Segmentation. | Israel U, Marks M, Dilip R, Li Q, Yu C, Laubscher E, Iqbal A, Pradhan E, Ates A, Abt M, Brown C, Pao E, Li S, Pearson-Goulart A, Perona P, Gkioxari G, Barnowski R, Yue Y, Van Valen D | bioRxiv : the preprint server for biology | 38045277 | bioRxiv | 2025 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/38045277 |
| Publication, funding, and experimental data in support of Human Reference Atlas construction and usage. | Kong Y, Börner K | Scientific data | 38834597 | Sci Data | 2024 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/38834597 |
| Benchmarking single cell transcriptome matching methods for incremental growth of reference atlases. | Hu J, Peng B, Pankajam AV, Xu B, Deshpande VA, Bueckle A, Herr BW 2nd, Börner K, Dupont C, Scheuermann RH, Zhang Y | bioRxiv : the preprint server for biology | 40568082 | bioRxiv | 2025 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/40568082 |
| Defining breast epithelial cell types in the single-cell era. | Gray GK, Carlson EG, Lev T, Marshall B, Reed AD, Sánchez-Covarrubias AP, Twigger AJ, Puig-Barbe A, Thennavan A, Omotoso A, Murrow LM, Chatterjee D, He S, Pensa S, Aevermann B, Tavares NK, Chen N, Hilton JA, Blake K, Liu Y, Phong K, Gartner ZJ, Lawson DA, Swarbrick A, Dos Santos CO, George SHL, Brugge JS, LaBarge MA, Nakshatri H, Navin N, Kessenbrock K, Khaled WT | Developmental cell | 40925326 | Dev Cell | 2025 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/40925326 |
| The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques. | Radtke AJ, Anidi IU, Arakkal L, Arroyo-Mejias AJ, Beuschel RT, Börner K, Chu CJ, Clark B, Clatworthy MR, Colautti J, Coscia F, Croteau J, Denha S, Dever R, Dutra WO, Fritzsche S, Fullam S, Gerner MY, Gola A, Gollob KJ, Hernandez JM, Hor JL, Ichise H, Jing Z, Jonigk D, Kandov E, Kastenmüller W, Koenig JFE, Kortekaas RK, Kothurkar A, Kreins AY, Lamborn IT, Lin Y, Luciano Pereira Morais K, Lunich A, Luz JCS, MacDonald RB, Makranz C, Maltez VI, McDonough JE, Moriarty RV, Ocampo-Godinez JM, Olyntho VM, Oxenius A, Padhan K, Remmert K, Richoz N, Schrom EC, Shang W, Shi L, Shih RM, Speranza E, Stierli S, Teichmann SA, Veres TZ, Vierhout M, Wachter BT, Wade-Vallance AK, Williams M, Zangger N, Germain RN, Yaniv Z | PLoS biology | 40106489 | PLoS Biol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/40106489 |
| The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality. | Bueckle A, Qing C, Luley S, Kumar Y, Pandey N, Börner K | bioRxiv : the preprint server for biology | 36824790 | bioRxiv | 2023 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/36824790 |
| The Cell Ontology in the age of single-cell omics. | Tan SZK, Puig-Barbe A, Goutte-Gattat D, Eastwood C, Aevermann B, Avola A, Balhoff JP, Bayindir IU, Belfiore J, Caron AR, Fischer DS, George N, Gyori BM, Haendel MA, Hoyt CT, Kir H, Lubiana T, Matentzoglu N, Overton JA, Peng B, Peters B, Quardokus EM, Ray PL, Roncaglia P, Rivera AD, Stefancsik R, Teh WK, Toro S, Vasilevsky N, Xu C, Zhang Y, Scheuermann RH, Mungall CJ, Diehl AD, Osumi-Sutherland D | Scientific data | 42031777 | Sci Data | 2026 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/42031777 |
| 3D virtual reality vs. 2D desktop registration user interface comparison. | Bueckle A, Buehling K, Shih PC, Börner K | PloS one | 34705835 | PLoS One | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34705835 |
| Functional Tissue Units in the Human Reference Atlas. | Bidanta S, Börner K, Herr BW 2nd, Nagy M, Gustilo KS, Bajema R, Maier L, Molontay R, Weber G | bioRxiv : the preprint server for biology | 37905079 | bioRxiv | 2023 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/37905079 |
| A general strategy for generating expert-guided, simplified views of ontologies. | Caron AR, Puig-Barbe A, Quardokus EM, Balhoff JP, Belfiore J, Chipampe NJ, Hardi J, Herr BW 2nd, Kir H, Roncaglia P, Musen MA, Parkinson H, McLaughlin JA, Börner K, Osumi-Sutherland D | bioRxiv : the preprint server for biology | 39763856 | bioRxiv | 2025 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/39763856 |
| Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys. | Jain Y, Walsh CL, Yagis E, Aslani S, Nandanwar S, Zhou Y, Ha J, Gustilo KS, Brunet J, Rahmani S, Tafforeau P, Bellier A, Weber GM, Lee PD, Börner K | bioRxiv : the preprint server for biology | 39253466 | bioRxiv | 2024 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/39253466 |
| The IBEX knowledge-base a community resource enabling adoption and development of immunofluorescence imaging methods. | Yaniv Z, Anidi IU, Arakkal L, Arroyo-Mejías AJ, Beuschel RT, Börner K, Chu CJ, Clark BH, Clatworthy MR, Colautti J, Coscia F, Croteau J, Denha S, Dever R, Dutra WO, Fritzsche S, Fullam S, Gerner MY, Gola A, Gollob KJ, Hernandez JM, Hor JL, Ichise H, Jing Z, Jonigk D, Kandov E, Kastenmüller W, Koenig JFE, Kothurkar A, Kortekaas RK, Kreins AY, Lamborn IT, Lin Y, Luciano Pereira Morais K, Lunich A, Luz JCS, MacDonald RB, Makranz C, Maltez VI, McDonough JE, Moriarty RV, Ocampo-Godinez JM, Murakami Olyntho V, Oxenius A, Padhan K, Remmert K, Richoz N, Schrom EC, Shang W, Shi L, Shih RM, Speranza E, Stierli S, Teichmann SA, Verse TZ, Vierhout M, Wachter BT, Wade-Vallance AK, Williams M, Zangger N, Germain RN, Radtke AJ | eLife | 41575186 | Elife | 2026 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/41575186 |
| CellSAM: a foundation model for cell segmentation. | Marks M, Israel U, Dilip R, Li Q, Yu C, Laubscher E, Iqbal A, Pradhan E, Ates A, Abt M, Brown C, Pao E, Li S, Pearson-Goulart A, Perona P, Gkioxari G, Barnowski R, Yue Y, Van Valen D | Nature methods | 41360960 | Nat Methods | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41360960 |
| Deep Learning for 3D Vascular Segmentation in Phase Contrast Tomography. | Yagis E, Aslani S, Jain Y, Zhou Y, Rahmani S, Brunet J, Bellier A, Werlein C, Ackermann M, Jonigk D, Tafforeau P, Lee PD, Walsh C | Research square | 39070623 | Res Sq | 2024 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/39070623 |
| Functional tissue units in the Human Reference Atlas. | Bidanta S, Börner K, Herr Ii BW, Quardokus EM, Nagy M, Gustilo KS, Bajema R, Maier E, Molontay R, Weber GM | Nature communications | 39934102 | Nat Commun | 2025 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/39934102 |
| The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods. | Yaniv Z, Anidi IU, Arakkal L, Arroyo-Mejías AJ, Beuschel RT, Börner K, Chu CJ, Clark B, Clatworthy MR, Colautti J, Coscia F, Croteau J, Denha S, Dever R, Dutra WO, Fritzsche S, Fullam S, Gerner MY, Gola A, Gollob KJ, Hernandez JM, Hor JL, Ichise H, Jing Z, Jonigk D, Kandov E, Kastenmüller W, Koenig JFE, Kothurkar A, Kortekaas RK, Kreins AY, Lamborn IT, Lin Y, Morais KLP, Lunich A, Luz JCS, MacDonald RB, Makranz C, Maltez VI, McDonough JE, Moriarty RV, Ocampo-Godinez JM, Olyntho VM, Oxenius A, Padhan K, Remmert K, Richoz N, Schrom EC, Shang W, Shi L, Shih RM, Speranza E, Stierli S, Teichmann SA, Veres TZ, Vierhout M, Wachter BT, Williams M, Zangger N, Germain RN, Radtke AJ | ArXiv | 39764400 | ArXiv | 2024 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/39764400 |
| Deep learning for 3D vascular segmentation in hierarchical phase contrast tomography: a case study on kidney. | Yagis E, Aslani S, Jain Y, Zhou Y, Rahmani S, Brunet J, Bellier A, Werlein C, Ackermann M, Jonigk D, Tafforeau P, Lee PD, Walsh CL | Scientific reports | 39516256 | Sci Rep | 2024 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/39516256 |
| A general strategy for generating expert-guided, simplified views of ontologies. | Caron AR, Puig-Barbe A, Quardokus EM, Balhoff JP, Belfiore J, Chipampe NJ, Hardi J, Herr BW 2nd, Kir H, Roncaglia P, Musen MA, Parkinson H, McLaughlin JA, Börner K, Osumi-Sutherland D | Scientific data | 41513678 | Sci Data | 2026 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/41513678 |
| ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology. | Mimar S, Paul AS, Lucarelli N, Border S, Santo BA, Naglah A, Barisoni L, Hodgin J, Rosenberg AZ, Clapp W, Sarder P, Kidney Precision Medicine Project | bioRxiv : the preprint server for biology | 38585837 | bioRxiv | 2024 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/38585837 |
| An Innovative Pilot Program Approach to Facilitating Interdisciplinary Collaboration Among STEM and Public Health Students in Biomedical AI and Clinical Translational Research. | Liu-Galvin R, Atchison L, Ray JM, Border S, Khan M, Afsari F, Sarder P, Levites Strekalova YA | Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology | 40996113 | Biochem Mol Biol Educ | 2025 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/40996113 |
| ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology. | Mimar S, Paul AS, Lucarelli N, Border S, Naglah A, Barisoni L, Hodgin J, Rosenberg AZ, Clapp W, Sarder P | Proceedings of SPIE--the International Society for Optical Engineering | 38813089 | Proc SPIE Int Soc Opt Eng | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38813089 |
| Investigating quantitative histological characteristics in renal pathology using HistoLens. | Border SP, Tomaszewski JE, Yoshida T, Kopp JB, Hodgin JB, Clapp WL, Rosenberg AZ, Buyon JP, Sarder P | Scientific reports | 39080444 | Sci Rep | 2024 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/39080444 |
| Mechanisms of young professional engagement in health policy development: a cultural domain approach. | Levites Strekalova YA, Modjarrad L, Midence S | Frontiers in public health | 39507656 | Front Public Health | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39507656 |
| Developing evaluation metrics to measure the US national institute of health plans to enhance diverse perspectives: a protocol for a consensus-based study. | Levites Strekalova YA, Jain S, Sarder P | BMJ open | 40010840 | BMJ Open | 2025 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/40010840 |
| Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. | Ginley B, Lucarelli N, Zee J, Jain S, Han SS, Rodrigues L, Ozrazgat-Baslanti T, Wong ML, Nadkarni G, Jen KY, Sarder P | bioRxiv : the preprint server for biology | 37292965 | bioRxiv | 2023 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/37292965 |
| Continuous-state HMMs for modeling time-series single-cell RNA-Seq data. | Lin C, Bar-Joseph Z | Bioinformatics (Oxford, England) | 31038684 | Bioinformatics | 2019 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/31038684 |
| Deep learning of gene relationships from single cell time-course expression data. | Yuan Y, Bar-Joseph Z | Briefings in bioinformatics | 33876191 | Brief Bioinform | 2021 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/33876191 |
| Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. | Goenka SD, Gorzynski JE, Shafin K, Fisk DG, Pesout T, Jensen TD, Monlong J, Chang PC, Baid G, Bernstein JA, Christle JW, Dalton KP, Garalde DR, Grove ME, Guillory J, Kolesnikov A, Nattestad M, Ruzhnikov MRZ, Samadi M, Sethia A, Spiteri E, Wright CJ, Xiong K, Zhu T, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA | Nature biotechnology | 35347328 | Nat Biotechnol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35347328 |
| Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. | Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, Sović I, Wood JMD, Zook JM, Phillippy AM, Rhie A | Nature methods | 35361931 | Nat Methods | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35361931 |
| scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. | Chen H, Lee YJ, Ovando JA, Rosas L, Rojas M, Mora AL, Bar-Joseph Z, Lugo-Martinez J | bioRxiv : the preprint server for biology | 38187629 | bioRxiv | 2023 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/38187629 |
| UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. | Li D, Ding J, Bar-Joseph Z | Journal of computational biology : a journal of computational molecular cell biology | 36036832 | J Comput Biol | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36036832 |
| Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering. | Hislop J, Alavi A, Song Q, Schoenberger R, Kamyar KF, LeGraw R, Velazquez J, Mokhtari T, Taheri MN, Rytel M, de Sousa Lopes SMC, Watkins S, Stolz D, Kiani S, Sozen B, Bar-Joseph Z, Ebrahimkhani MR | bioRxiv : the preprint server for biology | 37398391 | bioRxiv | 2023 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/37398391 |
| Temporal modelling using single-cell transcriptomics. | Ding J, Sharon N, Bar-Joseph Z | Nature reviews. Genetics | 35102309 | Nat Rev Genet | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35102309 |
| Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. | Shafin K, Pesout T, Chang PC, Nattestad M, Kolesnikov A, Goel S, Baid G, Kolmogorov M, Eizenga JM, Miga KH, Carnevali P, Jain M, Carroll A, Paten B | Nature methods | 34725481 | Nat Methods | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34725481 |
| Iterative point set registration for aligning scRNA-seq data. | Alavi A, Bar-Joseph Z | PLoS computational biology | 33108369 | PLoS Comput Biol | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33108369 |
| Interactive single-cell data analysis using Cellar. | Hasanaj E, Wang J, Sarathi A, Ding J, Bar-Joseph Z | Nature communications | 35422041 | Nat Commun | 2022 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/35422041 |
| Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data. | Rashid S, Shah S, Bar-Joseph Z, Pandya R | Bioinformatics (Oxford, England) | 30768159 | Bioinformatics | 2021 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/30768159 |
| Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. | Hurley K, Ding J, Villacorta-Martin C, Herriges MJ, Jacob A, Vedaie M, Alysandratos KD, Sun YL, Lin C, Werder RB, Huang J, Wilson AA, Mithal A, Mostoslavsky G, Oglesby I, Caballero IS, Guttentag SH, Ahangari F, Kaminski N, Rodriguez-Fraticelli A, Camargo F, Bar-Joseph Z, Kotton DN | Cell stem cell | 32004478 | Cell Stem Cell | 2020 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/32004478 |
| Inferring TF activation order in time series scRNA-Seq studies. | Lin C, Ding J, Bar-Joseph Z | PLoS computational biology | 32069291 | PLoS Comput Biol | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32069291 |
| Computational tools for analyzing single-cell data in pluripotent cell differentiation studies. | Ding J, Alavi A, Ebrahimkhani MR, Bar-Joseph Z | Cell reports methods | 35474899 | Cell Rep Methods | 2021 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/35474899 |
| Membrane marker selection for segmenting single cell spatial proteomics data. | Dayao MT, Brusko M, Wasserfall C, Bar-Joseph Z | Nature communications | 35422106 | Nat Commun | 2022 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/35422106 |
| Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. | Formenti G, Rhie A, Walenz BP, Thibaud-Nissen F, Shafin K, Koren S, Myers EW, Jarvis ED, Phillippy AM | Nature methods | 35361932 | Nat Methods | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35361932 |
| Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. | Bailey AD, Talkish J, Ding H, Igel H, Duran A, Mantripragada S, Paten B, Ares M | eLife | 35384842 | Elife | 2022 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/35384842 |
| Supervised Adversarial Alignment of Single-Cell RNA-seq Data. | Ge S, Wang H, Alavi A, Xing E, Bar-Joseph Z | Journal of computational biology : a journal of computational molecular cell biology | 33470876 | J Comput Biol | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33470876 |
| Identifying signaling genes in spatial single-cell expression data. | Li D, Ding J, Bar-Joseph Z | Bioinformatics (Oxford, England) | 32886099 | Bioinformatics | 2021 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/32886099 |
| Using single cell atlas data to reconstruct regulatory networks. | Song Q, Ruffalo M, Bar-Joseph Z | Nucleic acids research | 36762475 | Nucleic Acids Res | 2023 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/36762475 |
| SCS: cell segmentation for high-resolution spatial transcriptomics. | Chen H, Li D, Bar-Joseph Z | bioRxiv : the preprint server for biology | 37398213 | bioRxiv | 2023 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/37398213 |
| GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data. | Yuan Y, Bar-Joseph Z | Genome biology | 33303016 | Genome Biol | 2020 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/33303016 |
| Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. | Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B | Nature biotechnology | 32686750 | Nat Biotechnol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32686750 |
| Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures. | Ding H, Anastopoulos I, Bailey AD 4th, Stuart J, Paten B | Nature communications | 34764310 | Nat Commun | 2021 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/34764310 |
| Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. | Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, Rich SS, Rotter JI, Haussler D, Garrison E, Paten B | Science (New York, N.Y.) | 34914532 | Science | 2021 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/34914532 |
| Cell type ontologies of the Human Cell Atlas. | Osumi-Sutherland D, Xu C, Keays M, Levine AP, Kharchenko PV, Regev A, Lein E, Teichmann SA | Nature cell biology | 34750578 | Nat Cell Biol | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34750578 |
| scSTEM: clustering pseudotime ordered single-cell data. | Song Q, Wang J, Bar-Joseph Z | Genome biology | 35799304 | Genome Biol | 2022 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/35799304 |
| GBZ file format for pangenome graphs. | Sirén J, Paten B | Bioinformatics (Oxford, England) | 36179091 | Bioinformatics | 2022 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/36179091 |
| A complete reference genome improves analysis of human genetic variation. | Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC | Science (New York, N.Y.) | 35357935 | Science | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35357935 |
| SCS: cell segmentation for high-resolution spatial transcriptomics. | Chen H, Li D, Bar-Joseph Z | Nature methods | 37429992 | Nat Methods | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37429992 |
| Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. | Dayao MT, Trevino A, Kim H, Ruffalo M, D'Angio HB, Preska R, Duvvuri U, Mayer AT, Bar-Joseph Z | Bioinformatics (Oxford, England) | 37387167 | Bioinformatics | 2023 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/37387167 |
| Recovering single-cell expression profiles from spatial transcriptomics with scResolve. | Chen H, Lee YJ, Ovando-Ricardez JA, Rosas L, Rojas M, Mora AL, Bar-Joseph Z, Lugo-Martinez J | Cell reports methods | 39326411 | Cell Rep Methods | 2024 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/39326411 |
| Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. | Sibbesen JA, Eizenga JM, Novak AM, Sirén J, Chang X, Garrison E, Paten B | Nature methods | 36646895 | Nat Methods | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36646895 |
| Optimal gap-affine alignment in O(s) space. | Marco-Sola S, Eizenga JM, Guarracino A, Paten B, Garrison E, Moreto M | Bioinformatics (Oxford, England) | 36749013 | Bioinformatics | 2023 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/36749013 |
| TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data. | Li D, Velazquez JJ, Ding J, Hislop J, Ebrahimkhani MR, Bar-Joseph Z | Genome biology | 35255944 | Genome Biol | 2022 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/35255944 |
| Cell lineage inference from SNP and scRNA-Seq data. | Ding J, Lin C, Bar-Joseph Z | Nucleic acids research | 30820578 | Nucleic Acids Res | 2019 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/30820578 |
| Deep learning for inferring gene relationships from single-cell expression data. | Yuan Y, Bar-Joseph Z | Proceedings of the National Academy of Sciences of the United States of America | 31822622 | Proc Natl Acad Sci U S A | 2019 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/31822622 |
| Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data. | Zafar H, Lin C, Bar-Joseph Z | Nature communications | 32546686 | Nat Commun | 2020 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/32546686 |
| A complete pedigree-based graph workflow for rare candidate variant analysis. | Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B | Genome research | 35483961 | Genome Res | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35483961 |
| Complete genomic and epigenetic maps of human centromeres. | Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH | Science (New York, N.Y.) | 35357911 | Science | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35357911 |
| Highly accurate assembly polishing with DeepPolisher. | Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K | bioRxiv : the preprint server for biology | 39345401 | bioRxiv | 2024 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/39345401 |
| A unified analysis of atlas single-cell data. | Chen H, Nguyen ND, Ruffalo M, Bar-Joseph Z | Genome research | 39965934 | Genome Res | 2025 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/39965934 |
| Predicting lung aging using scRNA-Seq data. | Song Q, Singh A, McDonough JE, Adams TS, Vos R, De Man R, Myers G, Ceulemans LJ, Vanaudenaerde BM, Wuyts WA, Yan X, Schupp J, Hagood JS, Kaminski N, Bar-Joseph Z | PLoS computational biology | 39700255 | PLoS Comput Biol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39700255 |
| Highly accurate assembly polishing with DeepPolisher. | Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K, plus the Human Pangenome Reference Consortium | Genome research | 40389286 | Genome Res | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40389286 |
| scDOT: optimal transport for mapping senescent cells in spatial transcriptomics. | Nguyen ND, Rosas L, Khaliullin T, Jiang P, Hasanaj E, Ovando-Ricardez JA, Bueno M, Rahman I, Pryhuber GS, Li D, Ma Q, Finkel T, Königshoff M, Eickelberg O, Rojas M, Mora AL, Lugo-Martinez J, Bar-Joseph Z | Genome biology | 39516853 | Genome Biol | 2024 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/39516853 |
| Evaluation of cell segmentation methods without reference segmentations. | Chen H, Murphy RF | Molecular biology of the cell | 36515991 | Mol Biol Cell | 2023 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/36515991 |
| Multiset multicover methods for discriminative marker selection. | Hasanaj E, Alavi A, Gupta A, Póczos B, Bar-Joseph Z | Cell reports methods | 36452867 | Cell Rep Methods | 2022 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/36452867 |
| Modelling post-implantation human development to yolk sac blood emergence. | Hislop J, Song Q, Keshavarz F K, Alavi A, Schoenberger R, LeGraw R, Velazquez JJ, Mokhtari T, Taheri MN, Rytel M, Chuva de Sousa Lopes SM, Watkins S, Stolz D, Kiani S, Sozen B, Bar-Joseph Z, Ebrahimkhani MR | Nature | 38092041 | Nature | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38092041 |
| Unsupervised cell functional annotation for single-cell RNA-seq. | Li D, Ding J, Bar-Joseph Z | Genome research | 35764397 | Genome Res | 2022 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/35764397 |
| CINS: Cell Interaction Network inference from Single cell expression data. | Yuan Y, Cosme C Jr, Adams TS, Schupp J, Sakamoto K, Xylourgidis N, Ruffalo M, Li J, Kaminski N, Bar-Joseph Z | PLoS computational biology | 36095011 | PLoS Comput Biol | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36095011 |
| MITI minimum information guidelines for highly multiplexed tissue images. | Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Human Tumor Atlas Network, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK | Nature methods | 35277708 | Nat Methods | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35277708 |
| A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling. | Lekschas F, Zhou X, Chen W, Gehlenborg N, Bach B, Pfister H | IEEE transactions on visualization and computer graphics | 33026994 | IEEE Trans Vis Comput Graph | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33026994 |
| Guidelines for reporting single-cell RNA-seq experiments. | Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I | Nature biotechnology | 33188371 | Nat Biotechnol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33188371 |
| DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples. | Wang Q, L'Yi S, Gehlenborg N | Proceedings of the SIGCHI conference on human factors in computing systems. CHI Conference | 38074525 | Proc SIGCHI Conf Hum Factor Comput Syst | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38074525 |
| Markov models for clinical decision-making in radiation oncology: A systematic review. | McCullum LB, Karagoz A, Dede C, Garcia R, Nosrat F, Hemmati M, Hosseinian S, Schaefer AJ, Fuller CD, Rice/MD Anderson Center for Operations Research in Cancer (CORC), MD Anderson Head and Neck Cancer Symptom Working Group | Journal of medical imaging and radiation oncology | 38766899 | J Med Imaging Radiat Oncol | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38766899 |
| Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs. | Mohseni Ahooyi T, Stear B, Simmons JA, Nemarich CM, Silverstein JC, Taylor DM | Scientific data | 39799122 | Sci Data | 2025 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/39799122 |
| Head and neck cancer predictive risk estimator to determine control and therapeutic outcomes of radiotherapy (HNC-PREDICTOR): development, international multi-institutional validation, and web implementation of clinic-ready model-based risk stratification for head and neck cancer. | van Dijk LV, Mohamed AS, Ahmed S, Nipu N, Marai GE, Wahid K, Sijtsema NM, Gunn B, Garden AS, Moreno A, Hope AJ, Langendijk JA, Fuller CD | European journal of cancer (Oxford, England : 1990) | 36442460 | Eur J Cancer | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36442460 |
| Magnetic resonance linear accelerator technology and adaptive radiation therapy: An overview for clinicians. | Hall WA, Paulson E, Li XA, Erickson B, Schultz C, Tree A, Awan M, Low DA, McDonald BA, Salzillo T, Glide-Hurst CK, Kishan AU, Fuller CD | CA: a cancer journal for clinicians | 34792808 | CA Cancer J Clin | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34792808 |
| Unilateral Radiation Therapy for Tonsillar Cancer: Treatment Outcomes in the Era of Human Papillomavirus, Positron-Emission Tomography, and Intensity Modulated Radiation Therapy. | Taku N, Chronowski G, Brandon Gunn G, Morrison WH, Gross ND, Moreno AC, Ferrarotto R, Frank SJ, Fuller CD, Goepfert RP, Phan J, Lai SY, Reddy JP, Rosenthal DI, Garden AS | International journal of radiation oncology, biology, physics | 35504500 | Int J Radiat Oncol Biol Phys | 2022 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/35504500 |
| Prospective validation of diffusion-weighted MRI as a biomarker of tumor response and oncologic outcomes in head and neck cancer: Results from an observational biomarker pre-qualification study. | Joint Head and Neck Radiotherapy-MRI Development Cooperative, Mohamed ASR, Abusaif A, He R, Wahid KA, Salama V, Youssef S, McDonald BA, Naser M, Ding Y, Salzillo TC, AboBakr MA, Wang J, Lai SY, Fuller CD | Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology | 36990394 | Radiother Oncol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36990394 |
| Deep Learning-Based Dose Prediction for Automated, Individualized Quality Assurance of Head and Neck Radiation Therapy Plans. | Gronberg MP, Beadle BM, Garden AS, Skinner H, Gay S, Netherton T, Cao W, Cardenas CE, Chung C, Fuentes DT, Fuller CD, Howell RM, Jhingran A, Lim TY, Marquez B, Mumme R, Olanrewaju AM, Peterson CB, Vazquez I, Whitaker TJ, Wooten Z, Yang M, Court LE | Practical radiation oncology | 36697347 | Pract Radiat Oncol | 2023 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/36697347 |
| Clinical Implementation and Initial Experience With a 1.5 Tesla MR-Linac for MR-Guided Radiation Therapy for Gynecologic Cancer: An R-IDEAL Stage 1 and 2a First in Humans Feasibility Study of New Technology Implementation. | Lakomy DS, Yang J, Vedam S, Wang J, Lee B, Sobremonte A, Castillo P, Hughes N, Mohammedsaid M, Jhingran A, Klopp AH, Choi S, Fuller CD, Lin LL | Practical radiation oncology | 35278717 | Pract Radiat Oncol | 2022 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/35278717 |
| A molecular taxonomy of tumors independent of tissue-of-origin. | Nguyen PT, Coetzee SG, Lakeland DL, Hazelett DJ | iScience | 34611608 | iScience | 2021 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/34611608 |
| Machine-learning based investigation of prognostic indicators for oncological outcome of pancreatic ductal adenocarcinoma. | Chang J, Liu Y, Saey SA, Chang KC, Shrader HR, Steckly KL, Rajput M, Sonka M, Chan CHF | Frontiers in oncology | 36568148 | Front Oncol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36568148 |
| Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. | Stoeckius M, Zheng S, Houck-Loomis B, Hao S, Yeung BZ, Mauck WM 3rd, Smibert P, Satija R | Genome biology | 30567574 | Genome Biol | 2018 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/30567574 |
| Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. | Zhang B, Srivastava A, Mimitou E, Stuart T, Raimondi I, Hao Y, Smibert P, Satija R | Nature biotechnology | 35332340 | Nat Biotechnol | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35332340 |
| Integrated analysis of multimodal single-cell data. | Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P, Satija R | Cell | 34062119 | Cell | 2021 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/34062119 |
| Comparison and evaluation of statistical error models for scRNA-seq. | Choudhary S, Satija R | Genome biology | 35042561 | Genome Biol | 2022 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/35042561 |
| Single-cell chromatin state analysis with Signac. | Stuart T, Srivastava A, Madad S, Lareau CA, Satija R | Nature methods | 34725479 | Nat Methods | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34725479 |
| Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells. | Blair JD, Hartman A, Zenk F, Wahle P, Brancati G, Dalgarno C, Treutlein B, Satija R | Nature communications | 39905064 | Nat Commun | 2025 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/39905064 |
| Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. | Biancalani T, Scalia G, Buffoni L, Avasthi R, Lu Z, Sanger A, Tokcan N, Vanderburg CR, Segerstolpe Å, Zhang M, Avraham-Davidi I, Vickovic S, Nitzan M, Ma S, Subramanian A, Lipinski M, Buenrostro J, Brown NB, Fanelli D, Zhuang X, Macosko EZ, Regev A | Nature methods | 34711971 | Nat Methods | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34711971 |
| Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. | Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Göttgens B, Reik W, Nichols J, Cai L, Marioni JC | Nature biotechnology | 34489600 | Nat Biotechnol | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34489600 |
| Iterative, multimodal, and scalable single-cell profiling for discovery and characterization of signaling regulators. | Blair JD, Bradu A, Dalgarno C, Grabski IN, Satija R | bioRxiv : the preprint server for biology | 40909507 | bioRxiv | 2025 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/40909507 |
| A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space. | Harland LTG, Lohoff T, Koulena N, Pierson N, Pape C, Ameen F, Griffiths J, Theeuwes B, Wilson NK, Kreshuk A, Reik W, Nichols J, Cai L, Marioni JC, Göttgens B, Ghazanfar S | Cell reports | 40728928 | Cell Rep | 2025 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/40728928 |
| Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis. | Nakatsuka N, Adler D, Jiang L, Hartman A, Cheng E, Klann E, Satija R | Nature communications | 40796563 | Nat Commun | 2025 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/40796563 |
| Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. | Hafemeister C, Satija R | Genome biology | 31870423 | Genome Biol | 2019 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/31870423 |
| Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting. | Grabski IN, Lee J, Blair J, Dalgarno C, Mascio I, Bradu A, Knowles DA, Satija R | bioRxiv : the preprint server for biology | 41000753 | bioRxiv | 2025 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/41000753 |
| Comprehensive Integration of Single-Cell Data. | Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R | Cell | 31178118 | Cell | 2019 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/31178118 |
| Toward a Common Coordinate Framework for the Human Body. | Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G, Marioni JC, Regev A, Satija R | Cell | 31835027 | Cell | 2019 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/31835027 |
| Stabilized mosaic single-cell data integration using unshared features. | Ghazanfar S, Guibentif C, Marioni JC | Nature biotechnology | 37231260 | Nat Biotechnol | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37231260 |
| Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells. | Blair JD, Hartman A, Zenk F, Dalgarno C, Treutlein B, Satija R | bioRxiv : the preprint server for biology | 37034703 | bioRxiv | 2023 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/37034703 |
| A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Studies Uncovers Robust Differentially Expressed Genes. | Nakatsuka N, Adler D, Jiang L, Hartman A, Cheng E, Klann E, Satija R | bioRxiv : the preprint server for biology | 39463993 | bioRxiv | 2025 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/39463993 |
| Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. | Stuart T, Hao S, Zhang B, Mekerishvili L, Landau DA, Maniatis S, Satija R, Raimondi I | Nature biotechnology | 36536150 | Nat Biotechnol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36536150 |
| Visualizing learner engagement, performance, and trajectories to evaluate and optimize online course design. | Ginda M, Richey MC, Cousino M, Börner K | PloS one | 31059546 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31059546 |
| Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature. | Boppana A, Lee S, Malhotra R, Halushka M, Gustilo KS, Quardokus EM, Herr BW 2nd, Börner K, Weber GM | Scientific data | 37468503 | Sci Data | 2023 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/37468503 |
| The 2019 mathematical oncology roadmap. | Rockne RC, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, Macklin P, Hormuth DA, Jarrett AM, Lima EABF, Tinsley Oden J, Biros G, Yankeelov TE, Curtius K, Al Bakir I, Wodarz D, Komarova N, Aparicio L, Bordyuh M, Rabadan R, Finley SD, Enderling H, Caudell J, Moros EG, Anderson ARA, Gatenby RA, Kaznatcheev A, Jeavons P, Krishnan N, Pelesko J, Wadhwa RR, Yoon N, Nichol D, Marusyk A, Hinczewski M, Scott JG | Physical biology | 30991381 | Phys Biol | 2019 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/30991381 |
| The impact of air transport availability on research collaboration: A case study of four universities. | Ploszaj A, Yan X, Börner K | PloS one | 32886681 | PLoS One | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32886681 |
| Forecasting innovations in science, technology, and education. | Börner K, Rouse WB, Trunfio P, Stanley HE | Proceedings of the National Academy of Sciences of the United States of America | 30530683 | Proc Natl Acad Sci U S A | 2018 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/30530683 |
| Data visualization literacy: Definitions, conceptual frameworks, exercises, and assessments. | Börner K, Bueckle A, Ginda M | Proceedings of the National Academy of Sciences of the United States of America | 30718386 | Proc Natl Acad Sci U S A | 2019 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/30718386 |
| Toward a common standard for data and specimen provenance in life sciences. | Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, Allocca C, Betsou F, Burdett T, Cancio I, Chapman A, Chapman M, Courtot M, Curcin V, Eder J, Elliot M, Exter K, Goble C, Golebiewski M, Kisler B, Kremer A, Leo S, Lin-Gibson S, Marsano A, Mattavelli M, Moore J, Nakae H, Perseil I, Salman A, Sluka J, Soiland-Reyes S, Strambio-De-Castillia C, Sussman M, Swedlow JR, Zatloukal K, Geiger J | Learning health systems | 38249839 | Learn Health Syst | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38249839 |
