The Human BioMolecular Atlas Program (HuBMAP)
The Human BioMolecular Atlas Program (HuBMAP)
Program Publications
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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 |
|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A Novel Targeted Long-read Sequencing Approach Boosts Transcriptomic Profiling. | Tian X, Fan R | Genomics, proteomics & bioinformatics | 39724297 | Genomics Proteomics Bioinformatics | 2025 Jan 15 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Spatial pharmacology using mass spectrometry imaging. | Rajbhandari P, Neelakantan TV, Hosny N, Stockwell BR | Trends in pharmacological sciences | 38103980 | Trends Pharmacol Sci | 2024 Jan |
| 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 |
| Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications. | Stockwell BR | Cell | 35803244 | Cell | 2022 Jul 7 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Advances in Proximity Ligation in situ Hybridization (PLISH). | Nagendran M, Andruska AM, Harbury PB, Desai TJ | Bio-protocol | 33659462 | Bio Protoc | 2020 Nov 5 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Analyzing Spatial Transcriptomics Data Using Giotto. | Del Rossi N, Chen JG, Yuan GC, Dries R | Current protocols | 35384407 | Curr Protoc | 2022 Apr |
| 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 | 2024 Jul 29 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Emerging Computational Methods in Mass Spectrometry Imaging. | Hu H, Laskin J | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 36253139 | Adv Sci (Weinh) | 2022 Dec |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| Single-cell spatial mapping reveals alteration of cell type composition and tissue microenvironment during early colorectal cancer formation. | Guha TK, Esplin ED, Horning AM, Chiu R, Paul K, Weimer AK, Becker WR, Laquindanum R, Mills MA, Glen Esplin D, Shen J, Monte E, White S, Karathanos TV, Cotter D, Bi J, Ladabaum U, Longacre TA, Curtis C, Greenleaf WJ, Ford JM, Snyder MP | bioRxiv : the preprint server for biology | 39605357 | bioRxiv | 2024 Nov 21 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | 2024 Nov 15 |
| Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies. | Kotnala A, Anderson DMG, Patterson NH, Cantrell LS, Messinger JD, Curcio CA, Schey KL | Journal of mass spectrometry : JMS | 34881479 | J Mass Spectrom | 2021 Dec |
| 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 |
| 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 |
| 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 |
| 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 |
| X-CRISP: Domain-Adaptable and Interpretable CRISPR Repair Outcome Prediction. | Seale C, Gonçalves JP | bioRxiv : the preprint server for biology | 39974883 | bioRxiv | 2025 Feb 8 |
| 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 |
| 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 |
| 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 |
| Tetraspanin-7 regulation of L-type voltage-dependent calcium channels controls pancreatic β-cell insulin secretion. | Dickerson MT, Dadi PK, Butterworth RB, Nakhe AY, Graff SM, Zaborska KE, Schaub CM, Jacobson DA | The Journal of physiology | 32790176 | J Physiol | 2020 Nov |
| 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 |
| 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 |
| 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 |
| Overcoming selection bias in synthetic lethality prediction. | Seale C, Tepeli Y, Gonçalves JP | Bioinformatics (Oxford, England) | 35876858 | Bioinformatics | 2022 Sep 15 |
| 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 |
| 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 |
| 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 |
| 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 |
| Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. | Kruse ARS, Spraggins JM | Frontiers in physiology | 35222094 | Front Physiol | 2022 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| ELISL: early-late integrated synthetic lethality prediction in cancer. | Tepeli YI, Seale C, Gonçalves JP | Bioinformatics (Oxford, England) | 38113447 | Bioinformatics | 2024 Jan 2 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Spatial transcriptomics in health and disease. | Jain S, Eadon MT | Nature reviews. Nephrology | 38719971 | Nat Rev Nephrol | 2024 Oct |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Pharmacological inhibition and reversal of pancreatic acinar ductal metaplasia. | da Silva L, Jiang J, Perkins C, Atanasova KR, Bray JK, Bulut G, Azevedo-Pouly A, Campbell-Thompson M, Yang X, Hakimjavadi H, Chamala S, Ratnayake R, Gharaibeh RZ, Li C, Luesch H, Schmittgen TD | Cell death discovery | 36055991 | Cell Death Discov | 2022 Sep 2 |
| 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 |
| 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 |
| Transcriptional Profile of Human Pancreatic Acinar Ductal Metaplasia. | Jiang J, Hakimjavadi H, Bray JK, Perkins C, Gosling A, daSilva L, Bulut G, Ali J, Setiawan VW, Campbell-Thompson M, Chamala S, Schmittgen TD | Gastro hep advances | 37425649 | Gastro Hep Adv | 2023 |
| 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 |
| 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 |
| Erratum. Integrated Physiology of the Exocrine and Endocrine Compartments in Pancreatic Diseases: Workshop Proceedings. Diabetes 2023;72:433-448. | Mastracci TL, Apte M, Amundadottir LT, Alvarsson A, Artandi S, Bellin MD, Bernal-Mizrachi E, Caicedo A, Campbell-Thompson M, Cruz-Monserrate Z, Ouaamari AE, 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 | 37116182 | Diabetes | 2023 Aug 1 |
| Pancreas Optical Clearing and 3-D Microscopy in Health and Diabetes. | Campbell-Thompson M, Tang SC | Frontiers in endocrinology | 33981285 | Front Endocrinol (Lausanne) | 2021 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 | 2025 Apr 4 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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, McLaughlin JA, Börner K, Osumi-Sutherland D | bioRxiv : the preprint server for biology | 39763856 | bioRxiv | 2024 Dec 17 |
| 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 |
| 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 |
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| 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 |
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