Cellular Senescence Network (SenNet)
Cellular Senescence Network (SenNet)
Program Publications
Publications Search by Program
Search Results
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 |
|---|---|---|---|---|---|---|
| Single-cell transcriptomics of peripheral blood in the aging mouse. | Teo YV, Hinthorn SJ, Webb AE, Neretti N | Aging | 36622281 | Aging (Albany NY) | 2023 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/36622281 |
| Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery. | Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Rajaei M, Townsend JP, Muzumdar MD, Wang S | bioRxiv : the preprint server for biology | 37546882 | bioRxiv | 2024 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/37546882 |
| Cotranslational molecular condensation of cochaperones and assembly factors facilitates axonemal dynein biogenesis. | Li Y, Xu W, Cheng Y, Djenoune L, Zhuang C, Cox AL, Britto CJ, Yuan S, Wang S, Sun Z | Proceedings of the National Academy of Sciences of the United States of America | 39541357 | Proc Natl Acad Sci U S A | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39541357 |
| Heterogeneity of increased biological age in type 2 diabetes correlates with differential tissue DNA methylation, biological variables, and pharmacological treatments. | Cortez BN, Pan H, Hinthorn S, Sun H, Neretti N, Gloyn AL, Aguayo-Mazzucato C | GeroScience | 37987887 | Geroscience | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37987887 |
| PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning. | Deng Y, Zhang R, Xu P, Ma J, Gu Q | bioRxiv : the preprint server for biology | 37873233 | bioRxiv | 2023 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/37873233 |
| GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. | Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J | Nature genetics | 38744973 | Nat Genet | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38744973 |
| L2G: Repurposing Language Models for Genomics Tasks. | Cheng W, Shen J, Khodak M, Ma J, Talwalkar A | bioRxiv : the preprint server for biology | 39713364 | bioRxiv | 2024 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/39713364 |
| Single-Cell Transcriptomics Reveals Global Markers of Transcriptional Diversity across Different Forms of Cellular Senescence. | Evans SA, Teo YV, Hinthorn SJ, Clark K, Ito T, Sedivy JM, Neretti N | Aging biology | 39781544 | Aging Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/39781544 |
| POPARI: Modeling multisample variation in spatial transcriptomics. | Alam S, Zhou T, Haber E, Chidester B, Liu S, Chen F, Ma J | bioRxiv : the preprint server for biology | 40462963 | bioRxiv | 2025 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/40462963 |
| Spatial mapping of cellular senescence: emerging challenges and opportunities. | Gurkar AU, Gerencser AA, Mora AL, Nelson AC, Zhang AR, Lagnado AB, Enninful A, Benz C, Furman D, Beaulieu D, Jurk D, Thompson EL, Wu F, Rodriguez F, Barthel G, Chen H, Phatnani H, Heckenbach I, Chuang JH, Horrell J, Petrescu J, Alder JK, Lee JH, Niedernhofer LJ, Kumar M, Königshoff M, Bueno M, Sokka M, Scheibye-Knudsen M, Neretti N, Eickelberg O, Adams PD, Hu Q, Zhu Q, Porritt RA, Dong R, Peters S, Victorelli S, Pengo T, Khaliullin T, Suryadevara V, Fu X, Bar-Joseph Z, Ji Z, Passos JF | Nature aging | 37400722 | Nat Aging | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37400722 |
| Perturb-tracing enables high-content screening of multiscale 3D genome regulators. | Cheng Y, Hu M, Yang B, Jensen TB, Yang T, Yu R, Ma Z, Radda JSD, Jin S, Zang C, Wang S | bioRxiv : the preprint server for biology | 36778402 | bioRxiv | 2023 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/36778402 |
| Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. | Patterson B, Yang B, Tanaka Y, Kim KY, Cakir B, Xiang Y, Kim J, Wang S, Park IH | Science advances | 37540754 | Sci Adv | 2023 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/37540754 |
| Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. | Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J | bioRxiv : the preprint server for biology | 37546900 | bioRxiv | 2023 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/37546900 |
| SenNet recommendations for detecting senescent cells in different tissues. | Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver CM, Aguayo-Mazzucato C, Baker DJ, Bernlohr DA, Jurk D, Mangarova DB, Quardokus EM, Enninga EAL, Schmidt EL, Chen F, Duncan FE, Cambuli F, Kaur G, Kuchel GA, Lee G, Daldrup-Link HE, Martini H, Phatnani H, Al-Naggar IM, Rahman I, Nie J, Passos JF, Silverstein JC, Campisi J, Wang J, Iwasaki K, Barbosa K, Metis K, Nernekli K, Niedernhofer LJ, Ding L, Wang L, Adams LC, Ruiyang L, Doolittle ML, Teneche MG, Schafer MJ, Xu M, Hajipour M, Boroumand M, Basisty N, Sloan N, Slavov N, Kuksenko O, Robson P, Gomez PT, Vasilikos P, Adams PD, Carapeto P, Zhu Q, Ramasamy R, Perez-Lorenzo R, Fan R, Dong R, Montgomery RR, Shaikh S, Vickovic S, Yin S, Kang S, Suvakov S, Khosla S, Garovic VD, Menon V, Xu Y, Song Y, Suh Y, Dou Z, Neretti N | Nature reviews. Molecular cell biology | 38831121 | Nat Rev Mol Cell Biol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38831121 |
| DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks. | Cheng W, Song Z, Zhang Y, Wang S, Wang D, Yang M, Li L, Ma J | bioRxiv : the preprint server for biology | 39829833 | bioRxiv | 2025 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/39829833 |
| Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue. | Cheng Y, Dang S, Zhang Y, Chen Y, Yu R, Liu M, Jin S, Han A, Katz S, Wang S | bioRxiv : the preprint server for biology | 40161724 | bioRxiv | 2025 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/40161724 |
| Eykthyr reveals transcriptional regulators of spatial gene programs. | Krieger S, Haber E, Ma J | bioRxiv : the preprint server for biology | 40475415 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/40475415 |
| NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. | SenNet Consortium | Nature aging | 36936385 | Nat Aging | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36936385 |
| SPICEMIX enables integrative single-cell spatial modeling of cell identity. | Chidester B, Zhou T, Alam S, Ma J | Nature genetics | 36624346 | Nat Genet | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36624346 |
| scGHOST: identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | Nature methods | 38589516 | Nat Methods | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38589516 |
| Perturb-tracing enables high-content screening of multi-scale 3D genome regulators. | Cheng Y, Hu M, Yang B, Jensen TB, Zhang Y, Yang T, Yu R, Ma Z, Radda JSD, Jin S, Zang C, Wang S | Nature methods | 40211002 | Nat Methods | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40211002 |
| Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. | Chen V, Yang M, Cui W, Kim JS, Talwalkar A, Ma J | Nature methods | 39122941 | Nat Methods | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/39122941 |
| scGHOST: Identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | bioRxiv : the preprint server for biology | 37292994 | bioRxiv | 2023 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/37292994 |
| Comprehensive Identification of Regulatory Protein Networks. | Khoury L, Slavov N | Journal of proteome research | 34736325 | J Proteome Res | 2021 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/34736325 |
| Sampling the proteome by emerging single-molecule and mass spectrometry methods. | MacCoss MJ, Alfaro JA, Faivre DA, Wu CC, Wanunu M, Slavov N | Nature methods | 36899164 | Nat Methods | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36899164 |
| Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier. | Petelski AA, Slavov N, Specht H | Journal of visualized experiments : JoVE | 36571403 | J Vis Exp | 2022 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/36571403 |
| Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. | Huffman RG, Leduc A, Wichmann C, Di Gioia M, Borriello F, Specht H, Derks J, Khan S, Khoury L, Emmott E, Petelski AA, Perlman DH, Cox J, Zanoni I, Slavov N | Nature methods | 37012480 | Nat Methods | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37012480 |
| Data-Driven Optimization of DIA Mass Spectrometry by DO-MS. | Wallmann G, Leduc A, Slavov N | bioRxiv : the preprint server for biology | 36778474 | bioRxiv | 2023 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/36778474 |
| Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease. | Specht H, Slavov N | Journal of proteome research | 35114789 | J Proteome Res | 2022 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/35114789 |
| Driving Single Cell Proteomics Forward with Innovation. | Slavov N | Journal of proteome research | 34597050 | J Proteome Res | 2021 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/34597050 |
| Airway hillocks are injury-resistant reservoirs of unique plastic stem cells. | Lin B, Shah VS, Chernoff C, Sun J, Shipkovenska GG, Vinarsky V, Waghray A, Xu J, Leduc AD, Hintschich CA, Surve MV, Xu Y, Capen DE, Villoria J, Dou Z, Hariri LP, Rajagopal J | Nature | 38693267 | Nature | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38693267 |
| Controlling Pericellular Oxygen Tension in Cell Culture Reveals Distinct Breast Cancer Responses to Low Oxygen Tensions. | Rogers ZJ, Colombani T, Khan S, Bhatt K, Nukovic A, Zhou G, Woolston BM, Taylor CT, Gilkes DM, Slavov N, Bencherif SA | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 38874400 | Adv Sci (Weinh) | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38874400 |
| Alternate RNA decoding results in stable and abundant proteins in mammals. | Tsour S, Machne R, Leduc A, Widmer S, Guez J, Karczewski K, Slavov N | bioRxiv : the preprint server for biology | 39253435 | bioRxiv | 2024 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/39253435 |
| Limiting the impact of protein leakage in single-cell proteomics. | Leduc A, Xu Y, Shipkovenska G, Dou Z, Slavov N | Nature communications | 40324992 | Nat Commun | 2025 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/40324992 |
| Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. | Gatto L, Aebersold R, Cox J, Demichev V, Derks J, Emmott E, Franks AM, Ivanov AR, Kelly RT, Khoury L, Leduc A, MacCoss MJ, Nemes P, Perlman DH, Petelski AA, Rose CM, Schoof EM, Van Eyk J, Vanderaa C, Yates JR 3rd, Slavov N | Nature methods | 36864200 | Nat Methods | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36864200 |
| Upregulation of PD-L1 in Senescence and Aging. | Onorati A, Havas AP, Lin B, Rajagopal J, Sen P, Adams PD, Dou Z | Molecular and cellular biology | 36154662 | Mol Cell Biol | 2022 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/36154662 |
| Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA. | Derks J, Slavov N | Journal of proteome research | 36735898 | J Proteome Res | 2023 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/36735898 |
| Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. | Leduc A, Khoury L, Cantlon J, Khan S, Slavov N | Nature protocols | 39117766 | Nat Protoc | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39117766 |
| Impact of protein degradation and cell growth on mammalian proteomes. | Leduc A, Zheng S, Saxena P, Slavov N | bioRxiv : the preprint server for biology | 39990504 | bioRxiv | 2025 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/39990504 |
| Multiplexed single-cell proteomics using SCoPE2. | Petelski AA, Emmott E, Leduc A, Huffman RG, Specht H, Perlman DH, Slavov N | Nature protocols | 34716448 | Nat Protoc | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34716448 |
| Learning from natural variation across the proteomes of single cells. | Slavov N | PLoS biology | 34986167 | PLoS Biol | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34986167 |
| Counting protein molecules for single-cell proteomics. | Slavov N | Cell | 35063071 | Cell | 2022 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/35063071 |
| Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. | Leduc A, Koury L, Cantlon J, Slavov N | bioRxiv : the preprint server for biology | 38076795 | bioRxiv | 2023 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/38076795 |
| Dynamics of Single-Cell Protein Covariation during Epithelial-Mesenchymal Transition. | Khan S, Conover R, Asthagiri AR, Slavov N | Journal of proteome research | 38663020 | J Proteome Res | 2025 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/38663020 |
| Data-Driven Optimization of DIA Mass Spectrometry by DO-MS. | Wallmann G, Leduc A, Slavov N | Journal of proteome research | 37695820 | J Proteome Res | 2023 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/37695820 |
| Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes. | Galatidou S, Petelski AA, Pujol A, Lattes K, Latorraca LB, Fair T, Popovic M, Vassena R, Slavov N, Barragán M | Molecular human reproduction | 38870523 | Mol Hum Reprod | 2024 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/38870523 |
| Increasing the throughput of sensitive proteomics by plexDIA. | Derks J, Leduc A, Wallmann G, Huffman RG, Willetts M, Khan S, Specht H, Ralser M, Demichev V, Slavov N | Nature biotechnology | 35835881 | Nat Biotechnol | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35835881 |
| Single-cell proteomics: quantifying post-transcriptional regulation during development with mass-spectrometry. | Slavov N | Development (Cambridge, England) | 37387573 | Development | 2023 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/37387573 |
| Limiting the impact of protein leakage in single-cell proteomics. | Leduc A, Xu Y, Shipkovenska G, Dou Z, Slavov N | bioRxiv : the preprint server for biology | 39091738 | bioRxiv | 2024 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/39091738 |
| MRI detection of senescent cells in porcine knee joints with a β-galactosidase responsive Gd-chelate. | Nernekli K, Mangarova DB, Suryadevara V, Hajipour M, Tang JH, Wang J, Liang T, Harris M, Ueyama T, Lyons JK, Moseley ME, Roudi R, Pisani L, von Krüchten R, Duwa R, Lu-Liang SY, Shokri Varniab Z, Vasyliv I, Das N, Murayama M, Shinohara I, Pratx G, Goodman SB, Meade TJ, Daldrup-Link HE | Npj imaging.. | 40330124 | Npj Imaging | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40330124 |
| Pretherapy Ferumoxytol-enhanced MRI for Metastatic Breast Cancer: A New Approach for Predicting Tumor Delivery of Macromolecular Therapeutics? | Daldrup-Link HE | Radiology. Imaging cancer | 36734849 | Radiol Imaging Cancer | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36734849 |
| Musculoskeletal imaging of senescence. | Daldrup-Link HE, Suryadevara V, Tanyildizi Y, Nernekli K, Tang JH, Meade TJ | Skeletal radiology | 38329533 | Skeletal Radiol | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38329533 |
| Late Life Supplementation of 25-Hydroxycholesterol Reduces Aortic Stiffness and Cellular Senescence in Mice. | Mahoney SA, Darrah MA, Venkatasubramanian R, Ciotlos S, Rossman MJ, Campisi J, Seals DR, Melov S, Clayton ZS | Aging cell | 40401595 | Aging Cell | 2025 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/40401595 |
| Single nuclei profiling identifies cell specific markers of skeletal muscle aging, frailty, and senescence. | Perez K, Ciotlos S, McGirr J, Limbad C, Doi R, Nederveen JP, Nilsson MI, Winer DA, Evans W, Tarnopolsky M, Campisi J, Melov S | Aging | 36516485 | Aging (Albany NY) | 2022 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/36516485 |
| 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 |
| A Comprehensive Multiomics Signature of Doxorubicin-Induced Cellular Senescence in the Postmenopausal Human Ovary. | Devrukhkar PR, Watson MA, Soygur B, Wu F, Bons J, Anvari H, Atazhanova T, Martin N, Tran T, Schneider K, Rose JP, Winer D, Shanes E, Pavone MEG, Campisi J, Furman D, Melov S, Schilling B, Duncan FE | Aging cell | 40452152 | Aging Cell | 2025 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/40452152 |
| Senolytic Drugs: Reducing Senescent Cell Viability to Extend Health Span. | Robbins PD, Jurk D, Khosla S, Kirkland JL, LeBrasseur NK, Miller JD, Passos JF, Pignolo RJ, Tchkonia T, Niedernhofer LJ | Annual review of pharmacology and toxicology | 32997601 | Annu Rev Pharmacol Toxicol | 2021 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/32997601 |
| Neutrophils induce paracrine telomere dysfunction and senescence in ROS-dependent manner. | Lagnado A, Leslie J, Ruchaud-Sparagano MH, Victorelli S, Hirsova P, Ogrodnik M, Collins AL, Vizioli MG, Habiballa L, Saretzki G, Evans SA, Salmonowicz H, Hruby A, Geh D, Pavelko KD, Dolan D, Reeves HL, Grellscheid S, Wilson CH, Pandanaboyana S, Doolittle M, von Zglinicki T, Oakley F, Gallage S, Wilson CL, Birch J, Carroll B, Chapman J, Heikenwalder M, Neretti N, Khosla S, Masuda CA, Tchkonia T, Kirkland JL, Jurk D, Mann DA, Passos JF | The EMBO journal | 33764576 | EMBO J | 2021 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/33764576 |
| A chronic wound model to investigate skin cellular senescence. | Wyles SP, Dashti P, Pirtskhalava T, Tekin B, Inman C, Gomez LS, Lagnado AB, Prata L, Jurk D, Passos JF, Tchkonia T, Kirkland JL | Aging | 37086260 | Aging (Albany NY) | 2023 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/37086260 |
| Telomere dysfunction in ageing and age-related diseases. | Rossiello F, Jurk D, Passos JF, d'Adda di Fagagna F | Nature cell biology | 35165420 | Nat Cell Biol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35165420 |
| Targeted clearance of p21- but not p16-positive senescent cells prevents radiation-induced osteoporosis and increased marrow adiposity. | Chandra A, Lagnado AB, Farr JN, Doolittle M, Tchkonia T, Kirkland JL, LeBrasseur NK, Robbins PD, Niedernhofer LJ, Ikeno Y, Passos JF, Monroe DG, Pignolo RJ, Khosla S | Aging cell | 35363946 | Aging Cell | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35363946 |
| Senescent cardiomyocytes contribute to cardiac dysfunction following myocardial infarction. | Redgrave RE, Dookun E, Booth LK, Camacho Encina M, Folaranmi O, Tual-Chalot S, Gill JH, Owens WA, Spyridopoulos I, Passos JF, Richardson GD | npj aging | 37316516 | NPJ Aging | 2023 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/37316516 |
| Author Correction: Apoptotic stress causes mtDNA release during senescence and drives the SASP. | Victorelli S, Salmonowicz H, Chapman J, Martini H, Vizioli MG, Riley JS, Cloix C, Hall-Younger E, Machado Espindola-Netto J, Jurk D, Lagnado AB, Sales Gomez L, Farr JN, Saul D, Reed R, Kelly G, Eppard M, Greaves LC, Dou Z, Pirius N, Szczepanowska K, Porritt RA, Huang H, Huang TY, Mann DA, Masuda CA, Khosla S, Dai H, Kaufmann SH, Zacharioudakis E, Gavathiotis E, LeBrasseur NK, Lei X, Sainz AG, Korolchuk VI, Adams PD, Shadel GS, Tait SWG, Passos JF | Nature | 38168624 | Nature | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38168624 |
| Guidelines for minimal information on cellular senescence experimentation in vivo. | Ogrodnik M, Carlos Acosta J, Adams PD, d'Adda di Fagagna F, Baker DJ, Bishop CL, Chandra T, Collado M, Gil J, Gorgoulis V, Gruber F, Hara E, Jansen-Dürr P, Jurk D, Khosla S, Kirkland JL, Krizhanovsky V, Minamino T, Niedernhofer LJ, Passos JF, Ring NAR, Redl H, Robbins PD, Rodier F, Scharffetter-Kochanek K, Sedivy JM, Sikora E, Witwer K, von Zglinicki T, Yun MH, Grillari J, Demaria M | Cell | 39121846 | Cell | 2024 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/39121846 |
| Osteochondroprogenitor cells and neutrophils expressing p21 and senescence markers modulate fracture repair. | Saul D, Doolittle ML, Rowsey JL, Froemming MN, Kosinsky RL, Vos SJ, Ruan M, LeBrasseur NK, Chandra A, Pignolo RJ, Passos JF, Farr JN, Monroe DG, Khosla S | The Journal of clinical investigation | 38753433 | J Clin Invest | 2024 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/38753433 |
| Hyperoxia-induced senescence in fetal airway smooth muscle cells: role of mitochondrial reactive oxygen species and endoplasmic reticulum stress. | Koloko Ngassie ML, Thompson MA, Roos BB, Ayyalasomayajula S, Lagnado AB, Passos JF, Pabelick CM, Prakash YS | American journal of physiology. Lung cellular and molecular physiology | 40183670 | Am J Physiol Lung Cell Mol Physiol | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40183670 |
| Senescent cardiomyocytes contribute to cardiac dysfunction following myocardial infarction. | Redgrave R, Dookun E, Booth L, Folaranm O, Tual-Chalot S, Gill J, Owens A, Spyridopoulos I, Passos J, Richardson G | Research square | 37090497 | Res Sq | 2023 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/37090497 |
| BMAL1 modulates senescence programming via AP-1. | Jachim SK, Zhong J, Ordog T, Lee JH, Bhagwate AV, Nagaraj NK, Westendorf JJ, Passos JF, Matveyenko AV, LeBrasseur NK | Aging | 37819791 | Aging (Albany NY) | 2023 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/37819791 |
| Toll-like receptor 2 orchestrates a tumor suppressor response in non-small cell lung cancer. | Millar FR, Pennycuick A, Muir M, Quintanilla A, Hari P, Freyer E, Gautier P, Meynert A, Grimes G, Coll CS, Zdral S, Victorelli S, Teixeira VH, Connelly J, Passos JF, Ros MA, Wallace WAH, Frame MC, Sims AH, Boulter L, Janes SM, Wilkinson S, Acosta JC | Cell reports | 36351380 | Cell Rep | 2022 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/36351380 |
| Telomeres, cellular senescence, and aging: past and future. | Eppard M, Passos JF, Victorelli S | Biogerontology | 38150087 | Biogerontology | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38150087 |
| COPIng with senescence. | Victorelli S, Passos JF | Nature cell biology | 38012404 | Nat Cell Biol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38012404 |
| Mitochondrial RNA cytosolic leakage drives the SASP. | Victorelli S, Eppard M, Woo SH, Everts SPA, Martini H, Pirius N, Franco AC, Han Y, Saul D, Splinter PL, O'Hara SP, Valenzuela-Pérez L, Lee HSK, Jurk D, LaRusso NF, Hirsova P, Passos JF | Research square | 39257994 | Res Sq | 2024 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/39257994 |
| Longevity biotechnology: bridging AI, biomarkers, geroscience and clinical applications for healthy longevity. | Lyu YX, Fu Q, Wilczok D, Ying K, King A, Antebi A, Vojta A, Stolzing A, Moskalev A, Georgievskaya A, Maier AB, Olsen A, Groth A, Simon AK, Brunet A, Jamil A, Kulaga A, Bhatti A, Yaden B, Pedersen BK, Schumacher B, Djordjevic B, Kennedy B, Chen C, Huang CY, Correll CU, Murphy CT, Ewald CY, Chen D, Valenzano DR, Sołdacki D, Erritzoe D, Meyer D, Sinclair DA, Chini EN, Teeling EC, Morgen E, Verdin E, Vernet E, Pinilla E, Fang EF, Bischof E, Mercken EM, Finger F, Kuipers F, Pun FW, Gyülveszi G, Civiletto G, Zmudze G, Blander G, Pincus HA, McClure J, Kirkland JL, Peyer J, Justice JN, Vijg J, Gruhn JR, McLaughlin J, Mannick J, Passos J, Baur JA, Betts-LaCroix J, Sedivy JM, Speakman JR, Shlain J, von Maltzahn J, Andreasson KI, Moody K, Palikaras K, Fortney K, Niedernhofer LJ, Rasmussen LJ, Veenhoff LM, Melton L, Ferrucci L, Quarta M, Koval M, Marinova M, Hamalainen M, Unfried M, Ringel MS, Filipovic M, Topors M, Mitin N, Roy N, Pintar N, Barzilai N, Binetti P, Singh P, Kohlhaas P, Robbins PD, Rubin P, Fedichev PO, Kamya P, Muñoz-Canoves P, de Cabo R, Faragher RGA, Konrad R, Ripa R, Mansukhani R, Büttner S, Wickström SA, Brunemeier S, Jakimov S, Luo S, Rosenzweig-Lipson S, Tsai SY, Dimmeler S, Rando TA, Peterson TR, Woods T, Wyss-Coray T, Finkel T, Strauss T, Gladyshev VN, Longo VD, Dwaraka VB, Gorbunova V, Acosta-Rodríguez VA, Sorrentino V, Sebastiano V, Li W, Suh Y, Zhavoronkov A, Scheibye-Knudsen M, Bakula D | Aging | 39418098 | Aging (Albany NY) | 2024 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/39418098 |
| p53 enhances DNA repair and suppresses cytoplasmic chromatin fragments and inflammation in senescent cells. | Miller KN, Li B, Pierce-Hoffman HR, Patel S, Lei X, Rajesh A, Teneche MG, Havas AP, Gandhi A, Macip CC, Lyu J, Victorelli SG, Woo SH, Lagnado AB, LaPorta MA, Liu T, Dasgupta N, Li S, Davis A, Korotkov A, Hultenius E, Gao Z, Altman Y, Porritt RA, Garcia G, Mogler C, Seluanov A, Gorbunova V, Kaech SM, Tian X, Dou Z, Chen C, Passos JF, Adams PD | Nature communications | 40044657 | Nat Commun | 2025 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/40044657 |
| Linked regulation of genome integrity and senescence-associated inflammation by p53. | Miller KN, Li B, Pierce-Hoffman HR, Patel S, Lei X, Rajesh A, Teneche MG, Havas AP, Gandhi A, Macip CC, Lyu J, Victorelli SG, Woo SH, Lagnado AB, LaPorta MA, Liu T, Dasgupta N, Li S, Davis A, Korotkov A, Hultenius E, Gao Z, Altman Y, Porritt RA, Garcia G, Mogler C, Seluanov A, Gorbunova V, Kaech SM, Tian X, Dou Z, Chen C, Passos JF, Adams PD | bioRxiv : the preprint server for biology | 38045344 | bioRxiv | 2024 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/38045344 |
| Osteochondroprogenitor cells and neutrophils expressing p21 and senescence markers modulate fracture repair. | Saul D, Doolittle ML, Rowsey JL, Froemming MN, Kosinsky RL, Vos SJ, Ruan M, LeBrasseur N, Chandra A, Pignolo R, Passos JF, Farr JN, Monroe DG, Khosla S | bioRxiv : the preprint server for biology | 38370844 | bioRxiv | 2024 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/38370844 |
| A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues. | Saul D, Kosinsky RL, Atkinson EJ, Doolittle ML, Zhang X, LeBrasseur NK, Pignolo RJ, Robbins PD, Niedernhofer LJ, Ikeno Y, Jurk D, Passos JF, Hickson LJ, Xue A, Monroe DG, Tchkonia T, Kirkland JL, Farr JN, Khosla S | Nature communications | 35974106 | Nat Commun | 2022 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/35974106 |
| New Horizons in cellular senescence for clinicians. | Witham MD, Granic A, Miwa S, Passos JF, Richardson GD, Sayer AA | Age and ageing | 37466640 | Age Ageing | 2023 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/37466640 |
| Senolytic drugs: Beyond the promise and the hype. | Jurk D, Passos JF | Mechanisms of ageing and development | 35032547 | Mech Ageing Dev | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35032547 |
| Cellular senescence: all roads lead to mitochondria. | Martini H, Passos JF | The FEBS journal | 35048548 | FEBS J | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35048548 |
| Cytoplasmic DNA: sources, sensing, and role in aging and disease. | Miller KN, Victorelli SG, Salmonowicz H, Dasgupta N, Liu T, Passos JF, Adams PD | Cell | 34715021 | Cell | 2021 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/34715021 |
| Cytoplasmic innate immune sensing by the caspase-4 non-canonical inflammasome promotes cellular senescence. | Fernández-Duran I, Quintanilla A, Tarrats N, Birch J, Hari P, Millar FR, Lagnado AB, Smer-Barreto V, Muir M, Brunton VG, Passos JF, Acosta JC | Cell death and differentiation | 34916628 | Cell Death Differ | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34916628 |
| Therapeutic Potential of Senolytics in Cardiovascular Disease. | Dookun E, Passos JF, Arthur HM, Richardson GD | Cardiovascular drugs and therapy | 32979174 | Cardiovasc Drugs Ther | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32979174 |
| The Third Annual Symposium of the Midwest Aging Consortium. | Keller A, Bai H, Budinger S, Eliazer S, Hansen M, Konopka AR, Morales-Nebreda L, Najt CP, Prahlad V, Victorelli S, Vorland CJ, Yuan R, Rhoads TW, Mihaylova MM | The journals of gerontology. Series A, Biological sciences and medical sciences | 37804247 | J Gerontol A Biol Sci Med Sci | 2024 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/37804247 |
| Apoptotic stress causes mtDNA release during senescence and drives the SASP. | Victorelli S, Salmonowicz H, Chapman J, Martini H, Vizioli MG, Riley JS, Cloix C, Hall-Younger E, Machado Espindola-Netto J, Jurk D, Lagnado AB, Sales Gomez L, Farr JN, Saul D, Reed R, Kelly G, Eppard M, Greaves LC, Dou Z, Pirius N, Szczepanowska K, Porritt RA, Huang H, Huang TY, Mann DA, Masuda CA, Khosla S, Dai H, Kaufmann SH, Zacharioudakis E, Gavathiotis E, LeBrasseur NK, Lei X, Sainz AG, Korolchuk VI, Adams PD, Shadel GS, Tait SWG, Passos JF | Nature | 37821702 | Nature | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37821702 |
| Distinct secretomes in p16- and p21- positive senescent cells across tissues. | Saul D, Jurk D, Doolittle ML, Kosinsky RL, Monroe DG, LeBrasseur NK, Robbins PD, Niedernhofer LJ, Khosla S, Passos JF | bioRxiv : the preprint server for biology | 38106149 | bioRxiv | 2023 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/38106149 |
| Bone Marrow Adiposity in Models of Radiation- and Aging-Related Bone Loss Is Dependent on Cellular Senescence. | Chandra A, Lagnado AB, Farr JN, Schleusner M, Monroe DG, Saul D, Passos JF, Khosla S, Pignolo RJ | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 35247283 | J Bone Miner Res | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35247283 |
| Telomere dysfunction in chronic liver disease: The link from aging. | Penrice DD, Jalan-Sakrikar N, Jurk D, Passos JF, Simonetto DA | Hepatology (Baltimore, Md.) | 37102475 | Hepatology | 2024 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/37102475 |
| Local senolysis in aged mice only partially replicates the benefits of systemic senolysis. | Farr JN, Saul D, Doolittle ML, Kaur J, Rowsey JL, Vos SJ, Froemming MN, Lagnado AB, Zhu Y, Weivoda M, Ikeno Y, Pignolo RJ, Niedernhofer LJ, Robbins PD, Jurk D, Passos JF, LeBrasseur NK, Tchkonia T, Kirkland JL, Monroe DG, Khosla S | The Journal of clinical investigation | 36809340 | J Clin Invest | 2023 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/36809340 |
| Characterization of cellular senescence in aging skeletal muscle. | Zhang X, Habiballa L, Aversa Z, Ng YE, Sakamoto AE, Englund DA, Pearsall VM, White TA, Robinson MM, Rivas DA, Dasari S, Hruby AJ, Lagnado AB, Jachim SK, Granic A, Sayer AA, Jurk D, Lanza IR, Khosla S, Fielding RA, Nair KS, Schafer MJ, Passos JF, LeBrasseur NK | Nature aging | 36147777 | Nat Aging | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/36147777 |
| Cellular senescence is increased in airway smooth muscle cells of elderly persons with asthma. | Aghali A, Khalfaoui L, Lagnado AB, Drake LY, Teske JJ, Pabelick CM, Passos JF, Prakash YS | American journal of physiology. Lung cellular and molecular physiology | 36166734 | Am J Physiol Lung Cell Mol Physiol | 2022 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/36166734 |
| Determining the feasibility of characterising cellular senescence in human skeletal muscle and exploring associations with muscle morphology and physical function at different ages: findings from the MASS_Lifecourse Study. | Habiballa L, Hruby A, Granic A, Dodds RM, Hillman SJ, Jurk D, Passos JF, Sayer AA | GeroScience | 37434081 | Geroscience | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37434081 |
| Senescent cell transplantation into the skin induces age-related peripheral dysfunction and cognitive decline. | Franco AC, Martini H, Victorelli S, Lagnado AB, Wyles SP, Rowsey JL, Pirius N, Woo SH, Costa DG, Chaib S, Tullius SG, Tchkonia T, Kirkland JL, Khosla S, Jurk D, Cavadas C, Passos JF | Aging cell | 39374134 | Aging Cell | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39374134 |
| Mitochondrial metabolism and epigenetic crosstalk drive the SASP. | Passos J, Martini H, Birch J, Marques F, Victorelli S, Lagnado A, Pirius N, Franco A, Lee G, Han Y, Rowsey J, Gaspar-Maia A, Havas A, Murad R, Lei X, Porritt R, Maddocks O, Jurk D, Khosla S, Adams P | Research square | 39678326 | Res Sq | 2024 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/39678326 |
| Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain. | Fu X, Sun L, Dong R, Chen JY, Silakit R, Condon LF, Lin Y, Lin S, Palmiter RD, Gu L | Cell | 36368323 | Cell | 2022 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/36368323 |
| Single-cell and spatial detection of senescent cells using DeepScence. | Qu Y, Ji B, Dong R, Gu L, Chan C, Xie J, Glass C, Wang XF, Nixon A, Ji Z | bioRxiv : the preprint server for biology | 38045252 | bioRxiv | 2025 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/38045252 |
| STtools: A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data. | Xi J, Lee JH, Kang HM, Jun G | Bioinformatics advances | 36284674 | Bioinform Adv | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36284674 |
| Iditarod, a Drosophila homolog of the Irisin precursor FNDC5, is critical for exercise performance and cardiac autophagy. | Cobb T, Hwang I, Soukar M, Namkoong S, Cho US, Safdar M, Kim M, Wessells RJ, Lee JH | Proceedings of the National Academy of Sciences of the United States of America | 37722048 | Proc Natl Acad Sci U S A | 2023 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/37722048 |
| SiftCell: A robust framework to detect and isolate cell-containing droplets from single-cell RNA sequence reads. | Xi J, Park SR, Lee JH, Kang HM | Cell systems | 37473732 | Cell Syst | 2023 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/37473732 |
| Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution. | Anacleto A, Cheng W, Feng Q, Cho CS, Hwang Y, Kim Y, Si Y, Park A, Hsu JE, Schrank M, Teles R, Modlin RL, Plazyo O, Gudjonsson JE, Kim M, Kim CH, Han HS, Kang HM, Lee JH | bioRxiv : the preprint server for biology | 39975076 | bioRxiv | 2025 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/39975076 |
| TREM2 macrophages induced by human lipids drive inflammation in acne lesions. | Do TH, Ma F, Andrade PR, Teles R, de Andrade Silva BJ, Hu C, Espinoza A, Hsu JE, Cho CS, Kim M, Xi J, Xing X, Plazyo O, Tsoi LC, Cheng C, Kim J, Bryson BD, O'Neill AM, Colonna M, Gudjonsson JE, Klechevsky E, Lee JH, Gallo RL, Bloom BR, Pellegrini M, Modlin RL | Science immunology | 35867799 | Sci Immunol | 2022 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/35867799 |
| Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. | Ma F, Plazyo O, Billi AC, Tsoi LC, Xing X, Wasikowski R, Gharaee-Kermani M, Hile G, Jiang Y, Harms PW, Xing E, Kirma J, Xi J, Hsu JE, Sarkar MK, Chung Y, Di Domizio J, Gilliet M, Ward NL, Maverakis E, Klechevsky E, Voorhees JJ, Elder JT, Lee JH, Kahlenberg JM, Pellegrini M, Modlin RL, Gudjonsson JE | Nature communications | 37308489 | Nat Commun | 2023 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/37308489 |
| Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics. | Kim Y, Cheng W, Cho CS, Hwang Y, Si Y, Park A, Schrank M, Hsu JE, Xi J, Kim M, Pedersen E, Koues OI, Wilson T, Jun G, Kang HM, Lee JH | bioRxiv : the preprint server for biology | 38617262 | bioRxiv | 2024 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/38617262 |
| FICTURE: Scalable segmentation-free analysis of submicron resolution spatial transcriptomics. | Si Y, Lee C, Hwang Y, Yun JH, Cheng W, Cho CS, Quiros M, Nusrat A, Zhang W, Jun G, Zöllner S, Lee JH, Kang HM | bioRxiv : the preprint server for biology | 37961699 | bioRxiv | 2023 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/37961699 |
| FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics. | Si Y, Lee C, Hwang Y, Yun JH, Cheng W, Cho CS, Quiros M, Nusrat A, Zhang W, Jun G, Zöllner S, Lee JH, Kang HM | Nature methods | 39266749 | Nat Methods | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39266749 |
| Spatial Single-Cell Technologies for Exploring Gastrointestinal Tissue Transcriptome. | Kang HM, Lee JH | Comprehensive Physiology | 37358516 | Compr Physiol | 2023 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/37358516 |
| High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation. | Hsu JE, Ruiz L, Hwang Y, Guzman S, Cho CS, Cheng W, Si Y, Macpherson P, Schrank M, Jun G, Kang HM, Kim M, Brooks S, Lee JH | bioRxiv : the preprint server for biology | 38464282 | bioRxiv | 2024 Feb 29 | https://www.ncbi.nlm.nih.gov/pubmed/38464282 |
| Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics. | Kim Y, Cheng W, Cho CS, Hwang Y, Si Y, Park A, Schrank M, Hsu JE, Anacleto A, Xi J, Kim M, Pedersen E, Koues OI, Wilson T, Lee C, Jun G, Kang HM, Lee JH | Nature protocols | 39482362 | Nat Protoc | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39482362 |
| Is it the time to integrate novel sequencing technologies into clinical practice? | VanOudenhove J, Halene S, Mendez L | Current opinion in hematology | 36602939 | Curr Opin Hematol | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36602939 |
| 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 |
| 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 |
| 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 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 |
| Gene trajectory inference for single-cell data by optimal transport metrics. | Qu R, Cheng X, Sefik E, Stanley Iii JS, Landa B, Strino F, Platt S, Garritano J, Odell ID, Coifman R, Flavell RA, Myung P, Kluger Y | Nature biotechnology | 38580861 | Nat Biotechnol | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38580861 |
| Splicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis. | Maul-Newby HM, Halene S | Experimental hematology | 39393608 | Exp Hematol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39393608 |
| Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES. | Raredon MSB, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason LE, Kluger Y | Bioinformatics (Oxford, England) | 36458905 | Bioinformatics | 2023 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/36458905 |
| 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 |
| Scaling deep identifiable models enables zero-shot characterization of single-cell biological states. | Dong M, Agrawal K, Fan R, Sefik E, Flavell RA, Kluger Y | bioRxiv : the preprint server for biology | 38014345 | bioRxiv | 2024 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/38014345 |
| 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 |
| 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 |
| The Dyson equalizer: adaptive noise stabilization for low-rank signal detection and recovery. | Landa B, Kluger Y | Information and inference : a journal of the IMA | 39830802 | Inf inference | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39830802 |
| 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 |
| 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 |
| SIMVI reveals intrinsic and spatial-induced states in spatial omics data. | Dong M, Su D, Kluger H, Fan R, Kluger Y | bioRxiv : the preprint server for biology | 37693629 | bioRxiv | 2024 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/37693629 |
| 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 |
| 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 |
| 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, 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 |
| 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 |
| Deep unsupervised feature selection by discarding nuisance and correlated features. | Shaham U, Lindenbaum O, Svirsky J, Kluger Y | Neural networks : the official journal of the International Neural Network Society | 35500458 | Neural Netw | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35500458 |
| Biwhitening Reveals the Rank of a Count Matrix. | Landa B, Zhang TTCK, Kluger Y | SIAM journal on mathematics of data science | 37576699 | SIAM J Math Data Sci | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37576699 |
| Principled PCA separates signal from noise in omics count data. | Stanley JS 3rd, Yang J, Li R, Lindenbaum O, Kobak D, Landa B, Kluger Y | bioRxiv : the preprint server for biology | 39975320 | bioRxiv | 2025 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/39975320 |
| SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data. | Dong M, Su DG, Kluger H, Fan R, Kluger Y | Nature communications | 40148341 | Nat Commun | 2025 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/40148341 |
| Cellular senescence: a key therapeutic target in aging and diseases. | Zhang L, Pitcher LE, Yousefzadeh MJ, Niedernhofer LJ, Robbins PD, Zhu Y | The Journal of clinical investigation | 35912854 | J Clin Invest | 2022 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/35912854 |
| Analyzing somatic mutations by single-cell whole-genome sequencing. | Zhang L, Lee M, Maslov AY, Montagna C, Vijg J, Dong X | Nature protocols | 37996541 | Nat Protoc | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37996541 |
| Effect of Cellular Senescence in Disease Progression and Transplantation: Immune Cells and Solid Organs. | Kirchner VA, Badshah JS, Hong SK, Martinez O, Pruett TL, Niedernhofer LJ | Transplantation | 37953486 | Transplantation | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/37953486 |
| Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing. | Rivera-Mulia JC, Trevilla-Garcia C, Martinez-Cifuentes S | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 35781769 | Chromosome Res | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/35781769 |
| Targeting cellular senescence with senotherapeutics: senolytics and senomorphics. | Zhang L, Pitcher LE, Prahalad V, Niedernhofer LJ, Robbins PD | The FEBS journal | 35015337 | FEBS J | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35015337 |
| Predicting mutational function using machine learning. | Shea A, Bartz J, Zhang L, Dong X | Mutation research. Reviews in mutation research | 36965820 | Mutat Res Rev Mutat Res | 2023 Jan-Jun | https://www.ncbi.nlm.nih.gov/pubmed/36965820 |
| Progress in Discovering Transcriptional Noise in Aging. | Bartz J, Jung H, Wasiluk K, Zhang L, Dong X | International journal of molecular sciences | 36835113 | Int J Mol Sci | 2023 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/36835113 |
| Targeting Cellular Senescence with Senotherapeutics: Development of New Approaches for Skin Care. | Thompson EL, Pitcher LE, Niedernhofer LJ, Robbins PD | Plastic and reconstructive surgery | 36170431 | Plast Reconstr Surg | 2022 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/36170431 |
| Cellular Senescence in Obesity and Associated Complications: a New Therapeutic Target. | Narasimhan A, Flores RR, Camell CD, Bernlohr DA, Robbins PD, Niedernhofer LJ | Current diabetes reports | 36239841 | Curr Diab Rep | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36239841 |
| A nutrigeroscience approach: Dietary macronutrients and cellular senescence. | Calubag MF, Robbins PD, Lamming DW | Cell metabolism | 39178854 | Cell Metab | 2024 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/39178854 |
| Chronic social stress induces p16-mediated senescent cell accumulation in mice. | Lyons CE, Pallais JP, McGonigle S, Mansk RP, Collinge CW, Yousefzadeh MJ, Baker DJ, Schrank PR, Williams JW, Niedernhofer LJ, van Deursen JM, Razzoli M, Bartolomucci A | Nature aging | 39528642 | Nat Aging | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39528642 |
| Identification of lipid senolytics targeting senescent cells through ferroptosis induction. | Zhang LJ, Salekeen R, Soto-Palma C, Elsallabi O, Ye H, Hughes B, Zhang B, Nunes A, Lee K, Xu W, Mohamed A, Piepgras E, McGowan SJ, Angelini L, O'Kelly R, Han X, Niedernhofer LJ, Robbins PD | bioRxiv : the preprint server for biology | 39463954 | bioRxiv | 2024 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/39463954 |
| Attenuation of Cellular Senescence and Improvement of Osteogenic Differentiation Capacity of Human Liver Stem Cells Using Specific Senomorphic and Senolytic Agents. | Nunes ADC, Pitcher LE, Exner HA, Grassi DJ, Burns B, Sanchez MBH, Tetta C, Camussi G, Robbins PD | Stem cell reviews and reports | 40220121 | Stem Cell Rev Rep | 2025 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/40220121 |
| Developing transcriptomic signatures as a biomarker of cellular senescence. | Mahmud S, Pitcher LE, Torbenson E, Robbins PD, Zhang L, Dong X | Ageing research reviews | 38964507 | Ageing Res Rev | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38964507 |
| miR-96-5p expression is sufficient to induce and maintain the senescent cell fate in the absence of stress. | Santiago FE, Adige T, Mahmud S, Dong X, Niedernhofer LJ, Robbins PD | Proceedings of the National Academy of Sciences of the United States of America | 39325426 | Proc Natl Acad Sci U S A | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39325426 |
| Identification of Senomorphic miRNAs in Embryonic Progenitor and Adult Stem Cell-Derived Extracellular Vesicles. | Zhang T, Nunes ADC, Lee J, Larocca D, Camussi G, Lim SK, Bascones VU, Angelini L, O'Kelly RD, Dong X, Niedernhofer LJ, Robbins PD | Aging cell | 40275616 | Aging Cell | 2025 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/40275616 |
| The mouse Social Frailty Index (mSFI): a novel behavioral assessment for impaired social functioning in aging mice. | Collinge CW, Razzoli M, Mansk R, McGonigle S, Lamming DW, Pacak CA, van der Pluijm I, Niedernhofer L, Bartolomucci A | GeroScience | 38987495 | Geroscience | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38987495 |
| Epigenetics, DNA damage, and aging. | Soto-Palma C, Niedernhofer LJ, Faulk CD, Dong X | The Journal of clinical investigation | 35968782 | J Clin Invest | 2022 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/35968782 |
| High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. | Skok Gibbs C, Jackson CA, Saldi GA, Tjärnberg A, Shah A, Watters A, De Veaux N, Tchourine K, Yi R, Hamamsy T, Castro DM, Carriero N, Gorissen BL, Gresham D, Miraldi ER, Bonneau R | Bioinformatics (Oxford, England) | 35188184 | Bioinformatics | 2022 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/35188184 |
| The broken Alzheimer's disease genome. | Gouveia Roque C, Phatnani H, Hengst U | Cell genomics | 38697121 | Cell Genom | 2024 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/38697121 |
| Tissue and cellular spatiotemporal dynamics in colon aging. | Daly AC, Cambuli F, Äijö T, Lötstedt B, Marjanovic N, Kuksenko O, Smith-Erb M, Fernandez S, Domovic D, Van Wittenberghe N, Drokhlyansky E, Griffin GK, Phatnani H, Bonneau R, Regev A, Vickovic S | bioRxiv : the preprint server for biology | 38712088 | bioRxiv | 2024 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/38712088 |
| Biological sex matters in brain aging. | Dubal DB, Murphy CT, Suh Y, Benayoun BA | Neuron | 39788086 | Neuron | 2025 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/39788086 |
| Cell type-specific changes identified by single-cell transcriptomics in Alzheimer's disease. | Luquez T, Gaur P, Kosater IM, Lam M, Lee DI, Mares J, Paryani F, Yadav A, Menon V | Genome medicine | 36447241 | Genome Med | 2022 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/36447241 |
| Health AI Assurance Laboratories. | Stead WW, Aliferis C | JAMA | 38345804 | JAMA | 2024 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/38345804 |
| Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture. | Zhu Y, Rosenfeld MG, Suh Y | Proceedings of the National Academy of Sciences of the United States of America | 37922325 | Proc Natl Acad Sci U S A | 2023 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/37922325 |
| A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A. | Simon M, Yang J, Gigas J, Earley EJ, Hillpot E, Zhang L, Zagorulya M, Tombline G, Gilbert M, Yuen SL, Pope A, Van Meter M, Emmrich S, Firsanov D, Athreya A, Biashad SA, Han J, Ryu S, Tare A, Zhu Y, Hudgins A, Atzmon G, Barzilai N, Wolfe A, Moody K, Garcia BA, Thomas DD, Robbins PD, Vijg J, Seluanov A, Suh Y, Gorbunova V | The EMBO journal | 36215696 | EMBO J | 2022 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/36215696 |
| Ontogeny of the spinal cord dorsal horn. | Roome RB, Yadav A, Flores L, Puarr A, Nardini D, Richardson A, Waclaw RR, Arkell RM, Menon V, Johnson JE, Levine AJ | bioRxiv : the preprint server for biology | 40161840 | bioRxiv | 2025 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/40161840 |
| Multicellular communities are perturbed in the aging human brain and Alzheimer's disease. | Cain A, Taga M, McCabe C, Green GS, Hekselman I, White CC, Lee DI, Gaur P, Rozenblatt-Rosen O, Zhang F, Yeger-Lotem E, Bennett DA, Yang HS, Regev A, Menon V, Habib N, De Jager PL | Nature neuroscience | 37336975 | Nat Neurosci | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37336975 |
| A cellular taxonomy of the adult human spinal cord. | Yadav A, Matson KJE, Li L, Hua I, Petrescu J, Kang K, Alkaslasi MR, Lee DI, Hasan S, Galuta A, Dedek A, Ameri S, Parnell J, Alshardan MM, Qumqumji FA, Alhamad SM, Wang AP, Poulen G, Lonjon N, Vachiery-Lahaye F, Gaur P, Nalls MA, Qi YA, Maric D, Ward ME, Hildebrand ME, Mery PF, Bourinet E, Bauchet L, Tsai EC, Phatnani H, Le Pichon CE, Menon V, Levine AJ | Neuron | 36731429 | Neuron | 2023 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/36731429 |
| Targeted sequencing of the 9p21.3 region reveals association with reduced disease risks in Ashkenazi Jewish centenarians. | Zhu Y, Ryu S, Tare A, Barzilai N, Atzmon G, Suh Y | Aging cell | 37605876 | Aging Cell | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37605876 |
| Current Challenges and Solutions for Clinical Management and Care of People with HIV: Findings from the 12th Annual International HIV and Aging Workshop. | Yu X, Lobo JD, Sundermann E, Baker DJ, Tracy RP, Kuchel GA, Stephenson KE, Letendre SL, Brew B, Cysique LA, Dale SK, Wallen C, Kunisaki KM, Guaraldi G, Milic J, Winston A, Moore DJ, Margolick JB, Erlandson KM | AIDS research and human retroviruses | 36322713 | AIDS Res Hum Retroviruses | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36322713 |
| microRNA-449a reduces growth hormone-stimulated senescent cell burden through PI3K-mTOR signaling. | Noureddine S, Nie J, Schneider A, Menon V, Fliesen Z, Dhahbi J, Victoria B, Oyer J, Robles-Carrillo L, Nunes ADC, Ashiqueali S, Janusz A, Copik A, Robbins PD, Musi N, Masternak MM | Proceedings of the National Academy of Sciences of the United States of America | 36976763 | Proc Natl Acad Sci U S A | 2023 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/36976763 |
| The heterogeneity of cellular senescence: insights at the single-cell level. | Cohn RL, Gasek NS, Kuchel GA, Xu M | Trends in cell biology | 35599179 | Trends Cell Biol | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35599179 |
| HAND1, partially mediated through ape-specific LTR binding, is essential for human extra-embryonic mesenchyme derivation from iPSCs. | Liu Z, Tan Y, Flynn WF, Sun L, Pratumkaew P, Alcoforado Diniz J, Oliveira NAJ, McDonough JA, Skarnes WC, Robson P | Cell reports | 40220298 | Cell Rep | 2025 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/40220298 |
| Impact of Geroscience on Therapeutic Strategies for Older Adults With Cardiovascular Disease: JACC Scientific Statement. | Forman DE, Kuchel GA, Newman JC, Kirkland JL, Volpi E, Taffet GE, Barzilai N, Pandey A, Kitzman DW, Libby P, Ferrucci L | Journal of the American College of Cardiology | 37389519 | J Am Coll Cardiol | 2023 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/37389519 |
| Challenges and opportunities for modeling aging and cancer. | Anczuków O, Airhart S, Chuang JH, Coussens LM, Kuchel GA, Korstanje R, Li S, Lucido AL, McAllister SS, Politi K, Polyak K, Ratliff T, Ren G, Trowbridge JJ, Ucar D, Palucka K | Cancer cell | 37001528 | Cancer Cell | 2023 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/37001528 |
| Drugs Targeting Mechanisms of Aging to Delay Age-Related Disease and Promote Healthspan: Proceedings of a National Institute on Aging Workshop. | Espinoza SE, Khosla S, Baur JA, de Cabo R, Musi N | The journals of gerontology. Series A, Biological sciences and medical sciences | 37325957 | J Gerontol A Biol Sci Med Sci | 2023 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/37325957 |
| SenSkin™: a human skin-specific cellular senescence gene set. | Wyles SP, Yu GT, Ganier C, Tchkonia T, Lynch MD, Kuchel GA, Kirkland JL | GeroScience | 39998731 | Geroscience | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/39998731 |
| Identifying cell-type-specific spatially variable genes with ctSVG. | Zhuang H, Shang X, Hou W, Ji Z | Research square | 39764138 | Res Sq | 2024 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/39764138 |
| 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 |
| T cell transcriptional landscapes are shaped by TCR sequence similarity. | Wang H, Ji Z | bioRxiv : the preprint server for biology | 38076860 | bioRxiv | 2025 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/38076860 |
| 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 |
| Vispro improves imaging analysis for Visium spatial transcriptomics. | Ma H, Qu Y, Zhang AR, Ji Z | bioRxiv : the preprint server for biology | 39416029 | bioRxiv | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39416029 |
| Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. | Hou W, Ji Z | Nature methods | 38528186 | Nat Methods | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38528186 |
| PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns. | Zhuang H, Ji Z | bioRxiv : the preprint server for biology | 38585819 | bioRxiv | 2024 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/38585819 |
| Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering. | Fang J, Chan C, Owzar K, Wang L, Qin D, Li QJ, Xie J | Genome biology | 36575517 | Genome Biol | 2022 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/36575517 |
| Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. | Hou W, Ji Z | bioRxiv : the preprint server for biology | 37131626 | bioRxiv | 2023 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/37131626 |
| Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis. | Hou W, Ji Z | Research square | 37205379 | Res Sq | 2023 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/37205379 |
| 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 |
| Vispro improves imaging analysis for Visium spatial transcriptomics. | Ma H, Zhang X, Qu Y, Zhang AR, Ji Z | Genome biology | 40533768 | Genome Biol | 2025 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/40533768 |
| A systematic evaluation of computational methods for cell segmentation. | Wang Y, Zhao J, Xu H, Han C, Tao Z, Zhou D, Geng T, Liu D, Ji Z | Briefings in bioinformatics | 39154193 | Brief Bioinform | 2024 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/39154193 |
| Assessing large multimodal models for one-shot learning and interpretability in biomedical image classification. | Hou W, Liu Q, Ma H, Qu Y, Ji Z | bioRxiv : the preprint server for biology | 38260646 | bioRxiv | 2025 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/38260646 |
| Integrating multiple single-cell multi-omics samples with Smmit. | Wan C, Ji Z | bioRxiv : the preprint server for biology | 37066420 | bioRxiv | 2025 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/37066420 |
| Palo: spatially aware color palette optimization for single-cell and spatial data. | Hou W, Ji Z | Bioinformatics (Oxford, England) | 35642896 | Bioinformatics | 2022 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/35642896 |
| A systematic evaluation of computational methods for cell segmentation. | Wang Y, Zhao J, Xu H, Han C, Tao Z, Zhou D, Geng T, Liu D, Ji Z | bioRxiv : the preprint server for biology | 38352578 | bioRxiv | 2024 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/38352578 |
| B-Lightning: using bait genes for marker gene hunting in single-cell data with complex heterogeneity. | Shao Y, Gao Q, Wang L, Li D, Nixon AB, Chan C, Li QJ, Xie J | Briefings in bioinformatics | 39927857 | Brief Bioinform | 2024 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/39927857 |
| Comparative analysis of gene regulation in single cells using Compass. | Wan C, Qu Y, Ye Z, Zhang T, Ma H, Chen M, Hou W, Ji Z | Cell reports methods | 40345198 | Cell Rep Methods | 2025 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/40345198 |
| Tumour evolution and microenvironment interactions in 2D and 3D space. | Mo CK, Liu J, Chen S, Storrs E, Targino da Costa ALN, Houston A, Wendl MC, Jayasinghe RG, Iglesia MD, Ma C, Herndon JM, Southard-Smith AN, Liu X, Mudd J, Karpova A, Shinkle A, Goedegebuure SP, Abdelzaher ATMA, Bo P, Fulghum L, Livingston S, Balaban M, Hill A, Ippolito JE, Thorsson V, Held JM, Hagemann IS, Kim EH, Bayguinov PO, Kim AH, Mullen MM, Shoghi KI, Ju T, Reimers MA, Weimholt C, Kang LI, Puram SV, Veis DJ, Pachynski R, Fuh KC, Chheda MG, Gillanders WE, Fields RC, Raphael BJ, Chen F, Ding L | Nature | 39478210 | Nature | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39478210 |
| Senescence Defines a Distinct Subset of Myofibroblasts That Orchestrates Immunosuppression in Pancreatic Cancer. | Belle JI, Sen D, Baer JM, Liu X, Lander VE, Ye J, Sells BE, Knolhoff BL, Faiz A, Kang LI, Qian G, Fields RC, Ding L, Kim H, Provenzano PP, Stewart SA, DeNardo DG | Cancer discovery | 38683144 | Cancer Discov | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38683144 |
| Senescent CAFs Mediate Immunosuppression and Drive Breast Cancer Progression. | Ye J, Baer JM, Faget DV, Morikis VA, Ren Q, Melam A, Delgado AP, Luo X, Bagchi SM, Belle JI, Campos E, Friedman M, Veis DJ, Knudsen ES, Witkiewicz AK, Powers S, Longmore GD, DeNardo DG, Stewart SA | Cancer discovery | 38683161 | Cancer Discov | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38683161 |
| Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma. | Wu Y, Chen S, Yang X, Sato K, Lal P, Wang Y, Shinkle AT, Wendl MC, Primeau TM, Zhao Y, Gould A, Sun H, Mudd JL, Hoog J, Mashl RJ, Wyczalkowski MA, Mo CK, Liu R, Herndon JM, Davies SR, Liu D, Ding X, Evrard YA, Welm BE, Lum D, Koh MY, Welm AL, Chuang JH, Moscow JA, Meric-Bernstam F, Govindan R, Li S, Hsieh J, Fields RC, Lim KH, Ma CX, Zhang H, Ding L, Chen F | Cancer research | 38098449 | Cancer Res | 2023 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/38098449 |
| Combined KRAS-MAPK pathway inhibitors and HER2-directed drug conjugate is efficacious in pancreatic cancer. | Bulle A, Liu P, Seehra K, Bansod S, Chen Y, Zahra K, Somani V, Khawar IA, Chen HP, Dodhiawala PB, Li L, Geng Y, Mo CK, Mahsl J, Ding L, Govindan R, Davies S, Mudd J, Hawkins WG, Fields RC, DeNardo DG, Knoerzer D, Held JM, Grierson PM, Wang-Gillam A, Ruzinova MB, Lim KH | Nature communications | 38509064 | Nat Commun | 2024 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/38509064 |
| Epigenetic regulation during cancer transitions across 11 tumour types. | Terekhanova NV, Karpova A, Liang WW, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, Liu X, Wyczalkowski MA, Lu RJ, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo CK, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC, Chen F, Raphael BJ, Ding L | Nature | 37914932 | Nature | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37914932 |
| Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models. | Guo Z, Luo J, Mashl RJ, Hoog J, Maiti P, Fettig N, Davies SR, Aft R, Held JM, Govindan R, Ding L, Li S, von Morze C, Wulf GM, Shoghi KI, Ma CX | Cancer research communications | 38717161 | Cancer Res Commun | 2024 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/38717161 |
| Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics. | Ma C, Balaban M, Liu J, Chen S, Wilson MJ, Sun CH, Ding L, Raphael BJ | Nature methods | 39478176 | Nat Methods | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39478176 |
| Elevated p16Ink4a Expression Enhances Tau Phosphorylation in Neurons Differentiated From Human-Induced Pluripotent Stem Cells. | Holloway K, Neherin K, Song Y, Sato K, Houston A, Chen F, Ding L, Zhang H | Aging cell | 39757785 | Aging Cell | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39757785 |
| Multi-omic and spatial analysis of mouse kidneys highlights sex-specific differences in gene regulation across the lifespan. | Chen S, Liu R, Mo CK, Wendl MC, Houston A, Lal P, Zhao Y, Caravan W, Shinkle AT, Abedin-Do A, Naser Al Deen N, Sato K, Li X, Targino da Costa ALN, Li Y, Karpova A, Herndon JM, Artyomov MN, Rubin JB, Jain S, Li X, Stewart SA, Ding L, Chen F | Nature genetics | 40259083 | Nat Genet | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40259083 |
| Breast cancer risk based on a deep learning predictor of senescent cells in normal tissue. | Heckenbach I, Powell M, Fuller S, Henry J, Rysdyk S, Cui J, Teklu AA, Verdin E, Benz C, Scheibye-Knudsen M | medRxiv : the preprint server for health sciences | 37292628 | medRxiv | 2023 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/37292628 |
| Association of biological aging with frailty and post-transplant outcomes among adults with cirrhosis. | LaHue SC, Fuentealba M, Roa Diaz S, Seetharaman S, Garcia T, Furman D, Lai JC, Newman JC | GeroScience | 38246968 | Geroscience | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38246968 |
| A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers. | Neri F, Takajjart SN, Lerner CA, Desprez PY, Schilling B, Campisi J, Gerencser AA | bioRxiv : the preprint server for biology | 38187756 | bioRxiv | 2024 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/38187756 |
| Exosomes Released from Senescent Cells and Circulatory Exosomes Isolated from Human Plasma Reveal Aging-associated Proteomic and Lipid Signatures. | Patel SK, Bons J, Rose JP, Chappel JR, Beres RL, Watson MA, Webster C, Burton JB, Bruderer R, Desprez PY, Reiter L, Campisi J, Baker ES, Schilling B | bioRxiv : the preprint server for biology | 38979258 | bioRxiv | 2025 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/38979258 |
| Proteomic Analysis of the Senescence-Associated Secretory Phenotype: GDF-15, IGFBP-2, and Cystatin-C Are Associated With Multiple Aging Traits. | Evans DS, Young D, Tanaka T, Basisty N, Bandinelli S, Ferrucci L, Campisi J, Schilling B | The journals of gerontology. Series A, Biological sciences and medical sciences | 37982669 | J Gerontol A Biol Sci Med Sci | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/37982669 |
| Senescent cell heterogeneity and responses to senolytic treatment are related to cell cycle status during cell growth arrest. | Neri F, Zheng S, Watson M, Desprez PY, Gerencser AA, Campisi J, Wirtz D, Wu PH, Schilling B | bioRxiv : the preprint server for biology | 38979292 | bioRxiv | 2024 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/38979292 |
| Challenges and recommendations for the translation of biomarkers of aging. | Biomarkers of Aging Consortium, Herzog CMS, Goeminne LJE, Poganik JR, Barzilai N, Belsky DW, Betts-LaCroix J, Chen BH, Chen M, Cohen AA, Cummings SR, Fedichev PO, Ferrucci L, Fleming A, Fortney K, Furman D, Gorbunova V, Higgins-Chen A, Hood L, Horvath S, Justice JN, Kiel DP, Kuchel GA, Lasky-Su J, LeBrasseur NK, Maier AB, Schilling B, Sebastiano V, Slagboom PE, Snyder MP, Verdin E, Widschwendter M, Zhavoronkov A, Moqri M, Gladyshev VN | Nature aging | 39285015 | Nat Aging | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39285015 |
| Immunological biomarkers of aging. | Wu F, Mu WC, Markov NT, Fuentealba M, Halaweh H, Senchyna F, Manwaring-Mueller MN, Winer DA, Furman D | Journal of immunology (Baltimore, Md. : 1950) | 40443365 | J Immunol | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40443365 |
| Brain transcriptomic, metabolic and mitohormesis properties associated with N-propargylglycine treatment: A prevention strategy against neurodegeneration. | Teramayi F, Bons J, Scott M, Scott GK, Loureiro A, Lopez-Ramirez A, Schilling B, Ellerby LM, Benz CC | Brain research | 38128812 | Brain Res | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/38128812 |
| Therapeutic targeting of HYPDH/PRODH2 with N-propargylglycine offers a Hyperoxaluria treatment opportunity. | Bons J, Tadeo A, Scott GK, Teramayi F, Tanner JJ, Schilling B, Benz CC, Ellerby LM | Biochimica et biophysica acta. Molecular basis of disease | 37586438 | Biochim Biophys Acta Mol Basis Dis | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37586438 |
| Proteomic quantification of native and ECM-enriched mouse ovaries reveals an age-dependent fibro-inflammatory signature. | Dipali SS, King CD, Rose JP, Burdette JE, Campisi J, Schilling B, Duncan FE | Aging | 37899138 | Aging (Albany NY) | 2023 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/37899138 |
| Biochemical, structural, and cellular characterization of S-but-3-yn-2-ylglycine as a mechanism-based covalent inactivator of the flavoenzyme proline dehydrogenase. | Meeks KR, Ji J, Scott GK, Campbell AC, Nix JC, Tadeo A, Ellerby LM, Benz CC, Tanner JJ | Archives of biochemistry and biophysics | 39870289 | Arch Biochem Biophys | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39870289 |
| Nuclear morphology is a deep learning biomarker of cellular senescence. | Heckenbach I, Mkrtchyan GV, Ezra MB, Bakula D, Madsen JS, Nielsen MH, Oró D, Osborne B, Covarrubias AJ, Idda ML, Gorospe M, Mortensen L, Verdin E, Westendorp R, Scheibye-Knudsen M | Nature aging | 37118134 | Nat Aging | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37118134 |
| Chronic inflammation and the hallmarks of aging. | Baechle JJ, Chen N, Makhijani P, Winer S, Furman D, Winer DA | Molecular metabolism | 37329949 | Mol Metab | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37329949 |
| A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers. | Neri F, Takajjart SN, Lerner CA, Desprez PY, Schilling B, Campisi J, Gerencser AA | GeroScience | 38869711 | Geroscience | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38869711 |
| Deep learning assessment of senescence-associated nuclear morphologies in mammary tissue from healthy female donors to predict future risk of breast cancer: a retrospective cohort study. | Heckenbach I, Powell M, Fuller S, Henry J, Rysdyk S, Cui J, Teklu AA, Verdin E, Benz C, Scheibye-Knudsen M | The Lancet. Digital health | 39332852 | Lancet Digit Health | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39332852 |
| How a fibroblast ages: a role for bone morphogenetic protein 4 in protecting lung fibroblasts from senescence in pulmonary fibrosis. | Farkas L, Horowitz JC, Mora AL | The European respiratory journal | 36522139 | Eur Respir J | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36522139 |
| Senolytic vaccination: a new mandate for cardiovascular health? | Lear TB, Finkel T | The journal of cardiovascular aging | 36819765 | J Cardiovasc Aging | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36819765 |
| Impact of aging on immune function in the pathogenesis of pulmonary diseases: potential for therapeutic targets. | Shaikh SB, Goracci C, Tjitropranoto A, Rahman I | Expert review of respiratory medicine | 37078192 | Expert Rev Respir Med | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37078192 |
| Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning. | Chang Y, He F, Wang J, Chen S, Li J, Liu J, Yu Y, Su L, Ma A, Allen C, Lin Y, Sun S, Liu B, Javier Otero J, Chung D, Fu H, Li Z, Xu D, Ma Q | Computational and structural biotechnology journal | 36090815 | Comput Struct Biotechnol J | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36090815 |
| Editorial: Defining and Characterizing Respiratory Disease in an Aging Population. | Krick S, Geraghty P, Jourdan Le Saux C, Rojas M, Staab-Weijnitz CA | Frontiers in medicine | 35462999 | Front Med (Lausanne) | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35462999 |
| 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 |
| Dysregulation of mitochondrial complexes and dynamics by chronic cigarette smoke exposure Utilizing MitoQC reporter mice. | Wang Q, Unwalla H, Rahman I | Mitochondrion | 35032706 | Mitochondrion | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35032706 |
| multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results. | Khatiwada A, Yilmaz AS, Wolf BJ, Pietrzak M, Chung D | PLoS computational biology | 38060592 | PLoS Comput Biol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38060592 |
| Loss of ANT1 Increases Fibrosis and Epithelial Cell Senescence in Idiopathic Pulmonary Fibrosis. | Sui J, Boatz JC, Shi J, Hu Q, Li X, Zhang Y, Königshoff M, Kliment CR | American journal of respiratory cell and molecular biology | 37487137 | Am J Respir Cell Mol Biol | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37487137 |
| A platform for the biomedical application of large language models. | Lobentanzer S, Feng S, Bruderer N, Maier A, BioChatter Consortium, Wang C, Baumbach J, Abreu-Vicente J, Krehl N, Ma Q, Lemberger T, Saez-Rodriguez J | Nature biotechnology | 39843580 | Nat Biotechnol | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39843580 |
| Stimuli-Specific Senescence of Primary Human Lung Fibroblasts Modulates Alveolar Stem Cell Function. | Melo-Narváez MC, Bramey N, See F, Heinzelmann K, Ballester B, Steinchen C, Jain E, Federl K, Hu Q, Dhakad D, Behr J, Eickelberg O, Yildirim AÖ, Königshoff M, Lehmann M | Cells | 38994981 | Cells | 2024 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/38994981 |
| Stimuli-specific senescence of primary human lung fibroblasts modulates alveolar stem cell function. | Bramey N, Melo-Narvaez MC, See F, Ballester-Lllobell B, Steinchen C, Jain E, Hafner K, Yildirim AÖ, Königshoff M, Lehmann M | Research square | 38352619 | Res Sq | 2024 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/38352619 |
| 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 |
| Cold ischemia time alters cell-type specific senescence leading to loss of cellular integrity in mouse lungs. | Kaur G, Wang Q, Tjitropranoto A, Unwalla H, Rahman I | Experimental lung research | 39427288 | Exp Lung Res | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39427288 |
| Emerging roles of senolytics/senomorphics in HIV-related co-morbidities. | Kaur G, Sohanur Rahman M, Shaikh S, Panda K, Chinnapaiyan S, Santiago Estevez M, Xia L, Unwalla H, Rahman I | Biochemical pharmacology | 38556028 | Biochem Pharmacol | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38556028 |
| 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 |
| Intact mitochondrial function in the setting of telomere-induced senescence. | Sullivan DI, Bello FM, Silva AG, Redding KM, Giordano L, Hinchie AM, Loughridge KE, Mora AL, Königshoff M, Kaufman BA, Jurczak MJ, Alder JK | Aging cell | 37688329 | Aging Cell | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37688329 |
| The role of mitochondria in cellular senescence. | Ghosh-Choudhary SK, Liu J, Finkel T | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 34758157 | FASEB J | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34758157 |
| Romulus and Remus of Inflammation: The Conflicting Roles of MAP2K1 and MAP2K2 in Acute Respiratory Distress Syndrome. | Sarkar A, Chamucero-Millares JA, Rojas M | American journal of respiratory cell and molecular biology | 35238734 | Am J Respir Cell Mol Biol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35238734 |
| Biomechanical Force and Cellular Stiffness in Lung Fibrosis. | Nho RS, Ballinger MN, Rojas MM, Ghadiali SN, Horowitz JC | The American journal of pathology | 35183510 | Am J Pathol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35183510 |
| Clustering spatial transcriptomics data. | Teng H, Yuan Y, Bar-Joseph Z | Bioinformatics (Oxford, England) | 34623423 | Bioinformatics | 2022 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/34623423 |
| Mitohormesis. | Cheng YW, Liu J, Finkel T | Cell metabolism | 37939657 | Cell Metab | 2023 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/37939657 |
| Lysosomes in senescence and aging. | Tan JX, Finkel T | EMBO reports | 37811693 | EMBO Rep | 2023 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/37811693 |
| 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 |
| Scientific opportunities in resilience research for cardiovascular health and wellness. Report from a National Heart, Lung, and Blood Institute workshop. | Taylor HA, Finkel T, Gao Y, Ballinger SW, Campo R, Chen R, Chen SH, Davidson K, Iruela-Arispe ML, Jaquish C, LeBrasseur NK, Odden MC, Papanicolaou GJ, Picard M, Srinivas P, Tjurmina O, Wolz M, Galis ZS | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 36322029 | FASEB J | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36322029 |
| MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer. | Wang X, Duan M, Li J, Ma A, Xu D, Li Z, Liu B, Ma Q | bioRxiv : the preprint server for biology | 37645917 | bioRxiv | 2023 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/37645917 |
| DNA damage-induced stalling of transcription drives aging through gene expression imbalance. | Sims AA, Gurkar AU | DNA repair | 36921370 | DNA Repair (Amst) | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36921370 |
| 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 |
| scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. | Gu H, Cheng H, Ma A, Li Y, Wang J, Xu D, Ma Q | Bioinformatics (Oxford, England) | 36250784 | Bioinformatics | 2022 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/36250784 |
| 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 |
| Single-cell biological network inference using a heterogeneous graph transformer. | Ma A, Wang X, Li J, Wang C, Xiao T, Liu Y, Cheng H, Wang J, Li Y, Chang Y, Li J, Wang D, Jiang Y, Su L, Xin G, Gu S, Li Z, Liu B, Xu D, Ma Q | Nature communications | 36810839 | Nat Commun | 2023 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/36810839 |
| 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 |
| Environmental tobacco smoke exposure exaggerates bleomycin-induced collagen overexpression during pulmonary fibrogenesis. | Wang Q, Goracci C, Sundar IK, Rahman I | Journal of inflammation (London, England) | 38509574 | J Inflamm (Lond) | 2024 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/38509574 |
| 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 | 2024 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/39499861 |
| 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 |
| Network-based topic structure visualization. | Jeon Y, Park J, Jin IH, Chung D | Journal of applied statistics | 39926182 | J Appl Stat | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/39926182 |
| 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 |
| scBSP: A fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data. | Li J, Raina M, Wang Y, Xu C, Su L, Guo Q, Ferreira RM, Eadon MT, Ma Q, Wang J, Xu D | bioRxiv : the preprint server for biology | 39974940 | bioRxiv | 2025 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/39974940 |
| Relation equivariant graph neural networks to explore the mosaic-like tissue architecture of kidney diseases on spatially resolved transcriptomics. | Raina M, Cheng H, Ferreira RM, Stansfield T, Modak C, Cheng YH, Suryadevara HNSK, Xu D, Eadon MT, Ma Q, Wang J | Bioinformatics (Oxford, England) | 40358510 | Bioinformatics | 2025 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/40358510 |
| Analysis of community connectivity in spatial transcriptomics data. | Xie J, Jung KJ, Allen C, Chang Y, Paul S, Li Z, Ma Q, Chung D | Frontiers in applied mathematics and statistics | 40475302 | Front Appl Math Stat | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/40475302 |
| p16-3MR: A Novel Model to Study Cellular Senescence in Cigarette Smoke-Induced Lung Injuries. | Kaur G, Sundar IK, Rahman I | International journal of molecular sciences | 34063608 | Int J Mol Sci | 2021 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/34063608 |
| 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 |
| Graph Fourier transform for spatial omics representation and analyses of complex organs. | Chang Y, Liu J, Jiang Y, Ma A, Yeo YY, Guo Q, McNutt M, Krull J, Rodig SJ, Barouch DH, Nolan G, Xu D, Jiang S, Li Z, Liu B, Ma Q | Research square | 38410424 | Res Sq | 2024 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/38410424 |
| A molecular index for biological age identified from the metabolome and senescence-associated secretome in humans. | Hamsanathan S, Anthonymuthu T, Prosser D, Lokshin A, Greenspan SL, Resnick NM, Perera S, Okawa S, Narasimhan G, Gurkar AU | Aging cell | 38454639 | Aging Cell | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38454639 |
| 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 |
| A Chemoptogenetic Tool for Spatiotemporal Induction of Oxidative DNA Lesions In Vivo. | Han S, Sims A, Aceto A, Schmidt BF, Bruchez MP, Gurkar AU | Genes | 36833412 | Genes (Basel) | 2023 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/36833412 |
| Clearance of senescent cells reverts the cigarette smoke-induced lung senescence and airspace enlargement in p16-3MR mice. | Kaur G, Muthumalage T, Rahman I | Aging cell | 37078230 | Aging Cell | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37078230 |
| Single-cell transcriptome mapping identifies a local, innate B cell population driving chronic rejection after lung transplantation. | Smirnova NF, Riemondy K, Bueno M, Collins S, Suresh P, Wang X, Patel KN, Cool C, Königshoff M, Sharma NS, Eickelberg O | JCI insight | 36134664 | JCI Insight | 2022 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/36134664 |
| LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity. | Xie J, Jeon H, Xin G, Ma Q, Chung D | PLoS computational biology | 37428794 | PLoS Comput Biol | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37428794 |
| 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 |
| Graph Fourier transform for spatial omics representation and analyses of complex organs. | Chang Y, Liu J, Jiang Y, Ma A, Yeo YY, Guo Q, McNutt M, Krull JE, Rodig SJ, Barouch DH, Nolan GP, Xu D, Jiang S, Li Z, Liu B, Ma Q | Nature communications | 39209833 | Nat Commun | 2024 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/39209833 |
| Same-Slide Spatial Multi-Omics Integration Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment. | Yeo YY, Chang Y, Qiu H, Yiu SPT, Michel HA, Wu W, Jin X, Kure S, Parmelee L, Luo S, Cramer P, Lee JL, Wang Y, Yeung J, Ahmar NE, Simsek B, Mohanna R, Van Orden M, Lu W, Livak KJ, Li S, Shahryari J, Kingsley L, Al-Humadi RN, Nasr S, Nkosi D, Sadigh S, Rock P, Frauenfeld L, Kaufmann L, Zhu B, Basak A, Dhanikonda N, Chan CN, Krull J, Cho YW, Chen CY, Lee JYJ, Wang H, Zhao B, Loo LH, Kim DM, Boussiotis V, Zhang B, Shalek AK, Howitt B, Signoretti S, Schürch CM, Hodi FS, Burack WR, Rodig SJ, Ma Q, Jiang S | bioRxiv : the preprint server for biology | 39764057 | bioRxiv | 2024 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/39764057 |
| Interpretable machine learning uncovers epithelial transcriptional rewiring and a role for Gelsolin in COPD. | Sui J, Xiao H, Mbaekwe U, Ting NC, Murday K, Hu Q, Gregory AD, Kapellos TS, Yildirim AÖ, Königshoff M, Zhang Y, Sciurba F, Das J, Kliment CR | JCI insight | 39352744 | JCI Insight | 2024 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/39352744 |
| A signaling pathway map of plasminogen activator inhibitor-1 (PAI-1/SERPINE-1): a review of an innovative frontier in molecular aging and cellular senescence. | Shaikh SB, Balaya RDA, Dagamajalu S, Bhandary YP, Unwalla H, Prasad TSK, Rahman I | Cell communication and signaling : CCS | 39543686 | Cell Commun Signal | 2024 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/39543686 |
| Harnessing the Power of Single-Cell Large Language Models with Parameter Efficient Fine-Tuning using scPEFT. | He F, Fei R, Krull JE, Zhang X, Gao M, Su L, Chen Y, Yu Y, Li J, Jin B, Chang Y, Ma A, Ma Q, Xu D | Research square | 40313770 | Res Sq | 2025 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/40313770 |
| Airway-derived emphysema-specific alveolar type II cells exhibit impaired regenerative potential in COPD. | Hu Y, Hu Q, Ansari M, Riemondy K, Pineda R, Sembrat J, Leme AS, Ngo K, Morgenthaler O, Ha K, Gao B, Janssen WJ, Basil MC, Kliment CR, Morrisey E, Lehmann M, Evans CM, Schiller HB, Königshoff M | The European respiratory journal | 39147413 | Eur Respir J | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39147413 |
| FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis. | Preisendörfer S, Ishikawa Y, Hennen E, Winklmeier S, Schupp JC, Knüppel L, Fernandez IE, Binzenhöfer L, Flatley A, Juan-Guardela BM, Ruppert C, Guenther A, Frankenberger M, Hatz RA, Kneidinger N, Behr J, Feederle R, Schepers A, Hilgendorff A, Kaminski N, Meinl E, Bächinger HP, Eickelberg O, Staab-Weijnitz CA | Cells | 35456020 | Cells | 2022 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/35456020 |
| Fibroblast-derived extracellular vesicles contain SFRP1 and mediate pulmonary fibrosis. | Burgy O, Mayr CH, Schenesse D, Fousekis Papakonstantinou E, Ballester B, Sengupta A, She Y, Hu Q, Melo-Narvaéz MC, Jain E, Pestoni JC, Mozurak M, Estrada-Bernal A, Onwuka U, Coughlan C, Parimon T, Chen P, Heimerl T, Bange G, Schmeck BT, Lindner M, Hilgendorff A, Ruppert C, Güenther A, Mann M, Yildirim AÖ, Eickelberg O, Jung AL, Schiller HB, Lehmann M, Burgstaller G, Königshoff M | JCI insight | 39315549 | JCI Insight | 2024 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/39315549 |
| Integrating patients in time series clinical transcriptomics data. | Hasanaj E, Mathur S, Bar-Joseph Z | Bioinformatics (Oxford, England) | 38940139 | Bioinformatics | 2024 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/38940139 |
| A phosphoinositide signalling pathway mediates rapid lysosomal repair. | Tan JX, Finkel T | Nature | 36071159 | Nature | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36071159 |
| An evaluation of RNA-seq differential analysis methods. | Li D, Zand MS, Dye TD, Goniewicz ML, Rahman I, Xie Z | PloS one | 36112652 | PLoS One | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36112652 |
| Powering the formation of alveoli. | Hu Q, Königshoff M | eLife | 35678384 | Elife | 2022 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/35678384 |
| Mitochondrial Transfer between Airway Cells: Helping the Neighbors, or Sending Them Trash? | Calyeca J, Mora AL | American journal of respiratory cell and molecular biology | 35881957 | Am J Respir Cell Mol Biol | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35881957 |
| A Bayesian multivariate mixture model for high throughput spatial transcriptomics. | Allen C, Chang Y, Neelon B, Chang W, Kim HJ, Li Z, Ma Q, Chung D | Biometrics | 35895854 | Biometrics | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35895854 |
| Statistical Power Analysis for Designing Bulk, Single-Cell, and Spatial Transcriptomics Experiments: Review, Tutorial, and Perspectives. | Jeon H, Xie J, Jeon Y, Jung KJ, Gupta A, Chang W, Chung D | Biomolecules | 36830591 | Biomolecules | 2023 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/36830591 |
| 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 |
| 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 |
| Environmental tobacco smoke exposure exaggerates bleomycin- induced collagen overexpression during pulmonary fibrogenesis. | Wang Q, Goracci C, Sundar IK, Rahman I | Research square | 37886473 | Res Sq | 2023 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/37886473 |
| 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 |
| Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system. | Adameyko I, Bakken T, Bhaduri A, Chhatbar C, Filbin MG, Gate D, Hochgerner H, Kim CN, Krull J, La Manno G, Li Q, Linnarsson S, Ma Q, Mayer C, Menon V, Nano P, Prinz M, Quake S, Walsh CA, Yang J, Bayraktar OA, Gokce O, Habib N, Konopka G, Liddelow SA, Nowakowski TJ | Nature neuroscience | 39627588 | Nat Neurosci | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39627588 |
| Altered expression profile of plasma exosomal microRNAs in exclusive electronic cigarette adult users. | Li D, Xie Z, Shaikh SB, Rahman I | Scientific reports | 39837838 | Sci Rep | 2025 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/39837838 |
| Regulation of lung progenitor plasticity and repair by fatty acid oxidation. | Angeles-Lopez QD, Rodriguez-Lopez J, Agudelo Garcia P, Calyeca J, Álvarez D, Bueno M, Tu LN, Salazar-Terreros M, Vanegas-Avendaño N, Krull JE, Moldobaeva A, Bogamuwa S, Scott SS, Peters V, Reader BF, Shiva S, Jurczak M, Ghaedi M, Ma Q, Finkel T, Rojas M, Mora AL | JCI insight | 39927460 | JCI Insight | 2025 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/39927460 |
| Large-Scale Clustered Transcriptional Silencing Associated With Cellular Senescence. | Gurkar AU, Okawa S, Guillermier C, Chaddha K, Steinhauser ML | Aging cell | 39968744 | Aging Cell | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/39968744 |
| 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 |
| NSP7 Molecular Degrader Attenuates Coronaviral Infection Through the β-TrCP1/FBXO5 Axis. | Tong Y, Lear TB, Tuncer F, Villandre JJ, Boudreau ÁN, Lin B, Alfaras I, Kennerdell JR, Camarco DP, Larsen MB, Hua Y, Chen Y, Chandler ME, Pineda R, Barratt-Boyes SM, Evankovich JW, Finkel T, Liu Y, Chen BB | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 40577599 | Adv Sci (Weinh) | 2025 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/40577599 |
| Dietary methionine restriction started late in life promotes healthy aging in a sex-specific manner. | Hernández-Arciga U, Stamenkovic C, Yadav S, Nicoletti C, Albalawy WN, Al Hammood F, Gonzalez TF, Naikwadi MU, Graham A, Smarz C, Little GJ, Williams SG, McMahon B, Sipula IJ, Vandevender AM, Chuan B, Cooke D, Pinto AFM, Flores LC, Hartman HL, Diedrich JK, Brooke RT, Alder JK, Frahm KA, Pascal LE, Stolt E, Troensegaard H, Øvrebø B, Elshorbagy A, Molina E, Vinknes KJ, Tan RJ, Weisz OA, Bueno M, Eickelberg O, Steinhauser ML, Finkel T, Ables GP, Ikeno Y, Olsen T, Sacco A, Jurczak MJ, Sukoff Rizzo SJ, Parkhitko AA | Science advances | 40238871 | Sci Adv | 2025 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/40238871 |
| 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 |
| 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 |
| 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 |
| 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 | Frontiers in bioinformatics | 37181487 | Front Bioinform | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37181487 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39763856 |
| 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 |
