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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.

Title Author Journal Name PubMedID Journal Abbreviation Publication Date 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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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

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