Skip to main content

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
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
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
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
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
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
scGHOST: Identifying single-cell 3D genome subcompartments. Xiong K, Zhang R, Ma J bioRxiv : the preprint server for biology 37292994 bioRxiv 2023 May 25
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. SenNet Consortium Nature aging 36936385 Nat Aging 2022 Dec
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
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
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
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
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
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
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
scGHOST: identifying single-cell 3D genome subcompartments. Xiong K, Zhang R, Ma J Nature methods 38589516 Nat Methods 2024 May
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
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
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
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
Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease. Specht H, Slavov N Journal of proteome research 35114789 J Proteome Res 2022 Feb 4
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
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
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
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
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
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
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
Single-cell proteomics: quantifying post-transcriptional regulation during development with mass-spectrometry. Slavov N Development (Cambridge, England) 37387573 Development 2023 Jul 1
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
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
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
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
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
Learning from natural variation across the proteomes of single cells. Slavov N PLoS biology 34986167 PLoS Biol 2022 Jan
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
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
Comprehensive Identification of Regulatory Protein Networks. Khoury L, Slavov N Journal of proteome research 34736325 J Proteome Res 2021 Nov 5
Driving Single Cell Proteomics Forward with Innovation. Slavov N Journal of proteome research 34597050 J Proteome Res 2021 Nov 5
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
Protein degradation and growth dependent dilution substantially shape mammalian proteomes. Leduc A, Slavov N bioRxiv : the preprint server for biology 39990504 bioRxiv 2025 Mar 26
Counting protein molecules for single-cell proteomics. Slavov N Cell 35063071 Cell 2022 Jan 20
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
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
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
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
Musculoskeletal imaging of senescence. Daldrup-Link HE, Suryadevara V, Tanyildizi Y, Nernekli K, Tang JH, Meade TJ Skeletal radiology 38329533 Skeletal Radiol 2024 Sep
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
COPIng with senescence. Victorelli S, Passos JF Nature cell biology 38012404 Nat Cell Biol 2023 Dec
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
Cellular senescence: all roads lead to mitochondria. Martini H, Passos JF The FEBS journal 35048548 FEBS J 2023 Mar
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
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
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
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
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
Senolytic drugs: Beyond the promise and the hype. Jurk D, Passos JF Mechanisms of ageing and development 35032547 Mech Ageing Dev 2022 Mar
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
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
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
Telomeres, cellular senescence, and aging: past and future. Eppard M, Passos JF, Victorelli S Biogerontology 38150087 Biogerontology 2024 Apr
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
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
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
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
Single-cell and spatial detection of senescent cells using DeepScence. Qu Y, Dong R, Gu L, Chan C, Xie J, Glass C, Wang XF, Nixon AB, Ji Z bioRxiv : the preprint server for biology 38045252 bioRxiv 2024 Oct 14
Spatial Single-Cell Technologies for Exploring Gastrointestinal Tissue Transcriptome. Kang HM, Lee JH Comprehensive Physiology 37358516 Compr Physiol 2023 Jun 26
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
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
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
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
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
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
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
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
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
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
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
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
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
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq. Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Nam J, Gao F, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R Nature biotechnology 36823353 Nat Biotechnol 2023 Oct
Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus. Enninful A, Zhang Z, Klymyshyn D, Zong H, Bai Z, Farzad N, Su G, Baysoy A, Nam J, Yang M, Lu Y, Zhang NR, Braubach O, Xu ML, Ma Z, Fan R bioRxiv : the preprint server for biology 39605581 bioRxiv 2024 Nov 11
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
Splicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis. Maul-Newby HM, Halene S Experimental hematology 39393608 Exp Hematol 2024 Dec
A Novel Targeted Long-read Sequencing Approach Boosts Transcriptomic Profiling. Tian X, Fan R Genomics, proteomics & bioinformatics 39724297 Genomics Proteomics Bioinformatics 2025 Jan 15
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
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
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
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
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
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
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
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
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
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
Spatial epigenome-transcriptome co-profiling of mammalian tissues. Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R Nature 36922587 Nature 2023 Apr
Spatial profiling of chromatin accessibility in mouse and human tissues. Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R Nature 35978191 Nature 2022 Sep
Spatially 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
A nutrigeroscience approach: Dietary macronutrients and cellular senescence. Calubag MF, Robbins PD, Lamming DW Cell metabolism 39178854 Cell Metab 2024 Sep 3
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
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
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
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
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
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
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
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
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
The broken Alzheimer's disease genome. Gouveia Roque C, Phatnani H, Hengst U Cell genomics 38697121 Cell Genom 2024 May 8
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
Health AI Assurance Laboratories. Stead WW, Aliferis C JAMA 38345804 JAMA 2024 Mar 26
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
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
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
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
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
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
Palo: spatially aware color palette optimization for single-cell and spatial data. Hou W, Ji Z Bioinformatics (Oxford, England) 35642896 Bioinformatics 2022 Jul 11
T-cell receptor sequences correlate with and predict gene expression levels in T cells. Wang H, Ji Z bioRxiv : the preprint server for biology 38076860 bioRxiv 2023 Nov 28
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. Hou W, Ji Z Nature methods 38528186 Nat Methods 2024 Aug
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
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
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
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
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
Integrating multiple single-cell multi-omics samples with Smmit. Wan C, Ji Z bioRxiv : the preprint server for biology 37066420 bioRxiv 2025 Jan 4
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
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
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
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
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
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
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
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
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
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 Jan 5
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Senolytic vaccination: a new mandate for cardiovascular health? Lear TB, Finkel T The journal of cardiovascular aging 36819765 J Cardiovasc Aging 2022 Apr
Clustering spatial transcriptomics data. Teng H, Yuan Y, Bar-Joseph Z Bioinformatics (Oxford, England) 34623423 Bioinformatics 2022 Jan 27
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
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
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
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
SCS: cell segmentation for high-resolution spatial transcriptomics. Chen H, Li D, Bar-Joseph Z Nature methods 37429992 Nat Methods 2023 Aug
DNA damage-induced stalling of transcription drives aging through gene expression imbalance. Sims AA, Gurkar AU DNA repair 36921370 DNA Repair (Amst) 2023 May
Unsupervised cell functional annotation for single-cell RNA-seq. Li D, Ding J, Bar-Joseph Z Genome research 35764397 Genome Res 2022 Sep 27
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
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
Lysosomes in senescence and aging. Tan JX, Finkel T EMBO reports 37811693 EMBO Rep 2023 Nov 6
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
Integrating patients in time series clinical transcriptomics data. Hasanaj E, Mathur S, Bar-Joseph Z Bioinformatics (Oxford, England) 38940139 Bioinformatics 2024 Jun 28
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
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
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
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
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
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
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
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
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
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
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
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
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
A phosphoinositide signalling pathway mediates rapid lysosomal repair. Tan JX, Finkel T Nature 36071159 Nature 2022 Sep
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
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
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
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
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
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
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
Network-based topic structure visualization. Jeon Y, Park J, Jin IH, Chung D Journal of applied statistics 39926182 J Appl Stat 2025
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
Temporal modelling using single-cell transcriptomics. Ding J, Sharon N, Bar-Joseph Z Nature reviews. Genetics 35102309 Nat Rev Genet 2022 Jun
Mitohormesis. Cheng YW, Liu J, Finkel T Cell metabolism 37939657 Cell Metab 2023 Nov 7
Powering the formation of alveoli. Hu Q, Königshoff M eLife 35678384 Elife 2022 Jun 9
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
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
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
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
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
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
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
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
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
Identifying signaling genes in spatial single-cell expression data. Li D, Ding J, Bar-Joseph Z Bioinformatics (Oxford, England) 32886099 Bioinformatics 2021 May 17
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
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
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
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
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
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
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
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
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
scSTEM: clustering pseudotime ordered single-cell data. Song Q, Wang J, Bar-Joseph Z Genome biology 35799304 Genome Biol 2022 Jul 7
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
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
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
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
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
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
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

This page last reviewed on April 10, 2025