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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 https://www.ncbi.nlm.nih.gov/pubmed/39990504
Counting protein molecules for single-cell proteomics. Slavov N Cell 35063071 Cell 2022 Jan 20 https://www.ncbi.nlm.nih.gov/pubmed/35063071
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
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
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
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
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
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
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
Cytoplasmic innate immune sensing by the caspase-4 non-canonical inflammasome promotes cellular senescence. Fernández-Duran I, Quintanilla A, Tarrats N, Birch J, Hari P, Millar FR, Lagnado AB, Smer-Barreto V, Muir M, Brunton VG, Passos JF, Acosta JC Cell death and differentiation 34916628 Cell Death Differ 2022 Jun https://www.ncbi.nlm.nih.gov/pubmed/34916628
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
Local senolysis in aged mice only partially replicates the benefits of systemic senolysis. Farr JN, Saul D, Doolittle ML, Kaur J, Rowsey JL, Vos SJ, Froemming MN, Lagnado AB, Zhu Y, Weivoda M, Ikeno Y, Pignolo RJ, Niedernhofer LJ, Robbins PD, Jurk D, Passos JF, LeBrasseur NK, Tchkonia T, Kirkland JL, Monroe DG, Khosla S The Journal of clinical investigation 36809340 J Clin Invest 2023 Apr 17 https://www.ncbi.nlm.nih.gov/pubmed/36809340
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
Telomere dysfunction in chronic liver disease: The link from aging. Penrice DD, Jalan-Sakrikar N, Jurk D, Passos JF, Simonetto DA Hepatology (Baltimore, Md.) 37102475 Hepatology 2024 Oct 1 https://www.ncbi.nlm.nih.gov/pubmed/37102475
Linked regulation of genome integrity and senescence-associated inflammation by p53. Miller KN, Li B, Pierce-Hoffman HR, Patel S, Lei X, Rajesh A, Teneche MG, Havas AP, Gandhi A, Macip CC, Lyu J, Victorelli SG, Woo SH, Lagnado AB, LaPorta MA, Liu T, Dasgupta N, Li S, Davis A, Korotkov A, Hultenius E, Gao Z, Altman Y, Porritt RA, Garcia G, Mogler C, Seluanov A, Gorbunova V, Kaech SM, Tian X, Dou Z, Chen C, Passos JF, Adams PD bioRxiv : the preprint server for biology 38045344 bioRxiv 2024 Sep 19 https://www.ncbi.nlm.nih.gov/pubmed/38045344
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
Senescent cell transplantation into the skin induces age-related peripheral dysfunction and cognitive decline. Franco AC, Martini H, Victorelli S, Lagnado AB, Wyles SP, Rowsey JL, Pirius N, Woo SH, Costa DG, Chaib S, Tullius SG, Tchkonia T, Kirkland JL, Khosla S, Jurk D, Cavadas C, Passos JF Aging cell 39374134 Aging Cell 2025 Jan https://www.ncbi.nlm.nih.gov/pubmed/39374134
Mitochondrial metabolism and epigenetic crosstalk drive the SASP. Passos J, Martini H, Birch J, Marques F, Victorelli S, Lagnado A, Pirius N, Franco A, Lee G, Han Y, Rowsey J, Gaspar-Maia A, Havas A, Murad R, Lei X, Porritt R, Maddocks O, Jurk D, Khosla S, Adams P Research square 39678326 Res Sq 2024 Dec 5 https://www.ncbi.nlm.nih.gov/pubmed/39678326
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
Determining the feasibility of characterising cellular senescence in human skeletal muscle and exploring associations with muscle morphology and physical function at different ages: findings from the MASS_Lifecourse Study. Habiballa L, Hruby A, Granic A, Dodds RM, Hillman SJ, Jurk D, Passos JF, Sayer AA GeroScience 37434081 Geroscience 2024 Feb https://www.ncbi.nlm.nih.gov/pubmed/37434081
Cellular senescence is increased in airway smooth muscle cells of elderly persons with asthma. Aghali A, Khalfaoui L, Lagnado AB, Drake LY, Teske JJ, Pabelick CM, Passos JF, Prakash YS American journal of physiology. Lung cellular and molecular physiology 36166734 Am J Physiol Lung Cell Mol Physiol 2022 Nov 1 https://www.ncbi.nlm.nih.gov/pubmed/36166734
New Horizons in cellular senescence for clinicians. Witham MD, Granic A, Miwa S, Passos JF, Richardson GD, Sayer AA Age and ageing 37466640 Age Ageing 2023 Jul 1 https://www.ncbi.nlm.nih.gov/pubmed/37466640
Osteochondroprogenitor cells and neutrophils expressing p21 and senescence markers modulate fracture repair. Saul D, Doolittle ML, Rowsey JL, Froemming MN, Kosinsky RL, Vos SJ, Ruan M, LeBrasseur N, Chandra A, Pignolo R, Passos JF, Farr JN, Monroe DG, Khosla S bioRxiv : the preprint server for biology 38370844 bioRxiv 2024 Feb 7 https://www.ncbi.nlm.nih.gov/pubmed/38370844
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
Distinct secretomes in p16- and p21- positive senescent cells across tissues. Saul D, Jurk D, Doolittle ML, Kosinsky RL, Monroe DG, LeBrasseur NK, Robbins PD, Niedernhofer LJ, Khosla S, Passos JF bioRxiv : the preprint server for biology 38106149 bioRxiv 2023 Dec 5 https://www.ncbi.nlm.nih.gov/pubmed/38106149
Apoptotic stress causes mtDNA release during senescence and drives the SASP. Victorelli S, Salmonowicz H, Chapman J, Martini H, Vizioli MG, Riley JS, Cloix C, Hall-Younger E, Machado Espindola-Netto J, Jurk D, Lagnado AB, Sales Gomez L, Farr JN, Saul D, Reed R, Kelly G, Eppard M, Greaves LC, Dou Z, Pirius N, Szczepanowska K, Porritt RA, Huang H, Huang TY, Mann DA, Masuda CA, Khosla S, Dai H, Kaufmann SH, Zacharioudakis E, Gavathiotis E, LeBrasseur NK, Lei X, Sainz AG, Korolchuk VI, Adams PD, Shadel GS, Tait SWG, Passos JF Nature 37821702 Nature 2023 Oct https://www.ncbi.nlm.nih.gov/pubmed/37821702
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
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
COPIng with senescence. Victorelli S, Passos JF Nature cell biology 38012404 Nat Cell Biol 2023 Dec https://www.ncbi.nlm.nih.gov/pubmed/38012404
Characterization of cellular senescence in aging skeletal muscle. Zhang X, Habiballa L, Aversa Z, Ng YE, Sakamoto AE, Englund DA, Pearsall VM, White TA, Robinson MM, Rivas DA, Dasari S, Hruby AJ, Lagnado AB, Jachim SK, Granic A, Sayer AA, Jurk D, Lanza IR, Khosla S, Fielding RA, Nair KS, Schafer MJ, Passos JF, LeBrasseur NK Nature aging 36147777 Nat Aging 2022 Jul https://www.ncbi.nlm.nih.gov/pubmed/36147777
Cellular senescence: all roads lead to mitochondria. Martini H, Passos JF The FEBS journal 35048548 FEBS J 2023 Mar https://www.ncbi.nlm.nih.gov/pubmed/35048548
Bone Marrow Adiposity in Models of Radiation- and Aging-Related Bone Loss Is Dependent on Cellular Senescence. Chandra A, Lagnado AB, Farr JN, Schleusner M, Monroe DG, Saul D, Passos JF, Khosla S, Pignolo RJ Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 35247283 J Bone Miner Res 2022 May https://www.ncbi.nlm.nih.gov/pubmed/35247283
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
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Identification of lipid senolytics targeting senescent cells through ferroptosis induction. Zhang LJ, Salekeen R, Soto-Palma C, Elsallabi O, Ye H, Hughes B, Zhang B, Nunes A, Lee K, Xu W, Mohamed A, Piepgras E, McGowan SJ, Angelini L, O'Kelly R, Han X, Niedernhofer LJ, Robbins PD bioRxiv : the preprint server for biology 39463954 bioRxiv 2024 Oct 14 https://www.ncbi.nlm.nih.gov/pubmed/39463954
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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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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
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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
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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
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
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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
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
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
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
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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
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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
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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
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
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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
How a fibroblast ages: a role for bone morphogenetic protein 4 in protecting lung fibroblasts from senescence in pulmonary fibrosis. Farkas L, Horowitz JC, Mora AL The European respiratory journal 36522139 Eur Respir J 2022 Dec https://www.ncbi.nlm.nih.gov/pubmed/36522139
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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
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
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
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The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality. Bueckle A, Qing C, Luley S, Kumar Y, Pandey N, Börner K bioRxiv : the preprint server for biology 36824790 bioRxiv 2023 Feb 15 https://www.ncbi.nlm.nih.gov/pubmed/36824790
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The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods. Yaniv Z, Anidi IU, Arakkal L, Arroyo-Mejías AJ, Beuschel RT, Börner K, Chu CJ, Clark B, Clatworthy MR, Colautti J, Coscia F, Croteau J, Denha S, Dever R, Dutra WO, Fritzsche S, Fullam S, Gerner MY, Gola A, Gollob KJ, Hernandez JM, Hor JL, Ichise H, Jing Z, Jonigk D, Kandov E, Kastenmüller W, Koenig JFE, Kothurkar A, Kortekaas RK, Kreins AY, Lamborn IT, Lin Y, Morais KLP, Lunich A, Luz JCS, MacDonald RB, Makranz C, Maltez VI, McDonough JE, Moriarty RV, Ocampo-Godinez JM, Olyntho VM, Oxenius A, Padhan K, Remmert K, Richoz N, Schrom EC, Shang W, Shi L, Shih RM, Speranza E, Stierli S, Teichmann SA, Veres TZ, Vierhout M, Wachter BT, Williams M, Zangger N, Germain RN, Radtke AJ ArXiv 39764400 ArXiv 2024 Dec 17 https://www.ncbi.nlm.nih.gov/pubmed/39764400
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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
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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 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
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The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality. Bueckle A, Qing C, Luley S, Kumar Y, Pandey N, Börner K Frontiers in bioinformatics 37181487 Front Bioinform 2023 https://www.ncbi.nlm.nih.gov/pubmed/37181487
Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas. Herr BW 2nd, Hardi J, Quardokus EM, Bueckle A, Chen L, Wang F, Caron AR, Osumi-Sutherland D, Musen MA, Börner K Scientific data 36973309 Sci Data 2023 Mar 27 https://www.ncbi.nlm.nih.gov/pubmed/36973309
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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