Cellular Senescence Network (SenNet)
Cellular Senescence Network (SenNet)
Program Publications
Publications Search by Program
Search Results
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date |
|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| scGHOST: identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | Nature methods | 38589516 | Nat Methods | 2024 May |
| 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 |
| 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 |
| NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. | SenNet Consortium | Nature aging | 36936385 | Nat Aging | 2022 Dec |
| scGHOST: Identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | bioRxiv : the preprint server for biology | 37292994 | bioRxiv | 2023 May 25 |
| 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 |
| 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 |
| 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 |
| Counting protein molecules for single-cell proteomics. | Slavov N | Cell | 35063071 | Cell | 2022 Jan 20 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Learning from natural variation across the proteomes of single cells. | Slavov N | PLoS biology | 34986167 | PLoS Biol | 2022 Jan |
| 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 |
| Single-cell proteomics: quantifying post-transcriptional regulation during development with mass-spectrometry. | Slavov N | Development (Cambridge, England) | 37387573 | Development | 2023 Jul 1 |
| Protein degradation and growth dependent dilution substantially shape mammalian proteomes. | Leduc A, Slavov N | bioRxiv : the preprint server for biology | 39990504 | bioRxiv | 2025 Feb 12 |
| Driving Single Cell Proteomics Forward with Innovation. | Slavov N | Journal of proteome research | 34597050 | J Proteome Res | 2021 Nov 5 |
| Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease. | Specht H, Slavov N | Journal of proteome research | 35114789 | J Proteome Res | 2022 Feb 4 |
| 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 | 2024 Apr 25 |
| 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 |
| 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 |
| 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 |
| Comprehensive Identification of Regulatory Protein Networks. | Khoury L, Slavov N | Journal of proteome research | 34736325 | J Proteome Res | 2021 Nov 5 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Senolytic drugs: Beyond the promise and the hype. | Jurk D, Passos JF | Mechanisms of ageing and development | 35032547 | Mech Ageing Dev | 2022 Mar |
| 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 |
| Telomeres, cellular senescence, and aging: past and future. | Eppard M, Passos JF, Victorelli S | Biogerontology | 38150087 | Biogerontology | 2024 Apr |
| 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 |
| 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 |
| 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 |
| COPIng with senescence. | Victorelli S, Passos JF | Nature cell biology | 38012404 | Nat Cell Biol | 2023 Dec |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Cellular senescence: all roads lead to mitochondria. | Martini H, Passos JF | The FEBS journal | 35048548 | FEBS J | 2023 Mar |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 | 2024 Jun 24 |
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| 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 |
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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 |
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| 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 |
| Unsupervised cell functional annotation for single-cell RNA-seq. | Li D, Ding J, Bar-Joseph Z | Genome research | 35764397 | Genome Res | 2022 Sep 27 |
| 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 |
| 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 |
| DNA damage-induced stalling of transcription drives aging through gene expression imbalance. | Sims AA, Gurkar AU | DNA repair | 36921370 | DNA Repair (Amst) | 2023 May |
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| Integrating patients in time series clinical transcriptomics data. | Hasanaj E, Mathur S, Bar-Joseph Z | Bioinformatics (Oxford, England) | 38940139 | Bioinformatics | 2024 Jun 28 |
| 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 |
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| 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 |
| 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 |
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| 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 |
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| 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 |
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| Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning. | Chang Y, He F, Wang J, Chen S, Li J, Liu J, Yu Y, Su L, Ma A, Allen C, Lin Y, Sun S, Liu B, Javier Otero J, Chung D, Fu H, Li Z, Xu D, Ma Q | Computational and structural biotechnology journal | 36090815 | Comput Struct Biotechnol J | 2022 |
| 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 |
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| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| Powering the formation of alveoli. | Hu Q, Königshoff M | eLife | 35678384 | Elife | 2022 Jun 9 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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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 |
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