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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
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
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
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
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
POPARI: Modeling multisample variation in spatial transcriptomics. Alam S, Zhou T, Haber E, Chidester B, Liu S, Chen F, Ma J bioRxiv : the preprint server for biology 40462963 bioRxiv 2025 May 13 https://www.ncbi.nlm.nih.gov/pubmed/40462963
Non-disruptive 3D profiling of combinations of epigenetic marks in single cells. Chen Y, Radda JSD, Alderman MH 3rd, Jin S, Cheng Y, Zhang Y, Liu M, Xiao AZ, Wang S bioRxiv : the preprint server for biology 40666962 bioRxiv 2025 Jun 17 https://www.ncbi.nlm.nih.gov/pubmed/40666962
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
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
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
Eykthyr reveals transcriptional regulators of spatial gene programs. Krieger S, Haber E, Ma J bioRxiv : the preprint server for biology 40475415 bioRxiv 2025 May 23 https://www.ncbi.nlm.nih.gov/pubmed/40475415
Perturb-tracing enables high-content screening of multi-scale 3D genome regulators. Cheng Y, Hu M, Yang B, Jensen TB, Zhang Y, Yang T, Yu R, Ma Z, Radda JSD, Jin S, Zang C, Wang S Nature methods 40211002 Nat Methods 2025 May https://www.ncbi.nlm.nih.gov/pubmed/40211002
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
SenNet recommendations for detecting senescent cells in different tissues. Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver CM, Aguayo-Mazzucato C, Baker DJ, Bernlohr DA, Jurk D, Mangarova DB, Quardokus EM, Enninga EAL, Schmidt EL, Chen F, Duncan FE, Cambuli F, Kaur G, Kuchel GA, Lee G, Daldrup-Link HE, Martini H, Phatnani H, Al-Naggar IM, Rahman I, Nie J, Passos JF, Silverstein JC, Campisi J, Wang J, Iwasaki K, Barbosa K, Metis K, Nernekli K, Niedernhofer LJ, Ding L, Wang L, Adams LC, Ruiyang L, Doolittle ML, Teneche MG, Schafer MJ, Xu M, Hajipour M, Boroumand M, Basisty N, Sloan N, Slavov N, Kuksenko O, Robson P, Gomez PT, Vasilikos P, Adams PD, Carapeto P, Zhu Q, Ramasamy R, Perez-Lorenzo R, Fan R, Dong R, Montgomery RR, Shaikh S, Vickovic S, Yin S, Kang S, Suvakov S, Khosla S, Garovic VD, Menon V, Xu Y, Song Y, Suh Y, Dou Z, Neretti N Nature reviews. Molecular cell biology 38831121 Nat Rev Mol Cell Biol 2024 Dec https://www.ncbi.nlm.nih.gov/pubmed/38831121
DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks. Cheng W, Song Z, Zhang Y, Wang S, Wang D, Yang M, Li L, Ma J Nature communications 41253815 Nat Commun 2025 Nov 18 https://www.ncbi.nlm.nih.gov/pubmed/41253815
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
Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue. Cheng Y, Dang S, Zhang Y, Chen Y, Yu R, Liu M, Jin S, Han A, Katz S, Wang S bioRxiv : the preprint server for biology 40161724 bioRxiv 2025 Mar 29 https://www.ncbi.nlm.nih.gov/pubmed/40161724
Image-based 3D genomics through chromatin tracing. Yang T, Wang S Nature reviews. Methods primers 40756061 Nat Rev Methods Primers 2024 https://www.ncbi.nlm.nih.gov/pubmed/40756061
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
Unified integration of spatial transcriptomics across platforms. Haber E, Deshpande A, Ma J, Krieger S bioRxiv : the preprint server for biology 40236180 bioRxiv 2025 Apr 21 https://www.ncbi.nlm.nih.gov/pubmed/40236180
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
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
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
MIMYR: Generative modeling of missing tissue in spatial transcriptomics. Deshpande A, Bei Z, Ma J, Krieger S bioRxiv : the preprint server for biology 41394599 bioRxiv 2025 Nov 27 https://www.ncbi.nlm.nih.gov/pubmed/41394599
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
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
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
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
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
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution. Cheng Y, Dang S, Zhang Y, Chen Y, Yu R, Liu M, Jin S, Han A, Katz S, Wang S Cell 41038164 Cell 2025 Nov 26 https://www.ncbi.nlm.nih.gov/pubmed/41038164
Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Rajaei M, Li FY, Townsend JP, Muzumdar MD, Wang S Nature genetics 40825871 Nat Genet 2025 Dec https://www.ncbi.nlm.nih.gov/pubmed/40825871
Heimdall: A Modular Framework for Tokenization in Single-Cell Foundation Models. Haber E, Alam S, Ho N, Liu R, Trop E, Liang S, Yang M, Krieger S, Ma J bioRxiv : the preprint server for biology 41292913 bioRxiv 2025 Nov 10 https://www.ncbi.nlm.nih.gov/pubmed/41292913
TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models. Liu S, Tang J, Ma J, Liang S bioRxiv : the preprint server for biology 41394628 bioRxiv 2025 Nov 27 https://www.ncbi.nlm.nih.gov/pubmed/41394628
Senescence-Associated Chromatin Rewiring Promotes Inflammation and Transposable Element Activation. Dalgarno A, Evans SA, Kelsey MMG, Nunez TA, Rocha A, Clark K, Sedivy JM, Neretti N bioRxiv : the preprint server for biology 40666907 bioRxiv 2025 Jun 17 https://www.ncbi.nlm.nih.gov/pubmed/40666907
Unified integration of spatial transcriptomics across platforms with LLOKI. Haber E, Deshpande A, Ma J, Krieger S Genome research 41233159 Genome Res 2025 Dec 3 https://www.ncbi.nlm.nih.gov/pubmed/41233159
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
Impact of protein degradation and cell growth on mammalian proteomes. Leduc A, Zheng S, Saxena P, Slavov N bioRxiv : the preprint server for biology 39990504 bioRxiv 2025 Apr 26 https://www.ncbi.nlm.nih.gov/pubmed/39990504
Limiting the impact of protein leakage in single-cell proteomics. Leduc A, Xu Y, Shipkovenska G, Dou Z, Slavov N Nature communications 40324992 Nat Commun 2025 May 5 https://www.ncbi.nlm.nih.gov/pubmed/40324992
Metformin inhibits nuclear egress of chromatin fragments in senescence and aging. Kumazawa T, Xu Y, Wang Y, Lee JW, O'Brien TC, Ho CK, Cetinbas M, Weiner A, Hochedlinger K, Sadreyev RI, Bardeesy N, Cheng CW, He B, Dou Z Nature aging 41545663 Nat Aging 2026 Feb https://www.ncbi.nlm.nih.gov/pubmed/41545663
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
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
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
Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease. Specht H, Slavov N Journal of proteome research 35114789 J Proteome Res 2022 Feb 4 https://www.ncbi.nlm.nih.gov/pubmed/35114789
Driving Single Cell Proteomics Forward with Innovation. Slavov N Journal of proteome research 34597050 J Proteome Res 2021 Nov 5 https://www.ncbi.nlm.nih.gov/pubmed/34597050
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
RamanOmics Decodes Spatial Vibrational-Molecular Architecture and Rewiring in Aging and Repair. Zhang K, Chen X, Monticolo F, Sorrentino S, Huang H, Callahan C, Qiao Y, Zhou J, Brodowska S, Sapantzi S, Qi J, Wu Y, Dang TNS, Viggiani F, Ho CK, Xu Y, Kobayashi-Kirschvink KJ, Mung T, Phatnani H, Dou Z, Kang JW, So PTC, Shu J bioRxiv : the preprint server for biology 41427387 bioRxiv 2025 Dec 8 https://www.ncbi.nlm.nih.gov/pubmed/41427387
WSTF nuclear autophagy regulates chronic but not acute inflammation. Wang Y, Eapen VV, Liang Y, Kournoutis A, Sherman MS, Xu Y, Onorati A, Li X, Zhou X, Corey KE, Du K, Cabral Burkard AM, Ho CK, Xie J, Zhang H, Maeso-Díaz R, Ma X, Rieprecht U, O'Brien T, Cetinbas M, Wang L, Liu J, Bretz C, Havas AP, Zhou Z, Ho Sui SJ, Saladi SV, Sadreyev RI, Adams PD, Kingston RE, Diehl AM, Alman B, Goessling W, Yue Z, Wang XF, Johansen T, Dou Z Nature 40604282 Nature 2025 Aug https://www.ncbi.nlm.nih.gov/pubmed/40604282
Counting protein molecules for single-cell proteomics. Slavov N Cell 35063071 Cell 2022 Jan 20 https://www.ncbi.nlm.nih.gov/pubmed/35063071
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
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
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
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
Alternate RNA decoding results in stable and abundant proteins in mammals. Tsour S, Machne R, Leduc A, Widmer S, Koo E, Guez J, Karczewski K, Slavov N bioRxiv : the preprint server for biology 39253435 bioRxiv 2025 Oct 8 https://www.ncbi.nlm.nih.gov/pubmed/39253435
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
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
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
Principles of protein abundance regulation across single cells in a mammalian tissue. Leduc A, Shipkovenska G, Xu Y, Franks A, Slavov N bioRxiv : the preprint server for biology 41000751 bioRxiv 2025 Oct 28 https://www.ncbi.nlm.nih.gov/pubmed/41000751
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
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
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
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
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
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
MRI detection of senescent cells in porcine knee joints with a β-galactosidase responsive Gd-chelate. Nernekli K, Mangarova DB, Suryadevara V, Hajipour M, Tang JH, Wang J, Liang T, Harris M, Ueyama T, Lyons JK, Moseley ME, Roudi R, Pisani L, von Krüchten R, Duwa R, Lu-Liang SY, Shokri Varniab Z, Vasyliv I, Das N, Murayama M, Shinohara I, Pratx G, Goodman SB, Meade TJ, Daldrup-Link HE Npj imaging 40330124 Npj Imaging 2025 https://www.ncbi.nlm.nih.gov/pubmed/40330124
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
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
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
Production and Use of Customizable Agarose Molds for Scaffold-Free Mouse Ovarian Follicle Culture. Campo H, Hashim PH, Zaniker-Gomez EJ, Gauthier S, Yan Z, Zhang HF, Ankrum JA, Duncan FE Journal of visualized experiments : JoVE 41212809 J Vis Exp 2025 Oct 24 https://www.ncbi.nlm.nih.gov/pubmed/41212809
Late Life Supplementation of 25-Hydroxycholesterol Reduces Aortic Stiffness and Cellular Senescence in Mice. Mahoney SA, Darrah MA, Venkatasubramanian R, Ciotlos S, Rossman MJ, Campisi J, Seals DR, Melov S, Clayton ZS Aging cell 40401595 Aging Cell 2025 May 22 https://www.ncbi.nlm.nih.gov/pubmed/40401595
Single nuclei profiling identifies cell specific markers of skeletal muscle aging, frailty, and senescence. Perez K, Ciotlos S, McGirr J, Limbad C, Doi R, Nederveen JP, Nilsson MI, Winer DA, Evans W, Tarnopolsky M, Campisi J, Melov S Aging 36516485 Aging (Albany NY) 2022 Dec 13 https://www.ncbi.nlm.nih.gov/pubmed/36516485
A Comprehensive Multiomics Signature of Doxorubicin-Induced Cellular Senescence in the Postmenopausal Human Ovary. Devrukhkar PR, Watson MA, Soygur B, Wu F, Bons J, Anvari H, Atazhanova T, Martin N, Tran T, Schneider K, Rose JP, Winer D, Shanes E, Pavone MEG, Campisi J, Furman D, Melov S, Schilling B, Duncan FE Aging cell 40452152 Aging Cell 2025 Aug https://www.ncbi.nlm.nih.gov/pubmed/40452152
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
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
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
Inactivation of Histone Chaperone HIRA Unmasks a Link Between Normal Embryonic Development of Melanoblasts and Maintenance of Adult Melanocyte Stem Cells. Jaber-Hijazi F, Arnold R, Swaminathan K, Gilroy K, Wenzel AT, Lagnado A, Kirschner K, Robertson N, Reid C, Fullarton N, Pawlikowski J, Rai TS, Baranyk I, Shi CH, Yip KY, Blyth K, Mesirov JP, Harris ML, Passos JF, Machesky LM, Adams PD Aging cell 40669469 Aging Cell 2025 Jul https://www.ncbi.nlm.nih.gov/pubmed/40669469
Author Correction: Apoptotic stress causes mtDNA release during senescence and drives the SASP. Victorelli S, Salmonowicz H, Chapman J, Martini H, Vizioli MG, Riley JS, Cloix C, Hall-Younger E, Machado Espindola-Netto J, Jurk D, Lagnado AB, Sales Gomez L, Farr JN, Saul D, Reed R, Kelly G, Eppard M, Greaves LC, Dou Z, Pirius N, Szczepanowska K, Porritt RA, Huang H, Huang TY, Mann DA, Masuda CA, Khosla S, Dai H, Kaufmann SH, Zacharioudakis E, Gavathiotis E, LeBrasseur NK, Lei X, Sainz AG, Korolchuk VI, Adams PD, Shadel GS, Tait SWG, Passos JF Nature 38168624 Nature 2024 Jan https://www.ncbi.nlm.nih.gov/pubmed/38168624
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
Cytoplasmic DNA: sources, sensing, and role in aging and disease. Miller KN, Victorelli SG, Salmonowicz H, Dasgupta N, Liu T, Passos JF, Adams PD Cell 34715021 Cell 2021 Oct 28 https://www.ncbi.nlm.nih.gov/pubmed/34715021
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
A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues. Saul D, Kosinsky RL, Atkinson EJ, Doolittle ML, Zhang X, LeBrasseur NK, Pignolo RJ, Robbins PD, Niedernhofer LJ, Ikeno Y, Jurk D, Passos JF, Hickson LJ, Xue A, Monroe DG, Tchkonia T, Kirkland JL, Farr JN, Khosla S Nature communications 35974106 Nat Commun 2022 Aug 16 https://www.ncbi.nlm.nih.gov/pubmed/35974106
The Fourth Annual Symposium of the Midwest Aging Consortium. Kim J, Buffenstein R, Bronikowski AM, Pilar Vanegas ND, Rosas L, Agudelo-Garcia P, Mora AL, Rojas M, Englund DA, LeBrasseur NK, Nunes A, Robbins PD, Kohut ML, Kothadiya S, Bardhan R, Camell CD, Sturmlechner I, Goronzy JJ, Yeh CY, Lamming DW, Huang S, Leiser SF, Escorcia W, Gill MS, Taylor JR, Helfand SL, Korm S, Gribble KE, Pehar M, Blaszkiewicz M, Townsend KL, McGregor ER, Anderson RM, Stilgenbauer L, Sadagurski M, Taylor A, McNeill E, Stoeger T, Bai H The journals of gerontology. Series A, Biological sciences and medical sciences 39498863 J Gerontol A Biol Sci Med Sci 2024 Nov 1 https://www.ncbi.nlm.nih.gov/pubmed/39498863
Mitochondrial metabolism and epigenetic crosstalk drive the SASP. 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, Passos J Research square 39678326 Res Sq 2024 Dec 5 https://www.ncbi.nlm.nih.gov/pubmed/39678326
p53 enhances DNA repair and suppresses cytoplasmic chromatin fragments and inflammation in senescent cells. Miller KN, Li B, Pierce-Hoffman HR, Patel S, Lei X, Rajesh A, Teneche MG, Havas AP, Gandhi A, Macip CC, Lyu J, Victorelli SG, Woo SH, Lagnado AB, LaPorta MA, Liu T, Dasgupta N, Li S, Davis A, Korotkov A, Hultenius E, Gao Z, Altman Y, Porritt RA, Garcia G, Mogler C, Seluanov A, Gorbunova V, Kaech SM, Tian X, Dou Z, Chen C, Passos JF, Adams PD Nature communications 40044657 Nat Commun 2025 Mar 5 https://www.ncbi.nlm.nih.gov/pubmed/40044657
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
Mitochondrial RNA cytosolic leakage drives the SASP. Victorelli S, Eppard M, Martini H, Woo SH, Everts SPA, Lee G, Pirius N, Han N, Liang EY, Franco AC, Han Y, Saul D, Nóvoa E, Nogueiras R, Splinter PL, O'Hara SP, Morgenthaler O, Valenzuela-Pérez L, Kim Lee HS, Jurk D, LaRusso NF, Hirsova P, Passos JF Nature communications 41398033 Nat Commun 2025 Dec 15 https://www.ncbi.nlm.nih.gov/pubmed/41398033
Telomeres, cellular senescence, and aging: past and future. Eppard M, Passos JF, Victorelli S Biogerontology 38150087 Biogerontology 2024 Apr https://www.ncbi.nlm.nih.gov/pubmed/38150087
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
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
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
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
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
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
Determining the feasibility of characterising cellular senescence in human skeletal muscle and exploring associations with muscle morphology and physical function at different ages: findings from the MASS_Lifecourse Study. Habiballa L, Hruby A, Granic A, Dodds RM, Hillman SJ, Jurk D, Passos JF, Sayer AA GeroScience 37434081 Geroscience 2024 Feb https://www.ncbi.nlm.nih.gov/pubmed/37434081
Senescent cardiomyocytes contribute to cardiac dysfunction following myocardial infarction. Redgrave RE, Dookun E, Booth LK, Camacho Encina M, Folaranmi O, Tual-Chalot S, Gill JH, Owens WA, Spyridopoulos I, Passos JF, Richardson GD npj aging 37316516 NPJ Aging 2023 Jun 14 https://www.ncbi.nlm.nih.gov/pubmed/37316516
The Third Annual Symposium of the Midwest Aging Consortium. Keller A, Bai H, Budinger S, Eliazer S, Hansen M, Konopka AR, Morales-Nebreda L, Najt CP, Prahlad V, Victorelli S, Vorland CJ, Yuan R, Rhoads TW, Mihaylova MM The journals of gerontology. Series A, Biological sciences and medical sciences 37804247 J Gerontol A Biol Sci Med Sci 2024 Feb 1 https://www.ncbi.nlm.nih.gov/pubmed/37804247
Hyperoxia-induced senescence in fetal airway smooth muscle cells: role of mitochondrial reactive oxygen species and endoplasmic reticulum stress. Koloko Ngassie ML, Thompson MA, Roos BB, Ayyalasomayajula S, Lagnado AB, Passos JF, Pabelick CM, Prakash YS American journal of physiology. Lung cellular and molecular physiology 40183670 Am J Physiol Lung Cell Mol Physiol 2025 Jul 1 https://www.ncbi.nlm.nih.gov/pubmed/40183670
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
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
Cytosolic DNA crosstalk in senescence: a new axis of inflammatory signaling? Dou Z, Kreiling JA, Heynen-Genel S, Jurk D, Neretti N, Adams PD, Sedivy JM, Passos JF The EMBO journal 40883506 EMBO J 2025 Oct https://www.ncbi.nlm.nih.gov/pubmed/40883506
Advancing biological understanding of cellular senescence with computational multiomics. Li S, Agudelo Garcia PA, Aliferis C, Becich MJ, Calyeca J, Cosgrove BD, Elisseeff J, Farzad N, Fertig EJ, Glass C, Gu L, Hu Q, Ji Z, Königshoff M, LeBrasseur NK, Li D, Ma A, Ma Q, Menon V, Mitchell JT, Mora AL, Nagaraj S, Nelson AC, Niedernhofer LJ, Rojas M, Taha HB, Wang J, Wang S, Wu PH, Xie J, Xu M, Yu M, Zhang X, Zhao Y, Adams PD, Aguayo-Mazzucato C, Baker DJ, Benz C, Bernlohr DA, Bueno M, Chen J, Childs BG, Chuang JH, Chung D, Dileepan M, Ding L, Dong M, Duncan F, Enninful A, Flynn WF, Franco AC, Furman D, Garovic V, Halene S, Herman AB, Hertzel AV, Iwasaki K, Jeon H, Kang JW, Karmakar S, Kirkland JL, Korstanje R, Kummerfeld E, Lee JH, Liu Y, Lu Y, Lugo-Martinez J, Martini H, Melov S, Musi N, Passos JF, Peters ST, Rahman I, Ramasamy R, Rindone AN, Robbins PD, Robson P, Rodriguez-Lopez J, Rosas L, Rosenthal N, Schafer MJ, Schilling B, Schmidt EL, Schneider K, Sengupta K, Shu J, So PTC, Sun L, Tchkonia T, Teneche MG, Vanegas N, Wang J, Xie J, Yin S, Zhang K, Zhu Q, Fan R, SenNet Consortium Nature genetics 40954249 Nat Genet 2025 Oct https://www.ncbi.nlm.nih.gov/pubmed/40954249
Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues. Saul D, Jurk D, Doolittle ML, Kosinsky RL, Han Y, Zhang X, Franco AC, Kim SY, Wyles SP, Prakash YS, Monroe DG, Ferrucci L, LeBrasseur NK, Robbins PD, Niedernhofer LJ, Khosla S, Passos JF The EMBO journal 41162753 EMBO J 2025 Dec https://www.ncbi.nlm.nih.gov/pubmed/41162753
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
Comprehensive healthspan assessments and influence of sex as a biological variable in aging rats. Chandra A, Aversa Z, Zhang X, Farr JN, David A, Sharma R, Tchkonia T, Kirkland JL, Robbins PD, Niedernhofer LJ, Jurk D, Passos JF, Monroe DG, Miller J, LeBrasseur NK, Ikeno Y, Khosla S, Pignolo RJ bioRxiv : the preprint server for biology 41040156 bioRxiv 2025 Sep 22 https://www.ncbi.nlm.nih.gov/pubmed/41040156
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Senolytic drugs: Beyond the promise and the hype. Jurk D, Passos JF Mechanisms of ageing and development 35032547 Mech Ageing Dev 2022 Mar https://www.ncbi.nlm.nih.gov/pubmed/35032547
Therapeutic Potential of Senolytics in Cardiovascular Disease. Dookun E, Passos JF, Arthur HM, Richardson GD Cardiovascular drugs and therapy 32979174 Cardiovasc Drugs Ther 2022 Feb https://www.ncbi.nlm.nih.gov/pubmed/32979174
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 RNA cytosolic leakage drives the SASP. Victorelli S, Eppard M, Woo SH, Everts SPA, Martini H, Pirius N, Franco AC, Han Y, Saul D, Splinter PL, O'Hara SP, Valenzuela-Pérez L, Lee HSK, Jurk D, LaRusso NF, Hirsova P, Passos JF Research square 39257994 Res Sq 2024 Aug 27 https://www.ncbi.nlm.nih.gov/pubmed/39257994
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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
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
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Toll-like receptor 2 orchestrates a tumor suppressor response in non-small cell lung cancer. Millar FR, Pennycuick A, Muir M, Quintanilla A, Hari P, Freyer E, Gautier P, Meynert A, Grimes G, Coll CS, Zdral S, Victorelli S, Teixeira VH, Connelly J, Passos JF, Ros MA, Wallace WAH, Frame MC, Sims AH, Boulter L, Janes SM, Wilkinson S, Acosta JC Cell reports 36351380 Cell Rep 2022 Nov 8 https://www.ncbi.nlm.nih.gov/pubmed/36351380
Roadmap for alleviating the manifestations of ageing in the cardiovascular system. Liberale L, Tual-Chalot S, Sedej S, Ministrini S, Georgiopoulos G, Grunewald M, Bäck M, Bochaton-Piallat ML, Boon RA, Ramos GC, de Winther MPJ, Drosatos K, Evans PC, Ferguson JF, Forslund-Startceva SK, Goettsch C, Giacca M, Haendeler J, Kallikourdis M, Ketelhuth DFJ, Koenen RR, Lacolley P, Lutgens E, Maffia P, Miwa S, Monaco C, Montecucco F, Norata GD, Osto E, Richardson GD, Riksen NP, Soehnlein O, Spyridopoulos I, Van Linthout S, Vilahur G, Wentzel JJ, Andrés V, Badimon L, Benetos A, Binder CJ, Brandes RP, Crea F, Furman D, Gorbunova V, Guzik TJ, Hill JA, Lüscher TF, Mittelbrunn M, Nencioni A, Netea MG, Passos JF, Stamatelopoulos KS, Tavernarakis N, Ungvari Z, Wu JC, Kirkland JL, Camici GG, Dimmeler S, Kroemer G, Abdellatif M, Stellos K Nature reviews. Cardiology 39972009 Nat Rev Cardiol 2025 Aug https://www.ncbi.nlm.nih.gov/pubmed/39972009
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
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
COPIng with senescence. Victorelli S, Passos JF Nature cell biology 38012404 Nat Cell Biol 2023 Dec https://www.ncbi.nlm.nih.gov/pubmed/38012404
Optimized Synthetic Flavonols Support Senescence Clearance and Lung Fibrosis Resolution. Meridew JA, Vu JA, Chow D, Diaz Espinosa AM, Saraf N, Gao AY, Espindola-Netto JM, Dresler S, Whaley MG, Choi KM, Li Y, Martini H, Porquera EC, Link PA, Kollmeyer TM, Passos JF, Schafer MJ, LeBrasseur NK, Tschumperlin DJ, Haak AJ ACS pharmacology & translational science 40969882 ACS Pharmacol Transl Sci 2025 Sep 12 https://www.ncbi.nlm.nih.gov/pubmed/40969882
The Sixth Annual Symposium of the Midwest Aging Consortium. Sturmlechner I, Ashiqueali SA, Martini H, Valdivieso K, Franco AC, Guthikonda P, Dosch AJ, Prieto LI, Asmussen NC, Latham AS, Redden JT, Leitschuh EA, Mashek DG, Passos JF, Rodriguez-Lopez J, Monroe TB, Bernlohr DA, Robbins PD, Knopf BA, Lamming DW, Johnston MJ, Brown-Borg HM, Tye SA, Rhoads TW, Gate DM, Childs BG, Baker DJ, Li X, Jang IH, Camell CD, Miller Z, Phatnani H, Konopka AR, Haak AJ, Vanegas-Avendano N, Akula RN, Limkar AR, Ricke WA, Leiser SF, Correia J, Bai H, Olszewski S, Seldeen KL, Budinger GRS, Morales-Nebreda LC, Winter DR, McCrady-Spitzer SK, Anderson RM, Mihaylova MM, Rojas M, Mora AL, LeBrasseur NK, Schafer MJ The journals of gerontology. Series A, Biological sciences and medical sciences 41429578 J Gerontol A Biol Sci Med Sci 2026 Feb 5 https://www.ncbi.nlm.nih.gov/pubmed/41429578
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Heterogeneous pericoerulear neurons tune arousal and exploratory behaviours. Luskin AT, Li L, Fu X, Martin MM, Barcomb K, Girven KS, Blackburn T, Wells BA, Thai ST, Li EM, Rana AN, Simon RC, Sun L, Gao L, Murry AD, Golden SA, Stuber GD, Ford CP, Gu L, Bruchas MR Nature 40335695 Nature 2025 Jul https://www.ncbi.nlm.nih.gov/pubmed/40335695
High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation. Hsu JE, Ruiz L, Hwang Y, Guzman S, Cho CS, Cheng W, Si Y, Macpherson P, Schrank M, Jun G, Kang HM, Kim M, Brooks S, Lee JH bioRxiv : the preprint server for biology 38464282 bioRxiv 2024 Feb 29 https://www.ncbi.nlm.nih.gov/pubmed/38464282
Spatial omics enters the microscopic realm: opportunities and challenges. Si Y, Lee JS, Jun G, Kang HM, Lee JH Trends in genetics : TIG 40461389 Trends Genet 2025 Sep https://www.ncbi.nlm.nih.gov/pubmed/40461389
Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Ma F, Plazyo O, Billi AC, Tsoi LC, Xing X, Wasikowski R, Gharaee-Kermani M, Hile G, Jiang Y, Harms PW, Xing E, Kirma J, Xi J, Hsu JE, Sarkar MK, Chung Y, Di Domizio J, Gilliet M, Ward NL, Maverakis E, Klechevsky E, Voorhees JJ, Elder JT, Lee JH, Kahlenberg JM, Pellegrini M, Modlin RL, Gudjonsson JE Nature communications 37308489 Nat Commun 2023 Jun 12 https://www.ncbi.nlm.nih.gov/pubmed/37308489
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The developing tendon and enthesis are hypoxic and rely on hypoxia-inducible factor 1a (Hif1a) during postnatal development. Steltzer SS, Migotsky N, Phillips T, Lamia SN, Lee KW, Bae SH, Leek C, Grossman S, Shaik M, Risha A, Frey K, Loebel C, Lee JH, Shah YM, Abraham AC, Killian ML bioRxiv : the preprint server for biology 41446162 bioRxiv 2025 Dec 18 https://www.ncbi.nlm.nih.gov/pubmed/41446162
STtools: A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data. Xi J, Lee JH, Kang HM, Jun G Bioinformatics advances 36284674 Bioinform Adv 2022 https://www.ncbi.nlm.nih.gov/pubmed/36284674
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Iditarod, a Drosophila homolog of the Irisin precursor FNDC5, is critical for exercise performance and cardiac autophagy. Cobb T, Hwang I, Soukar M, Namkoong S, Cho US, Safdar M, Kim M, Wessells RJ, Lee JH Proceedings of the National Academy of Sciences of the United States of America 37722048 Proc Natl Acad Sci U S A 2023 Sep 26 https://www.ncbi.nlm.nih.gov/pubmed/37722048
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Exploring endothelial cell environments across organs in spatially resolved omics data. Jain Y, Jepson J, Chen R, Maier E, Herr BW 2nd, Puig-Barbe A, Quardokus EM, Qaurooni D, Yapp C, Ewing SL, Enninful A, Farzad N, Bueckle A, Easter QT, Matuck B, Zhu C, Monte EM, Purkerson JM, Jehrio M, Misra RS, Fan R, Ginty F, Karunamurthy A, Fan J, Campbell-Thompson M, Pryhuber GS, Byrd KM, Hickey JW, Börner K bioRxiv : the preprint server for biology 41040203 bioRxiv 2025 Sep 25 https://www.ncbi.nlm.nih.gov/pubmed/41040203
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Spatial analysis reveals the cellular microenvironments and mechanisms of inflammation and kidney injury in acute interstitial nephritis. Baker ML, Kakade VR, Budiman T, Weiß M, Cunningham JM, Sadarangani S, Lerner G, Moeckel G, Rosenberg AZ, Parikh CR, Kluger Y, Moledina DG, Cantley LG bioRxiv : the preprint server for biology 41278888 bioRxiv 2025 Oct 30 https://www.ncbi.nlm.nih.gov/pubmed/41278888
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Targeting Cellular Senescence with Senotherapeutics: Development of New Approaches for Skin Care. Thompson EL, Pitcher LE, Niedernhofer LJ, Robbins PD Plastic and reconstructive surgery 36170431 Plast Reconstr Surg 2022 Oct 1 https://www.ncbi.nlm.nih.gov/pubmed/36170431
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Predicting mutational function using machine learning. Shea A, Bartz J, Zhang L, Dong X Mutation research. Reviews in mutation research 36965820 Mutat Res Rev Mutat Res 2023 Jan-Jun https://www.ncbi.nlm.nih.gov/pubmed/36965820
miR-96-5p expression is sufficient to induce and maintain the senescent cell fate in the absence of stress. Santiago FE, Adige T, Mahmud S, Dong X, Niedernhofer LJ, Robbins PD Proceedings of the National Academy of Sciences of the United States of America 39325426 Proc Natl Acad Sci U S A 2024 Oct https://www.ncbi.nlm.nih.gov/pubmed/39325426
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The mouse Social Frailty Index (mSFI): a novel behavioral assessment for impaired social functioning in aging mice. Collinge CW, Razzoli M, Mansk R, McGonigle S, Lamming DW, Pacak CA, van der Pluijm I, Niedernhofer L, Bartolomucci A GeroScience 38987495 Geroscience 2025 Feb https://www.ncbi.nlm.nih.gov/pubmed/38987495
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Identification of Senomorphic miRNAs in Embryonic Progenitor and Adult Stem Cell-Derived Extracellular Vesicles. Zhang T, Nunes ADC, Lee J, Larocca D, Camussi G, Lim SK, Bascones VU, Angelini L, O'Kelly RD, Dong X, Niedernhofer LJ, Robbins PD Aging cell 40275616 Aging Cell 2025 Jul https://www.ncbi.nlm.nih.gov/pubmed/40275616
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Human Cell Aging Transcriptome Atlas (HCATA): a single-cell atlas of age-associated transcriptomic alterations across human tissues. Bartz J, Ma X, Zhang L, Dong X Communications biology 41068321 Commun Biol 2025 Oct 9 https://www.ncbi.nlm.nih.gov/pubmed/41068321
Space radiation induces distinct senescent phenotypes: Implications for space travel. Pitcher LE, Mukherjee B, Saathoff AM, Eduvas ZA, Bartz J, Zhang X, Giorgadze N, Pirtskhalava T, Habib AA, LeBrasseur NK, Tchkonia T, Kirkland JL, Dong X, Burma S, Robbins PD npj aging 41309663 NPJ Aging 2025 Nov 27 https://www.ncbi.nlm.nih.gov/pubmed/41309663
Select Small Non-Coding RNAs Are Determinants of Survival in Older Adults. Kraus VB, Ma S, Naz SI, Zhang X, Vann CG, Orenduff MC, Kraus WE, Shen S, Huebner JL, Chou CH, Kummerfeld E, Cohen HJ, Aliferis CF Aging cell 41736507 Aging Cell 2026 Mar https://www.ncbi.nlm.nih.gov/pubmed/41736507
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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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Proteomic Analysis of the Senescence-Associated Secretory Phenotype: GDF-15, IGFBP-2, and Cystatin-C Are Associated With Multiple Aging Traits. Evans DS, Young D, Tanaka T, Basisty N, Bandinelli S, Ferrucci L, Campisi J, Schilling B The journals of gerontology. Series A, Biological sciences and medical sciences 37982669 J Gerontol A Biol Sci Med Sci 2024 Mar 1 https://www.ncbi.nlm.nih.gov/pubmed/37982669
Proteomic quantification of native and ECM-enriched mouse ovaries reveals an age-dependent fibro-inflammatory signature. Dipali SS, King CD, Rose JP, Burdette JE, Campisi J, Schilling B, Duncan FE Aging 37899138 Aging (Albany NY) 2023 Oct 27 https://www.ncbi.nlm.nih.gov/pubmed/37899138
Senescence-Linked Fibrosis in the Aging Human Ovary Revealed by p16-Based Histological Profiling and Spatial Transcriptomics. Schilling B, Watson M, Devrukhkar P, Murad N, Wu F, Kim MJ, Anvari H, Tran U, Martin N, Tran T, Zaza G, Schneider K, Kaya BS, Shanes E, Wirtz D, Pavone M, Melov S, Wu PH, Furman D, Duncan F Research square 41674822 Res Sq 2026 Feb 6 https://www.ncbi.nlm.nih.gov/pubmed/41674822
Exosomes Released from Senescent Cells and Circulatory Exosomes Isolated from Human Plasma Reveal Aging-associated Proteomic and Lipid Signatures. Patel SK, Bons J, Rose JP, Chappel JR, Beres RL, Watson MA, Webster C, Burton JB, Bruderer R, Desprez PY, Reiter L, Campisi J, Baker ES, Schilling B bioRxiv : the preprint server for biology 38979258 bioRxiv 2025 Mar 22 https://www.ncbi.nlm.nih.gov/pubmed/38979258
Therapeutic targeting of HYPDH/PRODH2 with N-propargylglycine offers a Hyperoxaluria treatment opportunity. Bons J, Tadeo A, Scott GK, Teramayi F, Tanner JJ, Schilling B, Benz CC, Ellerby LM Biochimica et biophysica acta. Molecular basis of disease 37586438 Biochim Biophys Acta Mol Basis Dis 2024 Jan https://www.ncbi.nlm.nih.gov/pubmed/37586438
Brain transcriptomic, metabolic and mitohormesis properties associated with N-propargylglycine treatment: A prevention strategy against neurodegeneration. Teramayi F, Bons J, Scott M, Scott GK, Loureiro A, Lopez-Ramirez A, Schilling B, Ellerby LM, Benz CC Brain research 38128812 Brain Res 2024 Mar 1 https://www.ncbi.nlm.nih.gov/pubmed/38128812
Cold ischemia time alters cell-type specific senescence leading to loss of cellular integrity in mouse lungs. Kaur G, Wang Q, Tjitropranoto A, Unwalla H, Rahman I Experimental lung research 39427288 Exp Lung Res 2024 https://www.ncbi.nlm.nih.gov/pubmed/39427288
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
Graph Fourier transform for spatial omics representation and analyses of complex organs. Chang Y, Liu J, Jiang Y, Ma A, Yeo YY, Guo Q, McNutt M, Krull JE, Rodig SJ, Barouch DH, Nolan GP, Xu D, Jiang S, Li Z, Liu B, Ma Q Nature communications 39209833 Nat Commun 2024 Aug 29 https://www.ncbi.nlm.nih.gov/pubmed/39209833
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
Teatime: epigallocatechin gallate targets fibroblast-epithelial cell crosstalk to combat lung fibrosis. Burgy O, Königshoff M The Journal of clinical investigation 39286980 J Clin Invest 2024 Sep 17 https://www.ncbi.nlm.nih.gov/pubmed/39286980
Recovering single-cell expression profiles from spatial transcriptomics with scResolve. Chen H, Lee YJ, Ovando-Ricardez JA, Rosas L, Rojas M, Mora AL, Bar-Joseph Z, Lugo-Martinez J Cell reports methods 39326411 Cell Rep Methods 2024 Oct 21 https://www.ncbi.nlm.nih.gov/pubmed/39326411
A Bayesian multivariate mixture model for high throughput spatial transcriptomics. Allen C, Chang Y, Neelon B, Chang W, Kim HJ, Li Z, Ma Q, Chung D Biometrics 35895854 Biometrics 2023 Sep https://www.ncbi.nlm.nih.gov/pubmed/35895854
An evaluation of RNA-seq differential analysis methods. Li D, Zand MS, Dye TD, Goniewicz ML, Rahman I, Xie Z PloS one 36112652 PLoS One 2022 https://www.ncbi.nlm.nih.gov/pubmed/36112652
Single-cell transcriptome mapping identifies a local, innate B cell population driving chronic rejection after lung transplantation. Smirnova NF, Riemondy K, Bueno M, Collins S, Suresh P, Wang X, Patel KN, Cool C, Königshoff M, Sharma NS, Eickelberg O JCI insight 36134664 JCI Insight 2022 Sep 22 https://www.ncbi.nlm.nih.gov/pubmed/36134664
Dysregulation of mitochondrial complexes and dynamics by chronic cigarette smoke exposure Utilizing MitoQC reporter mice. Wang Q, Unwalla H, Rahman I Mitochondrion 35032706 Mitochondrion 2022 Mar https://www.ncbi.nlm.nih.gov/pubmed/35032706
Intact mitochondrial function in the setting of telomere-induced senescence. Sullivan DI, Bello FM, Silva AG, Redding KM, Giordano L, Hinchie AM, Loughridge KE, Mora AL, Königshoff M, Kaufman BA, Jurczak MJ, Alder JK Aging cell 37688329 Aging Cell 2023 Oct https://www.ncbi.nlm.nih.gov/pubmed/37688329
Graph Fourier transform for spatial omics representation and analyses of complex organs. Chang Y, Liu J, Jiang Y, Ma A, Yeo YY, Guo Q, McNutt M, Krull J, Rodig SJ, Barouch DH, Nolan G, Xu D, Jiang S, Li Z, Liu B, Ma Q Research square 38410424 Res Sq 2024 Feb 15 https://www.ncbi.nlm.nih.gov/pubmed/38410424
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. Chen H, Lee YJ, Ovando JA, Rosas L, Rojas M, Mora AL, Bar-Joseph Z, Lugo-Martinez J bioRxiv : the preprint server for biology 38187629 bioRxiv 2023 Dec 19 https://www.ncbi.nlm.nih.gov/pubmed/38187629
A molecular index for biological age identified from the metabolome and senescence-associated secretome in humans. Hamsanathan S, Anthonymuthu T, Prosser D, Lokshin A, Greenspan SL, Resnick NM, Perera S, Okawa S, Narasimhan G, Gurkar AU Aging cell 38454639 Aging Cell 2024 Apr https://www.ncbi.nlm.nih.gov/pubmed/38454639
Multiset multicover methods for discriminative marker selection. Hasanaj E, Alavi A, Gupta A, Póczos B, Bar-Joseph Z Cell reports methods 36452867 Cell Rep Methods 2022 Nov 21 https://www.ncbi.nlm.nih.gov/pubmed/36452867
Senolytic vaccination: a new mandate for cardiovascular health? Lear TB, Finkel T The journal of cardiovascular aging 36819765 J Cardiovasc Aging 2022 Apr https://www.ncbi.nlm.nih.gov/pubmed/36819765
Clearance of senescent cells reverts the cigarette smoke-induced lung senescence and airspace enlargement in p16-3MR mice. Kaur G, Muthumalage T, Rahman I Aging cell 37078230 Aging Cell 2023 Jul https://www.ncbi.nlm.nih.gov/pubmed/37078230
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
TrimNN: characterizing cellular community motifs for studying multicellular topological organization in complex tissues. Yu Y, Wang S, Li J, Yu M, McCrocklin K, Kang JQ, Ma A, Ma Q, Xu D, Wang J Nature communications 40830137 Nat Commun 2025 Aug 19 https://www.ncbi.nlm.nih.gov/pubmed/40830137
Multi-scaled transcriptomics of chronically inflamed nasal epithelium reveals immune-epithelial dynamics and tissue remodeling in nasal polyp formation. Liao G, Nakayama T, Zhu B, Lee IT, Yeung J, Yeo YY, Chang Y, Wang C, Liao SC, Nkosi D, Renteria A, Bravo DT, Overdevest JB, Yan CH, Zarabanda D, Gall PA, Dholakia SS, Borchard NA, Yang A, Kim D, Patel ZM, Hwang PH, Wagh D, Coller J, Phillips KM, Chang MT, Lechner M, Li Z, Yeh TH, Nolan G, Longhi MS, Boussiotis V, Barouch DH, Ma Q, Nayak JV, Jiang S Immunity 40945518 Immunity 2025 Oct 14 https://www.ncbi.nlm.nih.gov/pubmed/40945518
A Meta-Review of Spatial Transcriptomics Analysis Software. Gillespie J, Pietrzak M, Song MA, Chung D Cells 40710313 Cells 2025 Jul 10 https://www.ncbi.nlm.nih.gov/pubmed/40710313
SCS: cell segmentation for high-resolution spatial transcriptomics. Chen H, Li D, Bar-Joseph Z bioRxiv : the preprint server for biology 37398213 bioRxiv 2023 Jun 16 https://www.ncbi.nlm.nih.gov/pubmed/37398213
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
Mitohormesis. Cheng YW, Liu J, Finkel T Cell metabolism 37939657 Cell Metab 2023 Nov 7 https://www.ncbi.nlm.nih.gov/pubmed/37939657
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
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
Protocol to recover single-cell gene expression profiles from spatial transcriptomics data using cluster computing. Lee YJ, Chen H, Lugo-Martinez J STAR protocols 39946238 STAR Protoc 2025 Mar 21 https://www.ncbi.nlm.nih.gov/pubmed/39946238
Inhibition of epithelial cell YAP-TEAD/LOX signaling attenuates pulmonary fibrosis in preclinical models. Wagner DE, Alsafadi HN, Mitash N, Justet A, Hu Q, Pineda R, Staab-Weijnitz C, Korfei M, Gvazava N, Wannemo K, Onwuka U, Mozurak M, Estrada-Bernal A, Cala-Garcia J, Mutze K, Costa R, Bölükbas D, Stegmayr J, Skronska-Wasek W, Klee S, Ota C, Baarsma HA, Wang J, Sembrat J, Hilgendorff A, Ding J, Günther A, Chambers R, Rosas I, de Langhe S, Kaminski N, Lehmann M, Eickelberg O, Königshoff M Nature communications 40753090 Nat Commun 2025 Aug 2 https://www.ncbi.nlm.nih.gov/pubmed/40753090
Hallmarks of the ageing lung: 10 years later. Baker JR, Beaulieu D, Avci E, Huang E, Eickelberg O, Meiners S, Savai R, Lehmann M, Königshoff M The European respiratory journal 41819537 Eur Respir J 2026 Jun https://www.ncbi.nlm.nih.gov/pubmed/41819537
A phosphoinositide signalling pathway mediates rapid lysosomal repair. Tan JX, Finkel T Nature 36071159 Nature 2022 Sep https://www.ncbi.nlm.nih.gov/pubmed/36071159
Using single cell atlas data to reconstruct regulatory networks. Song Q, Ruffalo M, Bar-Joseph Z Nucleic acids research 36762475 Nucleic Acids Res 2023 Apr 24 https://www.ncbi.nlm.nih.gov/pubmed/36762475
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
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
A Chemoptogenetic Tool for Spatiotemporal Induction of Oxidative DNA Lesions In Vivo. Han S, Sims A, Aceto A, Schmidt BF, Bruchez MP, Gurkar AU Genes 36833412 Genes (Basel) 2023 Feb 14 https://www.ncbi.nlm.nih.gov/pubmed/36833412
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
An integrated cell atlas of the lung in health and disease. Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, Lung Biological Network Consortium, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ Nature medicine 37291214 Nat Med 2023 Jun https://www.ncbi.nlm.nih.gov/pubmed/37291214
Relation equivariant graph neural networks to explore the mosaic-like tissue architecture of kidney diseases on spatially resolved transcriptomics. Raina M, Cheng H, Ferreira RM, Stansfield T, Modak C, Cheng YH, Suryadevara HNSK, Xu D, Eadon MT, Ma Q, Wang J Bioinformatics (Oxford, England) 40358510 Bioinformatics 2025 Jun 2 https://www.ncbi.nlm.nih.gov/pubmed/40358510
An Intrinsic-hoc Framework for Heterogeneous Cellular Senescence Elucidation Using Deep Graph Representation Learning and Experimental Validation. Ma A, Cheng H, Vanegas NDP, Ghobashi A, Chen H, Rodriguez J, Rosas L, Wang C, Shao J, Jiang Y, Wang X, Rahman I, Lugo-Martinez J, Li D, Pryhuber GS, Bar-Joseph Z, Eickelberg O, Königshoff M, Chung D, Chen R, Finkel T, Mora A, Rojas M, Ma Q bioRxiv : the preprint server for biology 40631080 bioRxiv 2025 Jul 4 https://www.ncbi.nlm.nih.gov/pubmed/40631080
Perspectives on integrating artificial intelligence and single-cell omics for cellular plasticity research. Ghobashi A, Ma Q Quantitative biology (Beijing, China) 40874195 Quant Biol 2025 Dec https://www.ncbi.nlm.nih.gov/pubmed/40874195
Network-based topic structure visualization. Jeon Y, Park J, Jin IH, Chung D Journal of applied statistics 39926182 J Appl Stat 2025 https://www.ncbi.nlm.nih.gov/pubmed/39926182
MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer. Wang X, Duan M, Li J, Ma A, Xu D, Li Z, Liu B, Ma Q bioRxiv : the preprint server for biology 37645917 bioRxiv 2023 Aug 17 https://www.ncbi.nlm.nih.gov/pubmed/37645917
Environmental tobacco smoke exposure exaggerates bleomycin- induced collagen overexpression during pulmonary fibrogenesis. Wang Q, Goracci C, Sundar IK, Rahman I Research square 37886473 Res Sq 2023 Oct 10 https://www.ncbi.nlm.nih.gov/pubmed/37886473
Emerging roles of senolytics/senomorphics in HIV-related co-morbidities. Kaur G, Sohanur Rahman M, Shaikh S, Panda K, Chinnapaiyan S, Santiago Estevez M, Xia L, Unwalla H, Rahman I Biochemical pharmacology 38556028 Biochem Pharmacol 2024 Oct https://www.ncbi.nlm.nih.gov/pubmed/38556028
Environmental tobacco smoke exposure exaggerates bleomycin-induced collagen overexpression during pulmonary fibrogenesis. Wang Q, Goracci C, Sundar IK, Rahman I Journal of inflammation (London, England) 38509574 J Inflamm (Lond) 2024 Mar 20 https://www.ncbi.nlm.nih.gov/pubmed/38509574
Predicting lung aging using scRNA-Seq data. Song Q, Singh A, McDonough JE, Adams TS, Vos R, De Man R, Myers G, Ceulemans LJ, Vanaudenaerde BM, Wuyts WA, Yan X, Schupp J, Hagood JS, Kaminski N, Bar-Joseph Z PLoS computational biology 39700255 PLoS Comput Biol 2024 Dec https://www.ncbi.nlm.nih.gov/pubmed/39700255
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 2025 Jan https://www.ncbi.nlm.nih.gov/pubmed/39499861
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
Fibroblast-derived extracellular vesicles contain SFRP1 and mediate pulmonary fibrosis. Burgy O, Mayr CH, Schenesse D, Fousekis Papakonstantinou E, Ballester B, Sengupta A, She Y, Hu Q, Melo-Narvaéz MC, Jain E, Pestoni JC, Mozurak M, Estrada-Bernal A, Onwuka U, Coughlan C, Parimon T, Chen P, Heimerl T, Bange G, Schmeck BT, Lindner M, Hilgendorff A, Ruppert C, Güenther A, Mann M, Yildirim AÖ, Eickelberg O, Jung AL, Schiller HB, Lehmann M, Burgstaller G, Königshoff M JCI insight 39315549 JCI Insight 2024 Aug 15 https://www.ncbi.nlm.nih.gov/pubmed/39315549
A unified analysis of atlas single-cell data. Chen H, Nguyen ND, Ruffalo M, Bar-Joseph Z Genome research 39965934 Genome Res 2025 May 2 https://www.ncbi.nlm.nih.gov/pubmed/39965934
Large-Scale Clustered Transcriptional Silencing Associated With Cellular Senescence. Gurkar AU, Okawa S, Guillermier C, Chaddha K, Steinhauser ML Aging cell 39968744 Aging Cell 2025 Apr https://www.ncbi.nlm.nih.gov/pubmed/39968744
Dietary methionine restriction started late in life promotes healthy aging in a sex-specific manner. Hernández-Arciga U, Stamenkovic C, Yadav S, Nicoletti C, Albalawy WN, Al Hammood F, Gonzalez TF, Naikwadi MU, Graham A, Smarz C, Little GJ, Williams SG, McMahon B, Sipula IJ, Vandevender AM, Chuan B, Cooke D, Pinto AFM, Flores LC, Hartman HL, Diedrich JK, Brooke RT, Alder JK, Frahm KA, Pascal LE, Stolt E, Troensegaard H, Øvrebø B, Elshorbagy A, Molina E, Vinknes KJ, Tan RJ, Weisz OA, Bueno M, Eickelberg O, Steinhauser ML, Finkel T, Ables GP, Ikeno Y, Olsen T, Sacco A, Jurczak MJ, Sukoff Rizzo SJ, Parkhitko AA Science advances 40238871 Sci Adv 2025 Apr 18 https://www.ncbi.nlm.nih.gov/pubmed/40238871
SenSet defines cell-type specific senescence signatures in the aged human lung. Hasanaj E, Beaulieu D, Wang C, Hu Q, Rosas L, Bueno M, Sembrat JC, Pineda RH, Melo-Narvaez MC, Cardenes N, Yanwu Z, Yingze Z, Lafyatis R, Morris A, Mora A, Rojas M, Li D, Rahman I, Pryhuber GS, Lehmann M, Alder J, Gurkar A, Finkel T, Ma Q, Lugo-Martinez J, Póczos B, Bar-Joseph Z, Eickelberg O, Königshoff M The EMBO journal 41963555 EMBO J 2026 May https://www.ncbi.nlm.nih.gov/pubmed/41963555
Lysosomes in senescence and aging. Tan JX, Finkel T EMBO reports 37811693 EMBO Rep 2023 Nov 6 https://www.ncbi.nlm.nih.gov/pubmed/37811693
Loss of ANT1 Increases Fibrosis and Epithelial Cell Senescence in Idiopathic Pulmonary Fibrosis. Sui J, Boatz JC, Shi J, Hu Q, Li X, Zhang Y, Königshoff M, Kliment CR American journal of respiratory cell and molecular biology 37487137 Am J Respir Cell Mol Biol 2023 Nov https://www.ncbi.nlm.nih.gov/pubmed/37487137
Single-cell biological network inference using a heterogeneous graph transformer. Ma A, Wang X, Li J, Wang C, Xiao T, Liu Y, Cheng H, Wang J, Li Y, Chang Y, Li J, Wang D, Jiang Y, Su L, Xin G, Gu S, Li Z, Liu B, Xu D, Ma Q Nature communications 36810839 Nat Commun 2023 Feb 21 https://www.ncbi.nlm.nih.gov/pubmed/36810839
Statistical Power Analysis for Designing Bulk, Single-Cell, and Spatial Transcriptomics Experiments: Review, Tutorial, and Perspectives. Jeon H, Xie J, Jeon Y, Jung KJ, Gupta A, Chang W, Chung D Biomolecules 36830591 Biomolecules 2023 Jan 24 https://www.ncbi.nlm.nih.gov/pubmed/36830591
Clustering spatial transcriptomics data. Teng H, Yuan Y, Bar-Joseph Z Bioinformatics (Oxford, England) 34623423 Bioinformatics 2022 Jan 27 https://www.ncbi.nlm.nih.gov/pubmed/34623423
Mitochondrial Transfer between Airway Cells: Helping the Neighbors, or Sending Them Trash? Calyeca J, Mora AL American journal of respiratory cell and molecular biology 35881957 Am J Respir Cell Mol Biol 2022 Oct https://www.ncbi.nlm.nih.gov/pubmed/35881957
Stimuli-specific senescence of primary human lung fibroblasts modulates alveolar stem cell function. Bramey N, Melo-Narvaez MC, See F, Ballester-Lllobell B, Steinchen C, Jain E, Hafner K, Yildirim AÖ, Königshoff M, Lehmann M Research square 38352619 Res Sq 2024 Jan 29 https://www.ncbi.nlm.nih.gov/pubmed/38352619
multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results. Khatiwada A, Yilmaz AS, Wolf BJ, Pietrzak M, Chung D PLoS computational biology 38060592 PLoS Comput Biol 2023 Dec https://www.ncbi.nlm.nih.gov/pubmed/38060592
Altered expression profile of plasma exosomal microRNAs in exclusive electronic cigarette adult users. Li D, Xie Z, Shaikh SB, Rahman I Scientific reports 39837838 Sci Rep 2025 Jan 21 https://www.ncbi.nlm.nih.gov/pubmed/39837838
A platform for the biomedical application of large language models. Lobentanzer S, Feng S, Bruderer N, Maier A, BioChatter Consortium, Wang C, Baumbach J, Abreu-Vicente J, Krehl N, Ma Q, Lemberger T, Saez-Rodriguez J Nature biotechnology 39843580 Nat Biotechnol 2025 Feb https://www.ncbi.nlm.nih.gov/pubmed/39843580
Stimuli-Specific Senescence of Primary Human Lung Fibroblasts Modulates Alveolar Stem Cell Function. Melo-Narváez MC, Bramey N, See F, Heinzelmann K, Ballester B, Steinchen C, Jain E, Federl K, Hu Q, Dhakad D, Behr J, Eickelberg O, Yildirim AÖ, Königshoff M, Lehmann M Cells 38994981 Cells 2024 Jun 29 https://www.ncbi.nlm.nih.gov/pubmed/38994981
Impact of aging on immune function in the pathogenesis of pulmonary diseases: potential for therapeutic targets. Shaikh SB, Goracci C, Tjitropranoto A, Rahman I Expert review of respiratory medicine 37078192 Expert Rev Respir Med 2023 May https://www.ncbi.nlm.nih.gov/pubmed/37078192
scDOT: optimal transport for mapping senescent cells in spatial transcriptomics. Nguyen ND, Rosas L, Khaliullin T, Jiang P, Hasanaj E, Ovando-Ricardez JA, Bueno M, Rahman I, Pryhuber GS, Li D, Ma Q, Finkel T, Königshoff M, Eickelberg O, Rojas M, Mora AL, Lugo-Martinez J, Bar-Joseph Z Genome biology 39516853 Genome Biol 2024 Nov 8 https://www.ncbi.nlm.nih.gov/pubmed/39516853
scBSP: A fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data. Li J, Raina M, Wang Y, Xu C, Su L, Guo Q, Ferreira RM, Eadon MT, Ma Q, Wang J, Xu D bioRxiv : the preprint server for biology 39974940 bioRxiv 2025 Feb 7 https://www.ncbi.nlm.nih.gov/pubmed/39974940
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