Skip to main content

Program Publications

Publications Search by Program

Search Results

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

Title Authors Journal PubMedID Publication Date
Dictionary learning for integrative, multimodal and scalable single-cell analysis. Hao, Yuhan; Stuart, Tim; Kowalski, Madeline H; Choudhary, Saket; Hoffman, Paul; Hartman, Austin; Srivastava, Avi; Molla, Gesmira; Madad, Shaista; Fernandez-Granda, Carlos; Satija, Rahul Nature biotechnology 37231261 2024 Feb
Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery. Liu, Miao; Jin, Shengyan; Agabiti, Sherry S; Jensen, Tyler B; Yang, Tianqi; Radda, Jonathan S D; Ruiz, Christian F; Baldissera, Gabriel; Rajaei, Moein; Townsend, Jeffrey P; Muzumdar, Mandar Deepak; Wang, Siyuan bioRxiv : the preprint server for biology 37546882 2024 Sep 09
Analyzing somatic mutations by single-cell whole-genome sequencing. Zhang, Lei; Lee, Moonsook; Maslov, Alexander Y; Montagna, Cristina; Vijg, Jan; Dong, Xiao Nature protocols 37996541 2024 Feb
Musculoskeletal imaging of senescence. Daldrup-Link, Heike E; Suryadevara, Vidyani; Tanyildizi, Yasemin; Nernekli, Kerem; Tang, Jian-Hong; Meade, Thomas J Skeletal radiology 38329533 2024 Sep
Linked regulation of genome integrity and senescence-associated inflammation by p53. Miller, Karl N; Li, Brightany; Pierce-Hoffman, Hannah R; Patel, Shreeya; Lei, Xue; Rajesh, Adarsh; Teneche, Marcos G; Havas, Aaron P; Gandhi, Armin; Macip, Carolina Cano; Lyu, Jun; Victorelli, Stella G; Woo, Seung-Hwa; Lagnado, Anthony B; LaPorta, Michael A; Liu, Tianhui; Dasgupta, Nirmalya; Li, Sha; Davis, Andrew; Korotkov, Anatoly; Hultenius, Erik; Gao, Zichen; Altman, Yoav; Porritt, Rebecca A; Garcia, Guillermina; Mogler, Carolin; Seluanov, Andrei; Gorbunova, Vera; Kaech, Susan M; Tian, Xiao; Dou, Zhixun; Chen, Chongyi; Passos, João F; Adams, Peter D bioRxiv : the preprint server for biology 38045344 2024 Sep 19
Modelling post-implantation human development to yolk sac blood emergence. Hislop, Joshua; Song, Qi; Keshavarz F, Kamyar; Alavi, Amir; Schoenberger, Rayna; LeGraw, Ryan; Velazquez, Jeremy J; Mokhtari, Tahere; Taheri, Mohammad Naser; Rytel, Matthew; Chuva de Sousa Lopes, Susana M; Watkins, Simon; Stolz, Donna; Kiani, Samira; Sozen, Berna; Bar-Joseph, Ziv; Ebrahimkhani, Mo R Nature 38092041 2024 Feb
Senescent CAFs Mediate Immunosuppression and Drive Breast Cancer Progression. Ye, Jiayu; Baer, John M; Faget, Douglas V; Morikis, Vasilios A; Ren, Qihao; Melam, Anupama; Delgado, Ana Paula; Luo, Xianmin; Bagchi, Satarupa Mullick; Belle, Jad I; Campos, Edward; Friedman, Michael; Veis, Deborah J; Knudsen, Erik S; Witkiewicz, Agnieszka K; Powers, Scott; Longmore, Gregory D; DeNardo, David G; Stewart, Sheila A Cancer discovery 38683161 2024 Jul 01
Senescent CAFs Mediate Immunosuppression and Drive Breast Cancer Progression. Ye, Jiayu; Baer, John M; Faget, Douglas V; Morikis, Vasilios A; Ren, Qihao; Melam, Anupama; Delgado, Ana Paula; Luo, Xianmin; Mullick Bagchi, Satarupa; Belle, Jad I; Campos, Edward; Friedman, Michael; Veis, Deborah J; Knudsen, Erik S; Witkiewicz, Agnieszka K; Powers, Scott; Longmore, Gregory D; DeNardo, David G; Stewart, Sheila A Cancer discovery 38683543 2024 Apr 17
High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation. Hsu, Jer-En; Ruiz, Lloyd; Hwang, Yongha; Guzman, Steve; Cho, Chun-Seok; Cheng, Weiqiu; Si, Yichen; Macpherson, Peter; Schrank, Mitchell; Jun, Goo; Kang, Hyun-Min; Kim, Myungjin; Brooks, Susan; Lee, Jun Hee bioRxiv : the preprint server for biology 38464282 2024 Feb 29
Environmental tobacco smoke exposure exaggerates bleomycin-induced collagen overexpression during pulmonary fibrogenesis. Wang, Qixin; Goracci, Chiara; Sundar, Isaac Kirubakaran; Rahman, Irfan Journal of inflammation (London, England) 38509574 2024 Mar 20
Gene trajectory inference for single-cell data by optimal transport metrics. Qu, Rihao; Cheng, Xiuyuan; Sefik, Esen; Stanley Iii, Jay S; Landa, Boris; Strino, Francesco; Platt, Sarah; Garritano, James; Odell, Ian D; Coifman, Ronald; Flavell, Richard A; Myung, Peggy; Kluger, Yuval Nature biotechnology 38580861 2024 Apr 05
SenNet recommendations for detecting senescent cells in different tissues. Suryadevara, Vidyani; Hudgins, Adam D; Rajesh, Adarsh; Pappalardo, Alberto; Karpova, Alla; Dey, Amit K; Hertzel, Ann; Agudelo, Anthony; Rocha, Azucena; Soygur, Bikem; Schilling, Birgit; Carver, Chase M; Aguayo-Mazzucato, Cristina; Baker, Darren J; Bernlohr, David A; Jurk, Diana; Mangarova, Dilyana B; Quardokus, Ellen M; Enninga, Elizabeth Ann L; Schmidt, Elizabeth L; Chen, Feng; Duncan, Francesca E; Cambuli, Francesco; Kaur, Gagandeep; Kuchel, George A; Lee, Gung; Daldrup-Link, Heike E; Martini, Helene; Phatnani, Hemali; Al-Naggar, Iman M; Rahman, Irfan; Nie, Jia; Passos, João F; Silverstein, Jonathan C; Campisi, Judith; Wang, Julia; Iwasaki, Kanako; Barbosa, Karina; Metis, Kay; Nernekli, Kerem; Niedernhofer, Laura J; Ding, Li; Wang, Lichao; Adams, Lisa C; Ruiyang, Liu; Doolittle, Madison L; Teneche, Marcos G; Schafer, Marissa J; Xu, Ming; Hajipour, Mohammadjavad; Boroumand, Mozhgan; Basisty, Nathan; Sloan, Nicholas; Slavov, Nikolai; Kuksenko, Olena; Robson, Paul; Gomez, Paul T; Vasilikos, Periklis; Adams, Peter D; Carapeto, Priscila; Zhu, Quan; Ramasamy, Ramalakshmi; Perez-Lorenzo, Rolando; Fan, Rong; Dong, Runze; Montgomery, Ruth R; Shaikh, Sadiya; Vickovic, Sanja; Yin, Shanshan; Kang, Shoukai; Suvakov, Sonja; Khosla, Sundeep; Garovic, Vesna D; Menon, Vilas; Xu, Yanxin; Song, Yizhe; Suh, Yousin; Dou, Zhixun; Neretti, Nicola Nature reviews. Molecular cell biology 38831121 2024 Jun 03
FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics. Si, Yichen; Lee, ChangHee; Hwang, Yongha; Yun, Jeong H; Cheng, Weiqiu; Cho, Chun-Seok; Quiros, Miguel; Nusrat, Asma; Zhang, Weizhou; Jun, Goo; Zöllner, Sebastian; Lee, Jun Hee; Kang, Hyun Min Nature methods 39266749 2024 Sep 12
Developing transcriptomic signatures as a biomarker of cellular senescence. Mahmud, Shamsed; Pitcher, Louise E; Torbenson, Elijah; Robbins, Paul D; Zhang, Lei; Dong, Xiao Ageing research reviews 38964507 2024 Aug
The mouse Social Frailty Index (mSFI): a novel behavioral assessment for impaired social functioning in aging mice. Collinge, Charles W; Razzoli, Maria; Mansk, Rachel; McGonigle, Seth; Lamming, Dudley W; Pacak, Christina A; van der Pluijm, Ingrid; Niedernhofer, Laura; Bartolomucci, Alessandro GeroScience 38987495 2024 Jul 11
Osteochondroprogenitor cells and neutrophils expressing p21 and senescence markers modulate fracture repair. Saul, Dominik; Doolittle, Madison L; Rowsey, Jennifer L; Froemming, Mitchell N; Kosinsky, Robyn L; Vos, Stephanie J; Ruan, Ming; LeBrasseur, Nathan; Chandra, Abhishek; Pignolo, Robert; Passos, João F; Farr, Joshua N; Monroe, David G; Khosla, Sundeep bioRxiv : the preprint server for biology 38370844 2024 Feb 07
A molecular index for biological age identified from the metabolome and senescence-associated secretome in humans. Hamsanathan, Shruthi; Anthonymuthu, Tamil; Prosser, Denise; Lokshin, Anna; Greenspan, Susan L; Resnick, Neil M; Perera, Subashan; Okawa, Satoshi; Narasimhan, Giri; Gurkar, Aditi U Aging cell 38454639 2024 Apr
Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics. Kim, Yongsung; Cheng, Weiqiu; Cho, Chun-Seok; Hwang, Yongha; Si, Yichen; Park, Anna; Schrank, Mitchell; Hsu, Jer-En; Xi, Jingyue; Kim, Myungjin; Pedersen, Ellen; Koues, Olivia I; Wilson, Thomas; Jun, Goo; Kang, Hyun Min; Lee, Jun Hee bioRxiv : the preprint server for biology 38617262 2024 Apr 01
Dynamics of Single-Cell Protein Covariation during Epithelial-Mesenchymal Transition. Khan, Saad; Conover, Rachel; Asthagiri, Anand R; Slavov, Nikolai Journal of proteome research 38663020 2024 Apr 25
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. Börner, Katy; Blood, Philip D; Silverstein, Jonathan C; Ruffalo, Matthew; Satija, Rahul; Teichmann, Sarah A; Pryhuber, Gloria; Misra, Ravi S; Purkerson, Jeffrey; Fan, Jean; Hickey, John W; Molla, Gesmira; Xu, Chuan; Zhang, Yun; Weber, Griffin; Jain, Yashvardhan; Qaurooni, Danial; Kong, Yongxin; HRA Team; Bueckle, Andreas; Herr, Bruce W bioRxiv : the preprint server for biology 38826261 2024 Aug 14
Controlling Pericellular Oxygen Tension in Cell Culture Reveals Distinct Breast Cancer Responses to Low Oxygen Tensions. Rogers, Zachary J; Colombani, Thibault; Khan, Saad; Bhatt, Khushbu; Nukovic, Alexandra; Zhou, Guanyu; Woolston, Benjamin M; Taylor, Cormac T; Gilkes, Daniele M; Slavov, Nikolai; Bencherif, Sidi A Advanced science (Weinheim, Baden-Wurttemberg, Germany) 38874400 2024 Aug
Brain transcriptomic, metabolic and mitohormesis properties associated with N-propargylglycine treatment: A prevention strategy against neurodegeneration. Teramayi, Fadzai; Bons, Joanna; Scott, Madeleine; Scott, Gary K; Loureiro, Ashley; Lopez-Ramirez, Alejandro; Schilling, Birgit; Ellerby, Lisa M; Benz, Christopher C Brain research 38128812 2024 Mar 01
Telomeres, cellular senescence, and aging: past and future. Eppard, Madeline; Passos, João F; Victorelli, Stella Biogerontology 38150087 2024 Apr
Author Correction: Apoptotic stress causes mtDNA release during senescence and drives the SASP. Victorelli, Stella; Salmonowicz, Hanna; Chapman, James; Martini, Helene; Vizioli, Maria Grazia; Riley, Joel S; Cloix, Catherine; Hall-Younger, Ella; Machado Espindola-Netto, Jair; Jurk, Diana; Lagnado, Anthony B; Sales Gomez, Lilian; Farr, Joshua N; Saul, Dominik; Reed, Rebecca; Kelly, George; Eppard, Madeline; Greaves, Laura C; Dou, Zhixun; Pirius, Nicholas; Szczepanowska, Karolina; Porritt, Rebecca A; Huang, Huijie; Huang, Timothy Y; Mann, Derek A; Masuda, Claudio Akio; Khosla, Sundeep; Dai, Haiming; Kaufmann, Scott H; Zacharioudakis, Emmanouil; Gavathiotis, Evripidis; LeBrasseur, Nathan K; Lei, Xue; Sainz, Alva G; Korolchuk, Viktor I; Adams, Peter D; Shadel, Gerald S; Tait, Stephen W G; Passos, João F Nature 38168624 2024 Jan
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Zhou, Tianming; Zhang, Ruochi; Jia, Deyong; Doty, Raymond T; Munday, Adam D; Gao, Daniel; Xin, Li; Abkowitz, Janis L; Duan, Zhijun; Ma, Jian Nature genetics 38744973 2024 Aug
Combined KRAS-MAPK pathway inhibitors and HER2-directed drug conjugate is efficacious in pancreatic cancer. Bulle, Ashenafi; Liu, Peng; Seehra, Kuljeet; Bansod, Sapana; Chen, Yali; Zahra, Kiran; Somani, Vikas; Khawar, Iftikhar Ali; Chen, Hung-Po; Dodhiawala, Paarth B; Li, Lin; Geng, Yutong; Mo, Chia-Kuei; Mahsl, Jay; Ding, Li; Govindan, Ramaswamy; Davies, Sherri; Mudd, Jacqueline; Hawkins, William G; Fields, Ryan C; DeNardo, David G; Knoerzer, Deborah; Held, Jason M; Grierson, Patrick M; Wang-Gillam, Andrea; Ruzinova, Marianna B; Lim, Kian-Huat Nature communications 38509064 2024 Mar 20
PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns. Zhuang, Haotian; Ji, Zhicheng bioRxiv : the preprint server for biology 38585819 2024 Mar 25
Senescent cell heterogeneity and responses to senolytic treatment are related to cell cycle status during cell growth arrest. Neri, Francesco; Zheng, Shuyuan; Watson, Mark; Desprez, Pierre-Yves; Gerencser, Akos A; Campisi, Judith; Wirtz, Denis; Wu, Pei-Hsun; Schilling, Birgit bioRxiv : the preprint server for biology 38979292 2024 Jun 26
Deep Learning for 3D Vascular Segmentation in Phase Contrast Tomography. Yagis, Ekin; Aslani, Shahab; Jain, Yashvardhan; Zhou, Yang; Rahmani, Shahrokh; Brunet, Joseph; Bellier, Alexandre; Werlein, Christopher; Ackermann, Maximilian; Jonigk, Danny; Tafforeau, Paul; Lee, Peter D; Walsh, Claire Research square 39070623 2024 Jul 16
Limiting the impact of protein leakage in single-cell proteomics. Leduc, Andrew; Xu, Yanxin; Shipkovenska, Gergana; Dou, Zhixun; Slavov, Nikolai bioRxiv : the preprint server for biology 39091738 2024 Jul 27
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. Leduc, Andrew; Khoury, Luke; Cantlon, Joshua; Khan, Saad; Slavov, Nikolai Nature protocols 39117766 2024 Aug 08
A systematic evaluation of computational methods for cell segmentation. Wang, Yuxing; Zhao, Junhan; Xu, Hongye; Han, Cheng; Tao, Zhiqiang; Zhou, Dawei; Geng, Tong; Liu, Dongfang; Ji, Zhicheng Briefings in bioinformatics 39154193 2024 Jul 25
A nutrigeroscience approach: Dietary macronutrients and cellular senescence. Calubag, Mariah F; Robbins, Paul D; Lamming, Dudley W Cell metabolism 39178854 2024 Sep 03
Graph Fourier transform for spatial omics representation and analyses of complex organs. Chang, Yuzhou; Liu, Jixin; Jiang, Yi; Ma, Anjun; Yeo, Yao Yu; Guo, Qi; McNutt, Megan; Krull, Jordan E; Rodig, Scott J; Barouch, Dan H; Nolan, Garry P; Xu, Dong; Jiang, Sizun; Li, Zihai; Liu, Bingqiang; Ma, Qin Nature communications 39209833 2024 Aug 29
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, Leena; Hruby, Adam; Granic, Antoneta; Dodds, Richard M; Hillman, Susan J; Jurk, Diana; Passos, João F; Sayer, Avan A GeroScience 37434081 2024 Feb
Integrating patients in time series clinical transcriptomics data. Hasanaj, Euxhen; Mathur, Sachin; Bar-Joseph, Ziv Bioinformatics (Oxford, England) 38940139 2024 Jun 28
An open source knowledge graph ecosystem for the life sciences. Callahan, Tiffany J; Tripodi, Ignacio J; Stefanski, Adrianne L; Cappelletti, Luca; Taneja, Sanya B; Wyrwa, Jordan M; Casiraghi, Elena; Matentzoglu, Nicolas A; Reese, Justin; Silverstein, Jonathan C; Hoyt, Charles Tapley; Boyce, Richard D; Malec, Scott A; Unni, Deepak R; Joachimiak, Marcin P; Robinson, Peter N; Mungall, Christopher J; Cavalleri, Emanuele; Fontana, Tommaso; Valentini, Giorgio; Mesiti, Marco; Gillenwater, Lucas A; Santangelo, Brook; Vasilevsky, Nicole A; Hoehndorf, Robert; Bennett, Tellen D; Ryan, Patrick B; Hripcsak, George; Kahn, Michael G; Bada, Michael; Baumgartner Jr, William A; Hunter, Lawrence E Scientific data 38605048 2024 Apr 11
Therapeutic targeting of HYPDH/PRODH2 with N-propargylglycine offers a Hyperoxaluria treatment opportunity. Bons, Joanna; Tadeo, Ada; Scott, Gary K; Teramayi, Fadzai; Tanner, John J; Schilling, Birgit; Benz, Christopher C; Ellerby, Lisa M Biochimica et biophysica acta. Molecular basis of disease 37586438 2024 Jan
Effect of Cellular Senescence in Disease Progression and Transplantation: Immune Cells and Solid Organs. Kirchner, Varvara A; Badshah, Joshua S; Hong, Suk Kyun; Martinez, Olivia; Pruett, Timothy L; Niedernhofer, Laura J Transplantation 37953486 2024 Jul 01
Health AI Assurance Laboratories. Stead, William W; Aliferis, Constantin JAMA 38345804 2024 Mar 26
A systematic evaluation of computational methods for cell segmentation. Wang, Yuxing; Zhao, Junhan; Xu, Hongye; Han, Cheng; Tao, Zhiqiang; Zhou, Dawei; Geng, Tong; Liu, Dongfang; Ji, Zhicheng bioRxiv : the preprint server for biology 38352578 2024 Aug 25
Graph Fourier transform for spatial omics representation and analyses of complex organs. Chang, Yuzhou; Liu, Jixin; Jiang, Yi; Ma, Anjun; Yeo, Yao Yu; Guo, Qi; McNutt, Megan; Krull, Jordan; Rodig, Scott J; Barouch, Dan H; Nolan, Garry; Xu, Dong; Jiang, Sizun; Li, Zihai; Liu, Bingqiang; Ma, Qin Research square 38410424 2024 Feb 15
A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers. Neri, Francesco; Takajjart, Selma N; Lerner, Chad A; Desprez, Pierre-Yves; Schilling, Birgit; Campisi, Judith; Gerencser, Akos A bioRxiv : the preprint server for biology 38187756 2024 Mar 12
Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models. Guo, Zhanfang; Luo, Jingqin; Mashl, R Jay; Hoog, Jeremy; Maiti, Piyush; Fettig, Nikki; Davies, Sherri R; Aft, Rebecca; Held, Jason M; Govindan, Ramaswamy; Ding, Li; Li, Shunqiang; von Morze, Cornelius; Wulf, Gerburg M; Shoghi, Kooresh I; Ma, Cynthia X Cancer research communications 38717161 2024 Jun 05
Osteochondroprogenitor cells and neutrophils expressing p21 and senescence markers modulate fracture repair. Saul, Dominik; Doolittle, Madison L; Rowsey, Jennifer L; Froemming, Mitchell N; Kosinsky, Robyn L; Vos, Stephanie J; Ruan, Ming; LeBrasseur, Nathan K; Chandra, Abhishek; Pignolo, Robert J; Passos, João F; Farr, Joshua N; Monroe, David G; Khosla, Sundeep The Journal of clinical investigation 38753433 2024 May 16
Publication, funding, and experimental data in support of Human Reference Atlas construction and usage. Kong, Yongxin; Börner, Katy Scientific data 38834597 2024 Jun 04
A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers. Neri, Francesco; Takajjart, Selma N; Lerner, Chad A; Desprez, Pierre-Yves; Schilling, Birgit; Campisi, Judith; Gerencser, Akos A GeroScience 38869711 2024 Oct
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. Aihara, Gohta; Clifton, Kalen; Chen, Mayling; Li, Zhuoyan; Atta, Lyla; Miller, Brendan F; Satija, Rahul; Hickey, John W; Fan, Jean Bioinformatics (Oxford, England) 38902953 2024 Jul 01
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. Hou, Wenpin; Ji, Zhicheng Nature methods 38528186 2024 Aug
scGHOST: identifying single-cell 3D genome subcompartments. Xiong, Kyle; Zhang, Ruochi; Ma, Jian Nature methods 38589516 2024 May
Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys. Jain, Yashvardhan; Walsh, Claire L; Yagis, Ekin; Aslani, Shahab; Nandanwar, Sonal; Zhou, Yang; Ha, Juhyung; Gustilo, Katherine S; Brunet, Joseph; Rahmani, Shahrokh; Tafforeau, Paul; Bellier, Alexandre; Weber, Griffin M; Lee, Peter D; Börner, Katy bioRxiv : the preprint server for biology 39253466 2024 Aug 26
Exosomes Released from Senescent Cells and Circulatory Exosomes Isolated from Human Plasma Reveal Aging-associated Proteomic and Lipid Signatures. Patel, Sandip Kumar; Bons, Joanna; Rose, Jacob P; Chappel, Jessie R; Beres, Rebecca L; Watson, Mark A; Webster, Corey; Burton, Jordan B; Bruderer, Roland; Desprez, Pierre-Yves; Reiter, Lukas; Campisi, Judith; Baker, Erin S; Schilling, Birgit bioRxiv : the preprint server for biology 38979258 2024 Jun 24
Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping. Zhang, Di; Rubio Rodríguez-Kirby, Leslie A; Lin, Yingxin; Song, Mengyi; Wang, Li; Wang, Lijun; Kanatani, Shigeaki; Jimenez-Beristain, Tony; Dang, Yonglong; Zhong, Mei; Kukanja, Petra; Wang, Shaohui; Chen, Xinyi Lisa; Gao, Fu; Wang, Dejiang; Xu, Hang; Lou, Xing; Liu, Yang; Chen, Jinmiao; Sestan, Nenad; Uhlén, Per; Kriegstein, Arnold; Zhao, Hongyu; Castelo-Branco, Gonçalo; Fan, Rong bioRxiv : the preprint server for biology 39091821 2024 Jul 28
Proteomic Analysis of the Senescence-Associated Secretory Phenotype: GDF-15, IGFBP-2, and Cystatin-C Are Associated With Multiple Aging Traits. Evans, Daniel S; Young, Danielle; Tanaka, Toshiko; Basisty, Nathan; Bandinelli, Stefania; Ferrucci, Luigi; Campisi, Judith; Schilling, Birgit The journals of gerontology. Series A, Biological sciences and medical sciences 37982669 2024 Mar 01
Heterogeneity of increased biological age in type 2 diabetes correlates with differential tissue DNA methylation, biological variables, and pharmacological treatments. Cortez, Briana N; Pan, Hui; Hinthorn, Samuel; Sun, Han; Neretti, Nicola; Gloyn, Anna L; Aguayo-Mazzucato, Cristina GeroScience 37987887 2024 Apr
Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. Bai, Zhiliang; Zhang, Dingyao; Gao, Yan; Tao, Bo; Bao, Shuozhen; Enninful, Archibald; Zhang, Daiwei; Su, Graham; Tian, Xiaolong; Zhang, Ningning; Xiao, Yang; Liu, Yang; Gerstein, Mark; Li, Mingyao; Xing, Yi; Lu, Jun; Xu, Mina L; Fan, Rong bioRxiv : the preprint server for biology 38370833 2024 Feb 08
GPT-4V exhibits human-like performance in biomedical image classification. Hou, Wenpin; Ji, Zhicheng bioRxiv : the preprint server for biology 38260646 2024 Jan 01
Association of biological aging with frailty and post-transplant outcomes among adults with cirrhosis. LaHue, Sara C; Fuentealba, Matias; Roa Diaz, Stephanie; Seetharaman, Srilakshmi; Garcia, Thelma; Furman, David; Lai, Jennifer C; Newman, John C GeroScience 38246968 2024 Jun
Tissue and cellular spatiotemporal dynamics in colon aging. Daly, Aidan C; Cambuli, Francesco; Äijö, Tarmo; Lötstedt, Britta; Marjanovic, Nemanja; Kuksenko, Olena; Smith-Erb, Matthew; Fernandez, Sara; Domovic, Daniel; Van Wittenberghe, Nicholas; Drokhlyansky, Eugene; Griffin, Gabriel K; Phatnani, Hemali; Bonneau, Richard; Regev, Aviv; Vickovic, Sanja bioRxiv : the preprint server for biology 38712088 2024 Apr 26
Emerging roles of senolytics/senomorphics in HIV-related co-morbidities. Kaur, Gagandeep; Sohanur Rahman, Md; Shaikh, Sadiya; Panda, Kingshuk; Chinnapaiyan, Srinivasan; Santiago Estevez, Maria; Xia, Li; Unwalla, Hoshang; Rahman, Irfan Biochemical pharmacology 38556028 2024 Mar 29
Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes. Galatidou, Styliani; Petelski, Aleksandra A; Pujol, Aïda; Lattes, Karinna; Latorraca, Lais B; Fair, Trudee; Popovic, Mina; Vassena, Rita; Slavov, Nikolai; Barragán, Montserrat Molecular human reproduction 38870523 2024 Jun 26
miR-96-5p expression is sufficient to induce and maintain the senescent cell fate in the absence of stress. Santiago, Fernando E; Adige, Tanvi; Mahmud, Shamsed; Dong, Xiao; Niedernhofer, Laura J; Robbins, Paul D Proceedings of the National Academy of Sciences of the United States of America 39325426 2024 Oct
Stimuli-Specific Senescence of Primary Human Lung Fibroblasts Modulates Alveolar Stem Cell Function. Melo-Narváez, Maria Camila; Bramey, Nora; See, Fenja; Heinzelmann, Katharina; Ballester, Beatriz; Steinchen, Carina; Jain, Eshita; Federl, Kathrin; Hu, Qianjiang; Dhakad, Deepesh; Behr, Jürgen; Eickelberg, Oliver; Yildirim, Ali Önder; Königshoff, Melanie; Lehmann, Mareike Cells 38994981 2024 Jun 29
Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. Chen, Valerie; Yang, Muyu; Cui, Wenbo; Kim, Joon Sik; Talwalkar, Ameet; Ma, Jian Nature methods 39122941 2024 Aug
Identifying signaling genes in spatial single-cell expression data. Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv Bioinformatics (Oxford, England) 32886099 2021 05 17
SIRT1 - a new mammalian substrate of nuclear autophagy. Wang, Lu; Xu, Caiyue; Johansen, Terje; Berger, Shelley L; Dou, Zhixun Autophagy 33292048 2021 02
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Muus, Christoph; Luecken, Malte D; Eraslan, Gökcen; Sikkema, Lisa; Waghray, Avinash; Heimberg, Graham; Kobayashi, Yoshihiko; Vaishnav, Eeshit Dhaval; Subramanian, Ayshwarya; Smillie, Christopher; Jagadeesh, Karthik A; Duong, Elizabeth Thu; Fiskin, Evgenij; Triglia, Elena Torlai; Ansari, Meshal; Cai, Peiwen; Lin, Brian; Buchanan, Justin; Chen, Sijia; Shu, Jian; Haber, Adam L; Chung, Hattie; Montoro, Daniel T; Adams, Taylor; Aliee, Hananeh; Allon, Samuel J; Andrusivova, Zaneta; Angelidis, Ilias; Ashenberg, Orr; Bassler, Kevin; Bécavin, Christophe; Benhar, Inbal; Bergenstråhle, Joseph; Bergenstråhle, Ludvig; Bolt, Liam; Braun, Emelie; Bui, Linh T; Callori, Steven; Chaffin, Mark; Chichelnitskiy, Evgeny; Chiou, Joshua; Conlon, Thomas M; Cuoco, Michael S; Cuomo, Anna S E; Deprez, Marie; Duclos, Grant; Fine, Denise; Fischer, David S; Ghazanfar, Shila; Gillich, Astrid; Giotti, Bruno; Gould, Joshua; Guo, Minzhe; Gutierrez, Austin J; Habermann, Arun C; Harvey, Tyler; He, Peng; Hou, Xiaomeng; Hu, Lijuan; Hu, Yan; Jaiswal, Alok; Ji, Lu; Jiang, Peiyong; Kapellos, Theodoros S; Kuo, Christin S; Larsson, Ludvig; Leney-Greene, Michael A; Lim, Kyungtae; Litviňuková, Monika; Ludwig, Leif S; Lukassen, Soeren; Luo, Wendy; Maatz, Henrike; Madissoon, Elo; Mamanova, Lira; Manakongtreecheep, Kasidet; Leroy, Sylvie; Mayr, Christoph H; Mbano, Ian M; McAdams, Alexi M; Nabhan, Ahmad N; Nyquist, Sarah K; Penland, Lolita; Poirion, Olivier B; Poli, Sergio; Qi, CanCan; Queen, Rachel; Reichart, Daniel; Rosas, Ivan; Schupp, Jonas C; Shea, Conor V; Shi, Xingyi; Sinha, Rahul; Sit, Rene V; Slowikowski, Kamil; Slyper, Michal; Smith, Neal P; Sountoulidis, Alex; Strunz, Maximilian; Sullivan, Travis B; Sun, Dawei; Talavera-López, Carlos; Tan, Peng; Tantivit, Jessica; Travaglini, Kyle J; Tucker, Nathan R; Vernon, Katherine A; Wadsworth, Marc H; Waldman, Julia; Wang, Xiuting; Xu, Ke; Yan, Wenjun; Zhao, William; Ziegler, Carly G K; NHLBI LungMap Consortium; Human Cell Atlas Lung Biological Network Nature medicine 33654293 2021 03
p16-3MR: A Novel Model to Study Cellular Senescence in Cigarette Smoke-Induced Lung Injuries. Kaur, Gagandeep; Sundar, Isaac K; Rahman, Irfan International journal of molecular sciences 34063608 2021 May 03
Driving Single Cell Proteomics Forward with Innovation. Slavov, Nikolai Journal of proteome research 34597050 2021 Oct 01
Clustering Spatial Transcriptomics Data. Teng, Haotian; Yuan, Ye; Bar-Joseph, Ziv Bioinformatics (Oxford, England) 34623423 2021 Oct 08
Cytoplasmic DNA: sources, sensing, and role in aging and disease. Miller, Karl N; Victorelli, Stella G; Salmonowicz, Hanna; Dasgupta, Nirmalya; Liu, Tianhui; Passos, João F; Adams, Peter D Cell 34715021 2021 10 28
Multiplexed single-cell proteomics using SCoPE2. Petelski, Aleksandra A; Emmott, Edward; Leduc, Andrew; Huffman, R Gray; Specht, Harrison; Perlman, David H; Slavov, Nikolai Nature protocols 34716448 2021 Dec
Comprehensive Identification of Regulatory Protein Networks. Khoury, Luke; Slavov, Nikolai Journal of proteome research 34736325 2021 Nov 05
The role of mitochondria in cellular senescence. Ghosh-Choudhary, Shohini K; Liu, Jie; Finkel, Toren FASEB journal : official publication of the Federation of American Societies for Experimental Biology 34758157 2021 Dec
Scaling up single-cell proteomics. Slavov, Nikolai Molecular & cellular proteomics : MCP 34808355 2021 Nov 19
Cytoplasmic innate immune sensing by the caspase-4 non-canonical inflammasome promotes cellular senescence. Fernández-Duran, Irene; Quintanilla, Andrea; Tarrats, Núria; Birch, Jodie; Hari, Priya; Millar, Fraser R; Lagnado, Anthony B; Smer-Barreto, Vanessa; Muir, Morwenna; Brunton, Valerie G; Passos, João F; Acosta, Juan Carlos Cell death and differentiation 34916628 2021 Dec 16
Learning from natural variation across the proteomes of single cells. Slavov, Nikolai PLoS biology 34986167 2022 01
Senolytic drugs: Beyond the promise and the hype. Jurk, Diana; Passos, João F Mechanisms of ageing and development 35032547 2022 Mar
Dysregulation of mitochondrial complexes and dynamics by chronic cigarette smoke exposure Utilizing MitoQC reporter mice. Mitochondrion 35032706 2022 Jan 13
Cellular senescence: all roads lead to mitochondria. Martini, Hélène; Passos, João F The FEBS journal 35048548 2022 Jan 20
Counting protein molecules for single-cell proteomics. Slavov, Nikolai Cell 35063071 2022 Jan 20
Temporal modelling using single-cell transcriptomics. Ding, Jun; Sharon, Nadav; Bar-Joseph, Ziv Nature reviews. Genetics 35102309 2022 06
Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease. Journal of proteome research 35114789 2022 Feb 04
Telomere dysfunction in ageing and age-related diseases. Rossiello, Francesca; Jurk, Diana; Passos, João F; d'Adda di Fagagna, Fabrizio Nature cell biology 35165420 2022 02
Biomechanical Force and Cellular Stiffness in Lung Fibrosis. Nho, Richard S; Ballinger, Megan N; Rojas, Mauricio M; Ghadiali, Samir N; Horowitz, Jeffrey C The American journal of pathology 35183510 2022 05
High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0. Gibbs, Claudia Skok; Jackson, Christopher A; Saldi, Giuseppe-Antonio; Tjärnberg, Andreas; Shah, Aashna; Watters, Aaron; De Veaux, Nicholas; Tchourine, Konstantine; Yi, Ren; Hamamsy, Tymor; Castro, Dayanne M; Carriero, Nicholas; Gorissen, Bram L; Gresham, David; Miraldi, Emily R; Bonneau, Richard Bioinformatics (Oxford, England) 35188184 2022 Feb 21
Romulus and Remus of Inflammation: The Conflicting Roles of MAP2K1 and MAP2K2 in Acute Respiratory Distress Syndrome. Sarkar, Anasuya; Chamucero-Millares, Julián A; Rojas, Mauricio American journal of respiratory cell and molecular biology 35238734 2022 May
Bone Marrow Adiposity in Models of Radiation- and Aging-Related Bone Loss Is Dependent on Cellular Senescence. Chandra, Abhishek; Lagnado, Anthony B; Farr, Joshua N; Schleusner, Megan; Monroe, David G; Saul, Dominik; Passos, João F; Khosla, Sundeep; Pignolo, Robert J Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 35247283 2022 Mar 05
Targeted clearance of p21- but not p16-positive senescent cells prevents radiation-induced osteoporosis and increased marrow adiposity. Chandra, Abhishek; Lagnado, Anthony B; Farr, Joshua N; Doolittle, Madison; Tchkonia, Tamara; Kirkland, James L; LeBrasseur, Nathan K; Robbins, Paul D; Niedernhofer, Laura J; Ikeno, Yuji; Passos, João F; Monroe, David G; Pignolo, Robert J; Khosla, Sundeep Aging cell 35363946 2022 Apr 01
Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping. Fan, Rong; Liu, Yang; DiStasio, Marcello; Su, Graham; Asashima, Hiromitsu; Enninful, Archibald; Qin, Xiaoyu; Deng, Yanxiang; Bordignon, Pino; Cassano, Marco; Tomayko, Mary; Xu, Mina; Halene, Stephanie; Craft, Joseph; Hafler, David Research square 35378748 2022 Mar 30
Interactive single-cell data analysis using Cellar. Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, Ziv Nature communications 35422041 2022 04 14
FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis. Preisendörfer, Stefan; Ishikawa, Yoshihiro; Hennen, Elisabeth; Winklmeier, Stephan; Schupp, Jonas C; Knüppel, Larissa; Fernandez, Isis E; Binzenhöfer, Leonhard; Flatley, Andrew; Juan-Guardela, Brenda M; Ruppert, Clemens; Guenther, Andreas; Frankenberger, Marion; Hatz, Rudolf A; Kneidinger, Nikolaus; Behr, Jürgen; Feederle, Regina; Schepers, Aloys; Hilgendorff, Anne; Kaminski, Naftali; Meinl, Edgar; Bächinger, Hans Peter; Eickelberg, Oliver; Staab-Weijnitz, Claudia A Cells 35456020 2022 04 14
Editorial: Defining and Characterizing Respiratory Disease in an Aging Population. Krick, Stefanie; Geraghty, Patrick; Jourdan Le Saux, Claude; Rojas, Mauricio; Staab-Weijnitz, Claudia A Frontiers in medicine 35462999 2022
Deep unsupervised feature selection by discarding nuisance and correlated features. Shaham, Uri; Lindenbaum, Ofir; Svirsky, Jonathan; Kluger, Yuval Neural networks : the official journal of the International Neural Network Society 35500458 2022 Aug
The heterogeneity of cellular senescence: insights at the single-cell level. Cohn, Rachel L; Gasek, Nathan S; Kuchel, George A; Xu, Ming Trends in cell biology 35599179 2023 Jan
Palo: Spatially-aware color palette optimization for single-cell and spatial data. Hou, Wenpin; Ji, Zhicheng Bioinformatics (Oxford, England) 35642896 2022 Jun 01
Unsupervised cell functional annotation for single-cell RNA-seq. Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv Genome research 35764397 2022 Jun 28
Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing. Rivera-Mulia, Juan Carlos; Trevilla-Garcia, Claudia; Martinez-Cifuentes, Santiago Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 35781769 2022 Jul 04
scSTEM: clustering pseudotime ordered single-cell data. Song, Qi; Wang, Jingtao; Bar-Joseph, Ziv Genome biology 35799304 2022 07 07
Increasing the throughput of sensitive proteomics by plexDIA. Derks, Jason; Leduc, Andrew; Wallmann, Georg; Huffman, R Gray; Willetts, Matthew; Khan, Saad; Specht, Harrison; Ralser, Markus; Demichev, Vadim; Slavov, Nikolai Nature biotechnology 35835881 2022 Jul 14
TREM2 macrophages induced by human lipids drive inflammation in acne lesions. Do, Tran H; Ma, Feiyang; Andrade, Priscila R; Teles, Rosane; de Andrade Silva, Bruno J; Hu, Chanyue; Espinoza, Alejandro; Hsu, Jer-En; Cho, Chun-Seok; Kim, Myungjin; Xi, Jingyue; Xing, Xianying; Plazyo, Olesya; Tsoi, Lam C; Cheng, Carol; Kim, Jenny; Bryso Science immunology 35867799 2022 07 22
Mitochondrial Transfer between Airway Cells: Helping the Neighbors, or Sending Them Trash? Calyeca, Jazmin; Mora, Ana L American journal of respiratory cell and molecular biology 35881957 2022 Oct
A Bayesian multivariate mixture model for high throughput spatial transcriptomics. Allen, Carter; Chang, Yuzhou; Neelon, Brian; Chang, Won; Kim, Hang J; Li, Zihai; Ma, Qin; Chung, Dongjun Biometrics 35895854 2022 Jul 27
Cellular senescence: a key therapeutic target in aging and diseases. Zhang, Lei; Pitcher, Louise E; Yousefzadeh, Matthew J; Niedernhofer, Laura J; Robbins, Paul D; Zhu, Yi The Journal of clinical investigation 35912854 2022 Aug 01
Epigenetics, DNA damage, and aging. Soto-Palma, Carolina; Niedernhofer, Laura J; Faulk, Christopher D; Dong, Xiao The Journal of clinical investigation 35968782 2022 08 15
A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues. Saul, Dominik; Kosinsky, Robyn Laura; Atkinson, Elizabeth J; Doolittle, Madison L; Zhang, Xu; LeBrasseur, Nathan K; Pignolo, Robert J; Robbins, Paul D; Niedernhofer, Laura J; Ikeno, Yuji; Jurk, Diana; Passos, João F; Hickson, LaTonya J; Xue, Ailing; Monroe, David G; Tchkonia, Tamara; Kirkland, James L; Farr, Joshua N; Khosla, Sundeep Nature communications 35974106 2022 08 16
Spatial profiling of chromatin accessibility in mouse and human tissues. Deng, Yanxiang; Bartosovic, Marek; Ma, Sai; Zhang, Di; Kukanja, Petra; Xiao, Yang; Su, Graham; Liu, Yang; Qin, Xiaoyu; Rosoklija, Gorazd B; Dwork, Andrew J; Mann, J John; Xu, Mina L; Halene, Stephanie; Craft, Joseph E; Leong, Kam W; Boldrini, Maura; Castelo-Branco, Gonçalo; Fan, Rong Nature 35978191 2022 09
A phosphoinositide signalling pathway mediates rapid lysosomal repair. Tan, Jay Xiaojun; Finkel, Toren Nature 36071159 2022 Sep
An evaluation of RNA-seq differential analysis methods. Li, Dongmei; Zand, Martin S; Dye, Timothy D; Goniewicz, Maciej L; Rahman, Irfan; Xie, Zidian PloS one 36112652 2022
Characterization of cellular senescence in aging skeletal muscle. Zhang, Xu; Habiballa, Leena; Aversa, Zaira; Ng, Yan Er; Sakamoto, Ayumi E; Englund, Davis A; Pearsall, Vesselina M; White, Thomas A; Robinson, Matthew M; Rivas, Donato A; Dasari, Surendra; Hruby, Adam J; Lagnado, Anthony B; Jachim, Sarah K; Granic, Antoneta; Sayer, Avan A; Jurk, Diana; Lanza, Ian R; Khosla, Sundeep; Fielding, Roger A; Nair, K Sreekumaran; Schafer, Marissa J; Passos, João F; LeBrasseur, Nathan K Nature aging 36147777 2022 Jul
Upregulation of PD-L1 in Senescence and Aging. Onorati, Angelique; Havas, Aaron P; Lin, Brian; Rajagopal, Jayaraj; Sen, Payel; Adams, Peter D; Dou, Zhixun Molecular and cellular biology 36154662 2022 Oct 20
Cellular senescence is increased in airway smooth muscle cells of elderly persons with asthma. Aghali, Arbi; Khalfaoui, Latifa; Lagnado, Anthony B; Drake, Li Y; Teske, Jacob J; Pabelick, Christina M; Passos, João F; Prakash, Y S American journal of physiology. Lung cellular and molecular physiology 36166734 2022 Nov 01
Targeting Cellular Senescence with Senotherapeutics: Development of New Approaches for Skin Care. Thompson, Elizabeth L; Pitcher, Louise E; Niedernhofer, Laura J; Robbins, Paul D Plastic and reconstructive surgery 36170431 2022 10 01
A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A. Simon, Matthew; Yang, Jiping; Gigas, Jonathan; Earley, Eric J; Hillpot, Eric; Zhang, Lei; Zagorulya, Maria; Tombline, Greg; Gilbert, Michael; Yuen, Samantha L; Pope, Alexis; Van Meter, Michael; Emmrich, Stephan; Firsanov, Denis; Athreya, Advait; Biashad, Seyed Ali; Han, Jeehae; Ryu, Seungjin; Tare, Archana; Zhu, Yizhou; Hudgins, Adam; Atzmon, Gil; Barzilai, Nir; Wolfe, Aaron; Moody, Kelsey; Garcia, Benjamin A; Thomas, David D; Robbins, Paul D; Vijg, Jan; Seluanov, Andrei; Suh, Yousin; Gorbunova, Vera The EMBO journal 36215696 2022 Nov 02
Cellular Senescence in Obesity and Associated Complications: a New Therapeutic Target. Narasimhan, Akilavalli; Flores, Rafael R; Camell, Christina D; Bernlohr, David A; Robbins, Paul D; Niedernhofer, Laura J Current diabetes reports 36239841 2022 Nov
scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. Gu, Haocheng; Cheng, Hao; Ma, Anjun; Li, Yang; Wang, Juexin; Xu, Dong; Ma, Qin Bioinformatics (Oxford, England) 36250784 2022 Nov 30
STtools: A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data. Xi, Jingyue; Lee, Jun Hee; Kang, Hyun Min; Jun, Goo Bioinformatics advances 36284674 2022
Scientific opportunities in resilience research for cardiovascular health and wellness. Report from a National Heart, Lung, and Blood Institute workshop. Taylor, Herman A; Finkel, Toren; Gao, Yunling; Ballinger, Scott W; Campo, Rebecca; Chen, Rong; Chen, Shu Hui; Davidson, Karina; Iruela-Arispe, M Luisa; Jaquish, Cashell; LeBrasseur, Nathan K; Odden, Michelle C; Papanicolaou, George J; Picard, Martin; Srinivas, Pothur; Tjurmina, Olga; Wolz, Michael; Galis, Zorina S FASEB journal : official publication of the Federation of American Societies for Experimental Biology 36322029 2022 Dec
Current Challenges and Solutions for Clinical Management and Care of People with HIV: Findings from the 12th Annual International HIV and Aging Workshop. Yu, Xiaoying; Lobo, Judith D; Sundermann, Erin; Baker, Darren J; Tracy, Russell P; Kuchel, George A; Stephenson, Kathryn E; Letendre, Scott L; Brew, Bruce; Cysique, Lucette A; Dale, Sannisha K; Wallen, Chelsie; Kunisaki, Ken M; Guaraldi, Giovanni; Milic, Jovana; Winston, Alan; Moore, David J; Margolick, Joseph B; Erlandson, Kristine M AIDS research and human retroviruses 36322713 2023 Jan
Toll-like receptor 2 orchestrates a tumor suppressor response in non-small cell lung cancer. Millar, Fraser R; Pennycuick, Adam; Muir, Morwenna; Quintanilla, Andrea; Hari, Priya; Freyer, Elisabeth; Gautier, Philippe; Meynert, Alison; Grimes, Graeme; Coll, Carla Salomo; Zdral, Sofia; Victorelli, Stella; Teixeira, Vitor H; Connelly, John; Passos, João F; Ros, Marian A; Wallace, William A H; Frame, Margaret C; Sims, Andrew H; Boulter, Luke; Janes, Sam M; Wilkinson, Simon; Acosta, Juan Carlos Cell reports 36351380 2022 Nov 08
Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain. Fu, Xiaonan; Sun, Li; Dong, Runze; Chen, Jane Y; Silakit, Runglawan; Condon, Logan F; Lin, Yiing; Lin, Shin; Palmiter, Richard D; Gu, Liangcai Cell 36368323 2022 Nov 23
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer's disease. Luquez, Tain; Gaur, Pallavi; Kosater, Ivy M; Lam, Matti; Lee, Dylan I; Mares, Jason; Paryani, Fahad; Yadav, Archana; Menon, Vilas Genome medicine 36447241 2022 Nov 30
Multiset multicover methods for discriminative marker selection. Hasanaj, Euxhen; Alavi, Amir; Gupta, Anupam; Póczos, Barnabás; Bar-Joseph, Ziv Cell reports methods 36452867 2022 Nov 21
Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES. Raredon, Micha Sam Brickman; Yang, Junchen; Kothapalli, Neeharika; Lewis, Wesley; Kaminski, Naftali; Niklason, Laura E; Kluger, Yuval Bioinformatics (Oxford, England) 36458905 2023 Jan 01
Tissue registration and exploration user interfaces in support of a human reference atlas. Börner, Katy; Bueckle, Andreas; Herr 2nd, Bruce W; Cross, Leonard E; Quardokus, Ellen M; Record, Elizabeth G; Ju, Yingnan; Silverstein, Jonathan C; Browne, Kristen M; Jain, Sanjay; Wasserfall, Clive H; Jorgensen, Marda L; Spraggins, Jeffrey M; Patterson, N Heath; Weber, Griffin M Communications biology 36513738 2022 Dec 13
Single nuclei profiling identifies cell specific markers of skeletal muscle aging, frailty, and senescence. Perez, Kevin; Ciotlos, Serban; McGirr, Julia; Limbad, Chandani; Doi, Ryosuke; Nederveen, Joshua P; Nilsson, Mats I; Winer, Daniel A; Evans, William; Tarnopolsky, Mark; Campisi, Judith; Melov, Simon Aging 36516485 2022 Dec 13
How a fibroblast ages: a role for bone morphogenetic protein 4 in protecting lung fibroblasts from senescence in pulmonary fibrosis. Farkas, Laszlo; Horowitz, Jeffrey C; Mora, Ana L The European respiratory journal 36522139 2022 Dec
Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier. Petelski, Aleksandra A; Slavov, Nikolai; Specht, Harrison Journal of visualized experiments : JoVE 36571403 2022 Dec 09
Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering. Fang, Jiyuan; Chan, Cliburn; Owzar, Kouros; Wang, Liuyang; Qin, Diyuan; Li, Qi-Jing; Xie, Jichun Genome biology 36575517 2022 Dec 27
Is it the time to integrate novel sequencing technologies into clinical practice? VanOudenhove, Jennifer; Halene, Stephanie; Mendez, Lourdes Current opinion in hematology 36602939 2023 Mar 01
Single-cell transcriptomics of peripheral blood in the aging mouse. Teo, Yee Voan; Hinthorn, Samuel J; Webb, Ashley E; Neretti, Nicola Aging 36622281 2023 Jan 06
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Chidester, Benjamin; Zhou, Tianming; Alam, Shahul; Ma, Jian Nature genetics 36624346 2023 Jan
A cellular taxonomy of the adult human spinal cord. Yadav, Archana; Matson, Kaya J E; Li, Li; Hua, Isabelle; Petrescu, Joana; Kang, Kristy; Alkaslasi, Mor R; Lee, Dylan I; Hasan, Saadia; Galuta, Ahmad; Dedek, Annemarie; Ameri, Sara; Parnell, Jessica; Alshardan, Mohammad M; Qumqumji, Feras Abbas; Alhamad, Saud M; Wang, Alick Pingbei; Poulen, Gaetan; Lonjon, Nicolas; Vachiery-Lahaye, Florence; Gaur, Pallavi; Nalls, Mike A; Qi, Yue A; Maric, Dragan; Ward, Michael E; Hildebrand, Michael E; Mery, Pierre-Francois; Bourinet, Emmanuel; Bauchet, Luc; Tsai, Eve C; Phatnani, Hemali; Le Pichon, Claire E; Menon, Vilas; Levine, Ariel J Neuron 36731429 2023 Feb 01
Pretherapy Ferumoxytol-enhanced MRI for Metastatic Breast Cancer: A New Approach for Predicting Tumor Delivery of Macromolecular Therapeutics? Daldrup-Link, Heike E Radiology. Imaging cancer 36734849 2023 Mar
Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA. Derks, Jason; Slavov, Nikolai Journal of proteome research 36735898 2023 Mar 03
Using single cell atlas data to reconstruct regulatory networks. Song, Qi; Ruffalo, Matthew; Bar-Joseph, Ziv Nucleic acids research 36762475 2023 Apr 24
Perturb-tracing enables high-content screening of multiscale 3D genome regulators. Cheng, Yubao; Hu, Mengwei; Yang, Bing; Jensen, Tyler B; Yang, Tianqi; Yu, Ruihuan; Ma, Zhaoxia; Radda, Jonathan S D; Jin, Shengyan; Zang, Chongzhi; Wang, Siyuan bioRxiv : the preprint server for biology 36778402 2023 Nov 05
Data-Driven Optimization of DIA Mass Spectrometry by DO-MS. Wallmann, Georg; Leduc, Andrew; Slavov, Nikolai bioRxiv : the preprint server for biology 36778474 2023 Sep 03
Local senolysis in aged mice only partially replicates the benefits of systemic senolysis. Farr, Joshua N; Saul, Dominik; Doolittle, Madison L; Kaur, Japneet; Rowsey, Jennifer L; Vos, Stephanie J; Froemming, Mitchell N; Lagnado, Anthony B; Zhu, Yi; Weivoda, Megan M; Ikeno, Yuji; Pignolo, Robert J; Niedernhofer, Laura J; Robbins, Paul D; Jurk, Diana; Passos, João F; LeBrasseur, Nathan K; Tchkonia, Tamara; Kirkland, James L; Monroe, David G; Khosla, Sundeep The Journal of clinical investigation 36809340 2023 Feb 21
Single-cell biological network inference using a heterogeneous graph transformer. Ma, Anjun; Wang, Xiaoying; Li, Jingxian; Wang, Cankun; Xiao, Tong; Liu, Yuntao; Cheng, Hao; Wang, Juexin; Li, Yang; Chang, Yuzhou; Li, Jinpu; Wang, Duolin; Jiang, Yuexu; Su, Li; Xin, Gang; Gu, Shaopeng; Li, Zihai; Liu, Bingqiang; Xu, Dong; Ma, Qin Nature communications 36810839 2023 Feb 21
Senolytic vaccination: a new mandate for cardiovascular health? Lear, Travis B; Finkel, Toren The journal of cardiovascular aging 36819765 2022 Apr
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq. Liu, Yang; DiStasio, Marcello; Su, Graham; Asashima, Hiromitsu; Enninful, Archibald; Qin, Xiaoyu; Deng, Yanxiang; Nam, Jungmin; Gao, Fu; Bordignon, Pino; Cassano, Marco; Tomayko, Mary; Xu, Mina; Halene, Stephanie; Craft, Joseph E; Hafler, David; Fan, Rong Nature biotechnology 36823353 2023 Oct
Statistical Power Analysis for Designing Bulk, Single-Cell, and Spatial Transcriptomics Experiments: Review, Tutorial, and Perspectives. Jeon, Hyeongseon; Xie, Juan; Jeon, Yeseul; Jung, Kyeong Joo; Gupta, Arkobrato; Chang, Won; Chung, Dongjun Biomolecules 36830591 2023 Jan 24
A Chemoptogenetic Tool for Spatiotemporal Induction of Oxidative DNA Lesions In Vivo. Han, Suhao; Sims, Austin; Aceto, Anthony; Schmidt, Brigitte F; Bruchez, Marcel P; Gurkar, Aditi U Genes 36833412 2023 Feb 14
Progress in Discovering Transcriptional Noise in Aging. Bartz, Josh; Jung, Hannim; Wasiluk, Karen; Zhang, Lei; Dong, Xiao International journal of molecular sciences 36835113 2023 Feb 12
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Gatto, Laurent; Aebersold, Ruedi; Cox, Juergen; Demichev, Vadim; Derks, Jason; Emmott, Edward; Franks, Alexander M; Ivanov, Alexander R; Kelly, Ryan T; Khoury, Luke; Leduc, Andrew; MacCoss, Michael J; Nemes, Peter; Perlman, David H; Petelski, Aleksandra A; Rose, Christopher M; Schoof, Erwin M; Van Eyk, Jennifer; Vanderaa, Christophe; Yates 3rd, John R; Slavov, Nikolai Nature methods 36864200 2023 Mar
DNA damage-induced stalling of transcription drives aging through gene expression imbalance. Sims, Austin A; Gurkar, Aditi U DNA repair 36921370 2023 May
Spatial epigenome-transcriptome co-profiling of mammalian tissues. Zhang, Di; Deng, Yanxiang; Kukanja, Petra; Agirre, Eneritz; Bartosovic, Marek; Dong, Mingze; Ma, Cong; Ma, Sai; Su, Graham; Bao, Shuozhen; Liu, Yang; Xiao, Yang; Rosoklija, Gorazd B; Dwork, Andrew J; Mann, J John; Leong, Kam W; Boldrini, Maura; Wang, Liya; Haeussler, Maximilian; Raphael, Benjamin J; Kluger, Yuval; Castelo-Branco, Gonçalo; Fan, Rong Nature 36922587 2023 Apr
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. SenNet Consortium Nature aging 36936385 2022 Dec
Predicting mutational function using machine learning. Shea, Anthony; Bartz, Josh; Zhang, Lei; Dong, Xiao Mutation research. Reviews in mutation research 36965820 2023
Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas. Herr 2nd, Bruce W; Hardi, Josef; Quardokus, Ellen M; Bueckle, Andreas; Chen, Lu; Wang, Fusheng; Caron, Anita R; Osumi-Sutherland, David; Musen, Mark A; Börner, Katy Scientific data 36973309 2023 Mar 27
microRNA-449a reduces growth hormone-stimulated senescent cell burden through PI3K-mTOR signaling. Noureddine, Sarah; Nie, Jia; Schneider, Augusto; Menon, Vinal; Fliesen, Zoubeida; Dhahbi, Joseph; Victoria, Berta; Oyer, Jeremiah; Robles-Carrillo, Liza; Nunes, Allancer Divino De Carvalho; Ashiqueali, Sarah; Janusz, Artur; Copik, Alicja; Robbins, Paul D; Musi, Nicolas; Masternak, Michal M Proceedings of the National Academy of Sciences of the United States of America 36976763 2023 Apr 04
Challenges and opportunities for modeling aging and cancer. Anczuków, Olga; Airhart, Susie; Chuang, Jeffrey H; Coussens, Lisa M; Kuchel, George A; Korstanje, Ron; Li, Sheng; Lucido, Anna Lisa; McAllister, Sandra S; Politi, Katerina; Polyak, Kornelia; Ratliff, Timothy; Ren, Gary; Trowbridge, Jennifer J; Ucar, Duygu; Palucka, Karolina Cancer cell 37001528 2023 Apr 10
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. Huffman, R Gray; Leduc, Andrew; Wichmann, Christoph; Di Gioia, Marco; Borriello, Francesco; Specht, Harrison; Derks, Jason; Khan, Saad; Khoury, Luke; Emmott, Edward; Petelski, Aleksandra A; Perlman, David H; Cox, Jürgen; Zanoni, Ivan; Slavov, Nikolai Nature methods 37012480 2023 Apr 03
Integrating multiple single-cell multi-omics samples with Smmit. Wan, Changxin; Ji, Zhicheng bioRxiv : the preprint server for biology 37066420 2023 Apr 06
Impact of aging on immune function in the pathogenesis of pulmonary diseases: potential for therapeutic targets. Shaikh, Sadiya Bi; Goracci, Chiara; Tjitropranoto, Ariel; Rahman, Irfan Expert review of respiratory medicine 37078192 2023 May
Clearance of senescent cells reverts the cigarette smoke-induced lung senescence and airspace enlargement in p16-3MR mice. Kaur, Gagandeep; Muthumalage, Thivanka; Rahman, Irfan Aging cell 37078230 2023 Apr 20
A chronic wound model to investigate skin cellular senescence. Wyles, Saranya P; Dashti, Parisa; Pirtskhalava, Tamar; Tekin, Burak; Inman, Christina; Gomez, Lilian Sales; Lagnado, Anthony B; Prata, Larissa; Jurk, Diana; Passos, João F; Tchkonia, Tamar; Kirkland, James L Aging 37086260 2023 Apr 21
Senescent cardiomyocytes contribute to cardiac dysfunction following myocardial infarction. Redgrave, Rachael; Dookun, Emily; Booth, Laura; Folaranm, Omowumi; Tual-Chalot, Simon; Gill, Jason; Owens, Andrew; Spyridopoulos, Ioakim; Passos, Joao; Richardson, Gavin Research square 37090497 2023 Apr 10
Telomere dysfunction in chronic liver disease: The link from aging. Penrice, Daniel D; Jalan-Sakrikar, Nidhi; Jurk, Diana; Passos, João F; Simonetto, Douglas A Hepatology (Baltimore, Md.) 37102475 2023 Apr 28
Nuclear morphology is a deep learning biomarker of cellular senescence. Heckenbach, Indra; Mkrtchyan, Garik V; Ezra, Michael Ben; Bakula, Daniela; Madsen, Jakob Sture; Nielsen, Malte Hasle; Oró, Denise; Osborne, Brenna; Covarrubias, Anthony J; Idda, M Laura; Gorospe, Myriam; Mortensen, Laust; Verdin, Eric; Westendorp, Rudi; Scheibye-Knudsen, Morten Nature aging 37118134 2022 Aug
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. Hou, Wenpin; Ji, Zhicheng bioRxiv : the preprint server for biology 37131626 2023 Dec 13
The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality. Bueckle, Andreas; Qing, Catherine; Luley, Shefali; Kumar, Yash; Pandey, Naval; Börner, Katy Frontiers in bioinformatics 37181487 2023
Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis. Hou, Wenpin; Ji, Zhicheng Research square 37205379 2023 May 02
The technological landscape and applications of single-cell multi-omics. Baysoy, Alev; Bai, Zhiliang; Satija, Rahul; Fan, Rong Nature reviews. Molecular cell biology 37280296 2023 Oct
An integrated cell atlas of the lung in health and disease. Sikkema, Lisa; Ramírez-Suástegui, Ciro; Strobl, Daniel C; Gillett, Tessa E; Zappia, Luke; Madissoon, Elo; Markov, Nikolay S; Zaragosi, Laure-Emmanuelle; Ji, Yuge; Ansari, Meshal; Arguel, Marie-Jeanne; Apperloo, Leonie; Banchero, Martin; Bécavin, Christophe; Berg, Marijn; Chichelnitskiy, Evgeny; Chung, Mei-I; Collin, Antoine; Gay, Aurore C A; Gote-Schniering, Janine; Hooshiar Kashani, Baharak; Inecik, Kemal; Jain, Manu; Kapellos, Theodore S; Kole, Tessa M; Leroy, Sylvie; Mayr, Christoph H; Oliver, Amanda J; von Papen, Michael; Peter, Lance; Taylor, Chase J; Walzthoeni, Thomas; Xu, Chuan; Bui, Linh T; De Donno, Carlo; Dony, Leander; Faiz, Alen; Guo, Minzhe; Gutierrez, Austin J; Heumos, Lukas; Huang, Ni; Ibarra, Ignacio L; Jackson, Nathan D; Kadur Lakshminarasimha Murthy, Preetish; Lotfollahi, Mohammad; Tabib, Tracy; Talavera-López, Carlos; Travaglini, Kyle J; Wilbrey-Clark, Anna; Worlock, Kaylee B; Yoshida, Masahiro; Lung Biological Network Consortium; van den Berge, Maarten; Bossé, Yohan; Desai, Tushar J; Eickelberg, Oliver; Kaminski, Naftali; Krasnow, Mark A; Lafyatis, Robert; Nikolic, Marko Z; Powell, Joseph E; Rajagopal, Jayaraj; Rojas, Mauricio; Rozenblatt-Rosen, Orit; Seibold, Max A; Sheppard, Dean; Shepherd, Douglas P; Sin, Don D; Timens, Wim; Tsankov, Alexander M; Whitsett, Jeffrey; Xu, Yan; Banovich, Nicholas E; Barbry, Pascal; Duong, Thu Elizabeth; Falk, Christine S; Meyer, Kerstin B; Kropski, Jonathan A; Pe'er, Dana; Schiller, Herbert B; Tata, Purushothama Rao; Schultze, Joachim L; Teichmann, Sara A; Misharin, Alexander V; Nawijn, Martijn C; Luecken, Malte D; Theis, Fabian J Nature medicine 37291214 2023 Jun
Breast cancer risk based on a deep learning predictor of senescent cells in normal tissue. Heckenbach, Indra; Powell, Mark; Fuller, Sophia; Henry, Jill; Rysdyk, Sam; Cui, Jenny; Teklu, Amanuel Abraha; Verdin, Eric; Benz, Christopher; Scheibye-Knudsen, Morten medRxiv : the preprint server for health sciences 37292628 2023 May 23
Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Ma, Feiyang; Plazyo, Olesya; Billi, Allison C; Tsoi, Lam C; Xing, Xianying; Wasikowski, Rachael; Gharaee-Kermani, Mehrnaz; Hile, Grace; Jiang, Yanyun; Harms, Paul W; Xing, Enze; Kirma, Joseph; Xi, Jingyue; Hsu, Jer-En; Sarkar, Mrinal K; Chung, Yutein; Di Domizio, Jeremy; Gilliet, Michel; Ward, Nicole L; Maverakis, Emanual; Klechevsky, Eynav; Voorhees, John J; Elder, James T; Lee, Jun Hee; Kahlenberg, J Michelle; Pellegrini, Matteo; Modlin, Robert L; Gudjonsson, Johann E Nature communications 37308489 2023 Jun 12
Senescent cardiomyocytes contribute to cardiac dysfunction following myocardial infarction. Redgrave, Rachael E; Dookun, Emily; Booth, Laura K; Camacho Encina, Maria; Folaranmi, Omowumi; Tual-Chalot, Simon; Gill, Jason H; Owens, W Andrew; Spyridopoulos, Ioakim; Passos, João F; Richardson, Gavin D npj aging 37316516 2023 Jun 14
Drugs Targeting Mechanisms of Aging to Delay Age-Related Disease and Promote Healthspan: Proceedings of a National Institute on Aging Workshop. Espinoza, Sara E; Khosla, Sundeep; Baur, Joseph A; de Cabo, Rafael; Musi, Nicolas The journals of gerontology. Series A, Biological sciences and medical sciences 37325957 2023 Jun 16
Chronic inflammation and the hallmarks of aging. Baechle, Jordan J; Chen, Nan; Makhijani, Priya; Winer, Shawn; Furman, David; Winer, Daniel A Molecular metabolism 37329949 2023 Aug
Multicellular communities are perturbed in the aging human brain and Alzheimer's disease. Cain, Anael; Taga, Mariko; McCabe, Cristin; Green, Gilad S; Hekselman, Idan; White, Charles C; Lee, Dylan I; Gaur, Pallavi; Rozenblatt-Rosen, Orit; Zhang, Feng; Yeger-Lotem, Esti; Bennett, David A; Yang, Hyun-Sik; Regev, Aviv; Menon, Vilas; Habib, Naomi; De Jager, Philip L Nature neuroscience 37336975 2023 Jul
Spatial Single-Cell Technologies for Exploring Gastrointestinal Tissue Transcriptome. Kang, Hyun Min; Lee, Jun Hee Comprehensive Physiology 37358516 2023 Jun 26
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. Dayao, Monica T; Trevino, Alexandro; Kim, Honesty; Ruffalo, Matthew; D'Angio, H Blaize; Preska, Ryan; Duvvuri, Umamaheswar; Mayer, Aaron T; Bar-Joseph, Ziv Bioinformatics (Oxford, England) 37387167 2023 Jun 30
Single-cell proteomics: quantifying post-transcriptional regulation during development with mass-spectrometry. Slavov, Nikolai Development (Cambridge, England) 37387573 2023 Jul 01
Impact of Geroscience on Therapeutic Strategies for Older Adults With Cardiovascular Disease: JACC Scientific Statement. Forman, Daniel E; Kuchel, George A; Newman, John C; Kirkland, James L; Volpi, Elena; Taffet, George E; Barzilai, Nir; Pandey, Ambarish; Kitzman, Dalane W; Libby, Peter; Ferrucci, Luigi Journal of the American College of Cardiology 37389519 2023 Aug 15
SCS: cell segmentation for high-resolution spatial transcriptomics. Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv bioRxiv : the preprint server for biology 37398213 2023 Jun 16
Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering. Hislop, Joshua; Alavi, Amir; Song, Qi; Schoenberger, Rayna; Kamyar, Keshavarz F; LeGraw, Ryan; Velazquez, Jeremy; Mokhtari, Tahere; Taheri, Mohammad Nasser; Rytel, Matthew; de Sousa Lopes, Susana M Chuva; Watkins, Simon; Stolz, Donna; Kiani, Samira; Sozen, Berna; Bar-Joseph, Ziv; Ebrahimkhani, Mo R bioRxiv : the preprint server for biology 37398391 2023 Jul 24
Spatial mapping of cellular senescence: emerging challenges and opportunities. Gurkar, Aditi U; Gerencser, Akos A; Mora, Ana L; Nelson, Andrew C; Zhang, Anru R; Lagnado, Anthony B; Enninful, Archibald; Benz, Christopher; Furman, David; Beaulieu, Delphine; Jurk, Diana; Thompson, Elizabeth L; Wu, Fei; Rodriguez, Fernanda; Barthel, Grant; Chen, Hao; Phatnani, Hemali; Heckenbach, Indra; Chuang, Jeffrey H; Horrell, Jeremy; Petrescu, Joana; Alder, Jonathan K; Lee, Jun Hee; Niedernhofer, Laura J; Kumar, Manoj; Königshoff, Melanie; Bueno, Marta; Sokka, Miiko; Scheibye-Knudsen, Morten; Neretti, Nicola; Eickelberg, Oliver; Adams, Peter D; Hu, Qianjiang; Zhu, Quan; Porritt, Rebecca A; Dong, Runze; Peters, Samuel; Victorelli, Stella; Pengo, Thomas; Khaliullin, Timur; Suryadevara, Vidyani; Fu, Xiaonan; Bar-Joseph, Ziv; Ji, Zhicheng; Passos, João F Nature aging 37400722 2023 Jul
LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity. Xie, Juan; Jeon, Hyeongseon; Xin, Gang; Ma, Qin; Chung, Dongjun PLoS computational biology 37428794 2023 Jul
SCS: cell segmentation for high-resolution spatial transcriptomics. Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv Nature methods 37429992 2023 Aug
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, Leena; Hruby, Adam; Granic, Antoneta; Dodds, Richard M; Hillman, Susan J; Jurk, Diana; Passos, João F; Sayer, Avan A GeroScience 37434081 2023 Jul 11
New Horizons in cellular senescence for clinicians. Witham, Miles D; Granic, Antoneta; Miwa, Satomi; Passos, Joao F; Richardson, Gavin D; Sayer, Avan A Age and ageing 37466640 2023 Jul 01
Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging. Quardokus, Ellen M; Saunders, Diane C; McDonough, Elizabeth; Hickey, John W; Werlein, Christopher; Surrette, Christine; Rajbhandari, Presha; Casals, Anna Martinez; Tian, Hua; Lowery, Lisa; Neumann, Elizabeth K; Björklund, Frida; Neelakantan, Taruna V; Croteau, Josh; Wiblin, Anne E; Fisher, Jeremy; Livengood, April J; Dowell, Karen G; Silverstein, Jonathan C; Spraggins, Jeffrey M; Pryhuber, Gloria S; Deutsch, Gail; Ginty, Fiona; Nolan, Garry P; Melov, Simon; Jonigk, Danny; Caldwell, Michael A; Vlachos, Ioannis S; Muller, Werner; Gehlenborg, Nils; Stockwell, Brent R; Lundberg, Emma; Snyder, Michael P; Germain, Ronald N; Camarillo, Jeannie M; Kelleher, Neil L; Börner, Katy; Radtke, Andrea J Nature methods 37468619 2023 Aug
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Jain, Sanjay; Pei, Liming; Spraggins, Jeffrey M; Angelo, Michael; Carson, James P; Gehlenborg, Nils; Ginty, Fiona; Gonçalves, Joana P; Hagood, James S; Hickey, John W; Kelleher, Neil L; Laurent, Louise C; Lin, Shin; Lin, Yiing; Liu, Huiping; Naba, Alexandra; Nakayasu, Ernesto S; Qian, Wei-Jun; Radtke, Andrea; Robson, Paul; Stockwell, Brent R; Van de Plas, Raf; Vlachos, Ioannis S; Zhou, Mowei; HuBMAP Consortium; Börner, Katy; Snyder, Michael P Nature cell biology 37468756 2023 Aug
SiftCell: A robust framework to detect and isolate cell-containing droplets from single-cell RNA sequence reads. Xi, Jingyue; Park, Sung Rye; Lee, Jun Hee; Kang, Hyun Min Cell systems 37473732 2023 Jul 19
Loss of ANT1 Increases Fibrosis and Epithelial Cell Senescence in Idiopathic Pulmonary Fibrosis. Sui, Justin; Boatz, Jennifer C; Shi, Jian; Hu, Qianjiang; Li, Xiaoyun; Zhang, Yingze; Königshoff, Melanie; Kliment, Corrine R American journal of respiratory cell and molecular biology 37487137 2023 Nov
A genome-wide single-cell 3D genome atlas of lung cancer progression. Liu, Miao; Jin, Shengyan; Agabiti, Sherry S; Jensen, Tyler B; Yang, Tianqi; Radda, Jonathan S D; Ruiz, Christian F; Baldissera, Gabriel; Muzumdar, Mandar Deepak; Wang, Siyuan bioRxiv : the preprint server for biology 37546882 2023 Jul 24
Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. Zhou, Tianming; Zhang, Ruochi; Jia, Deyong; Doty, Raymond T; Munday, Adam D; Gao, Daniel; Xin, Li; Abkowitz, Janis L; Duan, Zhijun; Ma, Jian bioRxiv : the preprint server for biology 37546900 2023 Jul 25
Targeted sequencing of the 9p21.3 region reveals association with reduced disease risks in Ashkenazi Jewish centenarians. Zhu, Yizhou; Ryu, Seungjin; Tare, Archana; Barzilai, Nir; Atzmon, Gil; Suh, Yousin Aging cell 37605876 2023 Oct
MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer. Wang, Xiaoying; Duan, Maoteng; Li, Jingxian; Ma, Anjun; Xu, Dong; Li, Zihai; Liu, Bingqiang; Ma, Qin bioRxiv : the preprint server for biology 37645917 2023 Aug 17
Life's Essential 8: Optimizing Health in Older Adults. Kumar, Manish; Orkaby, Ariela; Tighe, Caitlan; Villareal, Dennis T; Billingsley, Hayley; Nanna, Michael G; Kwak, Min Ji; Rohant, Namit; Patel, Shreya; Goyal, Parag; Hummel, Scott; Al-Malouf, Christina; Kolimas, Amie; Krishnaswami, Ashok; Rich, Mike W; Kirkpatrick, James; Damluji, Abdulla A; Kuchel, George A; Forman, Daniel E; Alexander, Karen P JACC. Advances 37664644 2023 Sep
Intact mitochondrial function in the setting of telomere-induced senescence. Sullivan, Daniel I; Bello, Fiona M; Silva, Agustin Gil; Redding, Kevin M; Giordano, Luca; Hinchie, Angela M; Loughridge, Kelly E; Mora, Ana L; Königshoff, Melanie; Kaufman, Brett A; Jurczak, Michael J; Alder, Jonathan K Aging cell 37688329 2023 Oct
SIMVI reveals intrinsic and spatial-induced states in spatial omics data. Dong, Mingze; Kluger, Harriet; Fan, Rong; Kluger, Yuval bioRxiv : the preprint server for biology 37693629 2023 Aug 30
Data-Driven Optimization of DIA Mass Spectrometry by DO-MS. Wallmann, Georg; Leduc, Andrew; Slavov, Nikolai Journal of proteome research 37695820 2023 Oct 06
Iditarod, a Drosophila homolog of the Irisin precursor FNDC5, is critical for exercise performance and cardiac autophagy. Cobb, Tyler; Hwang, Irene; Soukar, Michael; Namkoong, Sim; Cho, Uhn-Soo; Safdar, Maryam; Kim, Myungjin; Wessells, Robert J; Lee, Jun Hee Proceedings of the National Academy of Sciences of the United States of America 37722048 2023 Sep 26
Lysosomes in senescence and aging. Tan, Jay Xiaojun; Finkel, Toren EMBO reports 37811693 2023 Nov 06
BMAL1 modulates senescence programming via AP-1. Jachim, Sarah K; Zhong, Jian; Ordog, Tamas; Lee, Jeong-Heon; Bhagwate, Aditya V; Nagaraj, Nagaswaroop Kengunte; Westendorf, Jennifer J; Passos, João F; Matveyenko, Aleksey V; LeBrasseur, Nathan K Aging 37819791 2023 Oct 10
Apoptotic stress causes mtDNA release during senescence and drives the SASP. Victorelli, Stella; Salmonowicz, Hanna; Chapman, James; Martini, Helene; Vizioli, Maria Grazia; Riley, Joel S; Cloix, Catherine; Hall-Younger, Ella; Machado Espindola-Netto, Jair; Jurk, Diana; Lagnado, Anthony B; Sales Gomez, Lilian; Farr, Joshua N; Saul, Dominik; Reed, Rebecca; Kelly, George; Eppard, Madeline; Greaves, Laura C; Dou, Zhixun; Pirius, Nicholas; Szczepanowska, Karolina; Porritt, Rebecca A; Huang, Huijie; Huang, Timothy Y; Mann, Derek A; Masuda, Claudio Akio; Khosla, Sundeep; Dai, Haiming; Kaufmann, Scott H; Zacharioudakis, Emmanouil; Gavathiotis, Evripidis; LeBrasseur, Nathan K; Lei, Xue; Sainz, Alva G; Korolchuk, Viktor I; Adams, Peter D; Shadel, Gerald S; Tait, Stephen W G; Passos, João F Nature 37821702 2023 Oct
PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning. Deng, Yihe; Zhang, Ruochi; Xu, Pan; Ma, Jian; Gu, Quanquan bioRxiv : the preprint server for biology 37873233 2023 Oct 02
Environmental tobacco smoke exposure exaggerates bleomycin- induced collagen overexpression during pulmonary fibrogenesis. Wang, Qixin; Goracci, Chiara; Sundar, Isaac Kirubakaran; Rahman, Irfan Research square 37886473 2023 Oct 10
Proteomic quantification of native and ECM-enriched mouse ovaries reveals an age-dependent fibro-inflammatory signature. Dipali, Shweta S; King, Christina D; Rose, Jacob P; Burdette, Joanna E; Campisi, Judith; Schilling, Birgit; Duncan, Francesca E Aging 37899138 2023 Oct 27
Functional Tissue Units in the Human Reference Atlas. Bidanta, Supriya; Börner, Katy; Herr 2nd, Bruce W; Nagy, Marcell; Gustilo, Katherine S; Bajema, Rachel; Maier, Libby; Molontay, Roland; Weber, Griffin bioRxiv : the preprint server for biology 37905079 2023 Oct 26
Epigenetic regulation during cancer transitions across 11 tumour types. Terekhanova, Nadezhda V; Karpova, Alla; Liang, Wen-Wei; Strzalkowski, Alexander; Chen, Siqi; Li, Yize; Southard-Smith, Austin N; Iglesia, Michael D; Wendl, Michael C; Jayasinghe, Reyka G; Liu, Jingxian; Song, Yizhe; Cao, Song; Houston, Andrew; Liu, Xiuting; Wyczalkowski, Matthew A; Lu, Rita Jui-Hsien; Caravan, Wagma; Shinkle, Andrew; Naser Al Deen, Nataly; Herndon, John M; Mudd, Jacqueline; Ma, Cong; Sarkar, Hirak; Sato, Kazuhito; Ibrahim, Omar M; Mo, Chia-Kuei; Chasnoff, Sara E; Porta-Pardo, Eduard; Held, Jason M; Pachynski, Russell; Schwarz, Julie K; Gillanders, William E; Kim, Albert H; Vij, Ravi; DiPersio, John F; Puram, Sidharth V; Chheda, Milan G; Fuh, Katherine C; DeNardo, David G; Fields, Ryan C; Chen, Feng; Raphael, Benjamin J; Ding, Li Nature 37914932 2023 Nov
Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture. Zhu, Yizhou; Rosenfeld, Michael G; Suh, Yousin Proceedings of the National Academy of Sciences of the United States of America 37922325 2023 Nov 07
Mitohormesis. Cheng, Yu-Wei; Liu, Jie; Finkel, Toren Cell metabolism 37939657 2023 Nov 07
Effect of Cellular Senescence in Disease Progression and Transplantation: Immune Cells and Solid Organs. Kirchner, Varvara A; Badshah, Joshua S; Hong, Suk Kyun; Martinez, Olivia; Pruett, Timothy L; Niedernhofer, Laura J Transplantation 37953486 2023 Nov 13
FICTURE: Scalable segmentation-free analysis of submicron resolution spatial transcriptomics. Si, Yichen; Lee, ChangHee; Hwang, Yongha; Yun, Jeong H; Cheng, Weiqiu; Cho, Chun-Seok; Quiros, Miguel; Nusrat, Asma; Zhang, Weizhou; Jun, Goo; Zöllner, Sebastian; Lee, Jun Hee; Kang, Hyun Min bioRxiv : the preprint server for biology 37961699 2023 Nov 07
Dimension-agnostic and granularity-based spatially variable gene identification using BSP. Wang, Juexin; Li, Jinpu; Kramer, Skyler T; Su, Li; Chang, Yuzhou; Xu, Chunhui; Eadon, Michael T; Kiryluk, Krzysztof; Ma, Qin; Xu, Dong Nature communications 37963892 2023 Nov 14
Proteomic Analysis of the Senescence Associated Secretory Phenotype (SASP): GDF-15, IGFBP-2, and Cystatin-C Are Associated with Multiple Aging Traits. Evans, Daniel S; Young, Danielle; Tanaka, Toshiko; Basisty, Nathan; Bandinelli, Stefania; Ferrucci, Luigi; Campisi, Judith; Schilling, Birgit The journals of gerontology. Series A, Biological sciences and medical sciences 37982669 2023 Nov 20
Analyzing somatic mutations by single-cell whole-genome sequencing. Zhang, Lei; Lee, Moonsook; Maslov, Alexander Y; Montagna, Cristina; Vijg, Jan; Dong, Xiao Nature protocols 37996541 2023 Nov 23
COPIng with senescence. Victorelli, Stella; Passos, João F Nature cell biology 38012404 2023 Dec
Deep identifiable modeling of single-cell atlases enables zero-shot query of cellular states. Dong, Mingze; Kluger, Yuval bioRxiv : the preprint server for biology 38014345 2023 Nov 15
A tissue ubiquitous gene set for cellular senescence. Qu, Yilong; Ji, Zhicheng bioRxiv : the preprint server for biology 38045252 2023 Nov 21
A mitochondria-regulated p53-CCF circuit integrates genome integrity with inflammation. Miller, Karl N; Li, Brightany; Pierce-Hoffman, Hannah R; Lei, Xue; Havas, Aaron P; Patel, Shreeya; Macip, Carolina Cano; Victorelli, Stella G; Woo, Seung-Hwa; Lagnado, Anthony B; Liu, Tianhui; Dasgupta, Nirmalya; Lyu, Jun; Altman, Yoav; Porritt, Rebecca A; Garcia, Guillermina; Mogler, Carolin; Dou, Zhixun; Chen, Chongyi; Passos, João F; Adams, Peter D bioRxiv : the preprint server for biology 38045344 2023 Nov 21
multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results. Khatiwada, Aastha; Yilmaz, Ayse Selen; Wolf, Bethany J; Pietrzak, Maciej; Chung, Dongjun PLoS computational biology 38060592 2023 Dec
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. Leduc, Andrew; Koury, Luke; Cantlon, Joshua; Slavov, Nikolai bioRxiv : the preprint server for biology 38076795 2023 Nov 28
T-cell receptor sequences correlate with and predict gene expression levels in T cells. Wang, Hao; Ji, Zhicheng bioRxiv : the preprint server for biology 38076860 2023 Nov 28
Modelling post-implantation human development to yolk sac blood emergence. Hislop, Joshua; Song, Qi; Keshavarz F, Kamyar; Alavi, Amir; Schoenberger, Rayna; LeGraw, Ryan; Velazquez, Jeremy J; Mokhtari, Tahere; Taheri, Mohammad Naser; Rytel, Matthew; Chuva de Sousa Lopes, Susana M; Watkins, Simon; Stolz, Donna; Kiani, Samira; Soze Nature 38092041 2024 Feb
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, Yige; Chen, Siqi; Yang, Xiaolu; Sato, Kazuhito; Lal, Preet; Wang, Yuefan; Shinkle, Andrew T; Wendl, Michael C; Primeau, Tina M; Zhao, Yanyan; Gould, Alanna; Sun, Hua; Mudd, Jacqueline L; Hoog, Jeremy; Mashl, R Jay; Wyczalkowski, Matthew A; Mo, Chia-Kuei; Liu, Ruiyang; Herndon, John M; Davies, Sherri R; Liu, Di; Ding, Xi; Evrard, Yvonne A; Welm, Bryan E; Lum, David; Koh, Mei Yee; Welm, Alana L; Chuang, Jeffrey H; Moscow, Jeffrey A; Meric-Bernstam, Funda; Govindan, Ramaswamy; Li, Shunqiang; Hsieh, James; Fields, Ryan C; Lim, Kian-Huat; Ma, Cynthia X; Zhang, Hui; Ding, Li; Chen, Feng Cancer research 38098449 2023 Dec 15
Distinct secretomes in p16- and p21- positive senescent cells across tissues. Saul, Dominik; Jurk, Diana; Doolittle, Madison L; Kosinsky, Robyn Laura; Monroe, David G; LeBrasseur, Nathan K; Robbins, Paul D; Niedernhofer, Laura J; Khosla, Sundeep; Passos, João F bioRxiv : the preprint server for biology 38106149 2023 Dec 05
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. Chen, Hao; Lee, Young Je; Ovando, Jose A; Rosas, Lorena; Rojas, Mauricio; Mora, Ana L; Bar-Joseph, Ziv; Lugo-Martinez, Jose bioRxiv : the preprint server for biology 38187629 2023 Dec 19
A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers. Neri, Francesco; Takajjart, Selma N; Lerner, Chad A; Desprez, Pierre-Yves; Schilling, Birgit; Campisi, Judith; Gerencser, Akos A bioRxiv : the preprint server for biology 38187756 2023 Dec 23
A systematic evaluation of computation methods for cell segmentation. Wang, Yuxing; Zhao, Junhan; Xu, Hongye; Han, Cheng; Tao, Zhiqiang; Zhao, Dongfang; Zhou, Dawei; Tong, Gang; Liu, Dongfang; Ji, Zhicheng bioRxiv : the preprint server for biology 38352578 2024 Jan 31
Stimuli-specific senescence of primary human lung fibroblasts modulates alveolar stem cell function. Bramey, Nora; Melo-Narvaez, Maria Camila; See, Fenja; Ballester-Lllobell, Beatriz; Steinchen, Carina; Jain, Eshita; Hafner, Kathrin; Yildirim, Ali Önder; Königshoff, Melanie; Lehmann, Mareike Research square 38352619 2024 Jan 29

This page last reviewed on December 3, 2024