Cellular Senescence Network (SenNet)
Cellular Senescence Network (SenNet)
Program Publications
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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 | 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 |
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| 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 |
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| Single-cell proteomics: quantifying post-transcriptional regulation during development with mass-spectrometry. | Slavov, Nikolai | Development (Cambridge, England) | 37387573 | 2023 Jul 01 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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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, 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 |
