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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.
Cellular Senescence Network (SenNet) (58)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| SPICEMIX enables integrative single-cell spatial modeling of cell identity. | Chidester, Benjamin; Zhou, Tianming; Alam, Shahul; Ma, Jian | Nature genetics | 2023 Jan | 36624346 | |
| Single-cell transcriptomics of peripheral blood in the aging mouse. | Teo, Yee Voan; Hinthorn, Samuel J; Webb, Ashley E; Neretti, Nicola | Aging | 2023 Jan 06 | 6-20 | 36622281 |
| 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 | 2022 Dec 27 | 36575517 | |
| 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 | 2022 Dec 13 | 9393-9422 | 36516485 |
| 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 | 2022 Dec 13 | 1369 | 36513738 |
| 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 | 2022 Nov 30 | 36447241 | |
| 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 | 2022 Nov 23 | 36368323 | |
| 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 | 2022 Nov 08 | 36351380 | |
| 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 | 2023 Jan | 1-12 | 36322713 |
| 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 | 2022 Dec | 36322029 | |
| STtools: A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data. | Xi, Jingyue; Lee, Jun Hee; Kang, Hyun Min; Jun, Goo | Bioinformatics advances | 2022 | 36284674 | |
| 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) | 2022 Nov 30 | 36250784 | |
| 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 | 2022 Nov | 36239841 | |
| 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 | 2022 10 01 | 36170431 | |
| 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 | 2022 Nov 01 | 36166734 | |
| 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 | 2022 Jul | 36147777 | |
| 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 | 2022 | 36112652 | |
| 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 | 2022 09 | 35978191 | |
| 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 | 2022 08 16 | 35974106 | |
| Epigenetics, DNA damage, and aging. | Soto-Palma, Carolina; Niedernhofer, Laura J; Faulk, Christopher D; Dong, Xiao | The Journal of clinical investigation | 2022 08 15 | 35968782 | |
| 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 | 2022 Aug 01 | 35912854 | |
| 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 | 2022 Jul 27 | 35895854 | |
| 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 | 2022 Oct | 417-418 | 35881957 |
| 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 | 2022 07 22 | 35867799 | |
| 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 | 2022 Jul 14 | 35835881 | |
| 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 | 2022 Jul 04 | 35781769 | |
| Palo: Spatially-aware color palette optimization for single-cell and spatial data. | Hou, Wenpin; Ji, Zhicheng | Bioinformatics (Oxford, England) | 2022 Jun 01 | 35642896 | |
| 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 | 2023 Jan | 35599179 | |
| 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 | 2022 Aug | 35500458 | |
| 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 | 2022 | 35462999 | |
| 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 | 2022 04 14 | 35456020 | |
| Interactive single-cell data analysis using Cellar. | Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, Ziv | Nature communications | 2022 04 14 | 35422041 | |
| 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 | 2022 Mar 30 | 35378748 | |
| 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 | 2022 Apr 01 | 35363946 | |
| 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 | 2022 Mar 05 | 35247283 | |
| 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 | 2022 May | 35238734 | |
| 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) | 2022 Feb 21 | 35188184 | |
| 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 | 2022 05 | 35183510 | |
| Telomere dysfunction in ageing and age-related diseases. | Rossiello, Francesca; Jurk, Diana; Passos, João F; d'Adda di Fagagna, Fabrizio | Nature cell biology | 2022 02 | 35165420 | |
| Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease. | Journal of proteome research | 2022 Feb 04 | 35114789 | ||
| Temporal modelling using single-cell transcriptomics. | Ding, Jun; Sharon, Nadav; Bar-Joseph, Ziv | Nature reviews. Genetics | 2022 06 | 35102309 | |
| Counting protein molecules for single-cell proteomics. | Slavov, Nikolai | Cell | 2022 Jan 20 | 35063071 | |
| Cellular senescence: all roads lead to mitochondria. | Martini, Hélène; Passos, João F | The FEBS journal | 2022 Jan 20 | 35048548 | |
| Dysregulation of mitochondrial complexes and dynamics by chronic cigarette smoke exposure Utilizing MitoQC reporter mice. | Mitochondrion | 2022 Jan 13 | 35032706 | ||
| Senolytic drugs: Beyond the promise and the hype. | Jurk, Diana; Passos, João F | Mechanisms of ageing and development | 2022 Mar | 35032547 | |
| Learning from natural variation across the proteomes of single cells. | Slavov, Nikolai | PLoS biology | 2022 01 | 34986167 | |
| 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 | 2021 Dec 16 | 34916628 | |
| Scaling up single-cell proteomics. | Slavov, Nikolai | Molecular & cellular proteomics : MCP | 2021 Nov 19 | 34808355 | |
| 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 | 2021 Dec | 34758157 | |
| Comprehensive Identification of Regulatory Protein Networks. | Khoury, Luke; Slavov, Nikolai | Journal of proteome research | 2021 Nov 05 | 34736325 | |
| 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 | 2021 Dec | 34716448 | |
| 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 | 2021 10 28 | 34715021 | |
| Clustering Spatial Transcriptomics Data. | Teng, Haotian; Yuan, Ye; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 2021 Oct 08 | 34623423 | |
| Driving Single Cell Proteomics Forward with Innovation. | Slavov, Nikolai | Journal of proteome research | 2021 Oct 01 | 34597050 | |
| 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 | 2021 May 03 | 34063608 | |
| 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 | 2021 03 | 33654293 | |
| SIRT1 - a new mammalian substrate of nuclear autophagy. | Wang, Lu; Xu, Caiyue; Johansen, Terje; Berger, Shelley L; Dou, Zhixun | Autophagy | 2021 02 | 33292048 | |
| Identifying signaling genes in spatial single-cell expression data. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 2021 05 17 | 32886099 |