Cellular Senescence Network (SenNet) (41)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Targeting Cellular Senescence with Senotherapeutics: Development of New Approaches for Skin Care.Thompson, Elizabeth L; Pitcher, Louise E; Niedernhofer, Laura J; Robbins, Paul DPlastic and reconstructive surgery2022 10 0136170431
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 KNature aging2022 Jul36147777
An evaluation of RNA-seq differential analysis methods.Li, Dongmei; Zand, Martin S; Dye, Timothy D; Goniewicz, Maciej L; Rahman, Irfan; Xie, ZidianPloS one202236112652
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, RongNature2022 0935978191
Epigenetics, DNA damage, and aging.Soto-Palma, Carolina; Niedernhofer, Laura J; Faulk, Christopher D; Dong, XiaoThe Journal of clinical investigation2022 08 1535968782
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, YiThe Journal of clinical investigation2022 Aug 0135912854
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, DongjunBiometrics2022 Jul 2735895854
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; BrysoScience immunology2022 07 2235867799
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, NikolaiNature biotechnology2022 Jul 1435835881
Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing.Rivera-Mulia, Juan Carlos; Trevilla-Garcia, Claudia; Martinez-Cifuentes, SantiagoChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology2022 Jul 0435781769
Palo: Spatially-aware color palette optimization for single-cell and spatial data.Hou, Wenpin; Ji, ZhichengBioinformatics (Oxford, England)2022 Jun 0135642896
Deep unsupervised feature selection by discarding nuisance and correlated features.Shaham, Uri; Lindenbaum, Ofir; Svirsky, Jonathan; Kluger, YuvalNeural networks : the official journal of the International Neural Network Society2022 Aug35500458
Editorial: Defining and Characterizing Respiratory Disease in an Aging Population.Krick, Stefanie; Geraghty, Patrick; Jourdan Le Saux, Claude; Rojas, Mauricio; Staab-Weijnitz, Claudia AFrontiers in medicine202235462999
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 ACells2022 04 1435456020
Interactive single-cell data analysis using Cellar.Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, ZivNature communications2022 04 1435422041
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, DavidResearch square2022 Mar 3035378748
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, SundeepAging cell2022 Apr 0135363946
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 JJournal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research2022 Mar 0535247283
Romulus and Remus of Inflammation: The Conflicting Roles of MAP2K1 and MAP2K2 in Acute Respiratory Distress Syndrome.Sarkar, Anasuya; Chamucero-Millares, Julián A; Rojas, MauricioAmerican journal of respiratory cell and molecular biology2022 May35238734
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, RichardBioinformatics (Oxford, England)2022 Feb 2135188184
Biomechanical Force and Cellular Stiffness in Lung Fibrosis.Nho, Richard S; Ballinger, Megan N; Rojas, Mauricio M; Ghadiali, Samir N; Horowitz, Jeffrey CThe American journal of pathology2022 0535183510
Telomere dysfunction in ageing and age-related diseases.Rossiello, Francesca; Jurk, Diana; Passos, João F; d'Adda di Fagagna, FabrizioNature cell biology2022 0235165420
Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease.Journal of proteome research2022 Feb 0435114789
Temporal modelling using single-cell transcriptomics.Ding, Jun; Sharon, Nadav; Bar-Joseph, ZivNature reviews. Genetics2022 0635102309
Counting protein molecules for single-cell proteomics.Slavov, NikolaiCell2022 Jan 2035063071
Cellular senescence: all roads lead to mitochondria.Martini, Hélène; Passos, João FThe FEBS journal2022 Jan 2035048548
Dysregulation of mitochondrial complexes and dynamics by chronic cigarette smoke exposure Utilizing MitoQC reporter mice.Mitochondrion2022 Jan 1335032706
Senolytic drugs: Beyond the promise and the hype.Jurk, Diana; Passos, João FMechanisms of ageing and development2022 Mar35032547
Learning from natural variation across the proteomes of single cells.Slavov, NikolaiPLoS biology2022 0134986167
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 CarlosCell death and differentiation2021 Dec 1634916628
Scaling up single-cell proteomics.Slavov, NikolaiMolecular & cellular proteomics : MCP2021 Nov 1934808355
The role of mitochondria in cellular senescence.Ghosh-Choudhary, Shohini K; Liu, Jie; Finkel, TorenFASEB journal : official publication of the Federation of American Societies for Experimental Biology2021 Dec34758157
Comprehensive Identification of Regulatory Protein Networks.Khoury, Luke; Slavov, NikolaiJournal of proteome research2021 Nov 0534736325
Multiplexed single-cell proteomics using SCoPE2.Petelski, Aleksandra A; Emmott, Edward; Leduc, Andrew; Huffman, R Gray; Specht, Harrison; Perlman, David H; Slavov, NikolaiNature protocols2021 Dec34716448
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 DCell2021 10 2834715021
Clustering Spatial Transcriptomics Data.Teng, Haotian; Yuan, Ye; Bar-Joseph, ZivBioinformatics (Oxford, England)2021 Oct 0834623423
Driving Single Cell Proteomics Forward with Innovation.Slavov, NikolaiJournal of proteome research2021 Oct 0134597050
p16-3MR: A Novel Model to Study Cellular Senescence in Cigarette Smoke-Induced Lung Injuries.Kaur, Gagandeep; Sundar, Isaac K; Rahman, IrfanInternational journal of molecular sciences2021 May 0334063608
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 NetworkNature medicine2021 0333654293
SIRT1 - a new mammalian substrate of nuclear autophagy.Wang, Lu; Xu, Caiyue; Johansen, Terje; Berger, Shelley L; Dou, ZhixunAutophagy2021 0233292048
Identifying signaling genes in spatial single-cell expression data.Li, Dongshunyi; Ding, Jun; Bar-Joseph, ZivBioinformatics (Oxford, England)2021 05 1732886099