Skip to main content
SenNet logo.

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
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
Single-cell proteomics: quantifying post-transcriptional regulation during development with mass-spectrometry. Slavov, Nikolai Development (Cambridge, England) 37387573 2023 Jul 01
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
Spatial Single-Cell Technologies for Exploring Gastrointestinal Tissue Transcriptome. Kang, Hyun Min; Lee, Jun Hee Comprehensive Physiology 37358516 2023 Jun 26
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
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
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
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
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
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
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
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
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
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
Integrating multiple single-cell multi-omics samples with Smmit. Wan, Changxin; Ji, Zhicheng bioRxiv : the preprint server for biology 37066420 2023 Apr 06
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
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
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
Predicting mutational function using machine learning. Shea, Anthony; Bartz, Josh; Zhang, Lei; Dong, Xiao Mutation research. Reviews in mutation research 36965820 2023
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. SenNet Consortium Nature aging 36936385 2022 Dec
DNA damage-induced stalling of transcription drives aging through gene expression imbalance. Sims, Austin A; Gurkar, Aditi U DNA repair 36921370 2023 May
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
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
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
Senolytic vaccination: a new mandate for cardiovascular health? Lear, Travis B; Finkel, Toren The journal of cardiovascular aging 36819765 2022 Apr
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
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
Using single cell atlas data to reconstruct regulatory networks. Song, Qi; Ruffalo, Matthew; Bar-Joseph, Ziv Nucleic acids research 36762475 2023 Apr 24
Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA. Derks, Jason; Slavov, Nikolai Journal of proteome research 36735898 2023 Mar 03
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
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
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Chidester, Benjamin; Zhou, Tianming; Alam, Shahul; Ma, Jian Nature genetics 36624346 2023 Jan
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
A phosphoinositide signalling pathway mediates rapid lysosomal repair. Tan, Jay Xiaojun; Finkel, Toren Nature 36071159 2022 Sep
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 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
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
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
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
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
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
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
scSTEM: clustering pseudotime ordered single-cell data. Song, Qi; Wang, Jingtao; Bar-Joseph, Ziv Genome biology 35799304 2022 07 07
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
Unsupervised cell functional annotation for single-cell RNA-seq. Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv Genome research 35764397 2022 Jun 28
Palo: Spatially-aware color palette optimization for single-cell and spatial data. Hou, Wenpin; Ji, Zhicheng Bioinformatics (Oxford, England) 35642896 2022 Jun 01
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
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
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
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
Interactive single-cell data analysis using Cellar. Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, Ziv Nature communications 35422041 2022 04 14
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
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
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
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
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
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
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
Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease. Journal of proteome research 35114789 2022 Feb 04
Temporal modelling using single-cell transcriptomics. Ding, Jun; Sharon, Nadav; Bar-Joseph, Ziv Nature reviews. Genetics 35102309 2022 06
Counting protein molecules for single-cell proteomics. Slavov, Nikolai Cell 35063071 2022 Jan 20
Cellular senescence: all roads lead to mitochondria. Martini, Hélène; Passos, João F The FEBS journal 35048548 2022 Jan 20
Dysregulation of mitochondrial complexes and dynamics by chronic cigarette smoke exposure Utilizing MitoQC reporter mice. Mitochondrion 35032706 2022 Jan 13
Senolytic drugs: Beyond the promise and the hype. Jurk, Diana; Passos, João F Mechanisms of ageing and development 35032547 2022 Mar
Learning from natural variation across the proteomes of single cells. Slavov, Nikolai PLoS biology 34986167 2022 01
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
Scaling up single-cell proteomics. Slavov, Nikolai Molecular & cellular proteomics : MCP 34808355 2021 Nov 19
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
Comprehensive Identification of Regulatory Protein Networks. Khoury, Luke; Slavov, Nikolai Journal of proteome research 34736325 2021 Nov 05
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
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
Clustering Spatial Transcriptomics Data. Teng, Haotian; Yuan, Ye; Bar-Joseph, Ziv Bioinformatics (Oxford, England) 34623423 2021 Oct 08
Driving Single Cell Proteomics Forward with Innovation. Slavov, Nikolai Journal of proteome research 34597050 2021 Oct 01
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
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
SIRT1 - a new mammalian substrate of nuclear autophagy. Wang, Lu; Xu, Caiyue; Johansen, Terje; Berger, Shelley L; Dou, Zhixun Autophagy 33292048 2021 02
Identifying signaling genes in spatial single-cell expression data. Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv Bioinformatics (Oxford, England) 32886099 2021 05 17

This page last reviewed on September 20, 2023