Program Publications
Program Publications
Publications Search by Program
Search Results
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| 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 |
