Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: AUCell
https://packages.ecosyste.ms/registries/bioconductor.org/packages/AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
1 version
Latest release: about 1 year ago
3 dependent packages
101,992 downloads total
Papers Mentioning AUCell 45
10.15252/msb.20209438
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomicsCited by: 49
Author(s): Carmen Bravo González-Blas, Xiao‐Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime De Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Software Mentions: 19
Published: over 4 years ago
10.1016/j.cell.2020.12.016
Spatiotemporal analysis of human intestinal development at single-cell resolutionCited by: 215
Author(s): David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren J. Fowler, Edward Morrissey, Christine M. Cunningham, Johnson Prv., Hashem Koohy, Alison Simmons
Software Mentions: 18
Published: almost 4 years ago
10.3389/fgene.2021.689406
Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA SequencingCited by: 26
Author(s): Júber Herrera-Uribe, Jayne E Wiarda, Sathesh K Sivasankaran, Lance Daharsh, Haibo Li, Kristen A Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 14
Published: over 3 years ago
10.1038/s41422-020-00453-x
Establishment of intestinal organoid cultures modeling injury-associated epithelial regenerationCited by: 39
Author(s): Molong Qu, Liang Xiong, Yulin Lyu, Xiannian Zhang, Jie Shen, Jingyang Guan, Peiyuan Chai, Lin Zheng, Boyao Nie, Cheng Li, Jun Xu, Hongkui Deng
Software Mentions: 13
Published: almost 4 years ago
10.1186/s13059-021-02293-3
Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cellsCited by: 47
Author(s): Drew Neavin, Quan Nguyen, Maciej Daniszewski, Helena Liang, Han Sheng Chiu, Yong Kiat Wee, Anne Senabouth, Samuel W. Lukowski, Duncan E. Crombie, Grace E. Lidgerwood, Damián Hernández, James C. Vickers, Anthony Cook, Nathan J. Palpant, Alice Pébay, Alex W. Hewitt, Joseph E. Powell
Software Mentions: 12
Published: over 3 years ago
10.1016/j.celrep.2019.05.026
ZIC3 Controls the Transition from Naive to Primed PluripotencyCited by: 41
Author(s): Shen Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D. Sharrocks
Software Mentions: 11
Published: over 5 years ago
10.3390/cancers13122903
Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct CarcinomaCited by: 6
Author(s): Chiara Gargiuli, Pierangela Sepe, Anna Tessari, Tyler Sheetz, Maurizio Colecchia, F.G.M. De Braud, Giuseppe Procopio, Marialuisa Sensi, Elena Verzoni, Matteo Dugo
Software Mentions: 11
Published: over 3 years ago
10.1038/s41421-021-00314-w
Single-cell RNA-Seq reveals transcriptional heterogeneity and immune subtypes associated with disease activity in human myasthenia gravisCited by: 12
Author(s): Jin Wu, Qi Yang, Yuyao Peng, Chengkai Yan, Yi Li, Zhaohui Luo, Bo Xiao, Liqun Xu, Huan Yang
Software Mentions: 11
Published: about 3 years ago
10.1038/s41422-021-00467-z
Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analysesCited by: 44
Author(s): Jian He, Yan Jing, Jianfang Wang, Liangyu Zhao, Xin Qian, Yang Zeng, Yuxi Sun, Han Zhang, Zhijie Bai, Zongcheng Li, Yanli Ni, Yandong Gong, Yunqiao Li, Han He, Zhilei Bian, Yu Lan, Chunyu Ma, Lihong Bian, Heng Zhu, Bing Liu, Rui Yue
Software Mentions: 10
Published: almost 4 years ago
10.1186/s12915-019-0709-6
Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitmentCited by: 31
Author(s): Hang Ruan, Yingnan Liao, Zongna Ren, Lin Mao, Fang Yao, Yu Peng, Youqiong Ye, Zhao Zhang, Shengli Li, Hanshi Xu, Jiewei Liu, Lixia Diao, Bingying Zhou, Leng Han, Li Wang
Software Mentions: 10
Published: about 5 years ago
10.26508/lsa.202000658
Predicting gene regulatory networks from cell atlasesCited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: about 4 years ago
10.1016/j.molcel.2020.04.008
Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific TargetsCited by: 101
Author(s): Bethan Psaila, Guanlin Wang, Alba Rodríguez-Meira, Rong Li, Elisabeth F. Heuston, Lauren C. Murphy, Daniel Yee, Ian S. Hitchcock, Nikolaos Sousos, Jennifer O’Sullivan, Stacie M. Anderson, Yotis A. Senis, Olga K. Weinberg, Monica L. Calicchio, Deena Iskander, Daniel Royston, Dragana Milojković, Irene Roberts, David M. Bodine, Supat Thongjuea, Adam J. Mead
Software Mentions: 9
Published: over 4 years ago
10.1016/j.celrep.2021.109698
Transitions in lineage specification and gene regulatory networks in hematopoietic stem/progenitor cells over human developmentCited by: 33
Author(s): Anindita Roy, Guanlin Wang, Deena Iskander, Sorcha O’Byrne, Natalina E. Elliott, Jennifer O’Sullivan, Gemma Buck, Elisabeth F. Heuston, Wei Wen, Alba Rodríguez-Meira, Peng Hua, Anastasios Karadimitris, Adam J. Mead, David M. Bodine, Irene Roberts, Bethan Psaila, Supat Thongjuea
Software Mentions: 9
Published: about 3 years ago
10.1016/j.celrep.2021.109118
Resident memory T cells in tumor-distant tissues fortify against metastasis formationCited by: 14
Author(s): Laura S. Christian, Liuyang Wang, Bryan Jian Wei Lim, Dachuan Deng, Haiyang Wu, Xiaofan Wang, Qi-Jing Li
Software Mentions: 8
Published: over 3 years ago
10.3389/fcell.2021.677697
Single-Cell RNA-Sequencing Portraying Functional Diversity and Clinical Implications of IFI6 in Ovarian CancerCited by: 7
Author(s): Hongyu Zhao, Zhefeng Li, Yan Gao, Jie Li, Xiaoting Zhao, Wentao Yue
Software Mentions: 8
Published: about 3 years ago
10.1038/s41422-018-0053-3
Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysisCited by: 162
Author(s): Xiaoying Fan, Ji Dong, Shaobo Zhong, Wei Yuan, Qian Wu, Liying Yan, Jun Yong, Le Sun, Xiaoye Wang, Yangyu Zhao, Wei Wang, Jie Yan, Xiaoqun Wang, Jie Qiao, Fuchou Tang
Software Mentions: 8
Published: over 6 years ago
10.1016/j.immuni.2019.02.006
Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative ColitisCited by: 121
Author(s): Tomas Castro‐Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J M Monk, Kourosh Saeb‐Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy
Software Mentions: 8
Published: over 5 years ago
10.1002/ctm2.500
Single‐cell transcriptomes reveal heterogeneity of high‐grade serous ovarian carcinomaCited by: 29
Author(s): Qian Hao, Jiajia Li, Qinghua Zhang, Fei Xu, Bangxiang Xie, Hua Lu, Xiaohua Wu, Xiang Zhou
Software Mentions: 7
Published: over 3 years ago
10.3390/cells10050973
Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA SequencingCited by: 5
Author(s): Shaojian Gao, Zhijie Wu, Jeerthi Kannan, Liza Mathews, Xingmin Feng, Sachiko Kajigaya, Neal S. Young
Software Mentions: 7
Published: over 3 years ago
10.1038/s41419-021-04067-y
Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: over 3 years ago
10.7150/thno.58433
Single-cell transcriptomic profiling provides insights into the toxic effects of Zearalenone exposure on primordial follicle assemblyCited by: 20
Author(s): Yu Tian, Mingyu Zhang, Ai-Hong Zhao, Li Kong, Junjie Wang, Wei Shen, Lan Li
Software Mentions: 6
Published: almost 4 years ago
10.1038/s41421-020-00200-x
Single-cell transcriptome atlas of lung adenocarcinoma featured with ground glass nodulesCited by: 45
Author(s): Tao Lu, Xiaodong Yang, Yu Shi, Mengnan Zhao, Guoshu Bi, Jiaqi Liang, Zhencong Chen, Yiwei Huang, Wei Jiang, Lin Zhang, Junjie Xi, Shuai Wang, Yong Yang, Cheng Zhan, Qun Wang, Liang Tan
Software Mentions: 6
Published: about 4 years ago
10.1038/s41422-020-00455-9
Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavagesCited by: 203
Author(s): Els Wauters, Pierre Van Mol, Abhishek D. Garg, S.L. Jansen, Yannick Van Herck, Lore Vanderbeke, Ayse Bassez, Bram Boeckx, Bert Malengier‐Devlies, Anna Timmerman, Thomas Van Brussel, Tina Van Buyten, Rogier Schepers, Elisabeth Heylen, Dieter Dauwe, Christophe Dooms, Jan Gunst, Greet Hermans, Philippe Meersseman, Dries Testelmans, Jonas Yserbyt, Sabine Tejpar, Walter De Wever, Patrick Matthys, Maria Bosisio, Michaël P Casaer, Frederik De Smet, Paul De Munter, Stéphanie Humblet-Baron, Adrian Liston, Natalie Lorent, Kim Martinod, Paul Proost, Jeroen Raes, Karin Thevissen, Robin Vos, Birgit Weynand, Carine Wouters, Johan Neyts, Joost Wauters, Junbin Qian, Diether Lambrechts
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13059-020-1949-z
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq dataCited by: 173
Author(s): Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan Gleixner, Manu P. Kumar, Elisabetta Mereu, Brian A. Joughin, Oliver Stegle, Douglas A. Lauffenburger, Holger Heyn, Bence Szalai, Julio Sáez-Rodríguez
Software Mentions: 6
Published: almost 5 years ago
10.7150/thno.54917
Single-cell transcriptome profiling reveals vascular endothelial cell heterogeneity in human skinCited by: 36
Author(s): Qingyang Li, Zhenlai Zhu, Lei Wang, Yi‐Ting Lin, Hui Fang, Jie Lei, Tianyu Cao, Gang Wang, Erle Dang
Software Mentions: 6
Published: almost 4 years ago
10.7150/ijbs.46645
Identification of a novel cancer stem cell subpopulation that promotes progression of human fatal renal cell carcinoma by single-cell RNA-seq analysisCited by: 25
Author(s): Xiuwu Pan, Hao Zhang, Da Xu, Jiaxin Chen, Wen-jin Chen, Sishun Gan, Fajun Qu, Chuanmin Chu, Jun Cao, Yong Fan, Shumin Xu, Jianqing Ye, Zhou Wang, Xingang Cui
Software Mentions: 6
Published: almost 5 years ago
10.1186/s13619-020-00042-8
Mapping a mammalian adult adrenal gland hierarchy across species by microwell-seqCited by: 7
Author(s): Shih–Wei Lai, Lifeng Ma, E Weigao, Fang Ye, Haide Chen, Xiaoping Han, Guoji Guo
Software Mentions: 5
Published: over 4 years ago
10.7554/eLife.60225
RUNX1 marks a luminal castration-resistant lineage established at the onset of prostate developmentCited by: 28
Author(s): Renaud Mével, Ivana Steiner, Susan Mason, Laura C.A. Galbraith, Rahima Patel, Muhammad Zaki Hidayatullah Fadlullah, Imran Ahmad, Hing Y. Leung, Pedro Oliveira, Karen Blyth, Esther Baena, Georges Lacaud
Software Mentions: 5
Published: about 4 years ago
10.1016/j.medj.2021.01.006
Identifying CNS-colonizing T cells as potential therapeutic targets to prevent progression of multiple sclerosisCited by: 39
Author(s): Max Kaufmann, Hayley G. Evans, Anna-Lena Schaupp, Jan Broder Engler, Gurman Kaur, Anne Willing, Nina Kursawe, Charlotte Schubert, Kathrine E. Attfield, Lars Fugger, Manuel A. Friese
Software Mentions: 5
Published: over 3 years ago
10.3390/cells10082143
Single-Cell Transcriptomics Reveals Core Regulatory Programs That Determine the Heterogeneity of Circulating and Tissue-Resident Memory CD8+ T CellsCited by: 12
Author(s): Yao Chen, Jian Shen, Moujtaba Y. Kasmani, Paytsar Topchyan, Weiguo Cui
Software Mentions: 5
Published: over 3 years ago
10.1038/s41419-021-03740-6
Single-cell analysis reveals urothelial cell heterogeneity and regenerative cues following cyclophosphamide-induced bladder injuryCited by: 12
Author(s): Xiaomu Cheng, Huadong Lai, Wenqin Luo, Man Zhang, Juju Miao, Weichen Song, Shunpeng Xing, Jia Wang, Wei‐Qiang Gao
Software Mentions: 5
Published: over 3 years ago
10.3389/fcvm.2020.615161
Comprehensive Integration of Single-Cell Transcriptional Profiling Reveals the Heterogeneities of Non-cardiomyocytes in Healthy and Ischemic HeartsCited by: 21
Author(s): Lingfang Zhuang, Lin Lü, Ruiyan Zhang, Kang Chen, Xiaoxiang Yan
Software Mentions: 5
Published: almost 4 years ago
10.1016/j.isci.2021.102402
Absence of Batf3 reveals a new dimension of cell state heterogeneity within conventional dendritic cellsCited by: 14
Author(s): Samuel W. Lukowski, Inga Rødahl, S. Thomas Kelly, Meihua Yu, James Gotley, Chenhao Zhou, Susan Millard, Stacey Andersen, Angelika N. Christ, Gabrielle T. Belz, Ian H. Frazer, Janin Chandra
Software Mentions: 5
Published: over 3 years ago
10.1186/s13073-021-00933-8
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19Cited by: 71
Author(s): John F. Fullard, Hao-Chih Lee, Georgios Voloudakis, Shengbao Suo, Behnam Javidfar, Zhiping Shao, Cyril J. Peter, Wen Zhang, Shan Jiang, André Corvelo, Heather Wargnier, Emma Woodoff-Leith, Dushyant P. Purohit, Sadhna Ahuja, Nadejda M. Tsankova, Nathalie Jetté, Gabriel E. Hoffman, Schahram Akbarian, Mary Fowkes, John F. Crary, Guo‐Cheng Yuan, Panos Roussos
Software Mentions: 4
Published: over 3 years ago
10.3389/fimmu.2021.623430
Multi-Modal Characterization of Monocytes in Idiopathic Pulmonary Fibrosis Reveals a Primed Type I Interferon Immune PhenotypeCited by: 28
Author(s): Emily Fraser, Laura Denney, Agne Antanaviciute, Karl Blirando, Chaitanya Vuppusetty, Yuejuan Zheng, Emmanouela Repapi, Valentina Iotchkova, Stephen Taylor, Neil Ashley, Victoria St Noble, Rachel Benamore, Rachel Hoyles, Colin Clelland, Joseph M. Rastrick, Clare S. Hardman, Nasullah Khalid Alham, Rachel E. Rigby, Alison Simmons, Jan Rehwinkel, Ling-Pei Ho
Software Mentions: 4
Published: over 3 years ago
10.7554/eLife.67436
Single-cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenesisCited by: 48
Author(s): Arantxa Cebrián-Silla, Marcos Assis Nascimento, Stephanie Redmond, Benjamin Mansky, David Wu, Kirsten Obernier, Ricardo Romero Rodriguez, Susana González-Granero, José Manuel García‐Verdugo, Daniel A. Lim, Arturo Álvarez-Buylla
Software Mentions: 4
Published: over 3 years ago
10.1172/jci.insight.141024
Single-cell omics analysis reveals functional diversification of hepatocytes during liver regenerationCited by: 34
Author(s): Tianyi Chen, Seh–Hoon Oh, Simon Gregory, Xiling Shen, Anna Mae Diehl
Software Mentions: 4
Published: about 4 years ago
10.1111/cpr.13007
Single‐cell transcriptomes of mouse bladder urothelium uncover novel cell type markers and urothelial differentiation characteristicsCited by: 10
Author(s): Yan Li, Yaxiao Liu, Zhengdong Gao, Lekai Zhang, Lipeng Chen, Zonglong Wu, Qinggang Liu, Shuai Wang, Nan Zhou, Toby C. Chai, Benkang Shi
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13024-021-00443-6
The CD33 short isoform is a gain-of-function variant that enhances Aβ1–42 phagocytosis in microgliaCited by: 41
Author(s): Abhishek Bhattacherjee, J. Jung, Sameera Zia, Madelene F. S. Ho, Ghazaleh Eskandari‐Sedighi, Chris D. St. Laurent, Kelli A. McCord, Arjun Bains, Gaurav Sidhu, Susmita Sarkar, Jason R. Plemel, Matthew Macauley
Software Mentions: 3
Published: over 3 years ago
10.3389/fpls.2018.01770
Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome DatasetsCited by: 45
Author(s): Keiichi Mochida, Satoru Koda, Komaki Inoue, Ryuei Nishii
Software Mentions: 3
Published: almost 6 years ago
10.1016/j.celrep.2018.11.034
Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born NeuronsCited by: 96
Author(s): Burak Tepe, Matthew C. Hill, Brandon Pekarek, Patrick J. Hunt, Thomas J. Martin, James F. Martin, Benjamin R. Arenkiel
Software Mentions: 3
Published: almost 6 years ago
10.1016/j.csbj.2021.06.043
UCell: Robust and scalable single-cell gene signature scoringCited by: 158
Author(s): Massimo Andreatta, Santiago J. Carmona
Software Mentions: 2
Published: almost 4 years ago
10.1073/pnas.2000943117
Macrophage metabolic reprogramming presents a therapeutic target in lupus nephritisCited by: 70
Author(s): Chenzhi Jing, Tomas Castro‐Dopico, Nathan Richoz, Zewen Kelvin Tuong, John R. Ferdinand, Laurence S.C. Lok, Kevin Loudon, Gemma D. Banham, Rebeccah J. Mathews, M Zaeem Cader, Susan F. Fitzpatrick, Kathleen R. Bashant, Mariana J. Kaplan, Arthur Kaser, Randall S. Johnson, Michael P. Murphy, Richard M. Siegel, Menna R. Clatworthy
Software Mentions: 2
Published: over 4 years ago
10.1186/s12920-020-0688-z
Highly robust model of transcription regulator activity predicts breast cancer overall survivalCited by: 3
Author(s): Chuanpeng Dong, Jiannan Liu, Steven Chen, Tianhan Dong, Guanglong Jiang, Yue Wang, Huanmei Wu, Jill L. Reiter, Yunlong Liu
Software Mentions: 2
Published: over 4 years ago
10.3389/fendo.2020.00259
Macrophage Subsets in Obesity, Aligning the Liver and Adipose TissueCited by: 31
Author(s): Anneleen Remmerie, Liesbet Martens, Charlotte Scott
Software Mentions: 1
Published: over 4 years ago