cran: cellranger | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0251194

A computational reproducibility study of PLOS ONE articles featuring longitudinal data analyses
Cited by: 15
Author(s): Heidi Seibold, Severin Czerny, Siona Decke, Roman Dieterle, Thomas Eder, Steffen Fohr, Nico Hahn, Rabea Hartmann, Christoph Heindl, Philipp Kopper, Dario Lepke, Verena Loidl, Maximilian Mandl, Sarah Musiol, Jessica Peter, Alexander Piehler, Elio Rojas, Stefanie Schmid, Hannah Schmidt, Melissa Schmoll, Lennart Schneider, Xiao-Yin To, Viêt Anh Tran, Antje Völker, Moritz Wagner, Joshua Wagner, Maria Waize, Hannah Wecker, Rui Yang, Simone Zellner, Malte Nalenz
Software Mentions: 46
Published: over 3 years ago

10.7554/eLife.51254

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
Cited by: 102
Author(s): Christopher Jackson, Dayanne M. Castro, Giuseppe-Antonio Saldi, Richard Bonneau, David Gresham
Software Mentions: 20
Published: almost 5 years ago

10.3390/cancers12040948

Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility
Cited by: 23
Author(s): Henry E. Miller, Aparna Gorthi, Nicklas Bassani, Liesl A. Lawrence, Brian S. Iskra, Alexander J.R. Bishop
Software Mentions: 19
Published: over 4 years ago

10.15252/msb.20209438

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
Cited 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.2021.04.048

Integrated analysis of multimodal single-cell data
Cited by: 4,423
Author(s): Yuhan Hao, Stephanie Hao, Erica Andersen‐Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Madeline Lee, Aaron J. Wilk, Charlotte A. Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, T.A. Stuart, Lamar M. Fleming, Bertrand Z. Yeung, Angela J. Rogers, Juliana McElrath, Catherine A. Blish, Raphaël Gottardo, Peter Smibert, Rahul Satija
Software Mentions: 13
Published: over 3 years ago

10.1038/s41422-020-00453-x

Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration
Cited 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 cells
Cited 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

10.7554/eLife.36187

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Cited by: 167
Author(s): Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 10
Published: about 6 years ago

10.1016/j.celrep.2020.108661

Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets
Cited by: 47
Author(s): Michael Fitzpatrick, Nicholas M. Provine, Lucy C. Garner, Kate Powell, Ali Amini, Sophie Irwin, Helen Ferry, Tim Ambrose, Peter J. Friend, Georgios Vrakas, Srikanth Reddy, Elizabeth Soilleux, Paul Klenerman, Philip Allan
Software Mentions: 9
Published: almost 4 years ago

10.20900/immunometab20210022

Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models
Cited by: 21
Author(s): Austin C. Conklin, Hitoo Nishi, Florencia Schlamp, Tiit Örd, Kadri Õunap, Minna U. Kaikkonen, Edward A. Fisher, Casey E. Romanoski
Software Mentions: 9
Published: over 3 years ago

10.12688/f1000research.22731.2

Fast analysis of scATAC-seq data using a predefined set of genomic regions
Cited by: 10
Author(s): Valentina Giansanti, Ming Tang, Davide Cittaro
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.65654

Quantitative control of noise in mammalian gene expression by dynamic histone regulation
Cited by: 2
Author(s): Tan D, Rui Chen, Yuejian Mo, Shu Gu, Jiao Ma, Wei Xu, Xibin Lu, Hongtao He, Fan Jiang, Weimin Fan, Yili Wang, Xi Chen, Wei Huang
Software Mentions: 8
Published: over 3 years ago

10.15252/msb.202010060

CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing
Cited by: 11
Author(s): Liang Fang, Guipeng Li, Zhiyuan Sun, Qionghua Zhu, Huanhuan Cui, Yunfei Li, Jingwen Zhang, Weizheng Liang, Wencheng Wei, Yuhui Hu, Wei Chen
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.69065

Cross-species analysis defines the conservation of anatomically segregated VMH neuron populations
Cited by: 16
Author(s): Alison H. Affinati, Paul V. Sabatini, Cadence True, Abigail J. Tomlinson, Melissa A. Kirigiti, Sarah R. Lindsley, Chien Li, David P. Olson, Paul Kievit, Martin G. Myers, Alan C. Rupp
Software Mentions: 8
Published: over 3 years ago

10.1126/sciadv.abd3311

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell
Cited by: 64
Author(s): Gerda Kildisiute, Waleed M. Kholosy, Matthew D. Young, Kenny Roberts, Rasa Elmentaite, Sander R. van Hooff, Clarissa N Pacyna, Eleonora Khabirova, Alice Piapi, Christine Thevanesan, Eva Bugallo-Blanco, Christina Burke, Lira Mamanova, KM Keller, Karin Langenberg-Ververgaert, Philip Lijnzaad, Thanasis Margaritis, Frank C. P. Holstege, Michelle L. Tas, Marc H. W. A. Wijnen, Max M. van Noesel, Ignacio del Valle, Giuseppe Barone, Reinier van der Linden, Catriona Duncan, John Anderson, John C. Achermann, Muzlifah Haniffa, Sarah A. Teichmann, Dyanne Rampling, Neil J. Sebire, Xiaoling He, Ronald R. de Krijger, Roger A. Barker, Kerstin B. Meyer, Ömer Bayraktar, Karin Straathof, Jan J. Molenaar, Sam Behjati
Software Mentions: 8
Published: almost 4 years ago

10.1016/j.celrep.2021.109118

Resident memory T cells in tumor-distant tissues fortify against metastasis formation
Cited 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

10.15252/embj.2020106423

Activation of endogenous retroviruses during brain development causes an inflammatory response
Cited by: 27
Author(s): Marie E. Jönsson, Raquel Garza, Yogita Sharma, Rebecca Petri, Erik Södersten, Jenny Johansson, Peter Johansson, Diahann A. M. Atacho, Karolina Pircs, Sofia Madsen, David Yudovich, Ramprasad Ramakrishnan, Johan Holmberg, Jonas Larsson, Patric Jern, Johan Jakobsson
Software Mentions: 8
Published: over 3 years ago

10.1186/s13059-019-1862-5

scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data
Cited by: 225
Author(s): José Alquicira-Hernández, Anuja Sathe, Hanlee P. Ji, Quan Nguyen, Joseph E. Powell
Software Mentions: 7
Published: almost 5 years ago

10.1016/j.ccell.2020.06.004

Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma
Cited by: 86
Author(s): Johannes Gojo, Bernhard Englinger, Li Jiang, Jens Martin Hübner, McKenzie Shaw, Olivia A. Hack, Sibylle Madlener, Dominik Kirchhofer, Ilon Liu, Jason W. Pyrdol, Volker Hovestadt, Emanuele Mazzola, Nathan D. Mathewson, Maria Trissal, Daniela Lötsch, Christian Dorfer, Christine Haberler, Angela Halfmann, Lisa Mayr, Andreas Peyrl, René Geyeregger, Benjamin Schwalm, Monica Mauermann, Kristian W. Pajtler, Till Milde, Marni E. Shore, Jack Geduldig, Kristine Pelton, Thomas Czech, Orr Ashenberg, Kai W. Wucherpfennig, Orit Rozenblatt-Rosen, Sanda Alexandrescu, Keith L. Ligon, Stefan M. Pfister, Aviv Regev, Irene Slavc, Walter Berger, Mario L. Suvà, Marcel Kool, Mariella G. Filbin
Software Mentions: 7
Published: over 4 years ago

10.3390/cancers13081934

Cannabinoid Receptor Type-2 in B Cells Is Associated with Tumor Immunity in Melanoma
Cited by: 3
Author(s): Thomas Gruber, Steve Robatel, Mirela Kremenovic, Lukas Bäriswyl, Jürg Gertsch, Mirjam Schenk
Software Mentions: 7
Published: over 3 years ago

10.1172/jci.insight.148035

Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells
Cited by: 7
Author(s): Ruoyi Jiang, Hailong Meng, Khadir Raddassi, Ira Fleming, Kenneth B. Hoehn, Kenneth R. Dardick, Alexia A. Belperron, Ruth R. Montgomery, Alex K. Shalek, David A. Hafler, Steven H. Kleinstein, Linda K. Bockenstedt
Software Mentions: 7
Published: over 3 years ago

10.1126/scitranslmed.abe9599

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro
Cited by: 57
Author(s): Miguel Reyes, Michael R. Filbin, Roby P. Bhattacharyya, Abraham Sonny, Arnav Mehta, Kianna Billman, Kyle R. Kays, Mayra Pinilla-Vera, Maura Benson, Lisa A. Cosimi, Deborah T. Hung, Bruce D. Levy, Alexandra Chloé Villani, Moshe Sade-Feldman, Rebecca M. Baron, Marcia B. Goldberg, Paul C. Blainey, Nir Hacohen
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.63632

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
Cited by: 119
Author(s): Elliott Swanson, Cara Lord, Julian Reading, Alexander T Heubeck, Palak C. Genge, Zachary Thomson, Morgan Weiss, Xiaojun Li, Adam K. Savage, Richard Green, Troy R. Torgerson, Thomas F. Bumol, Lucas T. Graybuck, Peter J. Skene
Software Mentions: 6
Published: over 3 years ago

10.1128/JVI.00500-19

Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity
Cited by: 81
Author(s): Alan D. Russell, Elizaveta Elshina, Jacob R. Kowalsky, Aartjan J.W. te Velthuis, Jesse D. Bloom
Software Mentions: 6
Published: over 5 years ago

10.3389/fcell.2021.653305

Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development
Cited by: 9
Author(s): Xiangmei Zhang, Igor Mandric, Kevin Nguyen, Thao T. T. Nguyen, Matteo Pellegrini, James C. R. Grove, Steven Barnes, Xian-Jie Yang
Software Mentions: 6
Published: over 3 years ago

10.3389/fimmu.2021.724015

Transcriptional, Epigenetic, and Functional Reprogramming of Monocytes From Non-Human Primates Following Chronic Alcohol Drinking
Cited by: 11
Author(s): Sloan A. Lewis, Suhas Sureshchandra, Brianna Doratt, Vanessa Jiménez, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: over 3 years ago

10.1016/j.cell.2020.05.039

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Cited by: 438
Author(s): Andrew L. Ji, Adam J. Rubin, Kim Thrane, Sizun Jiang, David L. Reynolds, Robin M. Meyers, Margaret Guo, Benson M. George, Annelie Mollbrink, Joseph Bergenstråhle, Ludvig Larsson, Yunhao Bai, Bokai Zhu, Aparna Bhaduri, Jordan M. Meyers, Xavier Rovira-Clavé, S. Tyler Hollmig, Sumaira Z. Aasi, Garry P. Nolan, Joakim Lundeberg, Paul A. Khavari
Software Mentions: 6
Published: over 4 years ago

10.1186/s13287-021-02354-1

Single-cell RNA sequencing of cultured human endometrial CD140b+CD146+ perivascular cells highlights the importance of in vivo microenvironment
Cited by: 11
Author(s): Dandan Cao, Rachel Chan, Ernest Hung Yu Ng, Kristina Gemzell‐Danielsson, William S.B. Yeung
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.59733

Activation of a neural stem cell transcriptional program in parenchymal astrocytes
Cited by: 41
Author(s): Jens P Magnusson, Margherita Zamboni, Giuseppe Santopolo, Jeff E. Mold, Mauricio Barrientos‐Somarribas, Carlos Talavera-López, Björn Andersson, Jonas Frisén
Software Mentions: 6
Published: over 4 years ago

10.1038/sdata.2018.192

Single-cell RNA sequencing of adult mouse testes
Cited by: 42
Author(s): Söeren Lukassen, Elisabeth Bosch, Arif B. Ekici, Andreas Winterpacht
Software Mentions: 6
Published: about 6 years ago

10.1186/s12864-021-07435-2

Blinatumomab-induced T cell activation at single cell transcriptome resolution
Cited by: 11
Author(s): Yi Huo, Zhonghua Sheng, Daniel Lu, Daniel C. Ellwanger, Chi-Ming Li, Oliver Homann, Songli Wang, Hong Mei Yin, Ruibao Ren
Software Mentions: 6
Published: over 3 years ago

10.15252/emmm.202114123

Mitogen‐activated protein kinase activity drives cell trajectories in colorectal cancer
Cited by: 33
Author(s): Florian Uhlitz, Philip Bischoff, Stefan Peidli, Anja Sieber, Alexandra Trinks, Mareen Lüthen, Benedikt Obermayer, Eric Blanc, Yana Ruchiy, Thomas Sell, Soulafa Mamlouk, Roberto Arsiè, Tzu-Ting Wei, Kathleen Klotz-Noack, Roland F. Schwarz, Birgit Sawitzki, Carsten Kamphues, Dieter Beule, Markus Landthaler, Christine Sers, David Horst, Nils Blüthgen, Markus Morkel
Software Mentions: 6
Published: over 3 years ago

10.1016/j.celrep.2020.03.063

A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level
Cited by: 71
Author(s): Florian Mair, Jami R. Erickson, Valentin Voillet, Yannick Simoni, Timothy Bi, Aaron J. Tyznik, Jody Martin, Raphaël Gottardo, Evan W. Newell, Martin Prlic
Software Mentions: 6
Published: over 4 years ago

10.1242/dev.183855

Aging induces aberrant state transition kinetics in murine muscle stem cells
Cited by: 50
Author(s): Jacob C. Kimmel, Ara B. Hwang, Annarita Scaramozza, Wallace F. Marshall, Andrew S. Brack
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pbio.3000435

Single-cell in vivo imaging of cellular circadian oscillators in zebrafish
Cited by: 13
Author(s): Haifang Wang, Zeyong Yang, Xingxing Li, Di Huang, Shuguang Yu, Jie He, Yuanhai Li, Jun Yan
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2021.711980

Characterization of Organ-Specific Regulatory B Cells Using Single-Cell RNA Sequencing
Cited by: 7
Author(s): Si Yu Yang, Jie Long, Meng Huang, Pan Luo, Zhen Bian, Ya Xu, Chengbo Wang, Shu Yang, Li Liang, Carlo Selmi, M. Eric Gershwin, Zhi Bin Zhao, Zhe Xiong Lian
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-018-24725-0

Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencing
Cited by: 68
Author(s): Söeren Lukassen, Elisabeth Bosch, Arif B. Ekici, Andreas Winterpacht
Software Mentions: 5
Published: over 6 years ago

10.1016/j.jtos.2021.03.010

A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells
Cited by: 84
Author(s): Joseph Collin, Rachel Queen, Darin Zerti, Sanja Bojić, Birthe Dorgau, Nicky Moyse, Marina Moya Molina, Chunbo Yang, Sunanda Dey, Gary Reynolds, Rafiqul Hussain, Jonathan Coxhead, Steven Lisgo, Deborah J. Henderson, Agatha Joseph, Paul Rooney, Saurabh Ghosh, Lucy Clarke, Che J. Connon, Muzlifah Haniffa, Francisco C Figueiredo, Lyle Armstrong, Majlinda Lako
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2021.625881

Epigenetic Landscapes of Single-Cell Chromatin Accessibility and Transcriptomic Immune Profiles of T Cells in COVID-19 Patients
Cited by: 28
Author(s): Shun Li, Bin Wu, Yun Ling, Mingquan Guo, Boyin Qin, Xu Ren, Chao Wang, Hua Yang, Lixiang Chen, Yixin Liao, Yang Liu, Xinjun Peng, Chunhua Xu, Zhenyan Wang, Yinzhong Shen, Jun Chen, Li Liu, Bowen Niu, Mengmin Zhu, Lingling Liu, Feng Li, Tongyu Zhu, Zhaoqin Zhu, Xiaohui Zhou, Hongzhou Lu
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-1928-4

scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens
Cited by: 35
Author(s): Lin Yang, Yuqing Zhu, Hua Yu, Xinhua Cheng, Sitong Chen, Yulan Chu, He Huang, Zhang Jin, Wei Li
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.cell.2021.05.020

Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota
Cited by: 68
Author(s): Djalma S. Lima-Júnior, Siddharth R. Krishnamurthy, Nicolas Bouladoux, Nicholas Collins, Seong-Ji Han, Erin Chen, Michael G. Constantinides, Verena M. Link, Ai Ing Lim, Michel Enamorado, Christophe Cataisson, Louis Gil, Indira Rao, Taylor K. Farley, G. I. Koroleva, Jan Attig, Stuart H. Yuspa, Michael A. Fischbach, George Kassiotis, Yasmine Belkaid
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-94186-5

Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties
Cited by: 6
Author(s): Sanshiro Kanazawa, H. Okada, Hironori Hojo, Shinsuke Ohba, Junichi Iwata, Makoto Komura, Atsuhiko Hikita
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-02006-2

Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets
Cited by: 29
Author(s): Brenda Marquina-Sanchez, Nikolaus Fortelny, Matthias Farlik, Andhira Vieira, Patrick Collombat, Christoph Bock, Stefan Kubicek
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2021.620386

CMV Status Drives Distinct Trajectories of CD4+ T Cell Differentiation
Cited by: 11
Author(s): Weiwen Zhang, Anna B. Morris, Erica V. Peek, Geeta Karadkhele, Jennifer Rosenstein, Haydn Kissick, Christian Larsen
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-02235-5

Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
Cited by: 36
Author(s): José Antonio Campoy, Hequan Sun, Manish Goel, Wen-Biao Jiao, Kat Folz-Donahue, Nan Wang, M. Rubio, Chang Liu, Christian Kukat, David Ruiz, Bruno Huettel, Korbinian Schneeberger
Software Mentions: 4
Published: almost 4 years ago

10.1038/s42003-021-01959-9

Genomic profiling reveals heterogeneous populations of ductal carcinoma in situ of the breast
Cited by: 31
Author(s): Satoi Nagasawa, Yuta Kuze, Ichiro Maeda, Yasuyuki Kojima, Ai Motoyoshi, Tatsuya Onishi, Tsuguo Iwatani, Takamichi Yokoe, Junki Koike, Motohiro Chosokabe, Manabu Kubota, Hibiki Seino, Ayako Suzuki, Masahide Seki, Katsuya Tsuchihara, Eisuke Inoue, Koichiro Tsugawa, Tomohiko Ohta, Yutaka Suzuki
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giaa151

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data
Cited by: 438
Author(s): Matthew D. Young, Sam Behjati
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.immuni.2018.07.004

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages
Cited by: 142
Author(s): Charlotte Scott, Wouter T’Jonck, Liesbet Martens, Helena Todorov, Dorine Sichien, Bieke Soen, Johnny Bonnardel, Sofie De Prijck, Niels Vandamme, Robrecht Cannoodt, Wouter Saelens, Bavo Vanneste, Wendy Toussaint, Pieter De Bleser, Nozomi Takahashi, Peter Vandenabeele, Sandrine Henri, Clare Pridans, David Hume, Bart N. Lambrecht, Patrick De Baetseĺier, Simon Milling, Jo A. Van Ginderachter, Bernard Malissen, Geert Berx, Alain Beck, Yvan Saeys, Martin Guilliams
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1009305

Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level
Cited by: 21
Author(s): Suraj Kannan, Michael Farid, Brian L. Lin, Matthew Miyamoto, Chulan Kwon
Software Mentions: 3
Published: about 3 years ago

10.1038/s42003-021-02610-3

NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data
Cited by: 80
Author(s): Alessandro Montemurro, Viktoria Schuster, Helle Rus Povlsen, Amalie Kai Bentzen, Vanessa Isabell Jurtz, William D. Chronister, Austin Crinklaw, Sine Reker Hadrup, Ole Winther, Bjoern Peters, Leon Eyrich Jessen, Morten Nielsen
Software Mentions: 3
Published: about 3 years ago

10.1038/s41422-018-0103-x

Expansion and differentiation of human hepatocyte-derived liver progenitor-like cells and their use for the study of hepatotropic pathogens
Cited by: 105
Author(s): Gongbo Fu, Weijian Huang, Min Zeng, Zhou Xu, Hongping Wu, Changcheng Liu, Han Wu, Jun Weng, Hong‐Dan Zhang, Yongchao Cai, Charles Ashton, Min Ding, Dan Tang, Baohua Zhang, Yi Gao, Weifeng Yu, Bo Zhai, Zhiying He, Hongyang Wang, He‐Xin Yan
Software Mentions: 3
Published: about 6 years ago

10.1016/j.celrep.2021.108863

Metabolic programs define dysfunctional immune responses in severe COVID-19 patients
Cited by: 82
Author(s): Elizabeth A. Thompson, Katherine Cascino, Alvaro A. Ordoñez, Weiqiang Zhou, Ajay Vaghasia, Anne Hamacher-Brady, Nathan R. Brady, Im-Hong Sun, Rulin Wang, Avi Z. Rosenberg, Michaël Delannoy, Richard E. Rothman, Katherine Fenstermacher, Lauren Sauer, Kathryn Shaw-Saliba, Evan M. Bloch, Andrew D. Redd, Aaron A.R. Tobian, Maureen R. Horton, Kellie N. Smith, Andrew Pekosz, Franco R. D’Alessio, Srinivasan Yegnasubramanian, Hongkai Ji, Andrea L. Cox, Jonathan D. Powell
Software Mentions: 3
Published: over 3 years ago

10.1007/s13238-020-00705-x

Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity
Cited by: 43
Author(s): Yugong Ho, Peng Hu, Michael T. Peel, Sixing Chen, Pablo G. Cámara, Douglas J. Epstein, Hao Wu, Stephen A. Liebhaber
Software Mentions: 3
Published: over 4 years ago

10.1186/s13619-021-00076-6

Canonical and early lineage-specific stem cell types identified in planarian SirNeoblasts
Cited by: 5
Author(s): Kaimeng Niu, Hao Xu, Yuanyi Zhou Xiong, Yun Zhao, Chong Gao, Chris Seidel, Xue Pan, Yuqing Ying, Kai Y. Lei
Software Mentions: 3
Published: over 3 years ago

10.1126/sciimmunol.abf6692

Clonal expansion and activation of tissue-resident memory-like T <sub>H</sub> 17 cells expressing GM-CSF in the lungs of patients with severe COVID-19
Cited by: 118
Author(s): Yu Zhao, Christoph Kilian, Jan-Eric Turner, Lidia Bosurgi, Kevin Roedl, Patricia Bartsch, Ann-Christin Gnirck, Filippo Cortesi, Christoph Schultheiß, Malte Hellmig, Leon U. B. Enk, Fabian Hausmann, Alina Borchers, Milagros Wong, Hans‐Joachim Paust, Francesco Siracusa, Nicola Scheibel, Marissa Herrmann, Elisa Rosati, Petra Bächer, Dominik Kylies, Dominik Jarczak, Marc Lütgehetmann, Susanne Pfefferle, Stefan Steurer, Julian Schulze zurWiesch, Victor G. Puelles, Jan‐Peter Sperhake, Marylyn M. Addo, Ansgar W. Lohse, Mascha Binder, Samuel Huber, Tobias B. Huber, Stefan Kluge, Stefan Bonn, Ulf Panzer, Nicola Gagliani, Christian Krebs
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41421-020-00213-6

Characterization and generation of human definitive multipotent hematopoietic stem/progenitor cells
Cited by: 18
Author(s): Yanling Zhu, Tianyu Wang, Jiaming Gu, Ke Huang, Tian Zhang, Zhishuai Zhang, He Liu, Jun Tang, Yuchan Mai, Yanqi Zhang, Yuhang Li, Yashu Feng, Baoqiang Kang, Jinbing Li, Yongli Shan, Qianyu Chen, Jian Zhang, Bing Liang, Junwei Wang, Minghui Gao, Di Zhang, Min Zhou, Xiaofen Zhong, Jiekai Chen, Duanqing Pei, Jinfu Nie, Bing Liu, Guangjin Pan
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13578-021-00541-4

Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells
Cited by: 5
Author(s): Chengbo Sun, Hailun Wang, Qiwang Ma, Chao Chen, Jianhui Yue, Bo Li, Xi Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1093/jmcb/mjy089

Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum
Cited by: 34
Author(s): Jian Peng, Ai-Li Sheng, Qi Xiao, Libing Shen, Xiang-Chun Ju, Min Zhang, Siting He, Chao Wu, Zhen-Ge Luo
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.62548

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees
Cited by: 11
Author(s): Briana E Mittleman, Sebastian Pott, Shane Warland, Kenneth Barr, Claudia Cuevas, Yoav Gilad
Software Mentions: 3
Published: almost 4 years ago

10.21203/rs.3.rs-664507/v1

Myeloid cell interferon responses correlate with clearance of SARS-CoV-2
Cited by: 2
Author(s): Dhiraj Kumar Singh, Ekaterina Aladyeva, Shibali Das, Bindu Singh, Ekaterina Esaulova, Amanda Swain, Mushtaq Ahmed, Journey Cole, Chivonne Moodley, Smriti Mehra, Larry S. Schlesinger, Maxim N. Artyomov, Shabaana A. Khader, Deepak Kaushal
Software Mentions: 2
Published: over 3 years ago

10.1016/j.xpro.2021.100581

Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis
Cited by: 1
Author(s): Aizhan Tastanova, Egle Ramelyte, Zsolt Balázs, Ulrike Menzel, Christian Beisel, Michael Krauthammer, Reinhard Dummer, Mitchell P. Levesque
Software Mentions: 2
Published: over 3 years ago

10.3390/cells8050503

Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis
Cited by: 138
Author(s): Oliver Krenkel, Jana Hundertmark, Thomas Ritz, Ralf Weiskirchen, Frank Tacke
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.57779

Bimodal function of chromatin remodeler Hmga1 in neural crest induction and Wnt-dependent emigration
Cited by: 17
Author(s): Shashank Gandhi, Erica J. Hutchins, Krystyna Maruszko, Jong H Park, Matt Thomson, Marianne E. Bronner
Software Mentions: 2
Published: about 4 years ago

10.14814/phy2.15013

<i>miR‐145</i> transgenic mice develop cardiopulmonary complications leading to postnatal death
Cited by: 1
Author(s): Shelby Thomas, Sathiyanarayanan Manivannan, Dwitiya Sawant, Karthik M. Kodigepalli, Vidu Garg, Simon J. Conway, Brenda Lilly
Software Mentions: 2
Published: about 3 years ago

10.1038/s41392-021-00610-7

Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq
Cited by: 38
Author(s): Bing He, Shuning Liu, Yuanyuan Wang, Mengxin Xu, Wei Cai, Jia Liu, Wendi Bai, Shupei Ye, Yong Ma, Hengrui Hu, Huicui Meng, Tao Sun, Yanling Li, Huanle Luo, Mǎng Shī, Xiangjun Du, Wenjing Zhao, Shoudeng Chen, Jingyi Yang, Haipeng Zhu, Yusheng Jie, Yuedong Yang, Deyin Guo, Qiao Wang, Yuwen Liu, Huimin Yan, Manli Wang, Yao-Qing Chen
Software Mentions: 2
Published: over 3 years ago

10.1186/s13287-020-01660-4

Single-cell RNA-seq highlights heterogeneity in human primary Wharton’s jelly mesenchymal stem/stromal cells cultured in vitro
Cited by: 47
Author(s): Chengbo Sun, Lei Wang, Hailun Wang, Tingrun Huang, Wenwen Yao, Jing Li, Xi Zhang
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-020-02103-2

Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics
Cited by: 42
Author(s): Kwangbom Choi, Yang Chen, Daniel A. Skelly, Gary A. Churchill
Software Mentions: 2
Published: over 4 years ago

10.1093/ecco-jcc/jjaa054

Lymphocyte Activation Gene (LAG)-3 Is Associated With Mucosal Inflammation and Disease Activity in Ulcerative Colitis
Cited by: 20
Author(s): Stephanie Slevin, Lucy C. Garner, Conor Lahiff, Min Tan, L M Wang, Helen Ferry, Borgel Greenaway, Kate D. Lynch, A Geremia, Stephen A. Hughes, Karen Leavens, David Krull, Marks Djb., Katherine Nevin, Kevin Page, Naren Srinivasan, Ruth M. Tarzi, Paul Klenerman, Simon Travis, Carolina V. Arancibia‐Cárcamo, Satish Keshav
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.62781

Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node
Cited by: 13
Author(s): Shannon M. Walsh, Ryan M. Sheridan, Erin D Lucas, Thu A Doan, Brian C. Ware, Johnathon Schafer, Rui Fu, Matthew A. Burchill, Jay R. Hesselberth, Beth Tamburini
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-95532-3

Immune cell residency in the nasal mucosa may partially explain respiratory disease severity across the age range
Cited by: 15
Author(s): Konner Winkley, Dithi Banerjee, Todd Bradley, Boryana Koseva, Warren A. Cheung, Rangaraj Selvarangan, Tomi Pastinen, Elin Grundberg
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0236477

Cloning antibodies from single cells in pooled sequence libraries by selective PCR
Cited by: 3
Author(s): Felix Horns, Stephen R. Quake
Software Mentions: 2
Published: over 4 years ago

10.3389/fmed.2021.665410

The Presence of Circulating Nucleated Red Blood Cells Is Associated With Disease Severity in Patients of Hemorrhagic Fever With Renal Syndrome
Cited by: 5
Author(s): George Zhang, Tae‐Young Kang, Yun Zhang, Ying Ma, Chunmei Zhang, Haiquan Hu, Xiaozhou Jia, Ran Zhuang, Boquan Jin, Meng Wang, Xiyue Zhang, Dalu Liu
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.ppat.1009165

Multi-clonal SARS-CoV-2 neutralization by antibodies isolated from severe COVID-19 convalescent donors
Cited by: 36
Author(s): Michael Mor, Michal Werbner, Joel Alter, Modi Safra, Elad Chomsky, Jamie C. Lee, Smadar Hada-Neeman, Ksenia Polonsky, Cameron J. Nowell, Alex E. Clark, Anna Roitburd-Berman, Noam Ben-Shalom, Michal Navon, Dor Rafael, Hila Sharim, Evgeny Kiner, Eric R. Griffis, Jonathan M. Gershoni, Oren Kobiler, Sandra L. Leibel, Oren Zimhony, Aaron F. Carlin, Gur Yaari, Moshe Dessau, Meital Gal-Tanamy, David Hagin, Ben A. Croker, Natalia T. Freund
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1009025

Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty
Cited by: 32
Author(s): Gurmannat Kalra, Béatrice Milon, Alex M. Casella, Brian R. Herb, Elizabeth Humphries, Yang Song, Kevin P. Rose, Ronna Hertzano, Seth A. Ament
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pbio.2006387

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics
Cited by: 215
Author(s): Kenneth D. Harris, Hannah Hochgerner, Nathan G. Skene, Lorenza Magno, Linda Katona, Carolina Bengtsson Gonzales, Péter Somogyi, Nicoletta Kessaris, Sten Linnarsson, Jens Hjerling-Leffler
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-021-80999-x

SHP2 blockade enhances anti-tumor immunity via tumor cell intrinsic and extrinsic mechanisms
Cited by: 30
Author(s): Ye Wang, Morvarid Mohseni, Angelo L. Grauel, Javier Estrada, Wei Guan, Simon Liang, Jiyoung Elizabeth Choi, Minying Pu, Dongshu Chen, Tyler Laszewski, Stephanie Schwartz, Jane Gu, Leandra Mansur, Tyler Burks, Lauren K. Brodeur, Roberto Velazquez, Steve G. Kovats, Bhavesh Pant, Giri Buruzula, Emily Deng, Julie Chen, Farid Sari‐Sarraf, Christina Dornelas, Malini Varadarajan, Haiyan Yu, Chen Liu, Joanne Lim, Huai-Xiang Hao, Xiaomo Jiang, Anthony S. Malamas, Matthew J. LaMarche, Felipe C. Geyer, Margaret E. McLaughlin, Carlotta Costa, Joel P. Wagner, David A. Ruddy, Pushpa Jayaraman, Nathaniel D. Kirkpatrick, Pu Zhang, Oleg Iartchouk, Kimberly Aardalen, Viviana Cremasco, Glenn Dranoff, Jeffrey A. Engelman, Serena J. Silver, Hongyun Wang, William D. Hastings, Silvia Goldoni
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.5578

Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments
Cited by: 30
Author(s): Jesse D. Bloom
Software Mentions: 1
Published: about 6 years ago

10.1200/CCI.18.00074

Leveraging Single-Cell RNA Sequencing Experiments to Model Intratumor Heterogeneity
Cited by: 15
Author(s): Meghan C. Ferrall‐Fairbanks, Markus Ball, Eric Padron, Philipp M. Altrock
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.cmet.2021.05.015

SARS-CoV-2 infection induces beta cell transdifferentiation
Cited by: 107
Author(s): Xiaoxue Tang, Skyler Uhl, Tuo Zhang, Dongxiang Xue, Bo Li, J. Jeya Vandana, Joshua A. Acklin, Lori L. Bonnycastle, Narisu Narisu, Michael R. Erdos, Yaron Bram, Vasuretha Chandar, Angie Chi Nok Chong, Lauretta A. Lacko, Zaw Min, Jean K. Lim, Alain C. Borczuk, Jenny Xiang, Ali Naji, Francis S. Collins, Todd Evans, Chengyang Liu, Benjamin R. tenOever, Robert E. Schwartz, Shuibing Chen
Software Mentions: 1
Published: over 3 years ago

Projects: cran: cellranger

Papers Mentioning cellranger 79