cran: Seurat | Projects | Ecosyste.ms: Papers

10.1172/jci.insight.149185

Th1 polarization defines the synovial fluid T cell compartment in oligoarticular juvenile idiopathic arthritis
Cited by: 16
Author(s): Amélie M. Julé, Kacie J. Hoyt, Kevin Wei, María Gutiérrez‐Arcelus, Maria Taylor, Julie Ng, James A. Lederer, Siobhan Case, Margaret H. Chang, Ezra Cohen, Fatma Dedeoğlu, Melissa Hazen, Jonathan S Hausmann, Olha Halyabar, Erin Janssen, Jeffrey Lo, Mindy S. Lo, Esra Meidan, Jay Roberts, Mary Beth Son, Robert P. Sundel, Pui Y. Lee, Talal Chatila, Peter A. Nigrović, Lauren A. Henderson
Software Mentions: 6
Published: about 3 years ago

10.7554/eLife.52648

Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
Cited by: 34
Author(s): Anneke Dixie Kakebeen, Alexander Daniel Chitsazan, Madison Corinne Williams, Lauren Saunders, Andrea E. Wills
Software Mentions: 6
Published: over 4 years ago

10.1172/jci.insight.147617

The impact of tumor epithelial and microenvironmental heterogeneity on treatment responses in HER2-positive breast cancer
Cited by: 19
Author(s): Michalina Janiszewska, Shayna Stein, Otto Metzger Filho, Jennifer Eng, Natalie L. Kingston, Nicholas W. Harper, Inga Hansine Rye, Maša Alečković, Anne Trinh, Katherine Murphy, Elisabetta Marangoni, Simona Cristea, B S Rachael Oakes, Eric P. Winer, Ian E. Krop, Hege G. Russnes, Paul T. Spellman, Elmar Bucher, Zhi Hu, Koei Chin, Joe W. Gray, Franziska Michor, Kornélia Polyák
Software Mentions: 6
Published: over 3 years ago

10.1186/s12915-021-01034-z

Single-cell transcriptomics reveals the effect of PD-L1/TGF-β blockade on the tumor microenvironment
Cited by: 14
Author(s): Yoong Wearn Lim, Garry L. Coles, Savreet K. Sandhu, D. S. Johnson, Adam S. Adler, Erica L. Stone
Software Mentions: 6
Published: over 3 years ago

10.26508/lsa.201900520

Dynamic changes in the regulatory T-cell heterogeneity and function by murine IL-2 mutein
Cited by: 11
Author(s): Daniel Lu, Hao Wu, Ian Driver, Sarah Ingersoll, Sue J. Sohn, Songli Wang, Chi-Ming Li, Hyewon Phee
Software Mentions: 6
Published: over 4 years ago

10.3389/fonc.2021.715552

Single-Cell RNA Sequencing Reveals the Migration of Osteoclasts in Giant Cell Tumor of Bone
Cited by: 14
Author(s): Wei Feng, Mingwei He, Xiaohong Jiang, Huijiang Liu, Tianyu Xie, Zhaojie Qin, Qian Huang, Shijie Liao, Chengsen Lin, Jun He, Jiake Xu, Jie Ma, Yun Liu, Qingjun Wei
Software Mentions: 6
Published: about 3 years ago

10.7554/eLife.46464

Molecular and anatomical organization of the dorsal raphe nucleus
Cited by: 120
Author(s): Kee Wui Huang, Nicole Ochandarena, Adrienne C. Philson, Minsuk Hyun, Jaclyn E Birnbaum, Marcelo Cicconet, Bernardo L. Sabatini
Software Mentions: 6
Published: over 5 years ago

10.3389/fnins.2021.591122

Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis
Cited by: 40
Author(s): Asif Adil, Vijay Kumar, Arif Tasleem Jan, M. Asger
Software Mentions: 6
Published: over 3 years ago

10.1186/s13578-021-00691-5

A single-cell interactome of human tooth germ from growing third molar elucidates signaling networks regulating dental development
Cited by: 7
Author(s): Yueqi Shi, Yinglan Yu, Yuqiong Zhou, Jing Zhao, Wenjie Zhang, Duohong Zou, Weichen Song, Shaoyi Wang
Software Mentions: 6
Published: about 3 years ago

10.1080/22221751.2021.1942228

Single-cell immune checkpoint landscape of PBMCs stimulated with <i>Candida albicans</i>
Cited by: 8
Author(s): Wei‐Wei Deng, Zhen Su, Panpan Liang, Yubo Ma, Yufang Liu, Kai Zhang, Yi Zhang, Ting Liang, Jinyan Shao, X. Liu, Wenling Han, Ruoyu Li
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.stem.2021.04.031

Naive stem cell blastocyst model captures human embryo lineage segregation
Cited by: 139
Author(s): Akira Yanagida, Daniel Spindlow, Jennifer Nichols, Anish Dattani, Austin Smith, Ge Guo
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

10.7554/eLife.54695

Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment
Cited by: 168
Author(s): Leilei Zhong, Lutian Yao, Robert J. Tower, Yulong Wei, Zhen Miao, Jihwan Park, Rojesh Shrestha, Luqiang Wang, Wei Yu, Nicholas Holdreith, Xiaobin Huang, Yejia Zhang, Wei Tong, Yanqing Gong, Jaimo Ahn, Katalin Suszták, Nathaniel A. Dyment, Mingyao Li, Fanxin Long, Chider Chen, Patrick Seale, Ling Qin
Software Mentions: 6
Published: over 4 years ago

10.3389/fnmol.2019.00316

Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis
Cited by: 62
Author(s): Soumya Korrapati, Ian Taukulis, Rafal T. Olszewski, Madeline Pyle, Shoujun Gu, Riya Singh, C. M. Griffiths, Daniel Martin, Erich T. Boger, Robert J. Morell, Michael Hoa
Software Mentions: 6
Published: almost 5 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

10.1186/s12915-021-01071-8

Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma
Cited by: 17
Author(s): Wenqin Luo, Guan Ning Lin, Weichen Song, Yu Zhang, Huadong Lai, Man Zhang, Juju Miao, Xiaomu Cheng, Yongjie Wang, Wang Li, Wenxiang Wei, Wei‐Qiang Gao, Ru Yang, Jia Wang
Software Mentions: 6
Published: over 3 years ago

10.1038/s41422-020-0374-x

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma
Cited by: 155
Author(s): Yu-Pei Chen, Jianhua Yin, Wenfei Li, Han-Jie Li, Dongping Chen, Cuijuan Zhang, Jiawei Lv, Yaqin Wang, Xiaomin Li, Junyan Li, Panpan Zhang, Ying‐Qin Li, Qing‐Mei He, Xiaojing Yang, Yuan Liu, Ling‐Long Tang, Guan-Qun Zhou, Yan‐Ping Mao, Wei Chen, Ke Xiong, Hongbo Zhang, Shida Zhu, Yong Hou, Ying Sun, Michael Dean, Ido Amit, Kui Wu, Dong-Ming Kuang, Guibo Li, Na Liu
Software Mentions: 6
Published: over 4 years ago

10.20892/j.issn.2095-3941.2020.0073

Single-cell RNA-seq reveals the immune escape and drug resistance mechanisms of mantle cell lymphoma
Cited by: 23
Author(s): Liang Wang, Steven Mo, Xin Li, Yuanyuan He, Jing Yang
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.immuni.2020.03.011

Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants
Cited by: 47
Author(s): Lucy H. Jackson-Jones, Peter Smith, Jordan Raymond Portman, Marlene S Magalhaes, Katie J. Mylonas, Matthieu Vermeren, Mark Nixon, Beth E. P. Henderson, Ross Dobie, Sonja Vermeren, Laura Denby, Neil C. Henderson, Damian J. Mole, C Benezech
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.61461

Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer
Cited by: 29
Author(s): Andrea Sacchetti, Miriam Teeuwssen, Mathijs Verhagen, Rosalie Joosten, Tong Xu, Roberto Stabile, Berdine van der Steen, Martin M. Watson, Alem Gusinac, Won Kyu Kim, Inge Ubink, Harmen J.G. van de Werken, Arianna Fumagalli, Madelon Paauwe, Jacco van Rheenen, Owen J. Sansom, Onno Kranenburg, Riccardo Fodde
Software Mentions: 6
Published: over 3 years ago

10.1016/j.immuni.2020.09.015

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
Cited by: 143
Author(s): Travis Hughes, Marc H. Wadsworth, Todd M. Gierahn, Tran Do, David I. Weiss, Priscila Ribeiro Andrade, Feiyang Ma, Bruno Jorge de Andrade Silva, Shuai Shao, Lam C. Tsoi, José Ordovás-Montañés, Jóhann E. Guðjónsson, Robert L. Modlin, J. Christopher Love, Alex K. Shalek
Software Mentions: 6
Published: about 4 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

10.1016/j.immuni.2019.01.001

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation
Cited by: 322
Author(s): Ricardo J. Miragaia, Tomás Gomes, Agnieszka Chomka, Laura Jardine, Angela Riedel, Ahmed N. Hegazy, Natasha Whibley, A. Tucci, Xi Chen, Ida Lindeman, Guy Emerton, Thomas Krausgruber, Jacqueline D. Shields, Muzlifah Haniffa, Fiona Powrie, Sarah A. Teichmann
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.63270

Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation
Cited by: 4
Author(s): Yogev Sela, Jinyang Li, Paola Kuri, Allyson J. Merrell, Ning Li, Chris Lengner, Pantelis Rompolas, Ben Z. Stanger
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giy059

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Cited by: 244
Author(s): Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2021.688493

Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes
Cited by: 4
Author(s): Martín A. Rivas, Ceyda Durmaz, Andreas Kloetgen, Cristopher R Chin, Zhengming Chen, Bhavneet Bhinder, Amnon Koren, Aaron D. Viny, Christopher D. Scharer, Jeremy M. Boss, Olivier Elemento, Christopher E. Mason, Ari Melnick
Software Mentions: 6
Published: about 3 years ago

10.1038/s41422-020-0300-2

Embryonic endothelial evolution towards first hematopoietic stem cells revealed by single-cell transcriptomic and functional analyses
Cited by: 80
Author(s): Siyuan Hou, Zongcheng Li, Xiaona Zheng, Yun Gao, Ji Dong, Yanli Ni, Xiaobo Wang, Yunqiao Li, Xiaochen Ding, Zhilin Chang, Shuaili Li, Yuqiong Hu, Xiaoying Fan, Yu Hou, Lu Wen, Bing Liu, Fuchou Tang, Yu Lan
Software Mentions: 6
Published: over 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 lavages
Cited 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/s13073-021-00939-2

Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes
Cited by: 17
Author(s): David Z. Pan, Min‐Hua Zong, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñóz-Hernández, Miguel Francisco Herrera-Hernández, Marı́a Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Kirsi H. Pietiläinen, Jussi Pihlajamäki, Markku Laakso, Kristina M. Garske, Päivi Pajukanta
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0218458

p73 regulates epidermal wound healing and induced keratinocyte programming
Cited by: 18
Author(s): J. Scott Beeler, Clayton B. Marshall, Paula I. González-Ericsson, Timothy M. Shaver, Gabriela L. Santos Guasch, Spencer Lea, Kimberly N. Johnson, Hailing Jin, Bryan J. Venters, Melinda E. Sanders, Jennifer A. Pietenpol
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-021-00861-7

Development of double-positive thymocytes at single-cell resolution
Cited by: 15
Author(s): Young Li, Kun Li, Lianbang Zhu, Bin Li, Dandan Zong, Pengfei Cai, Chen Jiang, Pengcheng Du, Jun Lin, Kun Qu
Software Mentions: 6
Published: over 3 years ago

10.1242/dev.195883

The BMP antagonist gremlin 1 contributes to the development of cortical excitatory neurons, motor balance and fear responses
Cited by: 4
Author(s): Mari Ichinose, Nobumi Suzuki, Tongtong Wang, Hiroki Kobayashi, Laura Vrbanac, Joseph Kim Fai Ng, Josephine Wright, Tamsin R.M. Lannagan, Krystyna A. Gieniec, Martin Lewis, Ryosuke Ando, Atsushi Enomoto, Simon Koblar, Paul Q. Thomas, Daniel L. Worthley, Susan L. Woods
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

10.3389/fimmu.2021.626255

Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell Function
Cited by: 13
Author(s): Adam P. Cribbs, P. Filippakopoulos, Martin Philpott, Graham Wells, Henry Penn, Henrik Oerum, Viia Valge-Archer, Marc Feldmann, U. Oppermann
Software Mentions: 6
Published: over 3 years ago

10.1155/2020/8537381

Autophagy Regulatory Genes MET and RIPK2 Play a Prognostic Role in Pancreatic Ductal Adenocarcinoma: A Bioinformatic Analysis Based on GEO and TCGA
Cited by: 10
Author(s): Xingyu Li, Zhiqiang Li, Hongwei Zhu, Xiao Yu
Software Mentions: 6
Published: about 4 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.2021.108990

Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancer
Cited by: 39
Author(s): Julienne L. Carstens, Stephen C. Yang, Pedro Corrêa de Sampaio, Xiaofeng Zheng, Souptik Barua, Kathleen M. McAndrews, Arvind Rao, Jared K. Burks, Andrew D. Rhim, Raghu Kalluri
Software Mentions: 6
Published: over 3 years ago

10.1016/j.celrep.2019.03.104

Notch Signaling Mediates Secondary Senescence
Cited by: 72
Author(s): Yee Voan Teo, Nattaphong Rattanavirotkul, Nelly Olova, Angela Salzano, Andrea Quintanilla, Núria Tarrats, Christos Kiourtis, Miryam Müller, Anthony Green, Peter D. Adams, Juan Carlos Acosta, Tom Bird, Kristina Kirschner, Nicola Neretti, Tamir Chandra
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0243360

DSAVE: Detection of misclassified cells in single-cell RNA-Seq data
Cited by: 2
Author(s): Johan Gustafsson, Jonathan L. Robinson, Juan Salvador Inda-Díaz, Elias Björnson, Rebecka Jörnsten, Jens Nielsen
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.celrep.2021.108739

Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer’s disease
Cited by: 40
Author(s): Hongtian Yang, Kristen D. Onos, Kwangbom Choi, Kelly J. Keezer, Daniel A. Skelly, Gregory W. Carter, Gareth R. Howell
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.cell.2021.07.023

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Cited by: 170
Author(s): Carly G.K. Ziegler, Vincent N. Miao, Anna H. Owings, Andrew W. Navia, Ying Tang, Joshua D. Bromley, Peter Lotfy, Meredith Sloan, Hannah Laird, Hibbard E. Williams, Micayla George, Riley S. Drake, Christian Taube, Adam Parker, Campbell B Sindel, Molly Burger, Yilianys Pride, Mohammad S Hasan, George Abraham, Michal Senitko, Tanya O. Robinson, Alex K. Shalek, Sarah C. Glover, Bruce H. Horwitz, José Ordovás-Montañés
Software Mentions: 6
Published: about 3 years ago

10.1136/jitc-2021-002856

IL-6 contributes to metastatic switch via the differentiation of monocytic-dendritic progenitors into prometastatic immune cells
Cited by: 15
Author(s): Ksenia Magidey-Klein, Tim J. Cooper, Ksenya Kveler, Rachelly Normand, Tongwu Zhang, Michael Timaner, Ziv Raviv, Brian P. James, Roi Gazit, Ze’ev Ronai, Shai S. Shen-Orr, Yuval Shaked
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1007552

High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor
Cited by: 56
Author(s): Tetsuji Yamashita, Fei Zheng, David Finkelstein, Zoe Kellard, Caroline Robert, Celeste Rosencrance, Ken Sugino, John Easton, Charles Gawad, Jian Zuo
Software Mentions: 6
Published: over 6 years ago

10.1038/s42003-021-02595-z

Single-cell profiling defines the prognostic benefit of CD39high tissue resident memory CD8+ T cells in luminal-like breast cancer
Cited by: 9
Author(s): Agnese Losurdo, Caterina Scirgolea, Giorgia Alvisi, Jolanda Brummelman, Valentina Errico, Luca Di Tommaso, Karolina Pilipow, Federico Colombo, Bethania Fernandes, Clelia Peano, Alberto Testori, Corrado Tinterri, Massimo Roncalli, Armando Santoro, Emilia Maria Cristina Mazza, Enrico Lugli
Software Mentions: 6
Published: about 3 years ago

10.1038/s42003-020-01476-1

Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
Cited by: 58
Author(s): Baijun Dong, Juju Miao, Yanqing Wang, Wenqin Luo, Zhongzhong Ji, Huadong Lai, Man Zhang, Xiaomu Cheng, Jinming Wang, Yuxiang Fang, Helen He Zhu, Chee Wai Chua, Liancheng Fan, Yao Zhu, Jiahua Pan, Jia Wang, Wei Xue, Wei‐Qiang Gao
Software Mentions: 6
Published: almost 4 years ago

10.3389/fimmu.2021.647209

PNOC Expressed by B Cells in Cholangiocarcinoma Was Survival Related and LAIR2 Could Be a T Cell Exhaustion Biomarker in Tumor Microenvironment: Characterization of Immune Microenvironment Combining Single-Cell and Bulk Sequencing Technology
Cited by: 20
Author(s): Zheng Chen, Ming Yu, Jiuliang Yan, Lei Guo, Bo Zhang, Shuang Liu, LJ Jin, Wentao Zhang, Bing Zhou, Jie Gao, Zhixu Yang, Xiaoqiang Li, Ji Zhou, Jia Fan, Qing–Hai Ye, Hui Li, Yongfeng Xu, Xiao Ye
Software Mentions: 6
Published: over 3 years ago

10.3389/fimmu.2019.02568

Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level
Cited by: 22
Author(s): Yannick F. Fuchs, Virag Sharma, Anne Eugster, Gloria Kraus, Robert Morgenstern, Andreas Dahl, Susanne Reinhardt, A. Petzold, Annett Lindner, Doreen Löbel, Ezio Bonifacio
Software Mentions: 6
Published: about 5 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 analysis
Cited 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

10.1371/journal.pcbi.1007939

Iterative point set registration for aligning scRNA-seq data
Cited by: 3
Author(s): Amir Alavi, Ziv Bar‐Joseph
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1007509

Clustering-independent analysis of genomic data using spectral simplicial theory
Cited by: 19
Author(s): Kiya W. Govek, Venkata S. Yamajala, Pablo G. Cámara
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.celrep.2020.107628

Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth
Cited by: 156
Author(s): Sarah Davidson, Mirjana Efremova, Angela Riedel, Bidesh Mahata, Jhuma Pramanik, Jani Huuhtanen, Gozde Kar, Roser Vento‐Tormo, Tzachi Hagai, Xi Chen, Muzlifah Haniffa, Jacqueline D. Shields, Sarah A. Teichmann
Software Mentions: 6
Published: over 4 years ago

10.1093/bioinformatics/btz726

bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
Cited by: 59
Author(s): Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei
Software Mentions: 6
Published: about 5 years ago

10.26508/lsa.202000707

Robust production of uniform human cerebral organoids from pluripotent stem cells
Cited by: 44
Author(s): Adam Sivitilli, Jessica Gosio, Bibaswan Ghoshal, Alesya Evstratova, Daniel Trcka, Parisa Ghiasi, J. Javier Hernández, Jean Martin Beaulieu, Jeffrey L. Wrana, Liliana Attisano
Software Mentions: 6
Published: over 4 years ago

10.1186/s13059-021-02280-8

iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks
Cited by: 25
Author(s): Dongfang Wang, Siyu Hou, Lei Zhang, Xiliang Wang, Baolin Liu, Zemin Zhang
Software Mentions: 6
Published: almost 4 years ago

10.1093/gigascience/giaa152

Tool recommender system in Galaxy using deep learning
Cited by: 7
Author(s): Anup Kumar, Helena Rasche, Björn Grüning, Rolf Backofen
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pbio.3001017

Single-cell RNA-seq analysis of mouse preimplantation embryos by third-generation sequencing
Cited by: 38
Author(s): Xiaoying Fan, Dong Tang, Yuhan Liao, Pidong Li, Yu Zhang, Minxia Wang, Fan Liang, Xiao Wang, Yun Gao, Lu Wen, Depeng Wang, Yan Wang, Fuchou Tang
Software Mentions: 5
Published: almost 4 years ago

10.18632/aging.104136

Single cell sequencing reveals cell populations that predict primary resistance to imatinib in chronic myeloid leukemia
Cited by: 5
Author(s): Weilong Zhang, Baofeng Yang, Linqian Weng, Jiangtao Li, Jinfeng Bai, Ting Wang, Jingwen Wang, Yue Jin, Hongmei Jing, Yuchen Jiao, Xixi Chen, Hui Liu, Yi‐Xin Zeng
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pbio.3000704

Single-cell mapping reveals new markers and functions of lymphatic endothelial cells in lymph nodes
Cited by: 83
Author(s): Noriki Fujimoto, Yuliang He, Marco D’Addio, Carlotta Tacconi, Michael Detmar, Lothar C. Dieterich
Software Mentions: 5
Published: over 4 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/fgene.2020.615680

Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma
Cited by: 5
Author(s): Miao Su, Kuangyuan Qiao, Xing Xie, Xinying Zhu, Fu-Lai Gao, Changjuan Li, Dongqiang Zhao
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-020-02048-6

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Cited by: 289
Author(s): Elena Denisenko, Belinda Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, C Olivier, Rebecca K. Simmons, Ryan Lister, Alistair R.R. Forrest
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-020-02054-8

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
Cited by: 14
Author(s): Zijian Ni, Shuyang Chen, Jared Brown, Christina Kendziorski
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-021-02201-2

Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis
Cited by: 28
Author(s): Kohei Saeki, Gregory Chang, Noriko Kanaya, Xiwei Wu, Jinhui Wang, Lauren Bernal, Desiree Ha, Susan L. Neuhausen, Shiuan Chen
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2019.00958

Single-Cell Analysis of Circulating Tumor Cells: How Far Have We Come in the -Omics Era?
Cited by: 52
Author(s): Elisabetta Rossi, Rita Zamarchi
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-020-02027-x

Accounting for cell type hierarchy in evaluating single cell RNA-seq clustering
Cited by: 19
Author(s): Zhijin Wu, Hao Wu
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-021-86070-z

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
Cited by: 7
Author(s): Karen Davey, Daniel Wong, Filip A. Konopacki, Eugene Kwa, Tony Ly, Heike Fiegler, Christopher R. Sibley
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-020-02032-0

Sampling time-dependent artifacts in single-cell genomics studies
Cited by: 50
Author(s): Ramón Massoni-Badosa, Giovanni Iacono, Cátia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodríguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elı́as Campo, Antonio Julià, José I. Martín‐Subero, Holger Heyn
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-021-90797-0

Targeting of the CD80/86 proinflammatory axis as a therapeutic strategy to prevent severe COVID-19
Cited by: 9
Author(s): Antonio Julià, Irene Bonafonte-Pardàs, Antonio Gómez, María López-Lasanta, Mireia López-Corbeto, Sergio H Martínez-Mateu, Jordi Lladós, Iván Rodríguez-Nunez, R Myers, Sara Marsal
Software Mentions: 5
Published: over 3 years ago

10.1038/s41385-019-0228-3

Commensal microbiota drive the functional diversification of colon macrophages
Cited by: 62
Author(s): Byunghyun Kang, Luigi J. Alvarado, Teayong Kim, Michael L. Lehmann, Hyeseon Cho, Jianping He, Peng Li, Bong-Hyun Kim, André Larochelle, Brian L. Kelsall
Software Mentions: 5
Published: over 4 years ago

10.1002/ctm2.246

Circulating tumor cell characterization of lung cancer brain metastases in the cerebrospinal fluid through single‐cell transcriptome analysis
Cited by: 33
Author(s): Haoyu Ruan, Yihang Zhou, Jie Shen, Yue Zhai, Ying Xu, Linyu Pi, Run Huang, Kun Chen, Xiangyu Li, Wendong Ma, Zhiyuan Wu, Xuan Deng, Xiaozhu Wang, Chao Zhang, Ming Guan
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-020-07302-6

JOINT for large-scale single-cell RNA-sequencing analysis via soft-clustering and parallel computing
Cited by: 4
Author(s): Tao Cui, Tingting Wang
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-019-1922-x

DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
Cited by: 31
Author(s): Zilu Zhou, Baocheng Xu, Andy J. Minn, Nancy R. Zhang
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-59808-4

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation
Cited by: 29
Author(s): Ian M. Traniello, Syed Bukhari, Jessica L. Kevill, Amy Cash Ahmed, Adam R. Hamilton, Nicholas L. Naeger, Declan C. Schroeder, Gene E. Robinson
Software Mentions: 5
Published: almost 5 years ago

10.3389/fgene.2021.681206

LISA2: Learning Complex Single-Cell Trajectory and Expression Trends
Cited by: 1
Author(s): Yang Chen, Yuping Zhang, Kairong Li, Zhengqing Ouyang
Software Mentions: 5
Published: about 3 years ago

10.1038/s42003-020-0989-y

IDO1+ Paneth cells promote immune escape of colorectal cancer
Cited by: 22
Author(s): Sandra Pflügler, Jasmin Svinka, Irene Scharf, Ilija Crnčec, Martin Filipits, Pornpimol Charoentong, Markus Tschurtschenthaler, Lukas Kenner, Monira Awad, Judith Stift, Marina Schernthanner, Romana Bischl, Dietmar Herndler‐Brandstetter, Elisabeth Glitzner, Herwig P. Moll, Emilio Casanova, Gerald Timelthaler, Maria Sibilia, Michael Gnant, Sigurd Lax, Josef Thaler, Mathias Müller, Birgit Strobl, Thomas Mohr, Arthur Kaser, Zlatko Trajanoski, Gerwin Heller, Robert Eferl
Software Mentions: 5
Published: over 4 years ago

10.1002/ctm2.350

Landscape and dynamics of single tumor and immune cells in early and advanced‐stage lung adenocarcinoma
Cited by: 43
Author(s): Zhencong Chen, Yiwei Huang, Zhengyang Hu, Mengnan Zhao, Ming Li, Guoshu Bi, Yuansheng Zheng, Jiaqi Liang, Tao Lu, Wei Jiang, Songtao Xu, Cheng Zhan, Junjie Xi, Qun Wang, Lijie Tan
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-57110-6

Single-cell transcriptional profiles in human skeletal muscle
Cited by: 160
Author(s): Aliza Rubenstein, Gregory R. Smith, Ulrika Raue, Gwénaëlle Begue, Kiril Minchev, Frederique Ruf-Zamojski, Venugopalan D. Nair, Xingyu Wang, Lan Zhou, Elena Zaslavsky, Todd A. Trappe, Scott Trappe, Stuart C. Sealfon
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-019-1764-6

BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
Cited by: 94
Author(s): Tongxin Wang, Travis Johnson, Wei Shao, Zixiao Lu, Bryan R. Helm, Jie Zhang, Kun Huang
Software Mentions: 5
Published: over 5 years ago

10.3389/fendo.2021.679582

Transcriptomic Profiling of Human Placenta in Gestational Diabetes Mellitus at the Single-Cell Level
Cited by: 31
Author(s): Yuqi Yang, Fang Guo, Yue Peng, Rong Chen, Wenbo Zhou, Huihui Wang, Jun Ouyang, Bin Yu, Zhengfeng Xu
Software Mentions: 5
Published: over 3 years ago

10.3389/fendo.2021.736286

Gene Signatures of NEUROGENIN3+ Endocrine Progenitor Cells in the Human Pancreas
Cited by: 2
Author(s): Hyo Jeong Yong, Gengqiang Xie, Chengyang Liu, Wei Wang, Ali Naji, Jerome Irianto, Yue J. Wang
Software Mentions: 5
Published: about 3 years ago

10.1186/s13024-021-00481-0

Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brains
Cited by: 9
Author(s): Julio Barrera, Lingyun Song, Julia Gamache, Melanie E. Garrett, Alexias Safi, Young Won Yun, Ivana Premasinghe, Daniel J. Sprague, Danielle Chipman, Jeffrey Li, Hélène Fradin, Karen Soldano, Raluca Gordân, Allison Ashley‐Koch, Gregory E. Crawford, Ornit Chiba‐Falek
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

10.3389/fcell.2021.700607

Comprehensive Analysis of a Nine-Gene Signature Related to Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 23
Author(s): Haihui Zhong, Jie Wang, Yaru Zhu, Yefeng Shen
Software Mentions: 5
Published: about 3 years ago

10.1126/sciimmunol.abe4782

Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2–reactive CD8 <sup>+</sup> T cells
Cited by: 163
Author(s): Anthony Kusnadi, Ciro Ramírez-Suástegui, Vicente Fajardo, Serena Chee, Benjamin J Meckiff, Hayley Simon, Emanuela Pelosi, Grégory Seumois, Ferhat Ay, Pandurangan Vijayanand, Christian Ottensmeier
Software Mentions: 5
Published: almost 4 years ago

10.1126/sciimmunol.abc3582

TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes
Cited by: 754
Author(s): Ruochen Zang, María Florencia Gómez Castro, Broc T. McCune, Qiru Zeng, Paul W. Rothlauf, Naomi Sonnek, Zhuoming Liu, Kevin Brulois, Xin Wang, Harry B. Greenberg, Michael S. Diamond, Matthew A. Ciorba, Sean P. J. Whelan, Siyuan Ding
Software Mentions: 5
Published: over 4 years ago

10.1038/s41423-020-00574-8

Single-cell profiling reveals the trajectories of natural killer cell differentiation in bone marrow and a stress signature induced by acute myeloid leukemia
Cited by: 48
Author(s): Adeline Crinier, Pierre‐Yves Dumas, Éric Bertrand, Christelle Pipéroglou, Laurine Gil, Arnaud Villacreces, Frédéric Vély, Zoran Ivanović, Pierre Milpied, Émilie Narni-Mancinelli, Éric Vivier
Software Mentions: 5
Published: almost 4 years ago

10.3389/fcell.2021.652408

Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver
Cited by: 21
Author(s): Xianliang Hou, Yane Yang, Ping Li, Zhipeng Zeng, Wenlong Hu, Ruilian Zhe, Xinqiong Liu, Donge Tang, Minglin Ou, Yong Dai
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.666771

scGPS: Determining Cell States and Global Fate Potential of Subpopulations
Cited by: 1
Author(s): Michael Thompson, Maika Matsumoto, Tianqi Ma, Anne Senabouth, Nathan J. Palpant, Joseph E. Powell, Quan Nguyen
Software Mentions: 5
Published: over 3 years ago

10.1038/s41421-020-00214-5

Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression
Cited by: 67
Author(s): Guohe Song, Yang Shi, Meiying Zhang, Shyamal Goswami, Saifullah Afridi, Ling Meng, Jiaqiang Ma, Yi Chen, Youpei Lin, Juan Zhang, Yuming Liu, Zijie Jin, Shenghong Yang, Dongning Rao, Shu Zhang, Aiwu Ke, Xiaoying Wang, Yang Cao, Jian Zhou, Jia Fan, Xiaoming Zhang, Ruibin Xi, Qiang Gao
Software Mentions: 5
Published: almost 4 years ago

10.3389/fcvm.2020.00052

A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature
Cited by: 86
Author(s): Menglan Xiang, Rubén Adrián Grosso, Akiko Takeda, Junliang Pan, Tove Bekkhus, Kevin Brulois, Denis Đermadi, Sofia Nordling, Michael Vanlandewijck, Sirpa Jalkanen, Maria H. Ulvmar, Eugene C. Butcher
Software Mentions: 5
Published: over 4 years ago

10.1186/s40779-021-00336-1

Advances in single-cell sequencing: insights from organ transplantation
Cited by: 7
Author(s): Ying Wang, Jian‐Ye Wang, Angelika Schnieke, Konrad Fischer
Software Mentions: 5
Published: over 3 years ago

10.3389/fcvm.2021.683074

A Multi-Omics Approach Using a Mouse Model of Cardiac Malformations for Prioritization of Human Congenital Heart Disease Contributing Genes
Cited by: 2
Author(s): Adrianna Matos‐Nieves, Sathiyanarayanan Manivannan, Uddalak Majumdar, Kim L. McBride, Peter White, Vidu Garg
Software Mentions: 5
Published: about 3 years ago

10.1186/s12864-020-07300-8

Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™
Cited by: 2
Author(s): Namit Kumar, Ryan Golhar, Kriti Sen Sharma, James L. Holloway, Srikant Sarangi, Isaac M. Neuhaus, Alice M. Walsh, Zachary W. Pitluk
Software Mentions: 5
Published: almost 4 years ago

10.1007/s13238-021-00852-9

Single-nucleus transcriptomic landscape of primate hippocampal aging
Cited by: 41
Author(s): Hui Zhang, Jiaming Li, Jie Ren, Shuhui Sun, Shuai Ma, Weiqi Zhang, Yang Yu, Yusheng Cai, Yan Ke, Wei Li, Baoyang Hu, Piu Chan, Guoguang Zhao, Juan Carlos Izpisúa Belmonte, Qi Zhou, Jing Qu, Si Wang, Guanghui Liu
Software Mentions: 5
Published: over 3 years ago

10.1038/s41421-020-00236-z

Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy loss
Cited by: 74
Author(s): Chuang Guo, Pengfei Cai, Lina Jin, Qing Sha, Qiaoni Yu, Wen Zhang, Chen Jiang, Qian Liu, Dandan Zong, Kun Li, Jingwen Fang, Fangting Lu, Yanshi Wang, Daojing Li, Jun Lin, Lü Li, Zhutian Zeng, Xianhong Tong, Haiming Wei, Kun Qu
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.medj.2021.01.006

Identifying CNS-colonizing T cells as potential therapeutic targets to prevent progression of multiple sclerosis
Cited 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

10.3389/fphys.2021.637924

A Subpopulation of Schwann Cell-Like Cells With Nerve Regeneration Signatures Is Identified Through Single-Cell RNA Sequencing
Cited by: 4
Author(s): Zairong Wei, Shenyou Shu, Mingjun Zhang, Sitian Xie, Shijie Tang, Kaiyu Nie, Haihong Li
Software Mentions: 5
Published: over 3 years ago

10.1007/s13238-020-00762-2

A human circulating immune cell landscape in aging and COVID-19
Cited by: 158
Author(s): Yingfeng Zheng, Xiuxing Liu, Wenqing Le, Lihui Xie, Li He, Wen Wen, Si Wang, Shuai Ma, Zhaofeng Huang, Jinguo Ye, Wen Shi, Yanxia Ye, Zunpeng Liu, Moshi Song, Weiqi Zhang, Jing‐Dong J. Han, Juan Carlos Izpisúa Belmonte, Chuan-Le Xiao, Jing Qu, Hongyang Wang, Guang‐Hui Liu, Wenru Su
Software Mentions: 5
Published: over 4 years ago

10.21203/rs.3.rs-25639/v1

A potential role for AHR in SARS-CoV-2 pathology
Cited by: 12
Author(s): Federico Giovannoni, Zhaorong Li, Cybele C. Garcı́a, Francisco J. Quintana
Software Mentions: 5
Published: over 4 years ago

10.3390/cells10082143

Single-Cell Transcriptomics Reveals Core Regulatory Programs That Determine the Heterogeneity of Circulating and Tissue-Resident Memory CD8+ T Cells
Cited by: 12
Author(s): Yao Chen, Jian Shen, Moujtaba Y. Kasmani, Paytsar Topchyan, Weiguo Cui
Software Mentions: 5
Published: over 3 years ago

Projects: cran: Seurat

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