cran: Seurat | Projects | Ecosyste.ms: Papers

10.7554/eLife.67481

SORBS2 is a genetic factor contributing to cardiac malformation of 4q deletion syndrome patients
Cited by: 7
Author(s): Fei Liang, Bo Wang, Juan Geng, Guoling You, Jingjing Fa, Min Zhang, Hunying Sun, Huiwen Chen, Qin Fu, Xiaoqing Zhang, Zhen Zhang
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

10.1002/iid3.362

What has single‐cell RNA sequencing revealed about microglial neuroimmunology?
Cited by: 15
Author(s): Norwin Kubick, Patrick C. Henckell Flournoy, Pavel Klimovich, Gina Manda, Michel‐Edwar Mickael
Software Mentions: 4
Published: about 4 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: over 3 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

10.7554/eLife.66954

Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process
Cited by: 45
Author(s): Keiichiro Koiwai, Takashi Koyama, Soichiro Tsuda, Atsushi Toyoda, Kiyoshi Kikuchi, Hiroaki Suzuki, Ryuji Kawano
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 neurogenesis
Cited 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

10.7554/eLife.55526

Delineating the early transcriptional specification of the mammalian trachea and esophagus
Cited by: 27
Author(s): Akela Kuwahara, Ace E. Lewis, Coohleen Coombes, Fang-Shiuan Leung, Michelle Percharde, Jeffrey O. Bush
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2018.02523

Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice
Cited by: 4
Author(s): Wendi Bacon, Russell S. Hamilton, Ziyi Yu, Jens Kieckbusch, Dean Hawkes, Ada Maria Krzak, Chris Abell, Francesco Colucci, D. Stephen Charnock-Jones
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.47138

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila
Cited by: 94
Author(s): Evan Witt, Sigi Benjamin, Nicolas Svetec, Li Zhao
Software Mentions: 4
Published: over 5 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

10.1093/gigascience/giz047

Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood
Cited by: 24
Author(s): Yi Zhao, Xiao Li, Weihua Zhao, Jingwan Wang, Jun Yu, Ziyun Wan, Kai Gao, Gang Ye, Wang Xie, Bingbing Fan, Qinkai Wu, Bangwei Chen, Feng Xie, Jinghua Wu, Wei Zhang, Fang Chen, Huanming Yang, Jian Wang, Xun Xu, Bin Li, Shiping Liu, Yong Hou, Xiao Liu
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.43882

Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury
Cited by: 349
Author(s): Nona Farbehi, Ralph Patrick, Aude Dorison, Munira Xaymardan, Vaibhao Janbandhu, Katharina Wystub-Lis, Joshua W. K. Ho, Robert E. Nordon, Richard P. Harvey
Software Mentions: 4
Published: over 5 years ago

10.1016/j.gpb.2018.10.003

SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data
Cited by: 29
Author(s): Xianwen Ren, Liangtao Zheng, Zemin Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.739605

Prednisone Reprograms the Transcriptional Immune Cell Landscape in CNS Autoimmune Disease
Cited by: 3
Author(s): Lin He, Yuehan Gao, Lihui Xie, Rong Wang, Runping Duan, Zhaohuai Li, Binyao Chen, Lei Zhu, Xianggui Wang, Wenru Su
Software Mentions: 4
Published: over 3 years ago

10.5808/GI.2020.18.3.e26

A semi-automatic cell type annotation method for single-cell RNA sequencing dataset
Cited by: 0
Author(s): Wan Kim, Sung Min Yoon, Sang Soo Kim
Software Mentions: 4
Published: about 4 years ago

10.1016/j.stem.2020.06.020

Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration
Cited by: 251
Author(s): Jinwook Choi, Jong-Eun Park, Georgia Tsagkogeorga, Motoko Yanagita, Bon‐Kyoung Koo, Namshik Han, Joo Hyeon Lee
Software Mentions: 4
Published: about 4 years ago

10.1186/s12865-019-0322-z

Subsets of mononuclear phagocytes are enriched in the inflamed colons of patients with IBD
Cited by: 45
Author(s): Hong Liu, Suryasarathi Dasgupta, Yu Fu, Brandi Bailey, Christian Roy, Eric S. Lightcap, Benjamin Faustin
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.66749

Murine muscle stem cell response to perturbations of the neuromuscular junction are attenuated with aging
Cited by: 11
Author(s): Jacqueline Larouche, Mahir Mohiuddin, Jeongmoon J. Choi, Peter Ulintz, Paula Fraczek, Kaitlyn Sabin, Sethuramasundaram Pitchiaya, Sarah J Kurpiers, Jesus A. Castor-Macias, Wenxuan Liu, Robert Louis Hastings, Lemuel A. Brown, James F. Markworth, Kanishka de Silva, Benjamin Levi, Sofía D. Merajver, Gregorio Valdez, Joe V. Chakkalakal, Young C. Jang, Susan V. Brooks, Carlos A. Aguilar
Software Mentions: 4
Published: over 3 years ago

10.1186/s40478-021-01204-8

CSF1R inhibition rescues tau pathology and neurodegeneration in an A/T/N model with combined AD pathologies, while preserving plaque associated microglia
Cited by: 20
Author(s): Chritica Lodder, Isabelle Scheyltjens, Ilie-Cosmin Stancu, Pablo Botella Lucena, Manuel Gutiérrez de Ravé, Sarah Vanherle, Tim Vanmierlo, Niels Cremers, Hannah Vanrusselt, Bert Brône, Bernard Hanseeuw, Jean‐Noël Octave, Astrid Bottelbergs, Kiavash Movahedi, Ilse Dewachter
Software Mentions: 4
Published: over 3 years ago

10.1172/jci.insight.147413

COVID-19 and RA share an SPP1 myeloid pathway that drives PD-L1+ neutrophils and CD14+ monocytes
Cited by: 23
Author(s): Lucy MacDonald, Stefano Alivernini, Barbara Tolusso, Aziza Elmesmari, Domenico Somma, Simone Perniola, Annamaria Paglionico, Luca Petricca, Silvia Laura Bosello, Angelo Carfì, Michela Sali, Egidio Stigliano, Antonella Cingolani, Rita Murri, Vincenzo Arena, Massimo Fantoni, Massimo Antonelli, Francesco Landi, Francesco Franceschi, Maurizio Sanguinetti, Iain B. McInnes, Charles McSharry, Antonio Gasbarrini, Thomas D. Otto, Mariola Kurowska‐Stolarska, Stefano Alivernini
Software Mentions: 4
Published: over 3 years ago

10.1038/s41422-020-00445-x

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
Cited by: 88
Author(s): Luca Mazzurana, Paulo Czarnewski, Viktor Jönsson, Leif Wigge, Markus Ringnér, Teresa C. Williams, Avinash Ravindran, Åsa K. Björklund, Jesper Säfholm, Gunnar Nilsson, Sven Erik Dahlén, Ann Charlotte Orre, Mamdoh Al‐Ameri, Charlotte Höög, Charlotte Hedin, Sylwester Szczegielniak, Sven Almér, Jenny Mjösberg
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41422-018-0066-y

Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta
Cited by: 242
Author(s): Yawei Liu, Xiaoying Fan, Rui Wang, Xiaoyin Lu, Yan-Li Dang, Huiying Wang, Haiyan Lin, Cheng Zhu, Hao Ge, James C. Cross, Hongmei Wang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41422-020-0378-6

Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level
Cited by: 49
Author(s): Xin Wang, Li Yang, Yanchun Wang, Ziran Xu, Yang Feng, Jing Zhang, Yi Wang, Cheng‐Ran Xu
Software Mentions: 4
Published: over 4 years ago

10.1186/s13075-020-02343-4

Single-cell transcriptome conservation in a comparative analysis of fresh and cryopreserved human skin tissue: pilot in localized scleroderma
Cited by: 17
Author(s): Emily Mirizio, Tracy Tabib, Xinjun Wang, Wei Chen, Christopher Liu, Robert Lafyatis, Heidi Jacobe, Kathryn S. Torok
Software Mentions: 4
Published: about 4 years ago

10.3389/fimmu.2020.594540

The Monocytes That Repopulate in Mice After Cyclophosphamide Treatment Acquire a Neutrophil Precursor Gene Signature and Immunosuppressive Activity
Cited by: 5
Author(s): Zhi Chun Ding, Nada S. Aboelella, Locke J. Bryan, Huidong Shi, Gang Zhou
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.celrep.2020.108337

Human and Mouse Transcriptome Profiling Identifies Cross-Species Homology in Pulmonary and Lymph Node Mononuclear Phagocytes
Cited by: 37
Author(s): Sonia M. Leach, Sophie L. Gibbings, Anita Tewari, Shaikh M. Atif, Brian Vestal, Thomas Danhorn, William J. Janssen, Tor D. Wager, Claudia Jakubzick
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-020-07289-0

Long non-coding RNA exploration for mesenchymal stem cell characterisation
Cited by: 2
Author(s): Sébastien Riquier, Marc Mathieu, Chloé Bessière, Anthony Boureux, Florence Rufflé, Jean-Marc Lemaı̂tre, Farida Djouad, Nicolas Gilbert, Thérèse Commes
Software Mentions: 4
Published: over 3 years ago

10.1186/s40425-018-0423-x

33rd Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)
Cited by: 24
Author(s): Adi Diab, Scott S. Tykodi, Brendan D. Curti, Daniel Cho, M. K. Wong, Igor Puzanov, Karl D. Lewis, Michele Maio, Gregory A. Daniels, Alexander I. Spira, Mary Tagliaferri, Alison L. Hannah, Wendy Clemens, Michael J. Imperiale, Chantale Bernatchez, Cara L. Haymaker, Salah Eddine Bentebibel, Jonathan Zalevsky, Ute Hoch, Christie Fanton, Ahsan Rizwan, Sandra Aung, Fiore Cattaruzza, Ernesto Iaccucci, Dariusz Sawka, Mehmet Asım Bilen, Paul Lorigan, Giovanni Grignani, James Larkin, Sekwon Jang, Ewa Kalinka Warzocha, Mario Sznol, Mike Hurwitz
Software Mentions: 4
Published: about 6 years ago

10.1186/s13073-020-0720-0

A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles
Cited by: 30
Author(s): Li Wang, Robert Sebra, John P. Sfakianos, Kimaada Allette, Wenhui Wang, Seungyeul Yoo, Nina Bhardwaj, Eric E. Schadt, Xin Yao, Matthew D. Galsky, Jun Zhu
Software Mentions: 4
Published: over 4 years ago

10.1186/s13073-021-00922-x

High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification
Cited by: 52
Author(s): Siel Olbrecht, Pieter Busschaert, Jun Qian, Adriaan Vanderstichele, Liselore Loverix, Toon Van Gorp, Els Van Nieuwenhuysen, Sileny Han, Annick Van den Broeck, An Coosemans, Anne‐Sophie Van Rompuy, Diether Lambrechts, Ignace Vergote
Software Mentions: 4
Published: over 3 years ago

10.1038/s41389-021-00311-4

Single-cell RNA sequencing reveals that targeting HSP90 suppresses PDAC progression by restraining mitochondrial bioenergetics
Cited by: 8
Author(s): Li-Peng Hu, Kaixia Zhou, Yan‐Miao Huo, Dejun Liu, Qing Li, Minwei Yang, Peng Huang, Chunjie Xu, Guang-Ang Tian, Lishuang Yao, Xueli Zhang, Yahui Wang, Jun Li, Zhigang Zhang, Shu-Heng Jiang, Xin Xing, Xu Wang, Weiting Qin, Qin Yang
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-021-02362-7

SpatialDWLS: accurate deconvolution of spatial transcriptomic data
Cited by: 107
Author(s): Rui Dong, Guo‐Cheng Yuan
Software Mentions: 4
Published: over 3 years ago

10.4049/jimmunol.1900940

<i>Malat1</i> Suppresses Immunity to Infection through Promoting Expression of Maf and IL-10 in Th Cells
Cited by: 45
Author(s): James P. Hewitson, Katie A West, Kylie R. James, Gulab Fatima Rani, Nidhi Sharma Dey, Audrey Romano, Najmeeyah Brown, Sarah A. Teichmann, Paul M. Kaye, Dimitrios Lagos
Software Mentions: 4
Published: over 4 years ago

10.1084/jem.20202446

GSAP regulates lipid homeostasis and mitochondrial function associated with Alzheimer’s disease
Cited by: 14
Author(s): Peng Xu, Jerry C. Chang, Xiaopu Zhou, Wei Wang, Michael Bamkole, Eitan Wong, Karima Bettayeb, LuLin Jiang, Timothy Huang, Wenjie Luo, Huaxi Xu, Angus C. Nairn, Marc Flajolet, Nancy Y. Ip, Yueming Li, Paul Greengard
Software Mentions: 4
Published: over 3 years ago

10.1186/s13024-021-00423-w

Methods to investigate intrathecal adaptive immunity in neurodegeneration
Cited by: 11
Author(s): Hamilton Oh, Olivia Leventhal, Divya Channappa, Victor W. Henderson, Tony Wyss‐Coray, Benoit Lehallier, David Gate
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-021-02364-5

scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing
Cited by: 6
Author(s): Gavin Wilson, Mathieu Derouet, Gail Darling, Jonathan C. Yeung
Software Mentions: 4
Published: over 3 years ago

10.1084/jem.20190730

Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid
Cited by: 47
Author(s): Guillermo L. Lehmann, Christin Hanke-Gogokhia, Yang Hu, Rohan Bareja, Zelda Salfati, Michael Ginsberg, Daniel J. Nolan, Santiago P. Méndez-Huergo, Tomás Dalotto-Moreno, Alexandre Wojcinski, Francisca Ochoa, Siyuan Zeng, Juan P. Cerliani, Lampros Panagis, Patrick J. Zager, Robert F. Mullins, Shuntaro Ogura, Gerard A. Lutty, Jakyung Bang, Jonathan H. Zippin, Carmelo Romano, Gabriel A. Rabinovich, Olivier Elemento, Alexandra L. Joyner, Shahin Rafii, Enrique Rodríguez-Boulan, Ignacio Benedicto
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-020-02238-2

scMC learns biological variation through the alignment of multiple single-cell genomics datasets
Cited by: 418
Author(s): Lihua Zhang, Qing Nie
Software Mentions: 4
Published: almost 4 years ago

10.3389/fimmu.2021.693608

Single-Cell RNA Sequencing Reveals the Immunological Profiles of Renal Allograft Rejection in Mice
Cited by: 11
Author(s): Qixia Shen, Yucheng Wang, Jiaoyi Chen, Lifeng Ma, Xiao‐Ru Huang, Sydney C. W. Tang, Hui‐Yao Lan, Hong Jiang, Jianghua Chen
Software Mentions: 4
Published: over 3 years ago

10.18632/aging.202857

Two reactive behaviors of chondrocytes in an IL-1β-induced inflammatory environment revealed by the single-cell RNA sequencing
Cited by: 4
Author(s): Chenghao Gao, Hongxu Pu, Qian Zhou, Tenghui Tao, Hui Liu, Xuying Sun, Ximiao He, Jun Xiao
Software Mentions: 4
Published: over 3 years ago

10.1007/s00018-021-03822-w

Immune cells lacking Y chromosome show dysregulation of autosomal gene expression
Cited by: 43
Author(s): Jan P. Dumanski, Jonatan Halvardson, Hanna Davies, Edyta Rychlicka-Buniowska, Jonas Mattisson, Behrooz Torabi Moghadam, Noémi Nagy, Kazimierz Węglarczyk, Karolina Bukowska-Straková, Marcus Danielsson, Paweł Olszewski, Arkadiusz Piotrowski, Erin Oerton, Aleksandra Ambicka, Marcin Przewoźnik, Łukasz Bełch, Tomasz Grodzicki, Piotr Chłosta, Stefan Imreh, Vilmantas Giedraitis, Lena Kilander, Jessica Nordlund, Adam Ameur, Ulf Gyllensten, Åsa Johansson, Alicja Józkowicz, Maciej Siedlar, Alicja Klich-Rączka, Janusz Jaszczyński, Stefan Enroth, Jarosław Baran, Martin Ingelsson, John Perry, Janusz Ryś, Lars A. Forsberg
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-021-02281-7

scSorter: assigning cells to known cell types according to marker genes
Cited by: 43
Author(s): Hongqian Guo, Jun Li
Software Mentions: 4
Published: almost 4 years ago

10.1084/jem.20201189

αβγδ T cells play a vital role in fetal human skin development and immunity
Cited by: 17
Author(s): René Reitermaier, Thomas Krausgruber, Nikolaus Fortelny, Tanya Ayub, Pablo A. Vieyra‐Garcia, Philip Kienzl, Peter Wolf, Anke Scharrer, Christian Fiala, Marita Kölz, Manuela Hiess, Martin Vierhapper, Christopher Schuster, Andreas Spittler, Christof Worda, Wolfgang Weninger, Christoph Bock, Wolfgang Eppel, Adelheid Elbe‐Bürger
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13073-021-00933-8

Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19
Cited 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

10.1093/hmg/ddab140

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
Cited by: 15
Author(s): Andrew P. Voigt, Nathaniel K. Mullin, S. Scott Whitmore, Adam P. DeLuca, Erin R Burnight, Xiuying Liu, Budd A. Tucker, Todd E. Scheetz, Edwin M Stone, Robert F. Mullins
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.66417

Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19
Cited by: 56
Author(s): Courtney Tindle, MacKenzie Fuller, Ayden G. Fonseca, Sahar Taheri, Stella‐Rita Ibeawuchi, Nathan Beutler, Gajanan D. Katkar, Amanraj Claire, Vanessa Castillo, Moises Hernandez, Hana Russo, Jason Duran, Laura E. Crotty Alexander, Ann Tipps, Grace Lin, Patricia A. Thistlethwaite, Ranajoy Chattopadhyay, Thomas F. Rogers, Debashis Sahoo, Pradipta Ghosh, Soumita Das
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-02084-2

GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing
Cited by: 34
Author(s): Hongyi Xin, Qiuyu Lian, Yale Jiang, Jianmin Luo, Xinjun Wang, Carla Erb, Zhongli Xu, Xiaoyi Zhang, Elisa Heidrich-O’Hare, Qi Yan, Richard H. Duerr, Kong Chen, Wei Chen
Software Mentions: 4
Published: over 4 years ago

10.3390/metabo10120513

Single-Cell Transcriptional Profiling of Mouse Islets Following Short-Term Obesogenic Dietary Intervention
Cited by: 12
Author(s): Annie R. Piñeros, Hongyu Gao, Wenting Wu, Yunlong Liu, Sarah A. Tersey, Raghavendra G. Mirmira
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-020-07334-y

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets
Cited by: 9
Author(s): Hongyu Liu, N M Prashant, Liam F. Spurr, Pavlos Bousounis, Nawaf Alomran, Helen Ibeawuchi, Justin Sein, Piotr Słowiński, Krasimira Tsaneva-Atanasova, Anélia Horvath
Software Mentions: 4
Published: almost 4 years ago

10.1097/MD.0000000000026775

Single-cell transcriptional profiling reveals the heterogeneity in embryonal rhabdomyosarcoma
Cited by: 1
Author(s): Bo Hong, Tian Xia, Chun-Jing Ye, Yong Zhan, Ran Yang, Jia Liu, Yang Li, Zhi-Xue Chen, Wei Yao, Kai Li, Jia Wang, Rui Dong
Software Mentions: 4
Published: over 3 years ago

10.1038/s41421-021-00271-4

Single-cell analysis of pancreatic ductal adenocarcinoma identifies a novel fibroblast subtype associated with poor prognosis but better immunotherapy response
Cited by: 90
Author(s): Yu Wang, Yongfeng Liang, Haiyan Xu, Xiao Zhang, Tiebo Mao, Jiujie Cui, Jiyong Yao, Yongchao Wang, Feng Jiao, Xiuying Xiao, Jiong Hu, Qing Xia, Xiaofei Zhang, Xujun Wang, Yongwei Sun, Deliang Fu, Lei Shen, Ximing Xu, Jing Xue, Liwei Wang
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.599261

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection
Cited by: 53
Author(s): Komudi Singh, Yunching Chen, Shakiba Hassanzadeh, Han Kim, Jennifer Judy, Fayaz Seifuddin, Ilker Tunc, Michael N. Sack, Mehdi Pirooznia
Software Mentions: 4
Published: over 3 years ago

10.1038/s41421-020-0157-z

Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human
Cited by: 119
Author(s): Juanjuan Zhao, Shuye Zhang, Yang Liu, Xiaomeng He, Mengmeng Qu, Gang Xu, Hongbo Wang, Man Huang, Jing Pan, Zhenwen Liu, Zhiwei Li, Lei Liu, Zheng Zhang
Software Mentions: 4
Published: over 4 years ago

10.1186/s13395-021-00269-2

Single cell RNA-seq analysis of the flexor digitorum brevis mouse myofibers
Cited by: 5
Author(s): Rohan Verma, Suraj Kannan, Brian L. Lin, Katherine M. Fomchenko, Tim O. Nieuwenhuis, Arun H. Patil, Clarisse Lukban, Xiao‐Ping Yang, Karen Fox-Talbot, Matthew N. McCall, Chulan Kwon, David A. Kass, Avi Rosenberg, Marc K. Halushka
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.719099

Interpretable, Scalable, and Transferrable Functional Projection of Large-Scale Transcriptome Data Using Constrained Matrix Decomposition
Cited by: 2
Author(s): Nicholas Panchy, Kazuhide Watanabe, Tian Hong
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-96837-z

Partitioning of gene expression among zebrafish photoreceptor subtypes
Cited by: 20
Author(s): Yohsuke Ogawa, Joseph C. Corbo
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-021-98806-y

Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis
Cited by: 36
Author(s): Zhongyi Wang, Adrian Keogh, Annick Waldt, Rachel Cuttat, Marilisa Neri, Shuchai Zhu, Sven Schuierer, Alexandra Ruchti, Christophe Crochemore, Judith Knehr, Julie Bastien, Iwona Ksiazek, Daniel Sánchez-Taltavull, Hui Ge, Jing Wu, Guglielmo Roma, Stephen B. Helliwell, Deborah Stroka, Florian Nigsch
Software Mentions: 4
Published: about 3 years ago

10.26508/lsa.201900443

De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments
Cited by: 7
Author(s): Hyung Jun Woo, Boris Winterhoff, Timothy K. Starr, Constantin F. Aliferis, Jinhua Wang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41419-021-03826-1

Gata2-L359V impairs primitive and definitive hematopoiesis and blocks cell differentiation in murine chronic myelogenous leukemia model
Cited by: 7
Author(s): Yanbin Fu, Yun Tan, Baichang Wu, Yuting Dai, Xiaoguang Xu, Mengmeng Pan, Zhiwei Chen, Na Qiao, Jing Wu, Lu Jiang, Jing Lu, Bing Chen, Avigail Rein, Shai Izraeli, Xiao Jian Sun, Jinyan Huang, Qiu-Hua Huang, Zhu Chen, Sai‐Juan Chen
Software Mentions: 4
Published: over 3 years ago

10.26508/lsa.201900561

Refining the adipose progenitor cell landscape in healthy and obese visceral adipose tissue using single-cell gene expression profiling
Cited by: 40
Author(s): Dong Seong Cho, Bolim Lee, Jason D. Doles
Software Mentions: 4
Published: almost 5 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

10.1038/s41419-021-03832-3

Comparison of the major cell populations among osteoarthritis, Kashin–Beck disease and healthy chondrocytes by single-cell RNA-seq analysis
Cited by: 35
Author(s): Wang Xi, Yujie Ning, Pan Zhang, Blandine Poulet, Ruitian Huang, Yi Gong, Minhan Hu, Cheng Li, Rong Zhou, Mikko J. Lammi, Xiong Guo
Software Mentions: 4
Published: over 3 years ago

10.1038/s41419-021-04075-y

A Catalogus Immune Muris of the mouse immune responses to diverse pathogens
Cited by: 0
Author(s): Céline Barlier, Diego Barriales, Alexey Samosyuk, Sascha Jung, Srikanth Ravichandran, Yulia A. Medvedeva, Juan Anguíta, Antonio del Sol
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-1932-8

scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles
Cited by: 91
Author(s): Suoqin Jin, Lihua Zhang
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2020.599834

An Integrated Transcriptome Analysis Reveals IGFBP7 Upregulation in Vasculature in Traumatic Brain Injury
Cited by: 3
Author(s): Jianhao Wang, Xiangyi Deng, Yuan Xie, Jiefu Tang, Ziwei Zhou, Fan Yang, Qiyuan He, Qingze Cao, Lei Zhang, Liqun He
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2020.572242

EC-PGMGR: Ensemble Clustering Based on Probability Graphical Model With Graph Regularization for Single-Cell RNA-seq Data
Cited by: 4
Author(s): Youwen Zhu, Dexin Zhang, Xiaofei Zhang, Ming Yi, Le Ou-Yang, Mengyun Wu
Software Mentions: 4
Published: about 4 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

10.1186/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

10.18632/aging.103945

Single-cell transcriptome analysis demonstrates inter-patient and intra-tumor heterogeneity in primary and metastatic lung adenocarcinoma
Cited by: 20
Author(s): Yafei Liu, Guanchao Ye, Lan Huang, Chunyang Zhang, Yinliang Sheng, Bin Wu, Lu Han, Chunli Wu, Bo Dong, Yu Qi
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-87805-8

Integrin αvβ5 heterodimer is a specific marker of human pancreatic beta cells
Cited by: 4
Author(s): Jacqueline V. Schiesser, Thomas Loudovaris, Helen E. Thomas, Andrew G. Elefanty
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-91625-1

Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Cited by: 24
Author(s): Brian Le, Gaia Andreoletti, Tomiko Oskotsky, Albert Vallejo-Gracia, Romel Rosales, Katharine Yu, Idit Kosti, Kristoffer E. Leon, Daniel Bunis, Christine Li, G. Renuka Kumar, Kris M. White, Adolfo Garcı́a-Sastre, Mélanie Ott, Marina Sirota
Software Mentions: 4
Published: over 3 years ago

10.1186/s12915-021-01122-0

Single-cell analysis of cell fate bifurcation in the chordate Ciona
Cited by: 4
Author(s): Konner Winkley, Wendy Reeves, Michael Veeman
Software Mentions: 4
Published: about 3 years ago

10.1111/cns.13396

Effect of intra‐ and inter‐tumoral heterogeneity on molecular characteristics of primary IDH‐wild type glioblastoma revealed by single‐cell analysis
Cited by: 22
Author(s): Zujian Xiong, Qi Yang, Xuejun Li
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers11101566

PD-1-Associated Gene Expression Signature of Neoadjuvant Trastuzumab-Treated Tumors Correlates with Patient Survival in HER2-Positive Breast Cancer
Cited by: 6
Author(s): William P.D. Hendricks, Natalia Briones, Rebecca F. Halperin, Salvatore Facista, Paul R. Heaton, Daruka Mahadevan, Suwon Kim
Software Mentions: 4
Published: about 5 years ago

10.1128/mBio.01959-21

Multifactorial Role of Mitochondria in Echinocandin Tolerance Revealed by Transcriptome Analysis of Drug-Tolerant Cells
Cited by: 13
Author(s): Rocio Garcia-Rubio, Cristina Jiménez‐Ortigosa, Lucius DeGregorio, Christopher Quinteros, Erika Shor, David S. Perlin
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-020-69182-w

Identification of TNFAIP3 as relapse biomarker and potential therapeutic target for MOG antibody associated diseases
Cited by: 9
Author(s): Shrishti Saxena, Hrishikesh Lokhande, Grace Gombolay, Radhika Raheja, Timothy B. Rooney, Tanuja Chitnis
Software Mentions: 4
Published: over 4 years ago

10.1186/s12915-020-00874-5

Automated identification of the mouse brain’s spatial compartments from in situ sequencing data
Cited by: 16
Author(s): Gabriele Partel, Markus M. Hilscher, Milli Giorgia, Leslie Solorzano, Anna H. Klemm, Mats Nilsson, Carolina Wählby
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-66848-3

Identification of cell types from single cell data using stable clustering
Cited by: 24
Author(s): Azam Peyvandipour, Adib Shafi, Nafiseh Saberian, Sorin Drăghici
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-70353-y

Single-cell RNA sequencing uncovers heterogenous transcriptional signatures in macrophages during efferocytosis
Cited by: 43
Author(s): Connor Lantz, Behram Radmanesh, Esther Liu, Edward B. Thorp, Jennie Lin
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2020.00867

Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts
Cited by: 13
Author(s): Wei Chen, Xuefei Wang, Gang Wei, Yin Huang, Yufang Shi, Dan Li, Shengnu Qiu, Bin Zhou, Junhong Cao, Meng Chen, Pengfei Qin, Wenfei Jin, Ting Ni
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-74598-5

Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19
Cited by: 36
Author(s): Anna A. Valyaeva, Anastasia A. Zharikova, Artem S. Kasianov, Yegor S. Vassetzky, Eugene V. Sheval
Software Mentions: 4
Published: about 4 years ago

10.3390/cancers12123639

Single-Cell RNA Sequencing of a Postmenopausal Normal Breast Tissue Identifies Multiple Cell Types That Contribute to Breast Cancer
Cited by: 13
Author(s): Sen Peng, Lora L. Hebert, Jennifer Eschbacher, Suwon Kim
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-018-1416-2

Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
Cited by: 135
Author(s): Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 6 years ago

10.1002/advs.202000938

Atlas of Musculoskeletal Stem Cells with the Soft and Hard Tissue Differentiation Architecture
Cited by: 7
Author(s): Zi Yin, Junxin Lin, Ruojin Yan, Richun Liu, Mengfei Liu, Bo Zhou, Wenyan Zhou, An Chen, Yangwu Chen, Yin Hu, Chunmei Fan, Kun Zhao, Bowen Wu, Xiaohui Zou, Jin Zhang, Ahmed El-Hashash, Xiao Chen
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-018-1426-0

Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing
Cited by: 79
Author(s): Xiaoping Han, Haide Chen, Daosheng Huang, Huidong Chen, Lijiang Fei, Chen Cheng, He Huang, Guo Cheng Yuan, Guoji Guo
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-019-2977-0

RESCUE: imputing dropout events in single-cell RNA-sequencing data
Cited by: 26
Author(s): Sam Tracy, Guo‐Cheng Yuan, Ruben Dries
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0258029

Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq
Cited by: 4
Author(s): Ying Yao, Łukasz Wyrozżemski, Knut E.A. Lundin, Geir Kjetil Sandve
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-020-64514-2

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype
Cited by: 12
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Kathryn A. Helmin, Basil Khuder, Cynthia Rothblum-Oviatt, Joseph M. Collaco, Jonathan H. Wright, Paul A. Reyfman, Howard M. Lederman, Benjamin D. Singer
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-76157-4

The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution
Cited by: 12
Author(s): Denise Anderson, Patrycja Skut, Anastasia M. Hughes, Emanuela Ferrari, Jennifer Tickner, Jiake Xu, Benjamin H. Mullin, Dave Tang, Sébastien Malinge, Ursula R. Kees, Rishi S. Kotecha, Timo Lassmann, Laurence C. Cheung
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-018-35365-9

Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA)
Cited by: 7
Author(s): Dong‐Hyung Lee, Anthony Cheng, Nathan Lawlor, Mohan Bolisetty, Duygu Ucar
Software Mentions: 4
Published: about 6 years ago

10.3390/genes11060709

Extensive Involvement of Alternative Polyadenylation in Single-Nucleus Neurons
Cited by: 3
Author(s): Ying Wang, Weixing Feng, Siwen Xu, Bo He
Software Mentions: 4
Published: over 4 years ago

10.3390/genes11040377

Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type Identification
Cited by: 15
Author(s): Maryam Zand, Jianhua Ruan
Software Mentions: 4
Published: over 4 years ago

10.1126/sciimmunol.abe1670

MAIT cell activation and dynamics associated with COVID-19 disease severity
Cited by: 138
Author(s): Tiphaine Parrot, Jean‐Baptiste Gorin, Andrea Ponzetta, Kimia T. Maleki, Tobias Kammann, Johanna Emgård, André Perez‐Potti, Takuya Sekine, Olga Rivera‐Ballesteros, Sara Gredmark‐Russ, Olav Rooyackers, Elin Folkesson, Lars Eriksson, Anna Norrby‐Teglund, Hans‐Gustaf Ljunggren, Niklas K. Björkström, Soo Aleman, Marcus Buggert, Jonas Klingström, Kristoffer Strålin, Johan K. Sandberg
Software Mentions: 4
Published: about 4 years ago

10.1534/g3.120.401160

Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment
Cited by: 31
Author(s): Yuheng Du, Qizhao Huang, Cédric Arisdakessian, Lana X. Garmire
Software Mentions: 4
Published: over 4 years ago

10.1038/s12276-020-00538-y

Tumor-promoting macrophages prevail in malignant ascites of advanced gastric cancer
Cited by: 39
Author(s): Hye Hyeon Eum, Minsuk Kwon, Daeun Ryu, Areum Jo, Wingyan Chung, Nayoung Kim, Yourae Hong, Dae‐Soon Son, Seung Tae Kim, Jeeyun Lee, Hae‐Ock Lee, Woong-Yang Park
Software Mentions: 4
Published: almost 4 years ago

10.1038/s12276-020-0420-2

Single-cell multiomics: technologies and data analysis methods
Cited by: 239
Author(s): Jeongwoo Lee, Do Young Hyeon, Daehee Hwang
Software Mentions: 4
Published: about 4 years ago

10.1038/s12276-020-00499-2

Single-cell sequencing techniques from individual to multiomics analyses
Cited by: 116
Author(s): Yukie Kashima, Yoshitaka Sakamoto, Keiya Kaneko, Masahide Seki, Yutaka Suzuki, Ayako Suzuki
Software Mentions: 4
Published: about 4 years ago

10.3389/fphar.2021.754933

Immune Cell Landscape of Patients With Diabetic Macular Edema by Single-Cell RNA Analysis
Cited by: 10
Author(s): Pingping Ma, Ping Zhang, Shuxia Chen, Wen Shi, Jinguo Ye, Shida Chen, Rong Ju, Bingqian Liu, Yingfeng Zheng, Yizhi Liu
Software Mentions: 4
Published: about 3 years ago

Projects: cran: Seurat

Papers Mentioning Seurat 1,512