cran: Seurat | Projects | Ecosyste.ms: Papers

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

10.1186/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

10.3389/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

10.3389/fimmu.2021.691142

Dynamic Network Biomarker of Pre-Exhausted CD8+ T Cells Contributed to T Cell Exhaustion in Colorectal Cancer
Cited by: 16
Author(s): Jiaqi Hu, Chongyin Han, Jiayuan Zhong, Huisheng Liu, Rui Li, Wei Luo, Pei Chen, Fei Ling
Software Mentions: 4
Published: over 3 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

10.3389/fimmu.2020.00216

FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells
Cited by: 26
Author(s): Noudjoud Attaf, Iñaki Cervera-Marzal, Chuang Dong, Laurine Gil, Amédée Renand, Lionel Spinelli, Pierre Milpied
Software Mentions: 4
Published: over 4 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

10.1186/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

10.1186/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

10.3389/fcvm.2021.628885

Single-Cell Transcriptome Analysis Decipher New Potential Regulation Mechanism of ACE2 and NPs Signaling Among Heart Failure Patients Infected With SARS-CoV-2
Cited by: 13
Author(s): Mengqiu Ma, Yanhua Xu, Yang Su, Sang‐Bing Ong, Xingdong Hu, Min Chai, Maojun Zhao, Hong Li, Xiaojuan Fan, Yingjie Chen, Dan Xu, Xiaojiang Xu
Software Mentions: 4
Published: over 3 years ago

10.3389/fbioe.2020.00348

Analysis of Gene Signatures of Tumor Microenvironment Yields Insight Into Mechanisms of Resistance to Immunotherapy
Cited by: 4
Author(s): Ben Wang, Mengmeng Liu, Zhujie Ran, Xin Li, Jie Li, Yunsheng Ou
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2021.623430

Multi-Modal Characterization of Monocytes in Idiopathic Pulmonary Fibrosis Reveals a Primed Type I Interferon Immune Phenotype
Cited by: 28
Author(s): Emily Fraser, Laura Denney, Agne Antanaviciute, Karl Blirando, Chaitanya Vuppusetty, Yuejuan Zheng, Emmanouela Repapi, Valentina Iotchkova, Stephen Taylor, Neil Ashley, Victoria St Noble, Rachel Benamore, Rachel Hoyles, Colin Clelland, Joseph M. Rastrick, Clare S. Hardman, Nasullah Khalid Alham, Rachel E. Rigby, Alison Simmons, Jan Rehwinkel, Ling-Pei Ho
Software Mentions: 4
Published: over 3 years ago

10.3389/fbioe.2020.00035

Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development
Cited by: 13
Author(s): Yongzhong Xing, Weihao Yang, Guoqing Liu, Xiangjun Cui, Hu Meng, Hongyu Zhao, Xingbo Zhao, Jun Li, Zhe Liu, Michael Q. Zhang, Liang Cai
Software Mentions: 4
Published: almost 5 years ago

10.3389/fcell.2021.668833

Detection of Hematopoietic Stem Cell Transcriptome in Human Fetal Kidneys and Kidney Organoids Derived From Human Induced Pluripotent Stem Cells
Cited by: 3
Author(s): Jin Wook Hwang, Christophe Desterke, Julien Loisel‐Duwattez, Frank Griscelli, Annelise Bennaceur‐Griscelli, Ali G Turhan
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

10.3389/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

10.1186/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

10.1038/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

10.3389/fcell.2018.00108

Experimental Considerations for Single-Cell RNA Sequencing Approaches
Cited by: 125
Author(s): Quy Nguyen, Nicholas Pervolarakis, Kevin Nee, Kai Kessenbrock
Software Mentions: 4
Published: about 6 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

10.5808/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

10.3389/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/s13072-021-00418-3

Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation
Cited by: 5
Author(s): Yujuan Gui, Kamil Grzyb, Mélanie Thomas, Jochen Ohnmacht, Pierre Garcia, Manuel Buttini, Alexander Skupin, Thomas Sauter, Lasse Sinkkonen
Software Mentions: 4
Published: about 3 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

10.1007/s00401-021-02322-2

Altered oligodendroglia and astroglia in chronic traumatic encephalopathy
Cited by: 25
Author(s): Kevin Blake Chancellor, Sarah E. Chancellor, Joseph E. Duke-Cohan, Bertrand R. Huber, Thor D. Stein, Victor E. Alvarez, Benjamin W. Okaty, Susan M. Dymecki, Ann C. McKee
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

10.1002/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

10.1186/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

10.1186/s13293-020-00335-2

Investigating transcriptome-wide sex dimorphism by multi-level analysis of single-cell RNA sequencing data in ten mouse cell types
Cited by: 18
Author(s): Tianyuan Lu, Jessica C. Mar
Software Mentions: 4
Published: about 4 years ago

10.18632/aging.203168

Cell landscape atlas for patients with chronic thromboembolic pulmonary hypertension after pulmonary endarterectomy constructed using single-cell RNA sequencing
Cited by: 8
Author(s): Ran Miao, Xingbei Dong, Juanni Gong, Yidan Li, Xiaojuan Guo, Jianfeng Wang, Qiang Huang, Ying Wang, Jifeng Li, Suqiao Yang, Tuguang Kuang, Jun Wan, Min Liu, Zhenguo Zhai, Jiuchang Zhong, Yuanhua Yang
Software Mentions: 4
Published: over 3 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

10.15252/embj.2019104159

Deciphering the regulatory landscape of fetal and adult γδ T‐cell development at single‐cell resolution
Cited by: 38
Author(s): Sagar, Maria Pokrovskii, Josip Stefan Herman, Shruti Naik, Elisabeth Sock, Patrice Zeis, Ute Lausch, Michael Wegner, Yakup Tanriver, Dan R. Littman, Dominic Grün
Software Mentions: 4
Published: over 4 years ago

10.1242/bio.047829

Heterogeneous beta-catenin activation is sufficient to cause hepatocellular carcinoma in zebrafish
Cited by: 13
Author(s): Sharanya Maanasi Kalasekar, Srishti Kotiyal, Christopher J. Conley, Cindy Phan, Annika Young, Kimberley Evason
Software Mentions: 4
Published: almost 6 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

10.1186/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/fcell.2021.735307

Transcriptomic Signatures of Airway Epithelium Infected With SARS-CoV-2: A Balance Between Anti-infection and Virus Load
Cited by: 3
Author(s): Lingzhang Meng, Houji Qin, Jingjie Zhao, Siyuan He, Qiuju Wei, Zechen Wang, Jiajia Shen, Suren R. Sooranna, Jian Song
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

10.3389/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

10.1093/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

10.1084/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

10.1371/journal.pcbi.1007488

Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process
Cited by: 9
Author(s): Jifan Shi, Tiejun Li, Luonan Chen, Kazuyuki Aihara
Software Mentions: 4
Published: about 5 years ago

10.1038/s42003-020-0888-2

Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cells
Cited by: 21
Author(s): Soyeong Jun, Hee‐Jung Lim, Honggu Chun, Ji Hyun Lee, Duhee Bang
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pcbi.1007040

PanoView: An iterative clustering method for single-cell RNA sequencing data
Cited by: 15
Author(s): Ming Hu, Dong Won Kim, Sheng Liu, Donald J. Zack, Seth Blackshaw, Jiang Qian
Software Mentions: 4
Published: about 5 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

10.1128/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

10.3389/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

10.3389/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

10.1186/s12859-019-2952-9

Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data
Cited by: 19
Author(s): Savvas Kinalis, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger
Software Mentions: 4
Published: over 5 years ago

10.1002/jbm4.10496

Single‐Cell <scp>RNA</scp>‐Sequencing Reveals the Breadth of Osteoblast Heterogeneity
Cited by: 11
Author(s): Hirotaka Yoshioka, Saki Okita, Masashi Nakano, Takeshi Minamizaki, Asako Nubukiyo, Yusuke Sotomaru, Edith Bonnelye, Katsuyuki Kozai, Kotaro Tanimoto, Jane E. Aubin, Yuji Yoshiko
Software Mentions: 4
Published: over 3 years ago

10.18632/aging.202950

Multiomics integrative analysis identifies APOE allele-specific blood biomarkers associated to Alzheimer’s disease etiopathogenesis
Cited by: 13
Author(s): Laura Madrid, Sonia Moreno‐Grau, Shahzad Ahmad, Antonio González‐Pérez, Itziar de Rojas, Rui Xia, Pamela Victoria Martino Adami, Pablo García‐González, Luca Kleineidam, Qiong Yang, Vincent Damotte, Joshua C. Bis, Fuensanta Noguera-Perea, Céline Bellenguez, Xueqiu Jian, Juan Marín-Muñoz, Benjamin Grenier‐Boley, Adela Orellana, M. Arfan Ikram, Philippe Amouyel, Claudia L. Satizábal, Alzheimer’s Disease Neuroimaging Initiative, Luis Miguel Real, Carmen Antúnez-Almagro, Anita L. DeStefano, Alfredo Cabrera-Socorro, Rebecca Sims, Cornelia M. van Duijn, Eric Boerwinkle, Alfredo Ramı́rez, Myriam Fornage, Jean‐Charles Lambert, Julie Williams, Sudha Seshadri, Janina S. Ried, Agustín Ruiz, María Eugenia Sáez
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-020-1028-8

Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures
Cited by: 31
Author(s): Åsa Wallén-Mackenzie, Sylvie Dumas, Maria Papathanou, Mihaela M. Martis, Bianca Vlcek, Niclas König, Åsa K. Björklund
Software Mentions: 4
Published: over 4 years ago

10.1093/bioinformatics/btab178

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples
Cited by: 13
Author(s): Antti Häkkinen, Kaiyang Zhang, Amjad Alkodsi, Noora Andersson, Erdoğan Pekcan Erkan, Jun Dai, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Anna Vähärautio, Olli Carpén, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 4
Published: over 3 years ago

10.1101/2021.03.26.21254445

Long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 are differentially expressed in severe COVID-19 patients: An integrated single cell analysis
Cited by: 5
Author(s): Huang Kai, Catherine Wang, Christen Vagts, Vanitha Raguveer, Patricia W. Finn, David L. Perkins
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

10.1038/s42003-021-02208-9

Systemic GLP-1R agonist treatment reverses mouse glial and neurovascular cell transcriptomic aging signatures in a genome-wide manner
Cited by: 5
Author(s): Zhongqi Li, Xinyi Chen, Joaquim S. L. Vong, Lei Zhao, Junzhe Huang, Leo Y. C. Yan, Bonaventure Ip, Yun Kwok Wing, H. M. Lai, Vincent Mok, Ho Ko
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-021-02562-8

Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma
Cited by: 13
Author(s): Alexander Bondoc, Kathryn Glaser, Kang Jin, Charissa Lake, Stefano Cairo, James I. Geller, Gregory M. Tiao, Bruce J. Aronow
Software Mentions: 3
Published: about 3 years ago

10.1126/scitranslmed.abe8146

Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys
Cited by: 128
Author(s): Emily Speranza, Brandi N. Williamson, Friederike Feldmann, Gail L. Sturdevant, Lizzette Pérez-Pérez, Kimberly Meade-White, Brian J Smith, Jamie Lovaglio, Craig Martens, Vincent J. Munster, Atsushi Okumura, Carl Shaia, Heinz Feldmann, Sonja M. Best, Emmie de Wit
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pbio.3000421

Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy
Cited by: 44
Author(s): Reshef Tal, Shafiq Shaikh, Pallavi Pallavi, Aya Tal, Francesc López-Giráldez, Fang Lyu, Yuanyuan Fang, Shruti Chinchanikar, Ying Liu, Harvey J. Kliman, Myles H. Alderman, Nicola Pluchino, Jehanzeb Kayani, Ramanaiah Mamillapalli, Diane S. Krause, Hugh S. Taylor
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-96195-w

Durable tracking anti-SARS-CoV-2 antibodies in cancer patients recovered from COVID-19
Cited by: 0
Author(s): Yongsheng Huang, Jing Yu, Dan Li, Kai He, Wenyang Liu, Lin Wang, Yeshan Chen, Conghua Xie, Xiaowei Wu
Software Mentions: 3
Published: about 3 years ago

10.1186/s12859-019-2817-2

A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification
Cited by: 7
Author(s): Douglas N. Abrams, Parveen Kumar, R. Krishna Murthy Karuturi, Joshy George
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-91846-4

High-resolution transcriptional landscape of xeno-free human induced pluripotent stem cell-derived cerebellar organoids
Cited by: 28
Author(s): Samuel Nayler, Devika Agarwal, Fabiola Curion, Rory Bowden, Esther B. E. Becker
Software Mentions: 3
Published: over 3 years ago

10.1002/advs.201801531

Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature‐on‐a‐Chip System Correlates with Tumor Heterogeneity and Subtypes
Cited by: 67
Author(s): Yang Xiao, Dongjoo Kim, Burak Dura, Kerou Zhang, Runchen Yan, Huamin Li, Edward Han, Joshua Ip, Pan Zou, Jun Li, Ann Tai Chen, Alexander O. Vortmeyer, Jiangbing Zhou, Rong Fan
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13395-020-00236-3

A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations
Cited by: 109
Author(s): Andrea De Micheli, Jason A. Spector, Olivier Elemento, Benjamin D. Cosgrove
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-90554-3

A potential role for somatostatin signaling in regulating retinal neurogenesis
Cited by: 5
Author(s): Kurt Weir, Dong Won Kim, Seth Blackshaw
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-021-03957-4

Selecting single cell clustering parameter values using subsampling-based robustness metrics
Cited by: 35
Author(s): Ryan B. Patterson Cross, Ariel J. Levine, Vilas Menon
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pbio.3001025

Single-cell transcriptome landscape of ovarian cells during primordial follicle assembly in mice
Cited by: 55
Author(s): Jun-Jie Wang, Wei Ge, Qiu-Yue Zhai, Jing-Cai Liu, Xiaowen Sun, Wen-Xiang Liu, Lan Li, Chuzhao Lei, Paul W. Dyce, Massimo De Felici, Wei Shen
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-82914-w

Single-cell RNA sequencing reveals developmental heterogeneity among Plasmodium berghei sporozoites
Cited by: 17
Author(s): Anthony A Ruberto, Caitlin Bourke, Nicolas Mérienne, Thomas Obadia, Rogério Amino, Ivo Müeller
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12920-018-0433-z

Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method
Cited by: 31
Author(s): Yanglan Gan, Ning Li, Guobing Zou, Yongchang Xin, Jihong Guan
Software Mentions: 3
Published: almost 6 years ago

10.3390/cells9051144

Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice
Cited by: 18
Author(s): Anne-Marie Galow, Markus Wolfien, Paula Müller, Madeleine Bartsch, Ronald M. Brunner, Andreas Hoeflich, Olaf Wolkenhauer, Róbert Dávid, Tom Goldammer
Software Mentions: 3
Published: over 4 years ago

10.3390/cells10010137

Single-Cell Profiling of Coding and Noncoding Genes in Human Dopamine Neuron Differentiation
Cited by: 7
Author(s): Fredrik Nilsson, Petter Storm, Edoardo Sozzi, David Gil, Marcella Birtele, Yogita Sharma, Malin Parmar, Alessandro Fiorenzano
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12920-021-00872-8

XenoCell: classification of cellular barcodes in single cell experiments from xenograft samples
Cited by: 6
Author(s): Stefano Cheloni, Roman Hillje, Lucilla Luzi, Pier Giuseppe Pelicci, Elena Gatti
Software Mentions: 3
Published: almost 4 years ago

10.3390/cells9020318

Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity
Cited by: 35
Author(s): Markus Wolfien, Anne-Marie Galow, Paula Müller, Madeleine Bartsch, Ronald M. Brunner, Tom Goldammer, Olaf Wolkenhauer, Andreas Hoeflich, Róbert Dávid
Software Mentions: 3
Published: almost 5 years ago

10.1007/s00441-021-03483-y

Single-cell biology to decode the immune cellular composition of kidney inflammation
Cited by: 4
Author(s): Yu Zhao, Ulf Panzer, Stefan Bonn, Christian Krebs
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-69096-7

Transcriptomic comparison of human and mouse brain microvessels
Cited by: 78
Author(s): Hannah Song, Koji L. Foreman, Benjamin D. Gastfriend, John S. Kuo, Sean P. Palecek, Eric V. Shusta
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-021-04033-7

Boosting scRNA-seq data clustering by cluster-aware feature weighting
Cited by: 2
Author(s): Ruiyi Li, Jihong Guan, Shuigeng Zhou
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-67513-5

Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM
Cited by: 50
Author(s): Marcus Alvarez, Elior Rahmani, Brandon Jew, Kristina M. Garske, Min‐Hua Zong, Jihane N. Benhammou, Chun Jimmie Ye, Joseph R. Pisegna, Kirsi H. Pietiläinen, Eran Halperin, Päivi Pajukanta
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-70673-z

Unique molecular signatures of antiviral memory CD8+ T cells associated with asymptomatic recurrent ocular herpes
Cited by: 2
Author(s): Swayam Prakash, Subhransu Roy, Ruchi Srivastava, Pierre-Gregoire A Coulon, Nisha R Dhanushkodi, Hawa Vahed, Allen Jankeel, Roger Geertsema, Cassandra Amezquita, Lan Nguyễn, Ilhem Messaoudi, Amanda M. Burkhardt, Lbachir BenMohamed
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-75657-7

Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation
Cited by: 12
Author(s): Hye‐Yeong Jo, Youngsun Lee, Hongryul Ahn, Heon-Seok Han, Ara Kwon, Boyoung Kim, Hye-Yeong Ha, Sang Cheol Kim, Jung-Hyun Kim, Yong-Ou Kim, Sun Kim, Soo Kyung Koo, Mi-Hyun Park
Software Mentions: 3
Published: about 4 years ago

10.1016/j.stem.2020.10.004

Three-Dimensional Human Alveolar Stem Cell Culture Models Reveal Infection Response to SARS-CoV-2
Cited by: 182
Author(s): Jeonghwan Youk, Taewoo Kim, Kelly V. Evans, Yoong Ki Jeong, Yong Suk Hur, Seon Pyo Hong, Je Hyoung Kim, Kijong Yi, Su Yeon Kim, Kwon Joong Na, Thomas Bleazard, Ho Min Kim, Mick D. Fellows, Krishnaa Mahbubani, Kourosh Saeb‐Parsy, Seon‐Young Kim, Young Tae Kim, Gou Young Koh, Boseung Choi, Young Seok Ju, Joo Hyeon Lee
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-019-1863-4

Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data
Cited by: 72
Author(s): Fenglin Liu, Yuanyuan Zhang, Lei Zhang, Ziyi Li, Fang Qiao, Ranran Gao
Software Mentions: 3
Published: about 5 years ago

10.3390/vaccines9060579

Predictive Markers of Immunogenicity and Efficacy for Human Vaccines
Cited by: 23
Author(s): Matthieu Van Tilbeurgh, Katia Lemdani, Anne-Sophie Beignon, Catherine Chapon, Nicolas Tchitchek, Lina Cheraitia, Ernesto Marcos López, Quentin Pascal, Roger Le Grand, Pauline Maisonnasse, Caroline Manet
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.203432

A comprehensive transcriptomic analysis of alternate interferon signaling pathways in peripheral blood mononuclear cells in rheumatoid arthritis
Cited by: 4
Author(s): Han Liang, Shenghao Tu, Pan Shen, Jiahui Yan, Yao Huang, Xin Ba, Tingting Li, Wei Chen Lin, Huihui Li, Kun Yu, Jing Guo, Ying Huang, Kai Qin, Yu Wang, Zhe Chen
Software Mentions: 3
Published: about 3 years ago

10.1186/s12859-020-03679-z

EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes
Cited by: 3
Author(s): Xiaoyang Chen, Shengquan Chen, Rui Jiang
Software Mentions: 3
Published: about 4 years ago

10.1186/s13059-018-1498-x

Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation
Cited by: 38
Author(s): Lakshmipuram S. Swapna, Alyssa M. Molinaro, Nicole Lindsay-Mosher, Bret J. Pearson, John Parkinson
Software Mentions: 3
Published: over 6 years ago

10.1038/s41422-018-0074-y

Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis
Cited by: 228
Author(s): Yao Chen, Yuxuan Zheng, Yun Gao, Zhen Lin, Suming Yang, Tongtong Wang, Qiu Wang, Nannan Xie, Rong Hua, Mingxi Liu, Jiahao Sha, Michael D. Griswold, Jinsong Li, Fuchou Tang, Ming-Han Tong
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-50310-0

Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component
Cited by: 9
Author(s): Dylan Sheerin, Daniel O’Connor, Christina Dold, Elizabeth A. Clutterbuck, Moustafa Attar, Christine S. Rollier, Manish Sadarangani, Andrew J. Pollard
Software Mentions: 3
Published: about 5 years ago

10.15252/msb.20209945

MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback
Cited by: 16
Author(s): Chung-Jung Li, Ee Shan Liau, Yi-Han Lee, Yang-Zhe Huang, Ziyi Liu, Andrew Willems, Victoria C. Garside, Edwina McGlinn, Jun-An Chen, Tian Hong
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-56038-1

LXR-inverse agonism stimulates immune-mediated tumor destruction by enhancing CD8 T-cell activity in triple negative breast cancer
Cited by: 34
Author(s): Katherine Carpenter, Aurore-Cécile Valfort, Nickolas Steinauer, Arindam Chatterjee, Suomia Abuirqeba, Shabnam Majidi, Monideepa Sengupta, Richard J. Di Paolo, Laurie P. Shornick, Jinsong Zhang, Colin A. Flaveny
Software Mentions: 3
Published: almost 5 years ago

10.1186/s40478-019-0665-y

Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral monocytes/macrophages in health and glioma
Cited by: 109
Author(s): Verena Haage, Marcus Semtner, Ramón Vidal, Daniel Hernández, Winnie W. Pong, Zhihong Chen, Dolores Hambardzumyan, Vincent Magrini, Amy Ly, Jason Walker, Elaine R. Mardis, Philipp Mertins, Sascha Sauer, Helmut Kettenmann, David H. Gutmann
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.crmeth.2021.100008

Double-jeopardy: scRNA-seq doublet/multiplet detection using multi-omic profiling
Cited by: 3
Author(s): Bo Sun, Emmanuel Bugarín-Estrada, Lauren Overend, Catherine Elizabeth Walker, Felicia Anna Tucci, Rachael Bashford-Rogers
Software Mentions: 3
Published: over 3 years ago

10.3390/genes12040509

Dynamic Expression of Imprinted Genes in the Developing and Postnatal Pituitary Gland
Cited by: 9
Author(s): Valeria Scagliotti, Ruben Esse, Thea L Willis, Mark Howard, Isabella Carrus, Emily J Lodge, Cynthia L. Andoniadou, Marika Charalambous
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-018-1603-1

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
Cited by: 608
Author(s): Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z. Yeung, William M. Mauck, Peter Smibert, Rahul Satija
Software Mentions: 3
Published: almost 6 years ago

10.15252/msb.20209866

TATA and paused promoters active in differentiated tissues have distinct expression characteristics
Cited by: 12
Author(s): Vivekanandan Ramalingam, Malini Natarajan, Jeff Johnston, Julia Zeitlinger
Software Mentions: 3
Published: almost 4 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

10.3390/genes12010028

Feature Selection for Topological Proximity Prediction of Single-Cell Transcriptomic Profiles in Drosophila Embryo Using Genetic Algorithm
Cited by: 4
Author(s): Shruti Gupta, Ajay Verma, Shandar Ahmad
Software Mentions: 3
Published: almost 4 years ago

10.3390/genes12050635

Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches
Cited by: 13
Author(s): Hyun-Hwan Jeong, Johnathan Jia, Yulin Dai, Lukas M. Simon, Zhongming Zhao
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-30551-1

In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells
Cited by: 29
Author(s): Tae-Yong Kim, Oscar Echeagaray, Bingyan Wang, Alexandria Casillas, Kathleen M. Broughton, Bong-Hyun Kim, Mark A. Sussman
Software Mentions: 3
Published: over 6 years ago

Projects: cran: Seurat

Papers Mentioning Seurat 1,512