bioconductor: SingleR | Projects | Ecosyste.ms: Papers

10.20517/jtgg.2020.51

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq
Cited by: 2
Author(s): Brandon Lieberman, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ning He, Yen‐Yi Ho, Josephine A. Taverna, Tim Hui-Ming Huang, Chun-Liang Chen
Software Mentions: 18
Published: almost 5 years ago

10.1038/s42003-020-01625-6

Mapping the immune environment in clear cell renal carcinoma by single-cell genomics
Cited by: 103
Author(s): Nicholas Borcherding, Ajaykumar Vishwakarma, Andrew P. Voigt, Andrew M. Bellizzi, Jacob Kaplan, Kenneth G. Nepple, Aliasger K. Salem, Russell W. Jenkins, Yousef Zakharia, Weizhou Zhang
Software Mentions: 14
Published: almost 4 years ago

10.3389/fgene.2021.665888

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
Cited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: over 3 years ago

10.1186/s12859-021-04028-4

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data
Cited by: 12
Author(s): Bobby Ranjan, Florian Schmidt, Wenjie Sun, Jinyu Park, Mohammad Amin Honardoost, Joanna H.J. Tan, Nirmala Arul Rayan, Shyam Prabhakar
Software Mentions: 12
Published: over 3 years ago

10.1186/s13059-021-02293-3

Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells
Cited by: 47
Author(s): Drew Neavin, Quan Nguyen, Maciej Daniszewski, Helena Liang, Han Sheng Chiu, Yong Kiat Wee, Anne Senabouth, Samuel W. Lukowski, Duncan E. Crombie, Grace E. Lidgerwood, Damián Hernández, James C. Vickers, Anthony Cook, Nathan J. Palpant, Alice Pébay, Alex W. Hewitt, Joseph E. Powell
Software Mentions: 12
Published: almost 4 years ago

10.1186/s13059-019-1795-z

A comparison of automatic cell identification methods for single-cell RNA sequencing data
Cited by: 361
Author(s): Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J. T. Reinders, Ahmed Mahfouz
Software Mentions: 12
Published: over 5 years ago

10.12688/f1000research.22969.2

clustifyr: an R package for automated single-cell RNA sequencing cluster classification
Cited by: 58
Author(s): Rui Fu, Austin E. Gillen, Ryan M. Sheridan, Chengzhe Tian, Michelle Daya, Yue Hao, Jay R. Hesselberth, Kent Riemondy
Software Mentions: 12
Published: over 4 years ago

10.3389/fbioe.2020.00101

The Integrated Transcriptome Bioinformatics Analysis Identifies Key Genes and Cellular Components for Spinal Cord Injury-Related Neuropathic Pain
Cited by: 8
Author(s): Runzhi Huang, Tong Meng, Rui Zhu, Lijuan Zhao, Dianwen Song, Huabin Yin, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: almost 5 years ago

10.1038/s41392-021-00753-7

Single-cell immune profiling reveals distinct immune response in asymptomatic COVID-19 patients
Cited by: 18
Author(s): Xiang-Na Zhao, Yue You, Xiaoming Cui, Han Gao, Guolin Wang, Shengbo Zhang, Lilin Ye, Lei Duan, Ka-Li Zhu, Yuling Wang, Li Li, Jianhua Lu, Haibin Wang, Jingfang Fan, Huanwei Zheng, Erfu Dai, Luyi Tian, Mai‐Juan Ma
Software Mentions: 11
Published: over 3 years ago

10.3389/fimmu.2021.622563

9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma
Cited by: 17
Author(s): Kexin Yan, Yuxiu Lu, Zhangyong Yan, Yutao Wang
Software Mentions: 10
Published: over 3 years ago

10.18632/aging.102434

Development and validation of a metastasis-associated prognostic signature based on single-cell RNA-seq in clear cell renal cell carcinoma
Cited by: 28
Author(s): Chuanjie Zhang, Hongchao He, Xin Hu, Ao Liu, Da Huang, Yu Xu, Lu Chen, Danfeng Xu
Software Mentions: 10
Published: about 5 years ago

10.1038/s42003-020-0842-3

Loss of the branched-chain amino acid transporter CD98hc alters the development of colonic macrophages in mice
Cited by: 17
Author(s): Philipp Wuggenig, Berna Kaya, Hassan Melhem, C. Korcan Ayata, Swiss Ibd Cohort Investigators, Petr Hrúz, Emre Sayan, Hideki Tsumura, Morihiro Ito, Julien Roux, Jan Hendrik Niess
Software Mentions: 10
Published: almost 5 years ago

10.3389/fcell.2021.722841

Classification of Estrogen Receptor-Positive Breast Cancer Based on Immunogenomic Profiling and Validation at Single-Cell Resolution
Cited by: 0
Author(s): Xianxiong Ma, Hengyu Chen, Ming Yang, Zunxiang Ke, Mengyi Wang, Tao Huang, Lei Li
Software Mentions: 10
Published: over 3 years ago

10.1186/s40425-019-0763-1

34th Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): part 1
Cited by: 31
Author(s):
Software Mentions: 9
Published: about 5 years ago

10.3390/biomedicines9040368

Single-Cell RNA Sequencing in Parkinson’s Disease
Cited by: 13
Author(s): Shi-Xun Ma, Su Bin Lim
Software Mentions: 9
Published: over 3 years ago

10.1186/s12859-020-3538-2

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments
Cited by: 39
Author(s): H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens, Ryan M. O’Connell
Software Mentions: 8
Published: over 4 years ago

10.3389/fimmu.2021.666355

Revealing the Immune Infiltration Landscape and Identifying Diagnostic Biomarkers for Lumbar Disc Herniation
Cited by: 32
Author(s): Linbang Wang, Tao He, Jingkun Liu, Jiaojiao Tai, Bing Wang, Lanyue Zhang, Zhengxue Quan
Software Mentions: 8
Published: over 3 years ago

10.1093/bib/bbz096

Evaluation of single-cell classifiers for single-cell RNA sequencing data sets
Cited by: 54
Author(s): Xinlei Zhao, Shuang Wu, Nan Fang, Xiao Sun, Jue Fan
Software Mentions: 8
Published: about 5 years ago

10.1038/s41418-021-00866-0

Fatal cytokine release syndrome by an aberrant FLIP/STAT3 axis
Cited by: 14
Author(s): Chiara Musiu, Simone Caligola, Alessandra Fiore, Alessia Lamolinara, Cristina Frusteri, Francesco Domenico Del Pizzo, Francesco De Sanctis, Stefania Canè, Annalisa Adamo, Francesca Hofer, Roza Maria Barouni, Andrea Grilli, Serena Zilio, Paolo Serafini, Evelina Tacconelli, Katia Donadello, Leonardo Gottin, Enrico Polati, Domenico Girelli, Ildo Polidoro, Piera Amelia Iezzi, Domenico Angelucci, Andrea Capece, Ying Chen, Shi Z, Peter J. Murray, Marco Chilosi, Ido Amit, Silvio Bicciato, Manuela Iezzi, Vincenzo Bronte, Stefano Ugel
Software Mentions: 8
Published: over 3 years ago

10.18632/aging.202515

Cell differentiation trajectory predicts patient potential immunotherapy response and prognosis in gastric cancer
Cited by: 18
Author(s): Renshen Xiang, Yuping Rong, Yuhang Ge, Wei Song, Jun Ren, Tao Fu
Software Mentions: 8
Published: almost 4 years ago

10.1038/s42003-021-01897-6

Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer
Cited by: 9
Author(s): Giorgia Maroni, Mahmoud A. Bassal, Indira Krishnan, Chee Wai Fhu, Virginia Savova, Rapolas Žilionis, Valerie A. Maymi, Nicole Pandell, Eva Csizmadia, Junyan Zhang, Barbara Storti, Julio Castaño, Riccardo Panella, Jia Li, Corinne E. Gustafson, Sam Fox, Rachel Levy, Claire Meyerovitz, Peter J. Tramontozzi, Kimberly Vermilya, Assunta De Rienzo, Stefania Crucitta, Daniela S. Bassères, Marla Weetall, Art Branstrom, Alessandra Giorgetti, Raffaele Ciampi, Marzia Del Re, Romano Danesi, Ranieri Bizzarri, Henry Yang, Olivier Kocher, Allon M. Klein, Robert S. Welner, Raphael Bueno, Maria Cristina Magli, John G. Clohessy, Azhar Ali, Daniel G. Tenen, Elena Levantini
Software Mentions: 7
Published: over 3 years ago

10.7150/jca.49707

Cancer-associated fibroblasts in gastric cancer affect malignant progression via the CXCL12-CXCR4 axis
Cited by: 20
Author(s): Qin Yan, Fang Wang, Hengli Ni, Yao Liu, Yuan Yin, Xinyi Zhou, Guihua Gao, Qing Li, Xiaowei Qi, Jianming Li
Software Mentions: 7
Published: almost 4 years ago

10.1016/j.gpb.2018.07.007

Deciphering Brain Complexity Using Single-cell Sequencing
Cited by: 50
Author(s): Quanhua Mu, Yiyun Chen, Jiguang Wang
Software Mentions: 7
Published: over 5 years ago

10.3389/fonc.2021.666829

Taming Cell-to-Cell Heterogeneity in Acute Myeloid Leukaemia With Machine Learning
Cited by: 2
Author(s): Yara E. Sánchez-Corrales, Ruben V.C. Pohle, Sergi Castellano, Alice Giustacchini
Software Mentions: 7
Published: over 3 years ago

10.3390/jpm11060448

Stromal Heterogeneity in the Human Proliferative Endometrium—A Single-Cell RNA Sequencing Study
Cited by: 22
Author(s): Suzanna Queckbörner, Carolina von Grothusen, Nageswara Rao Boggavarapu, Roy Mathew Francis, Lindsay C. Davies, Kristina Gemzell‐Danielsson
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

10.3389/fonc.2021.718644

N6-Methyladenosine Writer Gene ZC3H13 Predicts Immune Phenotype and Therapeutic Opportunities in Kidney Renal Clear Cell Carcinoma
Cited by: 10
Author(s): Tao Guo, Duan Huang, Jinbo Chen, Jinhui Liu, Belaydi Othmane, Jiao Hu, Huihuang Li, Xiongbing Zu
Software Mentions: 6
Published: over 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

10.1080/07853890.2021.1914343

Bioinformatics reveal macrophages marker genes signature in breast cancer to predict prognosis
Cited by: 21
Author(s): Ying Li, Xin Zhao, Qiang Liu, Yujie Liu
Software Mentions: 6
Published: almost 4 years ago

10.3389/fgene.2021.642012

Visual Genomics Analysis Studio as a Tool to Analyze Multiomic Data
Cited by: 12
Author(s): Rebecca J Hertzman, Pooja Deshpande, Shay Leary, Yueran Li, Ram Ramesh, Abha Chopra, Don Cooper, Mark W. Watson, Amy M. Palubinsky, S. Mallal, Andrew Gibson, Elizabeth Phillips
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

10.1016/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

10.1186/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

10.1038/s41392-020-00263-y

Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals
Cited by: 127
Author(s): Fan Zhang, Rui Gan, Ziqi Zhen, Xiaoli Hu, Xiang Li, Fengxia Zhou, Ying Liu, Chuangeng Chen, Shuangyu Xie, Bailing Zhang, Xiaoke Wu, Zhiwei Huang
Software Mentions: 6
Published: over 4 years ago

10.3390/genes12060898

A Literature-Derived Knowledge Graph Augments the Interpretation of Single Cell RNA-seq Datasets
Cited by: 4
Author(s): Deeksha Doddahonnaiah, Patrick Lenehan, Travis Hughes, David Zemmour, Enrique Garcia-Rivera, A J Venkatakrishnan, Ramakrishna Chilaka, Apoorv Khare, Akhil Kasaraneni, Abhinav Garg, Akash Anand, Rakesh Barve, Viswanathan Thiagarajan, Venky Soundararajan
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-021-07974-8

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Cited by: 8
Author(s): N M Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anélia Horvath
Software Mentions: 6
Published: about 3 years ago

10.21203/rs.3.rs-362886/v1

Maternal-Fetal Immune Responses in Pregnant Women Infected with SARS-CoV-2
Cited by: 6
Author(s): Valeria Garcia‐Flores, Roberto Romero, Yi Xu, Kevin R. Theis, Marcia Arenas-Hernández, Derek Miller, Azam Peyvandipour, José Galaz, Dustyn Levenson, Gaurav Bhatti, Meyer Gershater, Errile Pusod, David Kracht, Violetta Florova, Yaozhu Leng, Tao Li, Megan Faucett, Robert Para, Chaur‐Dong Hsu, Gary Zhang, Adi L. Tarca, Roger Piqué-Regi, Nardhy Gomez-López
Software Mentions: 6
Published: over 3 years ago

10.1111/cpr.13116

Single‐cell profiling reveals distinct immune phenotypes that contribute to ischaemia‐reperfusion injury after steatotic liver transplantation
Cited by: 19
Author(s): Xinyu Yang, Di Lu, Rui Wang, Zhengxing Lian, Zuyuan Lin, Jianyong Zhuo, Hao Chen, Modan Yang, Winyen Tan, Mengfan Yang, Xuyong Wei, Qiang Wei, Shusen Zheng, Xiao Xu
Software Mentions: 6
Published: over 3 years ago

10.1111/jcmm.16714

Single‐cell RNA sequencing identify SDCBP in ACE2‐positive bronchial epithelial cells negatively correlates with COVID‐19 severity
Cited by: 16
Author(s): Ding Ma, Shuwen Liu, Lili Hu, Qinyu He, Weiwei Shi, Dongming Yan, Chunyue Yin, Guang Zhang, Zhong‐Xia Wang, Junhua Wu, Chunping Jiang
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: about 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: about 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

10.7554/eLife.62270

The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline
Cited by: 66
Author(s): Danielle Janosevic, Jered Myslinski, Thomas McCarthy, Amy Zollman, Farooq Syed, Xiaoling Xuei, Hongyu Gao, Yunlong Liu, Kimberly S. Collins, Ying‐Hua Cheng, Seth Winfree, Tarek M. El‐Achkar, Bernhard Maier, Ricardo Melo Ferreira, Michael T. Eadon, Takashi Hato, Pierre C. Dagher
Software Mentions: 5
Published: almost 4 years ago

10.3389/fimmu.2021.670574

Single-Cell Transcriptional Heterogeneity of Neutrophils During Acute Pulmonary Cryptococcus neoformans Infection
Cited by: 14
Author(s): M. Elizabeth Deerhake, Estefany Y. Reyes, Shengjie Xu-Vanpala, Mari L. Shinohara
Software Mentions: 5
Published: over 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: over 3 years ago

10.3390/genes11070792

Integrating Deep Supervised, Self-Supervised and Unsupervised Learning for Single-Cell RNA-seq Clustering and Annotation
Cited by: 21
Author(s): Liang Chen, Yuyao Zhai, Qiuyan He, Weinan Wang, Minghua Deng
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.52004

Single cell transcriptional signatures of the human placenta in term and preterm parturition
Cited by: 173
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Edward Sendler, Yi Xu, Valeria Garcia‐Flores, Yaozhu Leng, Francesca Luca, Sonia S. Hassan, Nardhy Gomez-López
Software Mentions: 5
Published: about 5 years ago

10.1016/j.isci.2021.102402

Absence of Batf3 reveals a new dimension of cell state heterogeneity within conventional dendritic cells
Cited by: 14
Author(s): Samuel W. Lukowski, Inga Rødahl, S. Thomas Kelly, Meihua Yu, James Gotley, Chenhao Zhou, Susan Millard, Stacey Andersen, Angelika N. Christ, Gabrielle T. Belz, Ian H. Frazer, Janin Chandra
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22179228

SARS-CoV-2 Impairs Dendritic Cells and Regulates DC-SIGN Gene Expression in Tissues
Cited by: 13
Author(s): Guoshuai Cai, Mulong Du, Yohan Bossé, Helmut Albrecht, Fei Qin, Xizhi Luo, X Michelle Androulakis, Chao Cheng, Mitzi Nagarkatti, Mitzi Nagarkatti, David C. Christiani, Michael L. Whitfield, Christopher I. Amos, Feifei Xiao
Software Mentions: 5
Published: over 3 years ago

10.7150/jca.49409

Identification of marker genes and cell subtypes in castration-resistant prostate cancer cells
Cited by: 6
Author(s): Xiaodan Lin, Nanping Lin, Tingting Lin, Yupeng Wu, Peng Huang, Zhi‐Bin Ke, Yunzhi Lin, Shao‐Hao Chen, Qing‐Shui Zheng, Yong Wei, Xue-Yi Xue, Rongjin Lin, Ning Xu
Software Mentions: 5
Published: almost 4 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/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

10.18632/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/s41598-020-70353-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: over 4 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/ijms22010261

Transcriptomic Changes of Murine Visceral Fat Exposed to Intermittent Hypoxia at Single Cell Resolution
Cited by: 3
Author(s): Abdelnaby Khalyfa, Wesley C. Warren, Jorge Andrade, Christopher A. Bottoms, Edward S. Rice, Rene Cortese, Leila Kheirandish‐Gozal, David Gozal
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-66556-y

WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations
Cited by: 9
Author(s): Ian M. Rose, Mallikarjun Bidarimath, Alex Webster, Andrew K. Godwin, Andrea Flesken‐Nikitin, Alexander Yu. Nikitin
Software Mentions: 4
Published: over 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

10.1186/s12859-021-04278-2

Single-cell classification using graph convolutional networks
Cited by: 19
Author(s): Tianyu Wang, Junqiang Bai, Sheida Nabavi
Software Mentions: 4
Published: over 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

10.5808/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/fonc.2021.710695

Single-Cell Transcriptomics of Glioblastoma Reveals a Unique Tumor Microenvironment and Potential Immunotherapeutic Target Against Tumor-Associated Macrophage
Cited by: 17
Author(s): Xiaoteng Cui, Qixue Wang, Junhu Zhou, Yunfei Wang, Xu Cheng, Fei Tong, Hongjun Wang, Chunsheng Kang
Software Mentions: 3
Published: over 3 years ago

10.1007/s13238-020-00727-5

New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data
Cited by: 66
Author(s): Xin Shao, Xiaoyan Lu, Jie Liao, Huajun Chen, Xiaohui Fan
Software Mentions: 3
Published: over 4 years ago

10.15252/emmm.202013598

Myeloid cell‐based delivery of IFN‐γ reprograms the leukemia microenvironment and induces anti‐tumoral immune responses
Cited by: 10
Author(s): Adele Mucci, Gabriele Antonarelli, Carolina Caserta, Francesco Maria Vittoria, Giacomo Desantis, Riccardo Pagani, Béatrice Gréco, Monica Casucci, Giulia Escobar, Laura Passerini, Nico Lachmann, Francesca Sanvito, Matteo Barcella, Ivan Merelli, Luigi Naldini, Bernhard Gentner
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.103601

PDIA3 correlates with clinical malignant features and immune signature in human gliomas
Cited by: 29
Author(s): Hao Zhang, Yulai Zhou, Quan Cheng, Ziyu Dai, Zeyu Wang, Fangkun Liu, Fan Fan, Biqi Cui, Hui Cao
Software Mentions: 3
Published: over 4 years ago

10.1152/ajplung.00128.2019

PDGFRα and αSMA mark two distinct mesenchymal cell populations involved in parenchymal and vascular remodeling in pulmonary fibrosis
Cited by: 30
Author(s): Valentina Biasin, Slaven Crnković, Anita Sahu-Osen, Anna Birnhuber, Elie El Agha, Katharina Sinn, Walter Klepetko, Andrea Olschewski, Savério Bellusci, Leigh M. Marsh, Grażyna Kwapiszewska
Software Mentions: 3
Published: over 4 years ago

10.1038/s41392-020-00248-x

Nanoparticle enhanced combination therapy for stem-like progenitors defined by single-cell transcriptomics in chemotherapy-resistant osteosarcoma
Cited by: 24
Author(s): Li Wang, Xiaojia Huang, Xinru You, Tianqi Yi, Bing Lu, Jiali Liu, Guohao Lu, Minglin Ma, Changye Zou, Jun Wu, Wei Zhao
Software Mentions: 3
Published: about 4 years ago

10.1155/2021/9548648

Tumor Purity Coexpressed Genes Related to Immune Microenvironment and Clinical Outcomes of Lung Adenocarcinoma
Cited by: 7
Author(s): Ming Bai, Qi Pan, Chen Sun
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-82883-0

A non-invasive method to generate induced pluripotent stem cells from primate urine
Cited by: 17
Author(s): Johanna Geuder, Lucas E. Wange, Aleksandar Janjic, Jessica Radmer, Philipp Janssen, Johannes W. Bagnoli, Stefan Müller, Artur Kaul, Mari Ohnuki, Wolfgang Enard
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2019.00978

Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data
Cited by: 24
Author(s): Carlos Torroja, Fátima Sánchez‐Cabo
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2020.00490

SCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data
Cited by: 71
Author(s): Yinghao Cao, Xiaoyue Wang, Peng Guo
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.716760

Changes in the Gut Microbiome Contribute to the Development of Behcet’s Disease via Adjuvant Effects
Cited by: 8
Author(s): Qingfeng Wang, Shenglan Yi, Guannan Su, Ziyu Du, Pan S, Xinyue Huang, Qingfeng Cao, Guangjie Yuan, Aize Kijlstra, Peizeng Yang
Software Mentions: 3
Published: over 3 years ago

10.1155/2021/9960905

Identification of CD8+ T Cell-Related Genes: Correlations with Immune Phenotypes and Outcomes of Liver Cancer
Cited by: 6
Author(s): Qi Pan, Ying Cheng, Da‐Chuan Cheng
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.573429

Reconstructing the Developmental Trajectories of Multiple Subtypes in Pulmonary Parenchymal Epithelial Cells by Single-Cell RNA-seq
Cited by: 4
Author(s): Yiwei Huang, Yuansheng Zheng, Jiacheng Yin, Tao Lu, Ming Li, Jiaqi Liang, Zhengyang Hu, Guoshu Bi, Cheng Zhan, Xue Li, Wei Jiang, Qun Wang
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0244743

Transcriptional profiling of pediatric cholestatic livers identifies three distinct macrophage populations
Cited by: 20
Author(s): Sarah Taylor, Shang-Yang Chen, Gaurav Gadhvi, Liang Feng, Kyle D. Gromer, Hiam Abdala‐Valencia, Ki-Won Nam, Salina Dominguez, Anna B. Montgomery, Paul A. Reyfman, Lorena Ostilla, Joshua B. Wechsler, Carla M. Cuda, Richard M. Green, Harris Perlman, Deborah R. Winter
Software Mentions: 2
Published: almost 4 years ago

10.3390/cells10082129

Heterogeneity of Hepatic Stellate Cells in Fibrogenesis of the Liver: Insights from Single-Cell Transcriptomic Analysis in Liver Injury
Cited by: 16
Author(s): Wenjun Zhang, Simon J. Conway, Ying Liu, Paige Snider, Hanying Chen, Hongyu Gao, Yunlong Liu, Kadir Isidan, Kevin Lopez, Gonzalo Campaña, Ping Li, Burçin Ekser, Heather Francis, Weinian Shou, Chandrashekhar A. Kubal
Software Mentions: 2
Published: over 3 years ago

10.1002/ctm2.430

Identification of potential vaccine targets for COVID‐19 by combining single‐cell and bulk TCR sequencing
Cited by: 10
Author(s): Ping-ping Wang, Zhaochun Xu, Wenyang Zhou, Xiyun Jin, Chang Xu, Meng Luo, Kexin Ma, Huimin Cao, Yan Huang, Xiaoyu Lin, Fenglan Pang, Yiqun Li, Qinghua Jiang
Software Mentions: 2
Published: over 3 years ago

10.1093/bioinformatics/btz292

scMatch: a single-cell gene expression profile annotation tool using reference datasets
Cited by: 81
Author(s): Rui Hou, Elena Denisenko, Alistair R.R. Forrest
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.663487

Cryopreservation Preserves Cell-Type Composition and Gene Expression Profiles in Bone Marrow Aspirates From Multiple Myeloma Patients
Cited by: 8
Author(s): Duojiao Chen, Mohammad Abu Zaid, Jill L. Reiter, Magdalena Czader, Lin Wang, Patrick McGuire, Xiaoling Xuei, Hongyu Gao, Kun Huang, Rafat Abonour, Brian A Walker, Yunlong Liu
Software Mentions: 2
Published: over 3 years ago

10.3389/fphar.2021.673485

Therapeutic Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19
Cited by: 9
Author(s): Clarissa Stephanie Santoso, Zhaorong Li, Jaice T. Rottenberg, Xing Liu, Vivian Shen, Juan I. Fuxman Bass
Software Mentions: 2
Published: over 3 years ago

10.20900/immunometab20190008

Single-Cell RNA Sequencing of Visceral Adipose Tissue Leukocytes Reveals that Caloric Restriction Following Obesity Promotes the Accumulation of a Distinct Macrophage Population with Features of Phagocytic Cells
Cited by: 51
Author(s): Ada Weinstock, Emily J. Brown, Michela L. Garabedian, Stephanie Pena, Monika Sharma, Juan J. Lafaille, Kathryn J. Moore, Edward A. Fisher
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.140179

Risk-associated alterations in marrow T cells in pediatric leukemia
Cited by: 18
Author(s): Jithendra Kini Bailur, Samuel S. McCachren, Katherine E. Pendleton, Juan C. Vasquez, Hong Seo Lim, Alyssa Duffy, Deon B. Doxie, Akhilesh Kaushal, Connor Foster, Deborah DeRyckere, Sharon M. Castellino, Melissa L. Kemp, Peng Qiu, Madhav V. Dhodapkar, Kavita M. Dhodapkar
Software Mentions: 2
Published: over 4 years ago

10.1172/jci.insight.134170

Delta-like 4 is required for pulmonary vascular arborization and alveolarization in the developing lung
Cited by: 5
Author(s): Xia Sheng, Heather Menden, Nick Townley, Sherry M Mabry, Jeff Johnston, Michael F. Nyp, Daniel P. Heruth, Thomas R. Korfhagen, Venkatesh Sampath
Software Mentions: 2
Published: over 3 years ago

10.1172/jci.insight.149228

Distinctive waves of innate immune response in the retina in experimental autoimmune encephalomyelitis
Cited by: 10
Author(s): Andrés Cruz-Herranz, Frederike Cosima Oertel, Kicheol Kim, Ester Cantó, Garrett Timmons, Jung Hyung Sin, Michael Devereux, Nicholas S. Baker, Brady Michel, Ryan Schubert, Lakshmisahithi Rani, Christian Cordano, Sergio E. Baranzini, Ari J. Green
Software Mentions: 2
Published: over 3 years ago

10.1172/jci.insight.151981

Autophagy-mitophagy induction attenuates cardiovascular inflammation in a murine model of Kawasaki disease vasculitis
Cited by: 17
Author(s): Stefanie Marek-Iannucci, Asli Beyza Ozdemir, Debbie Moreira, Alejandro Raúl Gratacós Gómez, Malcolm Lane, Rebecca A. Porritt, Youngho Lee, Kenichi Shimada, Masanori Abe, Aleksandr Stotland, David Zemmour, Sarah J. Parker, Elsa Sánchez-López, Jennifer E. Van Eyk, Roberta A. Gottlieb, Michael C. Fishbein, Michael Karin, Timothy R. Crother, Magali Noval Rivas, Moshe Arditi
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-020-64158-2

Ly6cLo non-classical monocytes promote resolution of rhesus rotavirus-mediated perinatal hepatic inflammation
Cited by: 16
Author(s): Anas Alkhani, Claire S. Levy, Margaret Tsui, Katherine Rosenberg, Katya Polovina, Aras N. Mattis, Matthias Mack, Steven J. Van Dyken, Bruce M. Wang, Jacquelyn J. Maher, Amar Nijagal
Software Mentions: 2
Published: over 4 years ago

10.1007/s10911-021-09486-3

Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland
Cited by: 9
Author(s): Samantha Henry, Marygrace C. Trousdell, Samantha L. Cyrill, Yixin Zhao, Mary J. Feigman, Julia M Bouhuis, Dominik A. Aylard, Adam Siepel, Camila O. dos Santos
Software Mentions: 2
Published: almost 4 years ago

10.20900/immunometab20190010

Netrin-1 Alters Adipose Tissue Macrophage Fate and Function in Obesity
Cited by: 36
Author(s): Monika Sharma, Martin Schlegel, Emily J. Brown, Brian E. Sansbury, Ada Weinstock, Milessa da Silva Afonso, Emma M. Corr, Coen van Solingen, Lianne C. Shanley, Daniel Peled, Ravichandran Ramasamy, Ann Marie Schmidt, Matthew Spite, Edward A. Fisher, Kathryn J. Moore
Software Mentions: 1
Published: over 5 years ago

10.3390/mi11090815

Characterization of Diabetic and Non-Diabetic Foot Ulcers Using Single-Cell RNA-Sequencing
Cited by: 31
Author(s): Michael Januszyk, Kellen Chen, Dominic Henn, Deshka S. Foster, Mimi R. Borrelli, Clark A. Bonham, Dharshan Sivaraj, Dhananjay Wagh, Michael T. Longaker, Derrick C. Wan, Geoffrey C. Gurtner
Software Mentions: 1
Published: over 4 years ago

10.1186/s13073-019-0645-7

Dissecting lung development and fibrosis at single-cell resolution
Cited by: 9
Author(s): Donna L. Farber, Peter A. Sims
Software Mentions: 1
Published: over 5 years ago

10.1002/advs.202101462

Modeling Sporadic Alzheimer's Disease in Human Brain Organoids under Serum Exposure
Cited by: 51
Author(s): Xianwei Chen, Guoqiang Sun, Erpo Tian, Mingzi Zhang, Hayk Davtyan, Thomas G. Beach, Eric M. Reiman, Mathew Blurton‐Jones, David M. Holtzman, Yanhong Shi
Software Mentions: 1
Published: over 3 years ago

10.3389/fcell.2021.707073

HCG18 Participates in Vascular Invasion of Hepatocellular Carcinoma by Regulating Macrophages and Tumor Stem Cells
Cited by: 9
Author(s): Liwei Zhang, Zhiwei Wang, Mingxing Li, Peng Sun, Tao Bai, Wang Wang, Hualong Bai, Jianjun Gou, Zhiju Wang
Software Mentions: 1
Published: over 3 years ago

10.1186/s13578-019-0352-5

Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex
Cited by: 6
Author(s): Hailong Zhang, Jia-Wen Long, Wei Han, Jiuzhou Wang, Weichen Song, Guan Ning Lin, Dong-Min Yin
Software Mentions: 1
Published: about 5 years ago

10.3390/cancers13051006

Osteopontin Blockade Immunotherapy Increases Cytotoxic T Lymphocyte Lytic Activity and Suppresses Colon Tumor Progression
Cited by: 24
Author(s): John D. Klement, Dakota B. Poschel, Chunwan Lu, Alyssa D. Merting, Dafeng Yang, Priscilla S. Redd, Kebin Liu
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0246139

A microfluidic-based filtration system to enrich for bone marrow disseminated tumor cells from breast cancer patients
Cited by: 2
Author(s): Sreeraj G. Pillai, Chidananda M. Siddappa, Cynthia Ma, Jackie Snider, Madhurima Kaushal, Mark A. Watson, Rebecca Aft
Software Mentions: 1
Published: over 3 years ago

10.3389/pore.2021.604228

Single Cell Gene Transcriptome Analysis of Ovarian Mature Teratomas
Cited by: 0
Author(s): Sun Shin, Youn Jin Choi, Seung‐Hyun Jung, Yeun‐Jun Chung, Sug Hyung Lee
Software Mentions: 1
Published: over 3 years ago

10.1172/jci.insight.147282

Crosstalk between nonclassical monocytes and alveolar macrophages mediates transplant ischemia-reperfusion injury through classical monocyte recruitment
Cited by: 24
Author(s): Chitaru Kurihara, Emilia Lecuona, Qiang Wu, Wen‐Bin Yang, Felix Nunez-Santana, Mahzad Akbarpour, Xianpeng Liu, Ziyou Ren, Wenjun Li, Melissa Querrey, Sowmya Ravi, Megan L. Anderson, Emily Cerier, Haiying Sun, Megan E. Kelly, Hiam Abdala‐Valencia, Ali Shilatifard, Thalachallour Mohanakumar, G. R. Scott Budinger, Daniel Kreisel, Ankit Bharat
Software Mentions: 1
Published: almost 4 years ago

Projects: bioconductor: SingleR

Papers Mentioning SingleR 97