cran: Seurat | Projects | Ecosyste.ms: Papers

10.3389/fcell.2021.664868

SARS-CoV-2 Causes Acute Kidney Injury by Directly Infecting Renal Tubules
Cited by: 22
Author(s): Zhaohui Chen, Junyi Hu, Lilong Liu, Rong Chen, Miao Wang, Momiao Xiong, Zhenqiong Li, Yi Zhao, Liu Hong, Chuhuai Guan, Jie Zhang, Liang Liu, Ke Chen, Yumei Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.680947

Single-Cell Transcriptome Profiling Reveals the Suppressive Role of Retinal Neurons in Microglia Activation Under Diabetes Mellitus
Cited by: 5
Author(s): Yao Xiao, Xiaoyi Hu, Shuangshuang Fan, Jiawei Zhong, Xinzhi Mo, Xialin Liu, Youjin Hu
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.617853

Single-Cell RNA Sequencing and Quantitative Proteomics Analysis Elucidate Marker Genes and Molecular Mechanisms in Hypoplastic Left Heart Patients With Heart Failure
Cited by: 2
Author(s): Li Ma, Na Zhou, Rongjun Zou, Wu Shi, Yuanyuan Luo, Na Du, Jing Zhong, Xiaodong Zhao, Xinxin Chen, Huimin Xia, Xianyu Qin
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.647892

Transcriptome Profiling of the Ovarian Cells at the Single-Cell Resolution in Adult Asian Seabass
Cited by: 7
Author(s): Xiaoli Liu, Wei Li, Yanping Yang, Kaili Chen, Yulin Li, Xinping Zhu, Hua Ye, Hongyan Xu
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.643712

Toward a Consensus in the Repertoire of Hemocytes Identified in Drosophila
Cited by: 17
Author(s): Pierre B. Cattenoz, Sara Monticelli, Alexia Pavlidaki, Angela Giangrande
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.695546

Specific Transcriptomic Signatures and Dual Regulation of Steroidogenesis Between Fetal and Adult Mouse Leydig Cells
Cited by: 13
Author(s): Pauline Sararols, Isabelle Stévant, Yasmine Neirijnck, Diane Rebourcet, Annalucia Darbey, Martin Curley, Françoise Kühne, Emmanouil T. Dermitzakis, Lee B. Smith, Serge Nef
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.653308

Single-Cell Atlas Reveals Fatty Acid Metabolites Regulate the Functional Heterogeneity of Mesenchymal Stem Cells
Cited by: 6
Author(s): Jiayi Xie, Qi Lou, Yunxin Zeng, Yingying Liang, Siyu Xie, Quanhui Xu, Lisha Yuan, Jin Wang, Linjia Jiang, Lisha Mou, Dongjun Lin, Meng Zhao
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.596484

Immune Profiling Reveals Molecular Classification and Characteristic in Urothelial Bladder Cancer
Cited by: 6
Author(s): Yang Li, Aitian Li, Fengsen Liu, Qitai Zhao, Shaofei Ji, Wen Zhu, Wenbin Yu, Ru Zhang, Yaqing Liu, Wencai Li, Yi Zhang
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.42388

Specification of diverse cell types during early neurogenesis of the mouse cerebellum
Cited by: 57
Author(s): John Wizeman, Qiu Guo, Elliott M Wilion, Kairong Li
Software Mentions: 2
Published: almost 6 years ago

10.3389/fcell.2020.00398

Cathepsin S and Protease-Activated Receptor-2 Drive Alloimmunity and Immune Regulation in Kidney Allograft Rejection
Cited by: 9
Author(s): Yutian Lei, Benjamin Ehle, Sanjeev Kumar, Susanne Müller, Solange Moll, Andrew F. Malone, Benjamin D. Humphreys, Joachim Andrassy, Hans Joachim Anders
Software Mentions: 2
Published: over 4 years ago

10.3389/fcell.2019.00175

Cross-Species Analysis of Single-Cell Transcriptomic Data
Cited by: 66
Author(s): Maxwell E.R. Shafer
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0151664

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data
Cited by: 136
Author(s): Anne Bruun Krøigård, Mads Thomassen, Anne‐Vibeke Lænkholm, Torben A. Kruse, Martin Jakob Larsen
Software Mentions: 2
Published: over 8 years ago

10.3389/fncel.2021.703951

Single Cell Transcriptomics of Ependymal Cells Across Age, Region and Species Reveals Cilia-Related and Metal Ion Regulatory Roles as Major Conserved Ependymal Cell Functions
Cited by: 23
Author(s): Adam L. Macdonald, Brianna Lu, Maxime Caron, Nina Caporicci-Dinucci, Dale Hatrock, Kevin Petrecca, Guillaume Bourque, Jo Anne Stratton
Software Mentions: 2
Published: over 3 years ago

10.3389/fncel.2018.00410

Evidence of Müller Glia Conversion Into Retina Ganglion Cells Using Neurogenin2
Cited by: 26
Author(s): Roberta Pereira de Melo Guimarães, Bruna Soares Landeira, Diego Marques Coelho, Daiane Cristina Ferreira Golbert, Mariana S. Silveira, Rafael Linden, Ricardo Augusto de Melo Reis, Marcos Romualdo Costa
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.59328

Heterogeneous somatostatin-expressing neuron population in mouse ventral tegmental area
Cited by: 9
Author(s): Elina Nagaeva, Ivan Zubarev, Carolina Bengtsson Gonzales, Mikko Forss, Kasra Nikouei, Elena de Miguel, Lauri Elsilä, Anni‐Maija Lindén, Jens Hjerling-Leffler, George J Augustine, Esa R. Korpi
Software Mentions: 2
Published: over 4 years ago

10.3389/fendo.2021.609308

Using Single-Cell RNA-Seq Data to Trace Tissue Cells Responsive to Thyroid Hormones
Cited by: 1
Author(s): Liang Hu, Chao Wu
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00358

Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection
Cited by: 19
Author(s): Allen F. Ryan, Chanond A. Nasamran, Kwang Pak, Clara Draf, Kathleen M. Fisch, Nicholas J. G. Webster, Arwa Kurabi
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0242171

Age-associated changes in the transcriptomes of non-cultured adipose-derived stem cells from young and old mice assessed via single-cell transcriptome analysis
Cited by: 4
Author(s): Yuta Doshida, Haruka Sano, Sadahiro Iwabuchi, Toshiro Aigaki, Masayuki Yoshida, Shinichi Hashimoto, Akihito Ishigami
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1009497

Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images
Cited by: 36
Author(s): Hannah Currant, Pirro G. Hysi, Tomas Fitzgerald, Puya Gharahkhani, Pieter W.M. Bonnemaijer, Anne Senabouth, Alex W. Hewitt, UK Biobank Eye, Denize Atan, Tin Aung, Jason Charng, Hélène Choquet, Jamie E Craig, Peng Tee Khaw, Caroline C W Klaver, Michiaki Kubo, Jue‐Sheng Ong, Louis R. Pasquale, Charles Reisman, Maciej Daniszewski, Joseph E. Powell, Alice Pébay, Mark James Simcoe, Alberta A H J Thiadens, Cornelia M. van Duijn, Seyhan Yazar, Eric Jorgenson, Stuart MacGregor, Chris Hammond, David A. Mackey, Janey L. Wiggs, Paul J. Foster, Praveen J Patel, Ewan Birney, Anthony P Khawaja
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.511286

Patterns, Profiles, and Parsimony: Dissecting Transcriptional Signatures From Minimal Single-Cell RNA-Seq Output With SALSA
Cited by: 0
Author(s): Oswaldo A. Lozoya, Kathryn S. McClelland, Brian N. Papas, Jianliang Li, Hisayuki Yao
Software Mentions: 2
Published: about 4 years ago

10.3389/fgene.2021.698124

Visualization and Analysis of Gene Expression in Stanford Type A Aortic Dissection Tissue Section by Spatial Transcriptomics
Cited by: 13
Author(s): Yanhong Li, Ying Cao, Fen Liu, Qian Zhao, Dilare Adi, Qiang Huo, Zheng Liu, Junyi Luo, Binbin Fang, Ting Tian, Di Liu, Yi‐Ning Yang
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2019.00953

MTGO-SC, A Tool to Explore Gene Modules in Single-Cell RNA Sequencing Data
Cited by: 3
Author(s): Nelson Espinoza N., Danila Vella, Claudia Coronnello, Dario Di Silvestre, Riccardo Bellazzi, Simone Marini
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2021.658352

Enhancement and Imputation of Peak Signal Enables Accurate Cell-Type Classification in scATAC-seq
Cited by: 1
Author(s): Zhe Cui, Ya Cui, Yan Gao, Tao Jiang, Tianyi Zang, Yadong Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00662

Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics Technologies
Cited by: 17
Author(s): Q. Xing, Nadia Omega Cipta, Kiyofumi Hamashima, Yih‐Cherng Liou, Cheng-Gee Koh, Yuin-Han Loh
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2021.659500

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing
Cited by: 4
Author(s): Zhe Wang, Daofu Cheng, Chengang Fan, Cong Zhang, Chao Zhang, Zhongmin Liu
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.565955

Integrative Analysis Extracts a Core ceRNA Network of the Fetal Hippocampus With Down Syndrome
Cited by: 2
Author(s): Shengran Wang, Xia Tang, Litao Qin, Weili Shi, Shasha Bian, Zhaokun Wang, Qingqing Wang, Xin Wang, Jianqin Gu, Bingtao Hao, Keyue Ding, Shixiu Liao
Software Mentions: 2
Published: almost 4 years ago

10.3389/fgene.2020.596150

Expression Partitioning of Duplicate Genes at Single Cell Resolution in Arabidopsis Roots
Cited by: 19
Author(s): Jeremy E. Coate, Andrew Farmer, John Schiefelbein, Jeff J. Doyle
Software Mentions: 2
Published: about 4 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

10.3389/fgene.2020.572284

A Transcriptomics-Based Meta-Analysis Combined With Machine Learning Identifies a Secretory Biomarker Panel for Diagnosis of Pancreatic Adenocarcinoma
Cited by: 13
Author(s): Indu Khatri, Manoj Bhasin
Software Mentions: 2
Published: about 4 years ago

10.3389/fgene.2020.570546

A Systems Biology Approach to Identifying a Master Regulator That Can Transform the Fast Growing Cellular State to a Slowly Growing One in Early Colorectal Cancer Development Model
Cited by: 3
Author(s): Ji-Hye Choi, Jeong-Ryeol Gong, Chae Young Hwang, Chang Young Joung, Soobeom Lee, Kwang-Hyun Cho
Software Mentions: 2
Published: about 4 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

10.1371/journal.pcbi.1008804

JSOM: Jointly-evolving self-organizing maps for alignment of biological datasets and identification of related clusters
Cited by: 2
Author(s): Hong Seo Lim, Peng Qiu
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1009228

Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts
Cited by: 21
Author(s): Kaiyi Zhu, Lingyi Cai, Chenqian Cui, Juan R. de los Toyos, Dimitris Anastassiou
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.645988

A Partial Picture of the Single-Cell Transcriptomics of Human IgA Nephropathy
Cited by: 26
Author(s): Rong Tang, Ting Meng, Wei Lin, Cong Shen, Joshua D. Ooi, Peter J. Eggenhuizen, Peng Jin, Xiang Ding, Jinbiao Chen, Yangshuo Tang, Zhou Xiao, Xiang Ao, Weilin Peng, Qiaoling Zhou, Ping Xiao, Yong Zhong, Xiangcheng Xiao
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1008814

Predicting recognition between T cell receptors and epitopes with TCRGP
Cited by: 52
Author(s): Emmi Jokinen, Jani Huuhtanen, Satu Mustjoki, Markus Heinonen, Harri Lähdesmäki
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1008218

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion
Cited by: 18
Author(s): Zhuliu Li, Tianci Song, Jeongsik Yong, Rui Kuang
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.619932

Single-Cell Sequencing Reveals the Transcriptome and TCR Characteristics of pTregs and in vitro Expanded iTregs
Cited by: 7
Author(s): Zhenzhen Hui, Jiali Zhang, Yu Zheng, Lili Yang, Wenwen Yu, Yang An, Feng Wei, Xiubao Ren
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2018.02425

A Single-Cell Sequencing Guide for Immunologists
Cited by: 143
Author(s): Peter See, Josephine Lum, Jinmiao Chen, Florent Ginhoux
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pbio.3000538

A single-cell atlas of adult Drosophila ovary identifies transcriptional programs and somatic cell lineage regulating oogenesis
Cited by: 71
Author(s): Allison Jevitt, Deeptiman Chatterjee, Gengqiang Xie, Xianfeng Wang, Taylor Otwell, Yi-Chun Huang, Wu-Min Deng
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2020.594658

Single-Cell RNA Sequencing Reveals the Expansion of Cytotoxic CD4+ T Lymphocytes and a Landscape of Immune Cells in Primary Sjögren’s Syndrome
Cited by: 40
Author(s): Xiaoping Hong, Shuhui Meng, Donge Tang, Tingting Wang, Liping Ding, Haiyan Yu, Heng Li, Dongzhou Liu, Yong Dai, Min Yang
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2021.623280

Thymic Epithelial Cell-Derived IL-15 and IL-15 Receptor α Chain Foster Local Environment for Type 1 Innate Like T Cell Development
Cited by: 5
Author(s): Huishan Tao, Lei Li, Nan‐Shih Liao, Kimberly S. Schluns, Shirley Luckhart, John W. Sleasman, Xiao‐Ping Zhong
Software Mentions: 2
Published: over 3 years ago

10.3390/cells10061462

Single-Cell RNA-Seq Reveals Transcriptomic Heterogeneity and Post-Traumatic Osteoarthritis-Associated Early Molecular Changes in Mouse Articular Chondrocytes
Cited by: 35
Author(s): Aimy Sebastian, Jillian L. McCool, Nicholas R. Hum, Deepa K. Murugesh, Stephen Wilson, Blaine A. Christiansen, Gabriela G. Loots
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2020.587756

A Conserved TCRβ Signature Dominates a Highly Polyclonal T-Cell Expansion During the Acute Phase of a Murine Malaria Infection
Cited by: 9
Author(s): Natasha L. Smith, Wiebke Nahrendorf, Catherine Sutherland, Jason P. Mooney, Joanne Thompson, Philip J. Spence, Gillian Cowan
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2020.00580

YAP Attenuates CD8 T Cell-Mediated Anti-tumor Response
Cited by: 18
Author(s): Andriana Lebid, Liam Chung, Drew M. Pardoll, Ping Fan
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2021.702636

Exploiting Single-Cell Tools in Gene and Cell Therapy
Cited by: 15
Author(s): Daniel Bode, Alyssa Cull, Juan Rubio‐Lara, David G. Kent
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.694801

Multi-Omics Analysis Showed the Clinical Value of Gene Signatures of C1QC+ and SPP1+ TAMs in Cervical Cancer
Cited by: 16
Author(s): Li Xiong, Qinghua Zhang, Gang Chen, Danfeng Luo
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.666935

Single-Cell RNA Sequencing Reveals Tissue Compartment-Specific Plasticity of Mycosis Fungoides Tumor Cells
Cited by: 24
Author(s): Katharina Rindler, Wolfgang Bauer, Constanze Jonak, Matthias Wielscher, Lisa E. Shaw, Thomas B. Rojahn, Felix M. Thaler, Stefanie Porkert, Ingrid Simonitsch‐Klupp, Wolfgang Weninger, Marius E. Mayerhoefer, Matthias Farlik, Patrick M. Brunner
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.636720

Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28
Cited by: 29
Author(s): Nathan Lawlor, Djamel Nehar-Belaid, Jessica Grassmann, Marlon Stoeckius, Peter Smibert, Michael L. Stitzel, Virginia Pascual, Jacques Banchereau, Adam Williams, Duygu Ucar
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.683330

Single-Cell Profiling Reveals Transcriptional Signatures and Cell-Cell Crosstalk in Anti-PLA2R Positive Idiopathic Membranous Nephropathy Patients
Cited by: 17
Author(s): Jie Xu, Cong Shen, Wei Lin, Ting Meng, Joshua D. Ooi, Peter J. Eggenhuizen, Rong Tang, Gong Xiao, Peng Jin, Xiang Ding, Yangshuo Tang, Weilin Peng, Wannian Nie, Xiang Ao, Xiangcheng Xiao, Yong Zhong, Qiaoling Zhou
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.661551

Association of Premature Immune Aging and Cytomegalovirus After Solid Organ Transplant
Cited by: 12
Author(s): Lauren E. Higdon, Claire E. Gustafson, Xuhuai Ji, Malaya K. Sahoo, Benjamin A. Pinsky, Kenneth B. Margulies, Holden T. Maecker, Jörg J. Goronzy, Jonathan S. Maltzman
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.633201

Serum miRNA Signature in Rheumatoid Arthritis and “At-Risk Individuals”
Cited by: 32
Author(s): C Cunningham, Siobhan Wade, Achilleas Floudas, Carl Orr, Trudy McGarry, Siobhan Wade, Sian Cregan, Ursula Fearon, Douglas J. Veale
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pbio.3001032

Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis
Cited by: 45
Author(s): Michael David Brügger, Tomáš Valenta, Hassan Fazilaty, George Hausmann, Konrad Basler
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2021.655655

Dysfunction of Decidual Macrophages Is a Potential Risk Factor in the Occurrence of Preeclampsia
Cited by: 9
Author(s): Miaomiao Rong, Xiang-Ping Yan, Zhang Hong-ya, Chan Zhou, Cong Zhang
Software Mentions: 2
Published: over 3 years ago

10.3389/fmed.2021.665410

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

10.3389/fmicb.2021.637500

Single-Cell TCR Sequencing Reveals the Dynamics of T Cell Repertoire Profiling During Pneumocystis Infection
Cited by: 8
Author(s): Huqin Yang, Yishan Wang, Kan Zhai, Zhaohui Tong
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.568805

Single-Cell Transcriptomics Reveals That Metabolites Produced by Paenibacillus bovis sp. nov. BD3526 Ameliorate Type 2 Diabetes in GK Rats by Downregulating the Inflammatory Response
Cited by: 1
Author(s): Zhenyi Qiao, Xiaohua Wang, Huanchang Zhang, Jin Han, Huafeng Feng, Zhengjun Wu
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmolb.2021.664913

Dynamic Observation of Autophagy and Transcriptome Profiles in a Mouse Model of Bleomycin-Induced Pulmonary Fibrosis
Cited by: 3
Author(s): Yani Wang, Siqi Hu, Lisha Shen, Song Liu, Lin‐Yan Wan, Shuhui Yang, Mengjie Hou, Xinlun Tian, Hongbing Zhang, Kai‐Feng Xu
Software Mentions: 2
Published: over 3 years ago

10.3389/fnmol.2020.00134

Profiling Microglia From Alzheimer’s Disease Donors and Non-demented Elderly in Acute Human Postmortem Cortical Tissue
Cited by: 40
Author(s): Astrid M. Alsema, Qiong Jiang, Laura Kracht, Emma Gerrits, Marissa Dubbelaar, Anneke Miedema, Nieske Brouwer, Elly M. Hol, Jinte Middeldorp, Roland van Dijk, Maya E. Woodbury, Astrid Wachter, Simon Xi, Thomas Møller, Knut Biber, Susanne M. Kooistra, Erik Boddeke, Bart J. L. Eggen
Software Mentions: 2
Published: about 4 years ago

10.14814/phy2.15013

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

10.3390/ijms21217944

Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations
Cited by: 60
Author(s): Daniele Mattei, Andranik Ivanov, Marc van Oostrum, Stanislav Pantelyushin, Juliet Richetto, F Mueller, Michał Beffinger, Linda Schellhammer, Johannes vom Berg, Bernd Wollscheid, Dieter Beule, Rosa Chiara Paolicelli, Urs Meyer
Software Mentions: 2
Published: about 4 years ago

10.3390/pharmaceutics12050471

Osteoprotegerin Is more than a Possible Serum Marker in Liver Fibrosis: A Study into Its Function in Human and Murine Liver
Cited by: 14
Author(s): Adhyatmika Adhyatmika, Leonie Beljaars, Kurnia Sari Setio Putri, Habibie Habibie, Carian E. Boorsma, Catharina Reker‐Smit, Theerut Luangmonkong, Burak Güney, Axel Haak, Keri A. Mangnus, Eduard Post, Klaas Poelstra, Kim Ravnskjær, Peter Olinga, Barbro N. Melgert
Software Mentions: 2
Published: over 4 years ago

10.3389/fnins.2019.00240

Tanycyte-Independent Control of Hypothalamic Leptin Signaling
Cited by: 45
Author(s): Sooyeon Yoo, David Cha, Dong Won Kim, Thanh Hoang, Seth Blackshaw
Software Mentions: 2
Published: over 5 years ago

10.3390/pharmaceutics13040545

Drug Repurposing for COVID-19 Treatment by Integrating Network Pharmacology and Transcriptomics
Cited by: 15
Author(s): Danyang Liu, Jiachen Liu, Shuang Liang, Xiang-He Meng, Jonathan Greenbaum, Hong‐Mei Xiao, Lijun Tan, Hong‐Wen Deng
Software Mentions: 2
Published: over 3 years ago

10.3389/fonc.2021.711673

Intra-Tumoral Activation of Endosomal TLR Pathways Reveals a Distinct Role for TLR3 Agonist Dependent Type-1 Interferons in Shaping the Tumor Immune Microenvironment
Cited by: 7
Author(s): Graham D. Thomas, Luca Micci, Wenjing Yang, Joseph A. Katakowski, Cecilia Oderup, Purnima Sundar, Xiao Wang, Kenneth G. Geles, Shobha Potluri, Shahram Salek-Ardakani
Software Mentions: 2
Published: over 3 years ago

10.1007/s00424-021-02544-z

Keeping the ageing brain wired: a role for purine signalling in regulating cellular metabolism in oligodendrocyte progenitors
Cited by: 19
Author(s): Andrea Rivera, Irene Chacon-De-La-Rocha, Francesca Pieropan, Maria Papanikolau, Kasum Azim, Arthur M. Butt
Software Mentions: 2
Published: over 3 years ago

10.3389/fonc.2019.01493

Naturally-Occurring Invasive Urothelial Carcinoma in Dogs, a Unique Model to Drive Advances in Managing Muscle Invasive Bladder Cancer in Humans
Cited by: 44
Author(s): Deborah W. Knapp, Deepika Dhawan, José A. Ramos‐Vara, Timothy L. Ratliff, Gregory M. Cresswell, Sagar M. Utturkar, Breann C. Sommer, Christopher M. Fulkerson, Noah M. Hahn
Software Mentions: 2
Published: almost 5 years ago

10.3389/fonc.2021.649004

Differences in Tumor Immune Microenvironment in Metastatic Sites of Breast Cancer
Cited by: 16
Author(s): Hyun-Jong Lee, Kwon Joong Na, Hongyoon Choi
Software Mentions: 2
Published: over 3 years ago

10.3390/v13091757

Enrichment of SARS-CoV-2 Entry Factors and Interacting Intracellular Genes in Tissue and Circulating Immune Cells
Cited by: 2
Author(s): Abhinandan Devaprasad, Aridaman Pandit
Software Mentions: 2
Published: about 3 years ago

10.3389/fonc.2021.704857

Integrative Analysis Identified MCT4 as an Independent Prognostic Factor for Bladder Cancer
Cited by: 7
Author(s): Yang Zhao, Bin Zhao, Wei‐Hua Yan, Yan Xia, Zhi‐Hui Wang, Guoyang Zheng, Wenda Wang, Yushi Zhang
Software Mentions: 2
Published: about 3 years ago

10.3389/fonc.2020.566599

Single-Cell Sequencing of Glioblastoma Reveals Central Nervous System Susceptibility to SARS-CoV-2
Cited by: 8
Author(s): Bingshan Wu, Weihong Wang, Haopeng Wang, Quanli Zou, Benxia Hu, Lei Ye, Yangchun Hu, Yuhuan Xie, Nali Huang, Qing Lan, Hongwei Cheng, Jun Dong, Xingliang Dai
Software Mentions: 2
Published: about 4 years ago

10.3389/fonc.2021.587744

Prognostic Implication of the Expression Level of PECAM-1 in Non-small Cell Lung Cancer
Cited by: 4
Author(s): Shanshan Cao, Yue Wang, Jingwen Li, Xuxinyi Ling, Yao Zhang, Yan Zhou, Hua Zhong
Software Mentions: 2
Published: over 3 years ago

10.15252/msb.20209682

A single cell atlas of the human liver tumor microenvironment
Cited by: 77
Author(s): Hassan Massalha, Keren Bahar Halpern, Samir Abu‐Gazala, Tamar Jana, Efi E. Massasa, Andreas E. Moor, Lisa Buchauer, Milena Rozenberg, Eli Pikarsky, Ido Amit, Gideon Zamir, Shalev Itzkovitz
Software Mentions: 2
Published: almost 4 years ago

10.3389/fphar.2021.709343

Activation of FcRn Mediates a Primary Resistance Response to Sorafenib in Hepatocellular Carcinoma by Single-Cell RNA Sequencing
Cited by: 6
Author(s): Xin Yuan Guan, Yi Hui Wu, Shuqin Zhang, Zhiyi Liu, Qingjie Fan, Shuai Fang, Sennan Qiao, Fenyong Sun, Chaozhao Liang
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

10.3389/fphys.2020.591450

Flow-Induced Transcriptomic Remodeling of Endothelial Cells Derived From Human Induced Pluripotent Stem Cells
Cited by: 11
Author(s): Emmi Helle, Minna Ampuja, Laura Antola, Riikka Kivelä
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2020.603302

Single-Cell RNA Sequencing Efficiently Predicts Transcription Factor Targets in Plants
Cited by: 10
Author(s): Youming Xie, Shenfei Jiang, Lele Li, Xiangzhen Yu, Yupeng Wang, Cuiqin Luo, Qiuhua Cai, Wei He, Hong Xie, Yanmei Zheng, Huaan Xie, Chenglong Zhang
Software Mentions: 2
Published: almost 4 years ago

10.3390/genes5020366

Characterization of the Genomic Architecture and Mutational Spectrum of a Small Cell Prostate Carcinoma
Cited by: 9
Author(s): Alan F. Scott, David Mohr, Hua Ling, Robert B. Scharpf, Peng Zhang, Gregory S. Liptak
Software Mentions: 2
Published: over 10 years ago

10.3390/genes11050549

Single-Cell RNA Sequencing of Hematopoietic Stem and Progenitor Cells Treated with Gemcitabine and Carboplatin
Cited by: 2
Author(s): Niclas Björn, Ingrid Jakobsen Falk, Kourosh Lotfi, Henrik Gréen
Software Mentions: 2
Published: over 4 years ago

10.1038/s41380-020-0676-x

Glial cell diversity and methamphetamine-induced neuroinflammation in human cerebral organoids
Cited by: 54
Author(s): Jason Dang, Shashi Kant Tiwari, Kriti Agrawal, Hui Hui, Yue Qin, Tariq M. Rana
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41380-019-0369-5

A hypothalamus-habenula circuit controls aversion
Cited by: 101
Author(s): Iakovos Lazaridis, Ourania Tzortzi, Moritz Weglage, Antje Märtin, Yang Xuan, Marc A. Parent, Yvonne Johansson, János Fuzik, Daniel Fürth, Lief E. Fenno, Charu Ramakrishnan, Gilad Silberberg, Karl Deisseroth, Marie Carlén, Konstantinos Meletis
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-018-1576-0

Linking single-cell measurements of mass, growth rate, and gene expression
Cited by: 42
Author(s): Robert J. Kimmerling, Sanjay M. Prakadan, Apoorv Gupta, Nicholas L. Calistri, Mark M. Stevens, Selim Ölçüm, Nathan Cermak, Riley S. Drake, Kristine Pelton, Frederik De Smet, Keith L. Ligon, Alex K. Shalek, Scott R. Manalis
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.molmet.2019.09.001

Single cell transcriptomic profiling of large intestinal enteroendocrine cells in mice – Identification of selective stimuli for insulin-like peptide-5 and glucagon-like peptide-1 co-expressing cells
Cited by: 71
Author(s): Lawrence J. Billing, Pierre Larraufie, Jo Lewis, Andrew B. Leiter, Joyce H. Li, Brian Lam, Giles S.H. Yeo, Deborah A. Goldspink, Richard G. Kay, Fiona M. Gribble, Frank Reimann
Software Mentions: 2
Published: about 5 years ago

10.1016/j.molmet.2021.101248

Dysregulation of the Pdx1/Ovol2/Zeb2 axis in dedifferentiated β-cells triggers the induction of genes associated with epithelial–mesenchymal transition in diabetes
Cited by: 12
Author(s): Daniel Simões de Jesus, Tracy C S Mak, Yi Fang Wang, Yorrick von Ohlen, Ying Bai, Eva Kane, Pauline Chabosseau, Catherine Chahrour, Walter Distaso, Victoria Salem, Alejandra Tomás, Markus Stoffel, Guy A. Rutter, Mathieu Latreille
Software Mentions: 2
Published: about 3 years ago

10.1186/s13059-019-1812-2

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions
Cited by: 189
Author(s): Yael Baran, Akhiad Bercovich, Arnau Sebé-Pedrós, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz, Amos Tanay
Software Mentions: 2
Published: about 5 years ago

10.1016/j.mce.2021.111220

AKR1C2 and AKR1C3 expression in adipose tissue: Association with body fat distribution and regulatory variants
Cited by: 9
Author(s): Giada Ostinelli, Jinchu Vijay, Marie‐Claude Vohl, Elin Grundberg, André Tchernof
Software Mentions: 2
Published: over 3 years ago

10.1186/s12943-020-01264-9

Identification of a distinct luminal subgroup diagnosing and stratifying early stage prostate cancer by tissue-based single-cell RNA sequencing
Cited by: 42
Author(s): Xing-Hong Ma, Jinan Guo, Kaisheng Liu, Lipeng Chen, Dale Liu, Shaowei Dong, Jinquan Xia, Qiaoyun Long, Yongjian Yue, Pan Zhao, Fengyan Hu, Zhangang Xiao, Xinghua Pan, Kefeng Xiao, Zhiqiang Cheng, Zunfu Ke, Zhe‐Sheng Chen, Chang Zou
Software Mentions: 2
Published: about 4 years ago

10.1186/s12943-021-01419-2

Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma
Cited by: 17
Author(s): Katharina Rindler, Constanze Jonak, Natalia Alkon, Felix M. Thaler, Harald Kurz, Lisa E. Shaw, Georg Stingl, Wolfgang Weninger, Florian Halbritter, Wolfgang Bauer, Matthias Farlik, Patrick M. Brunner
Software Mentions: 2
Published: about 3 years ago

10.1186/s13059-020-01958-9

Linked optical and gene expression profiling of single cells at high-throughput
Cited by: 17
Author(s): Jesse Q. Zhang, Christian Siltanen, Leqian Liu, Kai‐Chun Chang, Zev J. Gartner, Adam R. Abate
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-020-02015-1

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data
Cited by: 285
Author(s): Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni, Oliver Stegle
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22105177

Cell–Cell Communication at the Embryo Implantation Site of Mouse Uterus Revealed by Single-Cell Analysis
Cited by: 10
Author(s): Yi Yang, Jia-Peng He, Ji‐Long Liu
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-020-02058-4

Analysis of endothelial-to-haematopoietic transition at the single cell level identifies cell cycle regulation as a driver of differentiation
Cited by: 32
Author(s): Giovanni Canu, Emmanouil Athanasiadis, Rodrigo A. Grandy, José Garcia‐Bernardo, Paulina M. Strzelecka, Ludovic Vallier, Daniel Ortmann, Ana Cvejic
Software Mentions: 2
Published: over 4 years ago

10.26508/lsa.202000744

An atlas of human proximal epididymis reveals cell-specific functions and distinct roles for CFTR
Cited by: 28
Author(s): Shih Hsing Leir, Shiyi Yin, Jenny L. Kerschner, Wilmel R. Cosme, Ann Harris
Software Mentions: 2
Published: about 4 years ago

10.1186/s13059-020-02103-2

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

10.1186/s12935-019-0911-1

Characteristics of a novel cell line ZJU-0430 established from human gallbladder carcinoma
Cited by: 6
Author(s): Fei Zhou, Yanhua Zhang, Jihong Sun, Xiaoming Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-020-02228-4

HiDeF: identifying persistent structures in multiscale ‘omics data
Cited by: 25
Author(s): Fan Zheng, She Zhang, Christopher Churas, Dexter Pratt, İvet Bahar, Trey Ideker
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13059-021-02279-1

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues
Cited by: 12
Author(s): Pawel F. Przytycki, Katherine S. Pollard
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13059-021-02301-6

Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
Cited by: 5
Author(s): Matan Sorek, Walaa Oweis, Malka Nissim-Rafinia, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi, Congyi Lu, Jen Q. Pan, Xiaohong Xu, Mahmoud A. Pouladi, Lisa M. Ellerby, Feng Zhang, Joshua Z. Levin, Eran Meshorer
Software Mentions: 2
Published: over 3 years ago

10.1186/s12935-021-02190-6

Single cell RNA-seq data and bulk gene profiles reveal a novel signature of disease progression in multiple myeloma
Cited by: 4
Author(s): Zhiyong Zeng, Jizhen Lin, Kejie Zhang, Xizhe Guo, Xiaoqiang Zheng, Apeng Yang, Junmin Chen
Software Mentions: 2
Published: about 3 years ago

10.3390/ijms22158109

Keratin Profiling by Single-Cell RNA-Sequencing Identifies Human Prostate Stem Cell Lineage Hierarchy and Cancer Stem-Like Cells
Cited by: 5
Author(s): Wen‐Yang Hu, Dongyan Hu, Lishi Xie, Larisa Nonn, Ranli Lu, Michael R. Abern, Toshihiro Shioda, Gail S. Prins
Software Mentions: 2
Published: over 3 years ago

10.1016/j.ccell.2017.11.001

Antibody Tumor Targeting Is Enhanced by CD27 Agonists through Myeloid Recruitment
Cited by: 51
Author(s): Anna H. Turaj, Khiyam Hussain, Kerry L. Cox, Matthew Rose-Zerilli, James Testa, Lekh N. Dahal, H T Claude Chan, Sonya James, Vikki L Field, Matthew Carter, Hyung J. Kim, Jonathan West, Lawrence J. Thomas, Lizhen He, Tibor Keler, Peter Johnson, Aymen Al‐Shamkhani, Stephen M. Thirdborough, Stephen A. Beers, Mark S. Cragg, Martin J. Glennie, Sean H. Lim
Software Mentions: 2
Published: almost 7 years ago

Projects: cran: Seurat

Papers Mentioning Seurat 1,512