cran: Seurat | Projects | Ecosyste.ms: Papers

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

10.15252/emmm.202013901

Glycolysis downregulation is a hallmark of HIV‐1 latency and sensitizes infected cells to oxidative stress
Cited by: 23
Author(s): Iart Luca Shytaj, Francesco A. Procopio, Mohammad Tarek, Irene Carlón-Andrés, Hsin‐Yao Tang, Aaron R. Goldman, MohamedHusen Munshi, Virender Kumar Pal, Mattia Forcato, Sheetal Sreeram, Konstantin Leskov, Fengchun Ye, Bojana Lucic, Nicolly Cruz, Lishomwa C. Ndhlovu, Silvio Bicciato, Sergi Padilla‐Parra, Ricardo Sobhie Diaz, Amit Singh, Marina Lušić, Jonathan Karn, David Alvarez-Carbonell, Andrea Savarino
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0185543

Diversity amongst trigeminal neurons revealed by high throughput single cell sequencing
Cited by: 119
Author(s): Minh Quang Nguyen, Youmei Wu, Lauren S. Bonilla, Lars J. von Buchholtz, Nicholas J. P. Ryba
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.65412

Fate mapping analysis reveals a novel murine dermal migratory Langerhans-like cell population
Cited by: 13
Author(s): Jianpeng Sheng, Qi Chen, Xiaoting Wu, Yu Wen Dong, Johannes U Mayer, Junlei Zhang, Lin Wang, Xueli Bai, Yang Ho Sung, Wilson Wen Bin Goh, Franca Ronchese, Christiane Ruedl
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

10.3389/fgene.2021.644211

CBA: Cluster-Guided Batch Alignment for Single Cell RNA-seq
Cited by: 1
Author(s): Wenbo Yu, Ahmed Mahfouz, Marcel J. T. Reinders
Software Mentions: 3
Published: over 3 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

10.1371/journal.pone.0224900

UM171 induces a homeostatic inflammatory-detoxification response supporting human HSC self-renewal
Cited by: 28
Author(s): Jalila Chagraoui, Bernhard Lehnertz, Simon Girard, Jean François Spinella, Iman Fares, Elisa Tomellini, Nadine Mayotte, Sophie Corneau, Tara MacRae, Laura Simon, Guy Sauvageau
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-019-6053-y

Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data
Cited by: 17
Author(s): Di Feng, Charles E. Whitehurst, Dechao Shan, Jon Hill, Yong Yue
Software Mentions: 3
Published: about 5 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

10.1111/acel.13296

Whole‐body senescent cell clearance alleviates age‐related brain inflammation and cognitive impairment in mice
Cited by: 148
Author(s): Mikołaj Ogrodnik, Shane A. Evans, Edward Fielder, Stella Victorelli, Patrick Krüger, Hanna Salmonowicz, Bettina M. Weigand, Ayush D. Patel, Tamar Pirtskhalava, Christine Inman, Kurt O. Johnson, Stephanie Dickinson, Azucena Rocha, Marissa J. Schafer, Yi Zhu, David B. Allison, Thomas von Zglinicki, Nathan K. LeBrasseur, Tamar Tchkonia, Nicola Neretti, João F. Passos, James L. Kirkland, Diana Jurk
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2020.610682

Single-Cell RNA Sequencing of Tocilizumab-Treated Peripheral Blood Mononuclear Cells as an in vitro Model of Inflammation
Cited by: 5
Author(s): Arya Zarinsefat, George C. Hartoularos, Dmitry Rychkov, Priyanka Rashmi, Sindhu Chandran, Flavio Vincenti, Chun J. Yee, Minnie M. Sarwal
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13100-021-00241-3

The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis
Cited by: 6
Author(s): Mahboubeh Rostami, Martina Bradić
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2019.00734

A Tool for Visualization and Analysis of Single-Cell RNA-Seq Data Based on Text Mining
Cited by: 13
Author(s): Gennaro Gambardella, Diego di Bernardo
Software Mentions: 3
Published: over 5 years ago

10.1101/2020.05.13.092536

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection
Cited by: 12
Author(s): Komudi Singh, Yunching Chen, Jennifer Judy, Fayaz Seifuddin, Ilker Tunc, Mehdi Pirooznia
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2020.00942

Single Cell RNA-seq Data Analysis Reveals the Potential Risk of SARS-CoV-2 Infection Among Different Respiratory System Conditions
Cited by: 7
Author(s): Qiang Zhang, Yuanyi Yue, Huiwen Tan, Yishu Liu, Zhang Yin, Li Xiao
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2021.741325

Multiomics Analysis Reveals the Prognostic Non-tumor Cell Landscape in Glioblastoma Niches
Cited by: 0
Author(s): Zixuan Xiao, Wei Zhang, Guanzhang Li, Wendong Li, Liang-In Lin, Taixiang Sun, Yufei He, Guang Liu, Lu Wang, Xiaohan Han, Hao Wen, Yong Liu, Yifan Chen, Haoyu Wang, Jing Li, Yubo Fan, Jing Zhang
Software Mentions: 3
Published: about 3 years ago

10.1016/j.celrep.2020.107742

Stem Cell Determinant SOX9 Promotes Lineage Plasticity and Progression in Basal-like Breast Cancer
Cited by: 29
Author(s): John R. Christin, Chunhui Wang, Chi Yeh Chung, Yu Liu, Christopher Dravis, Wei Tang, Maja H. Oktay, Geoffrey M. Wahl, Wenjun Guo
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2021.636743

DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data
Cited by: 21
Author(s): Floyd Maseda, Zixuan Cang, Qing Nie
Software Mentions: 3
Published: over 3 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

10.1002/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

10.1016/j.isci.2021.103030

Single-cell transcriptome identifies FCGR3B upregulated subtype of alveolar macrophages in patients with critical COVID-19
Cited by: 11
Author(s): Nasna Nassir, Richa Tambi, Asma Bankapur, Saba Al Heialy, Noushad Karuvantevida, Hamda Khansaheb, Binte Zehra, Ghausia Begum, Reem Abdel Hameid, Awab Ahmed, Zulfa Deesi, Abdulmajeed Alkhajeh, K. M. Furkan Uddin, Hosneara Akter, Seyed Ali Safizadeh Shabestari, Omar Almidani, Abu Zafor Md. Touhidul Islam, Mellissa Gaudet, Richard K. Kandasamy, Tom Loney, Ahmad Abou Tayoun, Norbert Nowotny, Marc Woodbury‐Smith, Proton Rahman, Wolfgang M. Kuebler, Mahmood Yaseen Hachim, Jean‐Laurent Casanova, Bakhrom K. Berdiev, Alawi A. Alsheikh‐Ali, Mohammed Uddin
Software Mentions: 3
Published: about 3 years ago

10.3390/ijms22063164

CaMKIIα Expressing Neurons to Report Activity-Related Endogenous Hypoxia upon Motor-Cognitive Challenge
Cited by: 4
Author(s): Umer Javed Butt, Imam Hassouna, Laura Fernandez Garcia-Agudo, Agnes A. Steixner-Kumar, Constanze Depp, Nadine Barnkothe, Matthias R. Zillmann, Anja Ronnenberg, Viktoria Bonet, Sandra Goebbels, Klaus‐Armin Nave
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

10.3389/fmicb.2021.709728

Spatially Resolved Immunometabolism to Understand Infectious Disease Progression
Cited by: 6
Author(s): Roel Tans, Shoumit Dey, Nidhi Sharma Dey, Grant Calder, Peter O’Toole, Paul M. Kaye, Ron M. A. Heeren
Software Mentions: 3
Published: over 3 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

10.1186/s13059-020-02064-6

Single-cell transcriptome and antigen-immunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer
Cited by: 92
Author(s): Jian Chen, Yun Tan, Fangyuan Sun, Likun Hou, Chi Zhang, Ge Tao, Hua Yu, Chunxiao Wu, Yuming Zhu, Liang Duan, Liang Wu, Nan Song, Liping Zhang, Wei Zhang, Di Wang, Chang Chen, Chunyan Wu, Gening Jiang, Peng Zhang
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2021.651656

Single-Cell RNA Sequencing Analysis of the Immunometabolic Rewiring and Immunopathogenesis of Coronavirus Disease 2019
Cited by: 21
Author(s): Furong Qi, Wenbo Zhang, Jialu Huang, Lili Fu, Jinfang Zhao
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-017-4019-5

SAIC: an iterative clustering approach for analysis of single cell RNA-seq data
Cited by: 29
Author(s): Lu Yang, Jiancheng Liu, Qiang Lü, Arthur D. Riggs, Xiwei Wu
Software Mentions: 3
Published: about 7 years ago

10.26508/lsa.202000867

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data
Cited by: 17
Author(s): Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Vu Viet Hoang Pham, Xiaomei Li, Thuc Duy Le, Adi L. Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gábor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Sáez-Rodríguez, Pablo Meyer
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.64875

Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans
Cited by: 30
Author(s): Trygve E. Bakken, Cindy Tj van Velthoven, Vilas Menon, Rebecca D. Hodge, Zizhen Yao, Thuc Nghi Nguyen, Lucas T. Graybuck, Gregory D. Horwitz, Darren Bertagnolli, Jeff Goldy, Anna Marie Yanny, Emma Garren, Sheana Parry, Tamara Casper, Soraya I. Shehata, Eliza Barkan, Aaron Szafer, Boaz P. Levi, Nick Dee, Kimberly A. Smith, Susan M. Sunkin, Amy Bernard, John W. Phillips, Michael Hawrylycz, Christof Koch, Gabe J. Murphy, Ed Lein, Hongkui Zeng, Bosiljka Tasic
Software Mentions: 3
Published: about 3 years ago

10.7554/eLife.48089

A scalable platform for the development of cell-type-specific viral drivers
Cited by: 59
Author(s): Siniša Hrvatin, Christopher P. Tzeng, Martina Nagy, Hume Stroud, Charalampia Koutsioumpa, Oren F Wilcox, Elena G. Assad, Jonathan Green, Christopher D. Harvey, Eric C. Griffith, Michael E. Greenberg
Software Mentions: 3
Published: about 5 years ago

10.1186/s12915-018-0580-x

Identification of cell types in a mouse brain single-cell atlas using low sampling coverage
Cited by: 15
Author(s): Aparna Bhaduri, Tomasz J. Nowakowski, Alex A. Pollen, Arnold R. Kriegstein
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1008772

Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance
Cited by: 18
Author(s): Anton J. M. Larsson, Christoph Ziegenhain, Michael Hagemann-Jensen, Björn Reinius, Tina Jacob, Tim Dalessandri, Gert‐Jan Hendriks, Maria Kasper, Rickard Sandberg
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

10.1186/s13619-021-00076-6

Canonical and early lineage-specific stem cell types identified in planarian SirNeoblasts
Cited by: 5
Author(s): Kaimeng Niu, Hao Xu, Yuanyi Zhou Xiong, Yun Zhao, Chong Gao, Chris Seidel, Xue Pan, Yuqing Ying, Kai Y. Lei
Software Mentions: 3
Published: over 3 years ago

10.1161/ATVBAHA.119.312399

Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mice Defined by Single-Cell RNA Sequencing
Cited by: 73
Author(s): Wenduo Gu, Zhichao Ni, Yuan Qing Tan, Jiacheng Deng, Si Jin Zhang, Zi Lv, Xiao Jian Wang, Ting Chen, Zhongyi Zhang, Yanhua Hu, Zhi‐Cheng Jing, Qingbo Xu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41375-020-0808-y

H3K79me2/3 controls enhancer–promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells
Cited by: 28
Author(s): Laura Godfrey, Nicholas T. Crump, Sorcha O’Byrne, I-Jun Lau, Siobhan Rice, Joe Harman, Thomas R. Jackson, Natalina E. Elliott, Gemma Buck, Christopher Connor, Ross Thorne, David J.H.F. Knapp, Olaf Heidenreich, Paresh Vyas, Pablo Menéndez, Sarah Inglott, Philip Ancliff, Huimin Geng, Irene Roberts, Anindita Roy, Thomas A. Milne
Software Mentions: 3
Published: over 4 years ago

10.1002/cam4.2113

Dissecting intratumoral myeloid cell plasticity by single cell RNA‐seq
Cited by: 89
Author(s): Qisheng Song, Gregory A. Hawkins, L. James Wudel, Ping-Chieh Chou, M. Elizabeth Forbes, Ashok Pullikuth, Liang Liu, Guangxu Jin, Lou Craddock, Ümit Topaloğlu, Gregory L. Kucera, Stacey S. O’Neill, Edward A. Levine, Peiqing Sun, Kounosuke Watabe, Yong Lu, Martha A. Alexander-Miller, Boris Pasche, Lance D. Miller, Wei Zhang
Software Mentions: 3
Published: over 5 years ago

10.1523/ENEURO.0252-21.2021

Cre Recombinase Driver Mice Reveal Lineage-Dependent and -Independent Expression of Brs3 in the Mouse Brain
Cited by: 1
Author(s): Allison S. Mogul, Colleen K. Hadley, Haley S. Province, Jordan L Pauli, Оксана Гаврилова, Cuiying Xiao, Richard D. Palmiter, Ramón A. Piñol, Marc L. Reitman
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-020-02145-6

Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction
Cited by: 24
Author(s): Norman Huang, Xiaochen Fan, Kathia Zaleta-Rivera, Tri C. Nguyen, Jiarong Zhou, Yingjun Luo, Jie Gao, Ronnie H. Fang, Zhangming Yan, Zhen Bouman Chen, Liangfang Zhang, Sheng Zhong
Software Mentions: 3
Published: about 4 years ago

10.3389/fphys.2021.562817

Single-Cell RNA Sequencing Analysis of Chicken Anterior Pituitary: A Bird’s-Eye View on Vertebrate Pituitary
Cited by: 11
Author(s): Jiannan Zhang, Can Lv, Chunheng Mo, Meng Li, Ying Wan, Juan Li, Yajun Wang
Software Mentions: 3
Published: over 3 years ago

10.1242/dev.196022

scRNA sequencing uncovers a TCF4-dependent transcription factor network regulating commissure development in mouse
Cited by: 6
Author(s): Marie-Theres Wittmann, Sayako Katada, Elisabeth Sock, Philipp Kirchner, Arif B. Ekici, Michael Wegner, Kinichi Nakashima, Dieter Chichung Lie, André Reis
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers13081776

Activated Regulatory T-Cells, Dysfunctional and Senescent T-Cells Hinder the Immunity in Pancreatic Cancer
Cited by: 22
Author(s): Shivan Sivakumar, Enas Abu-Shah, David Ahern, Edward H. Arbe-Barnes, Ashwin Kumar Jainarayanan, Nagina Mangal, Srikanth Reddy, Anikó Rendek, Alistair Easton, Elke Kurz, Michael Silva, Zahir Soonawalla, Lara Heij, Rachael Bashford-Rogers, Mark R. Middleton, Michael L. Dustin
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.53085

Chloride channels regulate differentiation and barrier functions of the mammalian airway
Cited by: 17
Author(s): Mu He, Bing Wu, Wenlei Ye, Daniel Le, Adriane Sinclair, Valeria Padovano, Yuzhang Chen, Ke-Xin Li, Rene Sit, Michelle Tan, Michael J. Caplan, Norma Neff, Yuh-Nung Jan, Spyros Darmanis, Yuh Nung Jan
Software Mentions: 3
Published: over 4 years ago

10.1186/s12935-021-01852-9

RNA sequencing reveals the expression profiles of circRNA and identifies a four-circRNA signature acts as a prognostic marker in esophageal squamous cell carcinoma
Cited by: 11
Author(s): Weiwei Wang, Di Zhu, Zhihua Zhao, Menghong Sun, Feng Wang, Wencai Li, Jianying Zhang, Guozhong Jiang
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.44423

Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons
Cited by: 26
Author(s): Disi An, Ryosuke Fujiki, Dylan E. Iannitelli, John W. Smerdon, Shuvadeep Maity, Matthew F. Rose, Alon Gelber, Elizabeth K. Wanaselja, Ilona Yagudayeva, Joun Y. Lee, Christine Vogel, Hynek Wichterle, Elizabeth C. Engle, Esteban O. Mazzoni
Software Mentions: 3
Published: over 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

10.1371/journal.pone.0251233

Mapping Rora expression in resting and activated CD4+ T cells
Cited by: 23
Author(s): Liora Haim-Vilmovsky, Johan Henriksson, Jennifer Walker, Zhichao Miao, Eviatar Natan, Gozde Kar, Simon Clare, Jillian L. Barlow, Evelina Charidemou, Lira Mamanova, Xi Chen, Valentina Proserpio, Jhuma Pramanik, Steven Woodhouse, Anna V. Protasio, Mirjana Efremova, Julian L. Griffin, Matt Berriman, Gordon Dougan, Jasmin Fisher, John C. Marioni, Andrew N. J. McKenzie, Sarah A. Teichmann
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22147696

Identification of Intercellular Crosstalk between Decidual Cells and Niche Cells in Mice
Cited by: 6
Author(s): Jia-Peng He, Qing Tian, Qiu-Yang Zhu, Ji‐Long Liu
Software Mentions: 3
Published: over 3 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

10.1371/journal.pcbi.1006053

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa
Cited by: 29
Author(s): Huanan Zhang, Catherine A. A. Lee, Zhuliu Li, John Garbe, Cindy R. Eide, Raphael Petegrosso, Jakub Tolar
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2021.639613

Single-Cell Transcriptomics and In Situ Morphological Analyses Reveal Microglia Heterogeneity Across the Nigrostriatal Pathway
Cited by: 24
Author(s): Oihane Uriarte Huarte, Dimitrios Kyriakis, Tony Heurtaux, Yolanda Pires‐Afonso, Kamil Grzyb, Rashi Halder, Manuel Buttini, Alexander Skupin, Michel Mittelbronn, Alessandro Michelucci
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers13133122

Overexpression of Replication-Dependent Histone Signifies a Subset of Dedifferentiated Liposarcoma with Increased Aggressiveness
Cited by: 5
Author(s): Yongjin Yoo, Soo‐Jin Park, Eun Byeol Jo, Minsu Choi, Kyo Won Lee, Doo-Pyo Hong, Sang Moon Lee, Cho Rong Lee, Youngha Lee, Jae Young Um, Jae Berm Park, Sung Wook Seo, Yoon La Choi, Sungjoo Kim, Seok-Geun Lee, Murim Choi
Software Mentions: 3
Published: over 3 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

10.1016/j.ccell.2020.03.022

C/EBPα and GATA-2 Mutations Induce Bilineage Acute Erythroid Leukemia through Transformation of a Neomorphic Neutrophil-Erythroid Progenitor
Cited by: 14
Author(s): Cristina Di Genua, Simona Valletta, Mario Buono, Bilyana Stoilova, Connor Sweeney, Alba Rodríguez-Meira, Amit Grover, Roy Drissen, Yiran Meng, Ryan Beveridge, Zahra Aboukhalil, Dimitris Karamitros, Mirjam E. Belderbos, Leonid Bystrykh, Supat Thongjuea, Paresh Vyas, Claus Nerlov
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-021-02445-5

MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data
Cited by: 14
Author(s): Siyao Liu, Aatish Thennavan, Joseph P. Garay, J. S. Marron, Charles M. Perou
Software Mentions: 3
Published: over 3 years ago

10.1186/s12885-020-07628-0

Analyses of metastasis-associated genes in IDH wild-type glioma
Cited by: 4
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 3
Published: about 4 years ago

10.3389/fcell.2020.00288

Hybrid Stem Cell States: Insights Into the Relationship Between Mammary Development and Breast Cancer Using Single-Cell Transcriptomics
Cited by: 18
Author(s): Tasha Thong, Yutong Wang, Michael Brooks, Christopher T. Lee, Clayton Scott, Laura Balzano, Max S. Wicha, Justin A. Colacino
Software Mentions: 3
Published: over 4 years ago

10.1016/j.isci.2021.102410

Induced lineage promiscuity undermines the efficiency of all-trans-retinoid-acid-induced differentiation of acute myeloid leukemia
Cited by: 1
Author(s): Yijia Tang, Xin Tian, Zihan Xu, Junke Cai, Han Liu, Nan Liu, Chen Zhu, Sai‐Juan Chen, Feng Liu
Software Mentions: 3
Published: over 3 years ago

10.1111/cpr.12931

Single‐cell analysis identified lung progenitor cells in COVID‐19 patients
Cited by: 18
Author(s): Zhongyang Zhao, Yu Zhao, Yueqing Zhou, Xiaofan Wang, Ting Zhang, Wei Zuo
Software Mentions: 3
Published: about 4 years ago

10.3389/fcell.2021.645276

Understanding the Adult Mammalian Heart at Single-Cell RNA-Seq Resolution
Cited by: 9
Author(s): Ernesto Marín-Sedeño, Xabier Martínez de Morentin, José M. Pérez‐Pomares, David Green, Adrián Ruiz‐Villalba
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2020.626820

CD52 Is Elevated on B cells of SLE Patients and Regulates B Cell Function
Cited by: 13
Author(s): Kartik Bhamidipati, John L. Silberstein, Yashaar Chaichian, Matthew Baker, Tobias V. Lanz, Amin Zia, Yusuf S. Rasheed, Jennifer R. Cochran, William H. Robinson
Software Mentions: 3
Published: almost 4 years ago

10.1093/jmcb/mjy089

Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum
Cited by: 34
Author(s): Jian Peng, Ai-Li Sheng, Qi Xiao, Libing Shen, Xiang-Chun Ju, Min Zhang, Siting He, Chao Wu, Zhen-Ge Luo
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.56086

Enteric glia as a source of neural progenitors in adult zebrafish
Cited by: 37
Author(s): Sarah E. McCallum, Yuichi Obata, Evangelia Fourli, Stefan Boeing, Christopher J. Peddie, Qiling Xu, Stuart Horswell, Robert N. Kelsh, Lucy Collinson, David Wilkinson, Carmen Pin, Vassilis Pachnis, Tiffany A. Heanue
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-04426-w

A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA
Cited by: 188
Author(s): Blue B. Lake, Simone Codeluppi, Yun C. Yung, Derek Gao, Jerold Chun, Peter V. Kharchenko, Sten Linnarsson, Kun Zhang
Software Mentions: 3
Published: over 7 years ago

10.1186/s13073-020-00756-z

Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis
Cited by: 48
Author(s): Dominik Trzupek, Melanie Dunstan, Antony J. Cutler, Mercede Lee, Leila Godfrey, Lorna B. Jarvis, Daniel B. Rainbow, Dominik Aschenbrenner, Joanne L. Jones, Holm H. Uhlig, Linda S. Wicker, John A. Todd, Ricardo C. Ferreira
Software Mentions: 3
Published: over 4 years ago

10.3390/genes10070531

SCINA: Semi-Supervised Analysis of Single Cells in Silico
Cited by: 127
Author(s): Ze Zhang, Danni Luo, Xue Zhong, Jin Huk Choi, Yuanqing Ma, Stacy Wang, Elena Mahrt, Wenfei Guo, Eric Stawiski, Zora Modrušan, Somasekar Seshagiri, Payal Kapur, Gary C. Hon, James Brugarolas, Tao Wang
Software Mentions: 3
Published: over 5 years ago

10.1126/sciimmunol.abf6692

Clonal expansion and activation of tissue-resident memory-like T <sub>H</sub> 17 cells expressing GM-CSF in the lungs of patients with severe COVID-19
Cited by: 118
Author(s): Yu Zhao, Christoph Kilian, Jan-Eric Turner, Lidia Bosurgi, Kevin Roedl, Patricia Bartsch, Ann-Christin Gnirck, Filippo Cortesi, Christoph Schultheiß, Malte Hellmig, Leon U. B. Enk, Fabian Hausmann, Alina Borchers, Milagros Wong, Hans‐Joachim Paust, Francesco Siracusa, Nicola Scheibel, Marissa Herrmann, Elisa Rosati, Petra Bächer, Dominik Kylies, Dominik Jarczak, Marc Lütgehetmann, Susanne Pfefferle, Stefan Steurer, Julian Schulze zurWiesch, Victor G. Puelles, Jan‐Peter Sperhake, Marylyn M. Addo, Ansgar W. Lohse, Mascha Binder, Samuel Huber, Tobias B. Huber, Stefan Kluge, Stefan Bonn, Ulf Panzer, Nicola Gagliani, Christian Krebs
Software Mentions: 3
Published: almost 4 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

10.1038/s42003-020-01232-5

Analysis of single-cell transcriptomes links enrichment of olfactory receptors with cancer cell differentiation status and prognosis
Cited by: 17
Author(s): Siddhant Kalra, Aayushi Mittal, Kavya Gupta, Vrinda Singhal, Anku Gupta, Tripti Mishra, Srivatsava Naidu, Debarka Sengupta, Gaurav Ahuja
Software Mentions: 3
Published: about 4 years ago

10.1111/cpr.13007

Single‐cell transcriptomes of mouse bladder urothelium uncover novel cell type markers and urothelial differentiation characteristics
Cited by: 10
Author(s): Yan Li, Yaxiao Liu, Zhengdong Gao, Lekai Zhang, Lipeng Chen, Zonglong Wu, Qinggang Liu, Shuai Wang, Nan Zhou, Toby C. Chai, Benkang Shi
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12915-020-00947-5

Single-cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse cell types including T-bet+ B cells
Cited by: 20
Author(s): Roosheel Patel, Joy E. Tomlinson, Thomas J. Divers, Gerlinde R. Van de Walle, Brad R. Rosenberg
Software Mentions: 3
Published: almost 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: about 3 years ago

10.1523/ENEURO.0108-21.2021

Forebrain Neural Precursor Cells Are Differentially Vulnerable to Zika Virus Infection
Cited by: 1
Author(s): Samantha M Shelton, Alexandra R Soucy, Ronni Kurzion, Ella Zeldich, John H. Connor, Tarik F. Haydar
Software Mentions: 3
Published: over 3 years ago

10.1038/s41388-020-01576-6

Merkel cell carcinoma-derived exosome-shuttle miR-375 induces fibroblast polarization by inhibition of RBPJ and p53
Cited by: 26
Author(s): Kaiji Fan, Ivelina Spassova, Jan Gravemeyer, Cathrin Ritter, Kai Horny, Anja Lange, Thilo Gambichler, Niels Ødum, David Schrama, Dirk Schadendorf, Selma Ugurel, Jürgen C. Becker
Software Mentions: 3
Published: almost 4 years ago

10.3390/biom11020177

Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines
Cited by: 10
Author(s): Daniele Mercatelli, Nicola Balboni, Alessandro Palma, Emanuela Aleo, Pietro Paolo Sanna, Giovanni Perini, Federico M. Giorgi
Software Mentions: 3
Published: almost 4 years ago

10.1002/sctm.19-0396

Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration
Cited by: 11
Author(s): Sandra Petrus‐Reurer, Pankaj Kumar, Sara Padrell Sánchez, Monica Aronsson, Helder André, Hammurabi Bartuma, Álvaro Plaza Reyes, Emeline F. Nandrot, Anders Kvanta, Fredrik Lanner
Software Mentions: 3
Published: over 4 years ago

10.1007/s41745-020-00178-1

Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art
Cited by: 9
Author(s): Justine Jia Wen Seow, Richard L. Wong, Rhea Pai, Ankur Sharma
Software Mentions: 3
Published: over 4 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

10.1038/s41597-019-0116-4

Single-cell RNA sequencing of a European and an African lymphoblastoid cell line
Cited by: 24
Author(s): Daniel Osorio, Xue Yu, Peng Yu, Erchin Serpedin, James J. Cai
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.55361

Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors
Cited by: 33
Author(s): Shiri Kult, Tsviya Olender, Marco Osterwalder, Svetalana Markman, Dena Leshkowitz, Sharon Krief, Ronnie Blecher‐Gonen, Shani Ben‐Moshe, Lydia Farack, Hadas Keren‐Shaul, Tomer-Meir Salame, Terence D. Capellini, Shalev Itzkovitz, Ido Amit, Axel Visel, Elazar Zelzer
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers12020284

Mechanism- and Immune Landscape-Based Ranking of Therapeutic Responsiveness of 22 Major Human Cancers to Next Generation Anti-CTLA-4 Antibodies
Cited by: 8
Author(s): Peng Zhang, Xinxin Xiong, Christian Rolfo, Xuexiang Du, Yan Zhang, Han Yang, Alessandro Russo, Martin Devenport, Penghui Zhou, Yang Liu, Pan Zheng
Software Mentions: 3
Published: almost 5 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

10.1186/s13287-021-02498-0

EGR1 dysregulation defines an inflammatory and leukemic program in cell trajectory of human-aged hematopoietic stem cells (HSC)
Cited by: 14
Author(s): Christophe Desterke, Annelise Bennaceur‐Griscelli, Ali G. Turhan
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2021.689019

The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss
Cited by: 40
Author(s): Pengfei Chen, Lei Zhou, Jiying Chen, Ying Lu, Chaoxia Cao, Shuangli Lv, Zhihong Wang, Liping Wang, Jiao Chen, Xinglin Hu, Zijing Wu, Xiaohua Zhou, Danna Su, Xiaofang Deng, Changchun Zeng, Huiyun Wang, Zuhui Pu, Ruiying Diao, Lisha Mou
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.62766

Developmental, cellular, and behavioral phenotypes in a mouse model of congenital hypoplasia of the dentate gyrus
Cited by: 1
Author(s): Amir Rattner, Chantelle E. Terrillion, Claudia Jou, Tina Kleven, Shun Felix Hu, John Williams, Zhipeng Hou, Manisha Aggarwal, Susumu Mori, Gloria Shin, Loyal A. Goff, Menno P. Witter, Mikhail V. Pletnikov, A. G. Fenton, Jeremy Nathans
Software Mentions: 3
Published: about 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

10.1038/s41421-021-00296-9

Dysregulated hematopoiesis in bone marrow marks severe COVID-19
Cited by: 34
Author(s): Xin Wang, Yanling Wen, Xiaowei Xie, Yang Liu, Xiaohua Tan, Qing-Qing Cai, Yawen Zhang, Lin Cheng, Gang Xu, Shengyuan Zhang, Haiyan Wang, Lanlan Wei, Xian Tang, Furong Qi, Juanjuan Zhao, Jing Yuan, Lei Liu, Ping Zhu, Florent Ginhoux, Shuye Zhang, Tao Cheng, Zheng Zhang
Software Mentions: 3
Published: over 3 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: about 3 years ago

10.1136/jitc-2021-003093

PI3Kα inhibitor CYH33 triggers antitumor immunity in murine breast cancer by activating CD8<sup>+</sup>T cells and promoting fatty acid metabolism
Cited by: 18
Author(s): Pu Sun, Xi Zhang, Rong-Jing Wang, Qingyang Ma, Lan Xu, Yi Wang, Huiping Liao, Hailong Wang, Landian Hu, Xiangyin Kong, Jian Ding, Linghua Meng
Software Mentions: 3
Published: over 3 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

10.3389/fimmu.2021.584538

Terminally Differentiated CD4+ T Cells Promote Myocardial Inflammaging
Cited by: 20
Author(s): Murilo Delgobo, Margarete Heinrichs, Nils Hapke, DiyaaElDin Ashour, Marc Appel, Mugdha Srivastava, Tobias Heckel, Ioakim Spyridopoulos, Ulrich Hofmann, Stefan Frantz, Gustavo Ramos
Software Mentions: 3
Published: almost 4 years ago

10.1126/sciadv.abe3024

Distinct inflammatory profiles distinguish COVID-19 from influenza with limited contributions from cytokine storm
Cited by: 187
Author(s): Philip A. Mudd, Jeremy Chase Crawford, Jackson S. Turner, Aisha Souquette, Daniel Reynolds, Diane Bender, James P. Bosanquet, Nitin Anand, David A. Striker, Roció Belén Martín, Adrianus C. M. Boon, Stacey L. House, Kenneth E. Remy, Richard S. Hotchkiss, Rachel Presti, Jane A. O’Halloran, William G. Powderly, Paul G. Thomas, Ali H. Ellebedy
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.xpro.2021.100561

A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells
Cited by: 1
Author(s): Kevin Chen, Kıvılcım Öztürk, Ted Liefeld, Michael Reich, Jill P. Mesirov, Hannah Carter, Stephanie I. Fraley
Software Mentions: 3
Published: over 3 years ago

10.3389/fnmol.2021.718241

Single-Cell RNA-Seq of Cisplatin-Treated Adult Stria Vascularis Identifies Cell Type-Specific Regulatory Networks and Novel Therapeutic Gene Targets
Cited by: 13
Author(s): Ian Taukulis, Rafal T. Olszewski, Soumya Korrapati, Katharine A. Fernandez, Erich T. Boger, Tracy S. Fitzgerald, Robert J. Morell, Lisa L. Cunningham, Michael Hoa
Software Mentions: 3
Published: about 3 years ago

10.3389/fimmu.2021.700152

Single-Cell Transcriptomic Profiling of MAIT Cells in Patients With COVID-19
Cited by: 16
Author(s): Jiandang Shi, Jianglin Zhou, Xiaochang Zhang, Wei Hu, Jinfang Zhao, Shengqi Wang, Fusheng Wang, Jiyuan Zhang
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.64444

A β-catenin-driven switch in TCF/LEF transcription factor binding to DNA target sites promotes commitment of mammalian nephron progenitor cells
Cited by: 27
Author(s): Qiuyu Guo, Albert D. Kim, Bin Li, Andrew Ransick, Helena Bugacov, Xi Chen, Nils O. Lindström, Aaron C. Brown, Leif Oxburgh, Bing Ren, Andrew P. McMahon
Software Mentions: 3
Published: almost 4 years ago

10.3389/fimmu.2021.737332

Full-Length Transcriptome: A Reliable Alternative for Single-Cell RNA-Seq Analysis in the Spleen of Teleost Without Reference Genome
Cited by: 8
Author(s): Lixing Huang, Ying Qiao, Wei Xü, Li Gong, Rongchao He, Weilu Qi, Qiancheng Gao, Hongyan Cai, Hans‐Peter Grossart, Qingpi Yan
Software Mentions: 3
Published: about 3 years ago

10.1242/bio.042754

Defining the dynamic chromatin landscape of mouse nephron progenitors
Cited by: 17
Author(s): Sylvia Hilliard, Renming Song, Hongbing Liu, Chao‐Hui Chen, Yuwen Li, Melody Baddoo, Erik Flemington, Alanna Wanek, Jay K. Kolls, Zubaida Saifudeen, Samir S. El‐Dahr
Software Mentions: 3
Published: almost 6 years ago

Projects: cran: Seurat

Papers Mentioning Seurat 1,512