pypi: velocyto | Projects | Ecosyste.ms: Papers

10.1038/s41422-020-00453-x

Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration
Cited by: 39
Author(s): Molong Qu, Liang Xiong, Yulin Lyu, Xiannian Zhang, Jie Shen, Jingyang Guan, Peiyuan Chai, Lin Zheng, Boyao Nie, Cheng Li, Jun Xu, Hongkui Deng
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pcbi.1008585

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
Cited by: 43
Author(s): Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Stadler
Software Mentions: 11
Published: over 3 years ago

10.1038/s41422-021-00467-z

Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses
Cited by: 44
Author(s): Jian He, Yan Jing, Jianfang Wang, Liangyu Zhao, Xin Qian, Yang Zeng, Yuxi Sun, Han Zhang, Zhijie Bai, Zongcheng Li, Yanli Ni, Yandong Gong, Yunqiao Li, Han He, Zhilei Bian, Yu Lan, Chunyu Ma, Lihong Bian, Heng Zhu, Bing Liu, Rui Yue
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pgen.1009773

Transcriptional progression during meiotic prophase I reveals sex-specific features and X chromosome dynamics in human fetal female germline
Cited by: 7
Author(s): Xueying Fan, Ioannis Moustakas, Vanessa Torrens-Juaneda, Qijing Lei, Geert Hamer, Leoni A. Louwé, Gonneke S. K. Pilgram, Károly Szuhai, Roberto Matorras, Cristina Eguizábal, Lucette van der Westerlaken, Hailiang Mei, Susana M. Chuva de Sousa Lopes
Software Mentions: 9
Published: about 3 years ago

10.7554/eLife.60188

Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells
Cited by: 42
Author(s): Kristen L. Wells, Corey N. Miller, Andreas R. Gschwind, Wei Wu, Jonah D Phipps, Mark S. Anderson, Lars M. Steinmetz
Software Mentions: 9
Published: almost 4 years ago

10.1126/sciadv.abd3311

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell
Cited by: 64
Author(s): Gerda Kildisiute, Waleed M. Kholosy, Matthew D. Young, Kenny Roberts, Rasa Elmentaite, Sander R. van Hooff, Clarissa N Pacyna, Eleonora Khabirova, Alice Piapi, Christine Thevanesan, Eva Bugallo-Blanco, Christina Burke, Lira Mamanova, KM Keller, Karin Langenberg-Ververgaert, Philip Lijnzaad, Thanasis Margaritis, Frank C. P. Holstege, Michelle L. Tas, Marc H. W. A. Wijnen, Max M. van Noesel, Ignacio del Valle, Giuseppe Barone, Reinier van der Linden, Catriona Duncan, John Anderson, John C. Achermann, Muzlifah Haniffa, Sarah A. Teichmann, Dyanne Rampling, Neil J. Sebire, Xiaoling He, Ronald R. de Krijger, Roger A. Barker, Kerstin B. Meyer, Ömer Bayraktar, Karin Straathof, Jan J. Molenaar, Sam Behjati
Software Mentions: 8
Published: over 3 years ago

10.3389/fcell.2020.593007

Exploring Additional Valuable Information From Single-Cell RNA-Seq Data
Cited by: 12
Author(s): Yunjin Li, Qiyue Xu, Duojiao Wu, Geng Chen
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13059-020-1945-3

Protein velocity and acceleration from single-cell multiomics experiments
Cited by: 43
Author(s): Gennady Gorin, Valentine Svensson, Lior Pachter
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-019-1699-y

CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
Cited by: 56
Author(s): Chuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, Xue Yang, Yuhei Kirita, Samantha A. Morris
Software Mentions: 7
Published: over 5 years ago

10.1186/s12915-021-01071-8

Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma
Cited by: 17
Author(s): Wenqin Luo, Guan Ning Lin, Weichen Song, Yu Zhang, Huadong Lai, Man Zhang, Juju Miao, Xiaomu Cheng, Yongjie Wang, Wang Li, Wenxiang Wei, Wei‐Qiang Gao, Ru Yang, Jia Wang
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pcbi.1008569

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data
Cited by: 16
Author(s): Andreas Tjärnberg, Omar Mahmood, Christopher Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen, Richard Bonneau
Software Mentions: 6
Published: over 3 years ago

10.1038/s42003-020-01476-1

Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
Cited by: 58
Author(s): Baijun Dong, Juju Miao, Yanqing Wang, Wenqin Luo, Zhongzhong Ji, Huadong Lai, Man Zhang, Xiaomu Cheng, Jinming Wang, Yuxiang Fang, Helen He Zhu, Chee Wai Chua, Liancheng Fan, Yao Zhu, Jiahua Pan, Jia Wang, Wei Xue, Wei‐Qiang Gao
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.immuni.2019.01.001

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation
Cited by: 322
Author(s): Ricardo J. Miragaia, Tomás Gomes, Agnieszka Chomka, Laura Jardine, Angela Riedel, Ahmed N. Hegazy, Natasha Whibley, A. Tucci, Xi Chen, Ida Lindeman, Guy Emerton, Thomas Krausgruber, Jacqueline D. Shields, Muzlifah Haniffa, Fiona Powrie, Sarah A. Teichmann
Software Mentions: 6
Published: over 5 years ago

10.1242/dev.183855

Aging induces aberrant state transition kinetics in murine muscle stem cells
Cited by: 50
Author(s): Jacob C. Kimmel, Ara B. Hwang, Annarita Scaramozza, Wallace F. Marshall, Andrew S. Brack
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-021-02414-y

Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation
Cited by: 38
Author(s): Melania Barile, Iván Imaz-Rosshandler, Isabella Inzani, Shila Ghazanfar, Jennifer Nichols, John C. Marioni, Carolina Guibentif, Berthold Göttgens
Software Mentions: 5
Published: about 3 years ago

10.1038/s41388-021-01940-0

Human cell transformation by combined lineage conversion and oncogene expression
Cited by: 10
Author(s): Biswajyoti Sahu, Päivi Pihlajamaa, Kaiyang Zhang, Kimmo Palin, Saija Ahonen, Alejandra Cervera, Ari Ristimäki, Lauri A. Aaltonen, Sampsa Hautaniemi, Jussi Taipale
Software Mentions: 5
Published: about 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: over 3 years ago

10.7554/eLife.68603

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair
Cited by: 49
Author(s): Shintaro Ide, Yoshihiko Kobayashi, Kana Ide, Sarah A. Strausser, Koki Abe, Savannah Herbek, Lori L. O’Brien, Steven D. Crowley, Laura Barisoni, Aleksandra Tata, Purushothama Rao Tata, Tomokazu Souma
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-021-02364-5

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

10.1038/s41422-020-0378-6

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

10.1038/s41598-020-76157-4

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

10.7554/eLife.60108

Novel cell types and developmental lineages revealed by single-cell RNA-seq analysis of the mouse crista ampullaris
Cited by: 21
Author(s): Brent A. Wilkerson, Heather L Zebroski, Connor Finkbeiner, Alex Chitsazan, Kathy Beach, Nilasha Sen, Renee C Zhang, Olivia Bermingham‐McDonogh
Software Mentions: 4
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

10.1038/s41421-021-00266-1

Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture
Cited by: 25
Author(s): Yanfang Lu, Miao Liu, Jennifer Yang, Sherman M. Weissman, Xinghua Pan, Samuel G. Katz, Siyuan Wang
Software Mentions: 3
Published: about 3 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: about 3 years ago

Ecosyste.ms: Papers

Projects: pypi: velocyto

Papers Mentioning velocyto 25