Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

by Christoph Hafemeister, Rahul Satija
Published 2019-12-01

Mesothelial cells are not a source of adipocytes in mice

by Gregory P. Westcott, Margo P. Emont, Jin Li, Christopher Jacobs, Linus Tsai, Evan D. Rosen
Published 2021-07-01

EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data

by Andrew E. Teschendorff, Tianyu Zhu, Charles E. Breeze, Stephan Beck
Published 2020-09-01

Accounting for cell type hierarchy in evaluating single cell RNA-seq clustering

by Zhijin Wu, Hao Wu
Published 2020-05-01

Single cell RNA-seq data clustering using TF-IDF based methods

by Marmar Moussa, Ion I. Măndoiu
Published 2018-08-01

Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters

by Fatemeh Behjati Ardakani, Kathrin Kattler, Karl Nordström, Nina Gasparoni, Gilles Gasparoni, Sarah Fuchs, Anupam Sinha, Matthias Barann, Peter Ebert, Jonas Fischer, Barbara Hutter, Gideon Zipprich, Charles D. Imbusch, Bärbel Felder, Jürgen Eils, Benedikt Brors, Thomas Lengauer, Thomas Manke, Philip Rosenstiel, Jörn Walter, Marcel H. Schulz
Published 2018-11-01

Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD

by Xiuying Li, Guillaume Noell, Tracy Tabib, Alyssa D. Gregory, Humberto E. Trejo Bittar, Ravi Vats, Tomasz W. Kaminski, John Sembrat, Mark E. Snyder, Divay Chandra, Kong Chen, Chunbin Zou, Yingze Zhang, Prithu Sundd, John F. McDyer, Frank Sciurba, Mauricio Rojas, Robert Lafyatis, Steve D. Shapiro, Rosa Faner, Toru Nyunoya
Published 2021-04-01

Identification of Intercellular Crosstalk between Decidual Cells and Niche Cells in Mice

by Jia-Peng He, Qing Tian, Qiu-Yang Zhu, Ji-Long Liu
Published 2021-07-01

Murine muscle stem cell response to perturbations of the neuromuscular junction are attenuated with aging

by Jacqueline A Larouche, Mahir Mohiuddin, Jeongmoon J Choi, Peter J Ulintz, Paula Fraczek, Kaitlyn Sabin, Sethuramasundaram Pitchiaya, Sarah J Kurpiers, Jesus Castor-Macias, Wenxuan Liu, Robert Louis Hastings, Lemuel A Brown, James F Markworth, Kanishka De Silva, Benjamin Levi, Sofia D Merajver, Gregorio Valdez, Joe V Chakkalakal, Young C Jang, Susan V Brooks, Carlos A Aguilar
Published 2021-07-01

The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline

by Danielle Janosevic, Jered Myslinski, Thomas W McCarthy, Amy Zollman, Farooq Syed, Xiaoling Xuei, Hongyu Gao, Yun-Long 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
Published 2021-01-01

Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes

by Qingxin Song, Atsumi Ando, Ning Jiang, Yoko Ikeda, Z. Jeffrey Chen
Published 2020-07-01

A robust semi-supervised NMF model for single cell RNA-seq data

by Peng Wu, Mo An, Hai-Ren Zou, Cai-Ying Zhong, Wei Wang, Chang-Peng Wu
Published 2020-10-01

SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data

by Tao Peng, Qin Zhu, Penghang Yin, Kai Tan
Published 2019-05-01

BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process

by Alexis Boukouvalas, James Hensman, Magnus Rattray
Published 2018-05-01

SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing

by Jinzhou Yuan, Jenny Sheng, Peter A. Sims
Published 2018-12-01

An interpretable framework for clustering single-cell RNA-Seq datasets

by Jesse M. Zhang, Jue Fan, H. Christina Fan, David Rosenfeld, David N. Tse
Published 2018-03-01

BRIE: transcriptome-wide splicing quantification in single cells

by Yuanhua Huang, Guido Sanguinetti
Published 2017-06-01

LAK: Lasso and K-Means Based Single-Cell RNA-Seq Data Clustering Analysis

by Jiao Hua, Hongkun Liu, Boyang Zhang, Shuilin Jin
Published 2020-01-01

Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker

by Andrew X. Chen, Robyn D. Gartrell, Junfei Zhao, Pavan S. Upadhyayula, Wenting Zhao, Jinzhou Yuan, Hanna E. Minns, Athanassios Dovas, Jeffrey N. Bruce, Anna Lasorella, Antonio Iavarone, Peter Canoll, Peter A. Sims, Raul Rabadan
Published 2021-05-01

Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation

by Hyeogsun Kwon, Mubasher Mohammed, Oscar Franzén, Johan Ankarklev, Ryan C Smith
Published 2021-07-01