Table of Contents

Methods

• Select this article

  Automated quality control and cell identification of droplet-based single-cell data using dropkick

  • Cody N. Heiser,
  • Victoria M. Wang,
  • Bob Chen,
  • Jacob J. Hughey,
  • and Ken S. Lau

  Genome Res. October 2021 31: 1742-1752; Published in Advance April 9, 2021, doi:10.1101/gr.271908.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics

  • Justin Lakkis,
  • David Wang,
  • Yuanchao Zhang,
  • Gang Hu,
  • Kui Wang,
  • Huize Pan,
  • Lyle Ungar,
  • Muredach P. Reilly,
  • Xiangjie Li,
  • and Mingyao Li

  Genome Res. October 2021 31: 1753-1766; Published in Advance May 25, 2021, doi:10.1101/gr.271874.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

  • Brian Aevermann,
  • Yun Zhang,
  • Mark Novotny,
  • Mohamed Keshk,
  • Trygve Bakken,
  • Jeremy Miller,
  • Rebecca Hodge,
  • Boudewijn Lelieveldt,
  • Ed Lein,
  • and Richard H. Scheuermann

  Genome Res. October 2021 31: 1767-1780; Published in Advance June 4, 2021, doi:10.1101/gr.275569.121
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Semisupervised adversarial neural networks for single-cell classification

  • Jacob C. Kimmel and
  • David R. Kelley

  Genome Res. October 2021 31: 1781-1793; Published in Advance February 24, 2021, doi:10.1101/gr.268581.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Likelihood-based deconvolution of bulk gene expression data using single-cell references

  • Dan D. Erdmann-Pham,
  • Jonathan Fischer,
  • Justin Hong,
  • and Yun S. Song

  Genome Res. October 2021 31: 1794-1806; Published in Advance July 22, 2021, doi:10.1101/gr.272344.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Bayesian estimation of cell type–specific gene expression with prior derived from single-cell data

  • Jiebiao Wang,
  • Kathryn Roeder,
  • and Bernie Devlin

  Genome Res. October 2021 31: 1807-1818; Published in Advance April 9, 2021, doi:10.1101/gr.268722.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Iterative epigenomic analyses in the same single cell

  • Hidetaka Ohnuki,
  • David J. Venzon,
  • Alexei Lobanov,
  • and Giovanna Tosato

  Genome Res. October 2021 31: 1819-1830; Published in Advance February 24, 2021, doi:10.1101/gr.269068.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing

  • Wai Lim Ku,
  • Lixia Pan,
  • Yaqiang Cao,
  • Weiwu Gao,
  • and Keji Zhao

  Genome Res. October 2021 31: 1831-1842; Published in Advance April 14, 2021, doi:10.1101/gr.260893.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities

  • Brendan F. Miller,
  • Dhananjay Bambah-Mukku,
  • Catherine Dulac,
  • Xiaowei Zhuang,
  • and Jean Fan

  Genome Res. October 2021 31: 1843-1855; Published in Advance May 25, 2021, doi:10.1101/gr.271288.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression

  • Yipeng Gao,
  • Lei Li,
  • Christopher I. Amos,
  • and Wei Li

  Genome Res. October 2021 31: 1856-1866; Published in Advance May 25, 2021, doi:10.1101/gr.271346.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data

  • Norah Alghamdi,
  • Wennan Chang,
  • Pengtao Dang,
  • Xiaoyu Lu,
  • Changlin Wan,
  • Silpa Gampala,
  • Zhi Huang,
  • Jiashi Wang,
  • Qin Ma,
  • Yong Zang,
  • Melissa Fishel,
  • Sha Cao,
  • and Chi Zhang

  Genome Res. October 2021 31: 1867-1884; Published in Advance July 22, 2021, doi:10.1101/gr.271205.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data

  • Shuze Wang,
  • Mary P. Lee,
  • Scott Jones,
  • Jie Liu,
  • and Joerg Waldhaus

  Genome Res. October 2021 31: 1885-1899; Published in Advance April 9, 2021, doi:10.1101/gr.271080.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Multimodal single-cell/nucleus RNA sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's disease

  • Jielin Xu,
  • Pengyue Zhang,
  • Yin Huang,
  • Yadi Zhou,
  • Yuan Hou,
  • Lynn M. Bekris,
  • Justin Lathia,
  • Chien-Wei Chiang,
  • Lang Li,
  • Andrew A. Pieper,
  • James B. Leverenz,
  • Jeffrey Cummings,
  • and Feixiong Cheng

  Genome Res. October 2021 31: 1900-1912; Published in Advance February 24, 2021, doi:10.1101/gr.272484.120
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE