Volume 31, Issue 10 | October 2021

Editorial
- - New frontiers in single-cell genomics
    Nicholas E. Navin
    Orit Rozenblatt-Rosen
    Nancy R. Zhang
    First Published October 1, 2021
Perspectives
- - Tagmentation-based single-cell genomics
    Andrew C. Adey
    First Published October 1, 2021
  - Advances in spatial transcriptomic data analysis
    Ruben Dries
    Jiaji Chen
    Natalie del Rossi
    Mohammed Muzamil Khan
    Adriana Sistig
    First Published October 1, 2021
  - Cancer cell states and emergent properties of the dynamic tumor system
    Dalia Barkley
    Anjali Rao
    Maayan Pour
    Gustavo S. França
    Itai Yanai
    First Published October 1, 2021
  - Applications of single-cell genomics and computational strategies to study common disease and population-level variation
    Benjamin J. Auerbach
    Jian Hu
    Muredach P. Reilly
    Mingyao Li
    First Published October 1, 2021
Methods
- - 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
    Ken S. Lau
    First Published April 9, 2021
  - 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
    ...[+1 authors]...,
    Lyle Ungar
    Muredach P. Reilly
    Xiangjie Li
    Mingyao Li
    First Published May 25, 2021
  - 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
    ...[+1 authors]...,
    Rebecca Hodge
    Boudewijn Lelieveldt
    Ed Lein
    Richard H. Scheuermann
    First Published June 4, 2021
  - Semisupervised adversarial neural networks for single-cell classification
    Jacob C. Kimmel
    David R. Kelley
    First Published February 24, 2021
  - Likelihood-based deconvolution of bulk gene expression data using single-cell references
    Dan D. Erdmann-Pham
    Jonathan Fischer
    Justin Hong
    Yun S. Song
    First Published July 22, 2021
  - Bayesian estimation of cell type–specific gene expression with prior derived from single-cell data
    Jiebiao Wang
    Kathryn Roeder
    Bernie Devlin
    First Published April 9, 2021
  - Iterative epigenomic analyses in the same single cell
    Hidetaka Ohnuki
    David J. Venzon
    Alexei Lobanov
    Giovanna Tosato
    First Published February 24, 2021
  - Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing
    Wai Lim Ku
    Lixia Pan
    Yaqiang Cao
    Weiwu Gao
    Keji Zhao
    First Published April 14, 2021
  - 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
    Jean Fan
    First Published May 25, 2021
  - 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
    Wei Li
    First Published May 25, 2021
  - 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
    ...[+4 authors]...,
    Yong Zang
    Melissa Fishel
    Sha Cao
    Chi Zhang
    First Published July 22, 2021
  - Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data
    Shuze Wang
    Mary P. Lee
    Scott Jones
    Jie Liu
    Joerg Waldhaus
    First Published April 9, 2021
  - 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
    ...[+4 authors]...,
    Andrew A. Pieper
    James B. Leverenz
    Jeffrey Cummings
    Feixiong Cheng
    First Published February 24, 2021
Resources
- - A single-cell tumor immune atlas for precision oncology
    Paula Nieto
    Marc Elosua-Bayes
    Juan L. Trincado
    Domenica Marchese
    Ramon Massoni-Badosa
    Maria Salvany Ana Henriques Juan Nieto Sergio Aguilar-Fernández Elisabetta Mereu Catia Moutinho Sara Ruiz Patricia Lorden Vanessa T. Chin Dominik Kaczorowski Chia-Ling Chan Richard Gallagher Angela Chou Ester Planas-Rigol Carlota Rubio-Perez Ivo Gut Josep M. Piulats
    ...[+17 authors]...,
    Joan Seoane
    Joseph E. Powell
    Eduard Batlle
    Holger Heyn
    First Published September 21, 2021
  - The Drosophila brain on cocaine at single-cell resolution
    Brandon M. Baker
    Sneha S. Mokashi
    Vijay Shankar
    Jeffrey S. Hatfield
    Rachel C. Hannah
    First Published May 25, 2021
  - A single-cell atlas reveals unanticipated cell type complexity in Drosophila ovaries
    Maija Slaidina
    Selena Gupta
    Torsten U. Banisch
    Ruth Lehmann
    First Published August 13, 2021
  - Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
    Timothy J. Durham
    Riza M. Daza
    Louis Gevirtzman
    Darren A. Cusanovich
    Olubusayo Bolonduro
    First Published April 22, 2021

Table of Contents

Volume 31, Issue 10 | October 2021

Editorial

New frontiers in single-cell genomics

Perspectives

Tagmentation-based single-cell genomics

Advances in spatial transcriptomic data analysis

Cancer cell states and emergent properties of the dynamic tumor system

Applications of single-cell genomics and computational strategies to study common disease and population-level variation

Methods

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

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

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

Semisupervised adversarial neural networks for single-cell classification

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

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

Iterative epigenomic analyses in the same single cell

Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing

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

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

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

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

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

Resources

A single-cell tumor immune atlas for precision oncology

The Drosophila brain on cocaine at single-cell resolution

A single-cell atlas reveals unanticipated cell type complexity in Drosophila ovaries

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

Table of Contents

Volume 31, Issue 10 | October 2021

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Editorial

Perspectives

Methods

Resources