Evaluating measures of association for single-cell transcriptomics

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

(2018) Shuonan Chen et al.   BMC BIOINFORMATICS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

(2018) Monique G. P. van der Wijst et al.   NATURE GENETICS

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

(2018) Megan Crow et al.   Nature Communications

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

(2018) Luke Zappia et al.   PLoS Computational Biology

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

(2018) Justin K. Huang et al.   Cell Systems

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

A molecular atlas of cell types and zonation in the brain vasculature

(2018) Michael Vanlandewijck et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration

(2018) Tobias Gerber et al.   SCIENCE

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

An integrative tissue-network approach to identify and test human disease genes

(2018) Victoria Yao et al.   NATURE BIOTECHNOLOGY

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

(2017) Thomas P. Quinn et al.   Scientific Reports

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes

(2016) Yurong Xin et al.   Cell Metabolism

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

Genome-wide changes in lncRNA, splicing and regional gene expression patterns in autism

(2016) Neelroop N. Parikshak et al.   NATURE

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks

(2016) Gregorio Alanis-Lobato et al.   NUCLEIC ACIDS RESEARCH

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

(2016) Graham Heimberg et al.   Cell Systems

A Single-Cell Transcriptome Atlas of the Human Pancreas

(2016) Mauro J. Muraro et al.   Cell Systems

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

(2015) S. Ballouz et al.   BIOINFORMATICS

Establishment and Dysfunction of the Blood-Brain Barrier

(2015) Zhen Zhao et al.   CELL

Comparing the performance of biomedical clustering methods

(2015) Christian Wiwie et al.   NATURE METHODS

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Association of zero-inflated continuous variables

(2015) Ronald S. Pimentel et al.   STATISTICS & PROBABILITY LETTERS

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

(2014) Bidesh Mahata et al.   Cell Reports

Spatial and Temporal Mapping of De Novo Mutations in Schizophrenia to a Fetal Prefrontal Cortical Network

(2013) Suleyman Gulsuner et al.   CELL

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Comparison of co-expression measures: mutual information, correlation, and model based indices

(2012) Lin Song et al.   BMC BIOINFORMATICS

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations

(2009) W. Yu et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

(2008) Arun K Ramani et al.   Molecular Systems Biology