Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

Human pre-implantation embryo development

(2012) K. K. Niakan et al.   DEVELOPMENT

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Transcript clearance during the maternal-to-zygotic transition

(2011) Claudia B Walser et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development

(2011) R. Vassena et al.   DEVELOPMENT

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

(2011) J. T. Eppig et al.   NUCLEIC ACIDS RESEARCH

Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres

(2011) Fuchou Tang et al.   PLoS One

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Novel Importin-α Family Member Kpna7 Is Required for Normal Fertility and Fecundity in the Mouse

(2010) Jianjun Hu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

(2010) Yingrui Li et al.   NATURE GENETICS

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

(2010) Jeremy A. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Transcriptome Profiling of Human Pre-Implantation Development

(2009) Pu Zhang et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Geometric Interpretation of Gene Coexpression Network Analysis

(2008) Steve Horvath et al.   PLoS Computational Biology