Single-cell genomics identifies cell type–specific molecular changes in autism

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

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

(2016) Neelroop N. Parikshak et al.   NATURE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

(2015) Stephan J. Sanders et al.   NEURON

Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism

(2014) Simone Gupta et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism

(2013) A. Jeremy Willsey et al.   CELL

Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism

(2013) Neelroop N. Parikshak et al.   CELL

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs)

(2013) Brett S Abrahams et al.   Molecular Autism

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH