Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

Avoiding the off-target effects of CRISPR/cas9 system is still a challenging accomplishment for genetic transformation

(2019) Roberto H. Herai   GENE

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development

(2019) Cleber A. Trujillo et al.   Cell Stem Cell

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

snpAD: an ancient DNA genotype caller

(2018) Kay Prüfer   BIOINFORMATICS

Synaptic activity induces input-specific rearrangements in a targeted synaptic protein interaction network

(2018) Jonathan D. Lautz et al.   JOURNAL OF NEUROCHEMISTRY

p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells

(2018) Robert J. Ihry et al.   NATURE MEDICINE

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

(2018) Emma Haapaniemi et al.   NATURE MEDICINE

Clustering the autisms using glutamate synapse protein interaction networks from cortical and hippocampal tissue of seven mouse models

(2018) Emily A. Brown et al.   Molecular Autism

SHANK proteins: roles at the synapse and in autism spectrum disorder

(2017) Patricia Monteiro et al.   NATURE REVIEWS NEUROSCIENCE

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex

(2016) Xiaochang Zhang et al.   CELL

Functional Impairment in Miro Degradation and Mitophagy Is a Shared Feature in Familial and Sporadic Parkinson’s Disease

(2016) Chung-Han Hsieh et al.   Cell Stem Cell

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

(2016) Neelroop N. Parikshak et al.   NATURE

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Multiplex matrix network analysis of protein complexes in the human TCR signalosome

(2016) Stephen E. P. Smith et al.   Science Signaling

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

(2016) Benjamin Lacar et al.   Nature Communications

The Strength of Selection against Neanderthal Introgression

(2016) Ivan Juric et al.   PLoS Genetics

A model for regulation by SynGAP-α1 of binding of synaptic proteins to PDZ-domain 'Slots' in the postsynaptic density

(2016) Ward G Walkup et al.   eLife

Multiplex matrix network analysis of protein complexes in the human TCR signalosome

(2016) Stephen E. P. Smith et al.   Science Signaling

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Lhx5 controls mamillary differentiation in the developing hypothalamus of the mouse

(2015) Michael Heide et al.   Frontiers in Neuroanatomy

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

(2014) B. Vernot et al.   SCIENCE

NPTX1 Regulates Neural Lineage Specification from Human Pluripotent Stem Cells

(2014) Nathan C. Boles et al.   Cell Reports

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

(2013) Y. Liao et al.   BIOINFORMATICS

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

(2013) Michael T Lovci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Disrupted Homer scaffolds mediate abnormal mGluR5 function in a mouse model of fragile X syndrome

(2012) Jennifer A Ronesi et al.   NATURE NEUROSCIENCE

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

(2011) L. Abi-Rached et al.   SCIENCE

Protein-RNA and Protein-Protein Recognition by Dual KH1/2 Domains of the Neuronal Splicing Factor Nova-1

(2011) Marianna Teplova et al.   STRUCTURE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Formation and patterning of the forebrain and olfactory system by zinc-finger genes Fezf1 and Fezf2

(2010) Takeshi Shimizu et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Conservation of an RNA regulatory map between Drosophila and mammals

(2010) A. N. Brooks 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

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Neuronatin Promotes Neural Lineage in ESCs via Ca2+ Signaling

(2010) Hsuan-Hwai Lin et al.   STEM CELLS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Pax6 3′ deletion results in aniridia, autism and mental retardation

(2008) L. K. Davis et al.   HUMAN GENETICS