High-resolution comparative analysis of great ape genomes

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

(2017) Matthias H. Weissensteiner et al.   GENOME RESEARCH

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data

(2017) Wen-Biao Jiao et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Selection in Europeans on Fatty Acid Desaturases Associated with Dietary Changes

(2017) Matthew T. Buckley et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques

(2017) Zhisong He et al.   NATURE NEUROSCIENCE

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

(2017) Panayotis Vlastaridis et al.   GigaScience

Dietary adaptation of FADS genes in Europe varied across time and geography

(2017) Kaixiong Ye et al.   Nature Ecology & Evolution

The evolution and population diversity of human-specific segmental duplications

(2017) Megan Y. Dennis et al.   Nature Ecology & Evolution

Simultaneous gene finding in multiple genomes

(2016) Stefanie König et al.   BIOINFORMATICS

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

(2016) Yuvia A. Pérez-Rico et al.   GENOME RESEARCH

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

(2016) Kiana Mohajeri et al.   GENOME RESEARCH

Characterizing polymorphic inversions in human genomes by single-cell sequencing

(2016) Ashley D. Sanders et al.   GENOME RESEARCH

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility

(2016) Xander Nuttle et al.   NATURE

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

(2016) Swapan Mallick et al.   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Mapping 3D genome architecture through in situ DNase Hi-C

(2016) Vijay Ramani et al.   Nature Protocols

Variation in the molecular clock of primates

(2016) Priya Moorjani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

The hominoid-specific gene TBC1D3 promotes generation of basal neural progenitors and induces cortical folding in mice

(2016) Xiang-Chun Ju et al.   eLife

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

(2016) Felipe Mora-Bermúdez et al.   eLife

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

(2015) Stephen W. Hartley et al.   BMC BIOINFORMATICS

Molecular Identity of Human Outer Radial Glia during Cortical Development

(2015) Alex A. Pollen et al.   CELL

Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex

(2015) J. Lomax Boyd et al.   CURRENT BIOLOGY

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays

(2015) A. C. Y. Mak et al.   GENETICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

(2015) J. Gray Camp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global diversity, population stratification, and selection of human copy-number variation

(2015) Peter H. Sudmant et al.   SCIENCE

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

(2015) M. Florio et al.   SCIENCE

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach

(2014) Gabriel Renaud et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Refining analyses of copy number variation identifies specific genes associated with developmental delay

(2014) Bradley P Coe et al.   NATURE GENETICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Induction of a Human Pluripotent State with Distinct Regulatory Circuitry that Resembles Preimplantation Epiblast

(2013) Yun-Shen Chan et al.   Cell Stem Cell

Differential L1 regulation in pluripotent stem cells of humans and apes

(2013) Maria C. N. Marchetto et al.   NATURE

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

A Penile Spine/Vibrissa Enhancer Sequence Is Missing in Modern and Extinct Humans but Is Retained in Multiple Primates with Penile Spines and Sensory Vibrissae

(2013) Philip L. Reno et al.   PLoS One

Rates and patterns of great ape retrotransposition

(2013) F. Hormozdiari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Adaptation of Fatty-Acid Metabolism: A Human-Specific Haplotype Increasing the Biosynthesis of Long-Chain Omega-3 and Omega-6 Fatty Acids

(2012) Adam Ameur et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation

(2012) Cécile Charrier et al.   CELL

Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication

(2012) Megan Y. Dennis et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Biosynthesis of the major brain gangliosides GD1a and GT1b

(2012) Elizabeth R Sturgill et al.   GLYCOBIOLOGY

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication

(2012) Maria Cardone et al.   GENOME BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

(2011) R. D. George et al.   GENOME RESEARCH

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

(2011) M. Ventura et al.   GENOME RESEARCH

Ultrasensitivity in the Regulation of Cdc25C by Cdk1

(2011) Nicole B. Trunnell et al.   MOLECULAR CELL

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The human brain in numbers: a linearly scaled-up primate brain

(2009) Suzana Herculano-Houzel   Frontiers in Human Neuroscience

A burst of segmental duplications in the genome of the African great ape ancestor

(2009) Tomas Marques-Bonet et al.   NATURE

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Primate chromosome evolution: Ancestral karyotypes, marker order and neocentromeres

(2008) R. Stanyon et al.   CHROMOSOME RESEARCH

Evolutionary toggling of the MAPT 17q21.31 inversion region

(2008) Michael C Zody et al.   NATURE GENETICS

Human uniqueness: genome interactions with environment, behaviour and culture

(2008) Ajit Varki et al.   NATURE REVIEWS GENETICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE