Research
Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources
- First Published May 14, 2026
Research
Epigenetic and evolutionary features of ape subterminal heterochromatin
- First Published October 22, 2025
Resource
An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- First Published December 5, 2024
Resource
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
- First Published October 2, 2024
Research
AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- First Published September 25, 2024
Research
Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- First Published August 6, 2024
Method
Phased nanopore assembly with Shasta and modular graph phasing with GFAse
- First Published April 16, 2024
Research
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- First Published December 7, 2023
Research
Gaps and complex structurally variant loci in phased genome assemblies
- First Published May 10, 2023
Research
Differences in the number of de novo mutations between individuals are due to small family-specific effects and stochasticity
- First Published July 23, 2021
Research
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
- First Published July 9, 2021
Resource
Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- First Published October 22, 2020
Method
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- First Published August 14, 2020
Resource
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- First Published September 19, 2019
Research
An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
- First Published January 3, 2019
Method
Transcriptional fates of human-specific segmental duplications in brain
- First Published September 18, 2018
Method
Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
- First Published June 8, 2018
Corrigendum
Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data
- First Published January 2, 2018
Method
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
- First Published October 11, 2017
Method
Co-expression networks reveal the tissue-specific regulation of transcription and splicing
- First Published October 11, 2017
Corrigendum
Corrigendum: The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2
- First Published September 1, 2017
Resource
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- First Published April 10, 2017
Research
Discovery and genotyping of structural variation from long-read haploid genome sequence data
- First Published November 28, 2016
Research
Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- First Published October 7, 2016
Corrigendum
Corrigendum: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
- First Published August 3, 2015
Research
Characteristics of de novo structural changes in the human genome
- First Published April 16, 2015
Method
MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
- First Published February 6, 2015
Method
The discovery of integrated gene networks for autism and related disorders
- First Published November 5, 2014
Resource
Single haplotype assembly of the human genome from a hydatidiform mole
- First Published November 4, 2014
Resource
Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- First Published July 1, 2014
Resource
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
- First Published July 1, 2014
Resource
Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline
- First Published March 27, 2014
Research
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- First Published January 15, 2014
Method
Reconstructing complex regions of genomes using long-read sequencing technology
- First Published January 13, 2014
Method
Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
- First Published December 5, 2013
Resource
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
- First Published October 29, 2013
Research
Hominoid fission of chromosome 14/15 and the role of segmental duplications
- First Published September 27, 2013
Research
Evolution and diversity of copy number variation in the great ape lineage
- First Published July 3, 2013
Method
Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
- First Published May 2, 2013
Research
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
- First Published April 17, 2013
Research
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
- First Published March 19, 2013
Research
Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence
- First Published November 2, 2012
Resource
GENCODE: The reference human genome annotation for The ENCODE Project
- First Published September 5, 2012
Resource
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- First Published September 5, 2012
Method
Copy number variation detection and genotyping from exome sequence data
- First Published May 14, 2012