Method
Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
- First Published April 15, 2026
Method
Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- First Published April 15, 2026
Research
Drosophila innate immune response" > A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- First Published April 15, 2026
Research
Epigenetic characterization of pseudogenes across human tissues
- First Published April 15, 2026
Method
Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- First Published April 13, 2026
Resource
Lignature provides a curated resource of ligand induced transcriptomic signatures for signaling inference
- First Published April 8, 2026
Method
Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- First Published April 8, 2026
Method
Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
- First Published April 8, 2026
Method
Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses
- First Published March 26, 2026
Resource
Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- First Published March 26, 2026
Method
k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants" > k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- First Published March 23, 2026
Method
High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- First Published March 23, 2026
Method
Restoring the potency of neutralizing antibody via guided hypermutation with hyper-antibody editor
- First Published March 19, 2026
Research
Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- First Published October 22, 2025
Resource
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- First Published October 6, 2025
Resource
Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- First Published February 21, 2025
Perspective
Reading TE leaves: New approaches to the identification of transposable element insertions
- First Published June 1, 2011
Perspective
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
- First Published February 4, 2011
Perspective
Transgenerational epigenetic inheritance: More questions than answers
- First Published November 1, 2010
Perspective
Assembly of large genomes using second-generation sequencing
- First Published May 27, 2010
Perspective
Phylogenomics of primates and their ancestral populations
- First Published October 3, 2009
RESOURCE
De novo fragment assembly with short mate-paired reads: Does the read length matter?
- First Published December 3, 2008
RESOURCE
Dissecting the effects of mtDNA variations on complex traits using mouse conplastic strains
- First Published November 26, 2008
Methods
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
- First Published November 26, 2008
RESOURCE
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
- First Published November 24, 2008
RESOURCE
Caenorhabditis elegans microRNA promoter activity" > Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- First Published November 3, 2008
Methods
Hox cis-regulatory elements" > Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- First Published November 3, 2008
Methods
cis-regulatory variation in human haplotypes" > Targeted screening of cis-regulatory variation in human haplotypes
- First Published October 29, 2008
RESOURCE
A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: The NIH heterogeneous stock
- First Published October 29, 2008
RESOURCE
Whole population, genome-wide mapping of hidden relatedness
- First Published October 29, 2008
Insight/Outlook
Ethical, legal, and social considerations in conducting the Human Microbiome Project
- First Published October 29, 2008
Methods
DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression
- First Published October 29, 2008
Methods
Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
- First Published October 27, 2008
Methods
Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes
- First Published October 10, 2008
Methods
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- First Published October 10, 2008
Methods
Genome-wide nucleotide-level mammalian ancestor reconstruction
- First Published October 10, 2008
RESOURCE
genBlastA: Enabling BLAST to identify homologous gene sequences
- First Published October 6, 2008
RESOURCE
Haplotype sorting using human fosmid clone end-sequence pairs
- First Published October 3, 2008
Methods
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
- First Published October 2, 2008
RESOURCE
Arabidopsis thaliana with short reads" > Sequencing of natural strains of Arabidopsis thaliana with short reads
- First Published September 25, 2008
Methods
cis-regulatory elements" > Ab initio identification of functionally interacting pairs of cis-regulatory elements
- First Published September 17, 2008
RESOURCE
Large-scale gene trapping in C57BL/6N mouse embryonic stem cells
- First Published September 17, 2008
Methods
Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification
- First Published September 16, 2008
Methods
Rapid whole-genome mutational profiling using next-generation sequencing technologies
- First Published September 4, 2008
Methods
MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
- First Published September 2, 2008
Methods
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
- First Published August 29, 2008
RESOURCE
Mapping short DNA sequencing reads and calling variants using mapping quality scores
- First Published August 19, 2008
Methods
An MCMC algorithm for haplotype assembly from whole-genome sequence data
- First Published August 1, 2008
PERSPECTIVE
The opossum genome: Insights and opportunities from an alternative mammal
- First Published August 1, 2008
PERSPECTIVE
Genomic medicine in Mexico: Initial steps and the road ahead
- First Published August 1, 2008
PERSPECTIVE
Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- First Published July 30, 2008
Methods
C. elegans gene annotations" > Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
- First Published July 24, 2008
Methods
Confounding between recombination and selection, and the Ped/Pop method for detecting selection
- First Published July 10, 2008
RESOURCE
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- First Published June 24, 2008
Methods
Inferring causal relationships among different histone modifications and gene expression
- First Published June 18, 2008
RESOURCE
EagleView: A genome assembly viewer for next-generation sequencing technologies
- First Published June 11, 2008
Methods
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
- First Published June 11, 2008
RESOURCE
DupMasker: A tool for annotating primate segmental duplications" > DupMasker: A tool for annotating primate segmental duplications
- First Published May 23, 2008
Methods
A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations
- First Published May 23, 2008
RESOURCE
A novel DNA sequence database for analyzing human demographic history
- First Published May 20, 2008
RESOURCE
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
- First Published May 9, 2008
Methods
Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
- First Published April 25, 2008
Methods
Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions
- First Published April 25, 2008
Methods
Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
- First Published April 21, 2008
Methods
Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
- First Published April 16, 2008
RESOURCE
Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
- First Published April 14, 2008
RESOURCE
New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
- First Published April 2, 2008
PERSPECTIVE
A new way to explore the world of extracellular protein interactions
- First Published April 1, 2008
Methods
Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
- First Published March 27, 2008
Methods
Power and SNP tagging in whole mitochondrial genome association studies
- First Published March 20, 2008
RESOURCE
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- First Published March 18, 2008
RESOURCE
ALLPATHS: De novo assembly of whole-genome shotgun microreads
- First Published March 13, 2008