The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

BlobToolKit - Interactive Quality Assessment of Genome Assemblies

(2020) Richard Challis et al.   G3-Genes Genomes Genetics

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

(2020) Rémi Allio et al.   Molecular Ecology Resources

Insecticides, biologics and nematicides: Updates to IRAC’s mode of action classification - a tool for resistance management

(2020) Thomas C. Sparks et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Inner Workings: Researchers peek into chromosomes’ 3D structure in unprecedented detail

(2020) Amber Dance   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

(2019) Sarah Kingan et al.   Genes

Apollo: Democratizing genome annotation

(2019) Nathan A. Dunn et al.   PLoS Computational Biology

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

Has Resistance Taken Root in U.S. Corn Fields? Demand for Insect Control

(2018) Seth Wechsler et al.   AMERICAN JOURNAL OF AGRICULTURAL ECONOMICS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increase in crop losses to insect pests in a warming climate

(2018) Curtis A. Deutsch et al.   SCIENCE

Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species

(2017) Brian P.H. Metzger et al.   Genome Biology and Evolution

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Surge in insect resistance to transgenic crops and prospects for sustainability

(2017) Bruce E Tabashnik et al.   NATURE BIOTECHNOLOGY

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

P8008 The NCBI Eukaryotic Genome Annotation Pipeline

(2016) F. Thibaud-Nissen et al.   JOURNAL OF ANIMAL SCIENCE

Global threat to agriculture from invasive species

(2016) Dean R. Paini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Lessons from modENCODE

(2015) James B. Brown et al.   Annual Review of Genomics and Human Genetics

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

Best practices in insect genome sequencing: what works and what doesn’t

(2015) Stephen Richards et al.   Current Opinion in Insect Science

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes

(2014) Monica Poelchau et al.   NUCLEIC ACIDS RESEARCH

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements

(2012) S. Dimitrieva et al.   BIOINFORMATICS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

miRNA-Mediated Gene Silencing by Translational Repression Followed by mRNA Deadenylation and Decay

(2012) S. Djuranovic et al.   SCIENCE

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

(2011) Frank Jühling et al.   NUCLEIC ACIDS RESEARCH

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE