Origins and evolution of extreme life span in Pacific Ocean rockfishes

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

GenMap: ultra-fast computation of genome mappability

(2020) Christopher Pockrandt et al.   BIOINFORMATICS

Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts

(2020) Jonathan Rolland et al.   MOLECULAR BIOLOGY AND EVOLUTION

TRAF3IP3 negatively regulates cytosolic RNA induced anti-viral signaling by promoting TBK1 K48 ubiquitination

(2020) Meng Deng et al.   Nature Communications

Massive haplotypes underlie ecotypic differentiation in sunflowers

(2020) Marco Todesco et al.   NATURE

Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity

(2020) Xuming Zhou et al.   Cell Reports

CAFE 5 models variation in evolutionary rates among gene families

(2020) Fábio K Mendes et al.   BIOINFORMATICS

Emerging roles of DYRK2 in cancer

(2020) Vasudha Tandon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

(2019) Guanliang Meng et al.   NUCLEIC ACIDS RESEARCH

The Genetics of Aging: A Vertebrate Perspective

(2019) Param Priya Singh et al.   CELL

RERconverge: an R package for associating evolutionary rates with convergent traits

(2019) Amanda Kowalczyk et al.   BIOINFORMATICS

Relaxed Selection Limits Lifespan by Increasing Mutation Load

(2019) Rongfeng Cui et al.   CELL

Mechanisms of radiocesium depuration in Sebastes cheni derived by simulation analysis of measured 137Cs concentrations off southern Fukushima 2014–2016

(2019) Takashi Ishimaru et al.   JOURNAL OF ENVIRONMENTAL RADIOACTIVITY

Using otolith morphometric analysis to improve species discrimination of blackspotted rockfish (Sebastes melanostictus) and rougheye rockfish (S. aleutianus)

(2019) Jeremy P. Harris et al.   FISHERY BULLETIN

A Prospective Analysis of Genetic Variants Associated with Human Lifespan

(2019) Kevin M. Wright et al.   G3-Genes Genomes Genetics

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

(2019) Jay Ghurye et al.   PLoS Computational Biology

Dynamic turnover of centromeres drives karyotype evolution in Drosophila

(2019) Ryan Bracewell et al.   eLife

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

OUP accepted manuscript

(2018)   BIOINFORMATICS

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

Fish reproductive-energy output increases disproportionately with body size

(2018) Diego R. Barneche et al.   SCIENCE

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

(2018) Tomáš Flouri et al.   MOLECULAR BIOLOGY AND EVOLUTION

An inverse latitudinal gradient in speciation rate for marine fishes

(2018) Daniel L. Rabosky et al.   NATURE

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Giant tortoise genomes provide insights into longevity and age-related disease

(2018) Víctor Quesada et al.   Nature Ecology & Evolution

A meta-analysis of fecundity in rockfishes (genus Sebastes )

(2017) E.J. Dick et al.   FISHERIES RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser 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

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

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

Parental influence on human germline de novo mutations in 1,548 trios from Iceland

(2017) Hákon Jónsson et al.   NATURE

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Rapid evolution of the human mutation spectrum

(2017) Kelley Harris et al.   eLife

Evolution of the immune system influences speciation rates in teleost fishes

(2016) Martin Malmstrøm et al.   NATURE GENETICS

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

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

(2016) Vijay Ramani et al.   Nature Protocols

Eye lens radiocarbon reveals centuries of longevity in the Greenland shark (Somniosus microcephalus)

(2016) J. Nielsen et al.   SCIENCE

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

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

Longevity Is Linked to Mitochondrial Mutation Rates in Rockfish: A Test Using Poisson Regression

(2015) Xia Hua et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Peter H. Sudmant et al.   SCIENCE

Insights into the Evolution of Longevity from the Bowhead Whale Genome

(2015) Michael Keane et al.   Cell Reports

Determinants of Mutation Rate Variation in the Human Germline

(2014) Laure Ségurel et al.   Annual Review of Genomics and Human Genetics

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Evaluating the predictive performance of empirical estimators of natural mortality rate using information on over 200 fish species

(2014) Amy Y Then et al.   ICES JOURNAL OF MARINE SCIENCE

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

(2012) Hiroaki Iwata et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES

(2011) Melissa A. Wilson Sayres et al.   EVOLUTION

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

(2011) Eun Bae Kim et al.   NATURE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution