Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance

(2018) Elliott Ferris et al.   Cell Reports

Growing old, yet staying young: The role of telomeres in bats’ exceptional longevity

(2018) Nicole M. Foley et al.   Science Advances

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

(2018) Úlfur Árnason et al.   Science Advances

Multinucleotide mutations cause false inferences of lineage-specific positive selection

(2018) Aarti Venkat et al.   Nature Ecology & Evolution

Size matters: height, cell number and a person's risk of cancer

(2018) Leonard Nunney   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Novel Evolution of the Sperm Whale Genome

(2017) Wesley C Warren et al.   Genome Biology and Evolution

Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics

(2017) Graham J. Slater et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Prolonged particulate chromate exposure does not inhibit homologous recombination repair in North Atlantic right whale ( Eubalaena glacialis ) lung cells

(2017) Cynthia L. Browning et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Differences between germline and somatic mutation rates in humans and mice

(2017) Brandon Milholland et al.   Nature Communications

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

The ethmoid and presphenoid of cetaceans

(2016) Hiroto Ichishima   JOURNAL OF MORPHOLOGY

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Non-catalytic Roles for XPG with BRCA1 and BRCA2 in Homologous Recombination and Genome Stability

(2016) Kelly S. Trego et al.   MOLECULAR CELL

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Gigantism and Its Implications for the History of Life

(2016) Geerat J. Vermeij   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

Potential Mechanisms for Cancer Resistance in Elephants and Comparative Cellular Response to DNA Damage in Humans

(2015) Lisa M. Abegglen et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

Solutions to Peto's paradox revealed by mathematical modelling and cross-species cancer gene analysis

(2015) Aleah F. Caulin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptive evolution toward larger size in mammals

(2015) Joanna Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cope's rule in the evolution of marine animals

(2015) N. A. Heim et al.   SCIENCE

Insights into the Evolution of Longevity from the Bowhead Whale Genome

(2015) Michael Keane et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae)

(2014) J. A. Jackson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage

(2014) Roger B. J. Benson et al.   PLOS BIOLOGY

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC

(2013) Walid H. Gharib et al.   MOLECULAR BIOLOGY AND EVOLUTION

Minke whale genome and aquatic adaptation in cetaceans

(2013) Hyung-Soon Yim et al.   NATURE GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure

(2012) Kristen Ruegg et al.   CONSERVATION GENETICS

The Evolution of Intron Size in Amniotes: A Role for Powered Flight?

(2012) Qu Zhang et al.   Genome Biology and Evolution

Inferring recent historic abundance from current genetic diversity

(2012) Per J. Palsbøll et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

(2012) Robi Tacutu et al.   NUCLEIC ACIDS RESEARCH

PRDM proteins: Important players in differentiation and disease

(2011) Cathrine K. Fog et al.   BIOESSAYS

Making whole genome multiple alignments usable for biologists

(2011) Daniel Blankenberg et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt 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

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

(2011) Jarrod A. Chapman et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Peto's Paradox: evolution's prescription for cancer prevention

(2011) Aleah F. Caulin et al.   TRENDS IN ECOLOGY & EVOLUTION

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Phylogenetic Targeting of Research Effort in Evolutionary Biology

(2010) Christian Arnold et al.   AMERICAN NATURALIST

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Retinoblastoma Protein-Interacting Zinc Finger 1 (RIZ1) Regulates the Proliferation of Monocytic Leukemia Cells via Activation of p53

(2010) Noman Mohammod Abu Shadat et al.   CANCER INVESTIGATION

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals

(2009) Kate E. Jones et al.   ECOLOGY

Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics

(2009) Susanne A. Fritz et al.   ECOLOGY LETTERS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Sighting history of a naturally marked humpback whale (Megaptera novaeangliae) suggests ear plug growth layer groups are deposited annually

(2009) Christine M. Gabriele et al.   MARINE MAMMAL SCIENCE

Big and Slow: Phylogenetic Estimates of Molecular Evolution in Baleen Whales (Suborder Mysticeti)

(2009) J. A. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Radiation of Extant Cetaceans Driven by Restructuring of the Oceans

(2009) Mette E. Steeman et al.   SYSTEMATIC BIOLOGY

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

(2008) Mario Stanke et al.   BIOINFORMATICS

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils

(2007) Maureen A. O'Leary et al.   CLADISTICS