Recurrent loss of HMGCS2 shows that ketogenesis is not essential for the evolution of large mammalian brains

A comprehensive genomic history of extinct and living elephants

(2018) Eleftheria Palkopoulou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genomics approach reveals insights into the importance of gene losses for mammalian adaptations

(2018) Virag Sharma et al.   Nature Communications

Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals

(2018) Virag Sharma et al.   PLOS BIOLOGY

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

(2018) Úlfur Árnason et al.   Science Advances

Chitinase genes ( CHIA s) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals

(2018) Christopher A. Emerling et al.   Science Advances

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

(2018) Vincent Ranwez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals

(2018) Wynn K. Meyer et al.   SCIENCE

Transition to an aquatic habitat permitted the repeated loss of the pleiotropic KLK8 gene in mammals

(2017) Nikolai Hecker et al.   Genome Biology and Evolution

Unusual loss of chymosin in mammalian lineages parallels neo-natal immune transfer strategies

(2017) Mónica Lopes-Marques et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation

(2017) Virag Sharma et al.   NUCLEIC ACIDS RESEARCH

Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades

(2017) Michael J. Gaudry et al.   Science Advances

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

(2016) Virag Sharma et al.   NUCLEIC ACIDS RESEARCH

Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus

(2015) Puli Chandramouli Reddy et al.   JOURNAL OF BIOSCIENCES

A new method of estimating brain mass through cranial capacity in extinct proboscideans to account for the non-neural tissues surrounding their brain

(2015) Julien Benoit   JOURNAL OF VERTEBRATE PALEONTOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Vocal learning in a social mammal: Demonstrated by isolation and playback experiments in bats

(2015) Y. Prat et al.   Science Advances

Ketogenesis prevents diet-induced fatty liver injury and hyperglycemia

(2014) David G. Cotter et al.   JOURNAL OF CLINICAL INVESTIGATION

Metabolism as a tool for understanding human brain evolution: Lipid energy metabolism as an example

(2014) Shu Pei Wang et al.   JOURNAL OF HUMAN EVOLUTION

Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency: urinary organic acid profiles and expanded spectrum of mutations

(2014) James J. Pitt et al.   JOURNAL OF INHERITED METABOLIC DISEASE

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

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

Eyes underground: Regression of visual protein networks in subterranean mammals

(2014) Christopher A. Emerling et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

An Adaptive Threshold in Mammalian Neocortical Evolution

(2014) Eric Lewitus et al.   PLOS BIOLOGY

New case of mitochondrial HMG-CoA synthase deficiency. Functional analysis of eight mutations

(2013) Mónica Ramos et al.   European Journal of Medical Genetics

THE EVOLUTIONARY HISTORY OF CETACEAN BRAIN AND BODY SIZE

(2013) Stephen H. Montgomery et al.   EVOLUTION

Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history

(2013) L. F. C. Castro et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Mini Review of Dolphin Carbohydrate Metabolism and Suggestions for Future Research Using Exhaled Air

(2013) Sam H. Ridgway   Frontiers in Endocrinology

Quantitative analysis of neocortical gyrencephaly in African elephants (Loxodonta africana) and six species of cetaceans: Comparison with other mammals

(2012) Paul R. Manger et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Comparative analysis of encephalization in mammals reveals relaxed constraints on anthropoid primate and cetacean brain scaling

(2012) A. M. BODDY et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Hundreds of conserved non-coding genomic regions are independently lost in mammals

(2012) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

Insightful Problem Solving in an Asian Elephant

(2011) Preston Foerder et al.   PLoS One

Brain size comparison in Chiroptera

(2010) H. Stephan et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Recapitulating the evolution of Afrotheria: 57 genes and rare genomic changes (RGCs) consolidate their history

(2010) N. Poulakakis et al.   SYSTEMATICS AND BIODIVERSITY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals

(2009) Robert W. Meredith et al.   PLoS Genetics