Platypus and echidna genomes reveal mammalian biology and evolution

Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales

(2019) Mark S. Springer et al.   BMC EVOLUTIONARY BIOLOGY

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals

(2019) Kelsie E Hunnicutt et al.   Genome Biology and Evolution

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Adaptation and conservation insights from the koala genome

(2018) Rebecca N. Johnson et al.   NATURE GENETICS

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

A fast adaptive algorithm for computing whole-genome homology maps

(2018) Chirag Jain et al.   BIOINFORMATICS

Haptoglobin Is a Divergent MASP Family Member That Neofunctionalized To Recycle Hemoglobin via CD163 in Mammals

(2018) Anthony K. Redmond et al.   JOURNAL OF IMMUNOLOGY

Influence of recombination and GC-biased gene conversion on the adaptive and non-adaptive substitution rate in mammals vs. birds

(2018) M Rousselle et al.   MOLECULAR BIOLOGY AND EVOLUTION

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Reconstruction and evolutionary history of eutherian chromosomes

(2017) Jaebum Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

(2017) Ryohei Seki et al.   Nature Communications

Differential cohesin loading marks paired and unpaired regions of platypus sex chromosomes at prophase I

(2017) Aaron E. Casey et al.   Scientific Reports

Dietary specialization drives multiple independent losses and gains in the bitter taste gene repertoire of Laurasiatherian Mammals

(2016) Zhijin Liu et al.   Frontiers in Zoology

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Frequent Expansions of the Bitter Taste Receptor Gene Repertoire during Evolution of Mammals in the Euarchontoglires Clade

(2014) Takashi Hayakawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

(2014) Daniel W. Bellott et al.   NATURE

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

Translocations of Chromosome End-Segments and Facultative Heterochromatin Promote Meiotic Ring Formation in Evening Primroses

(2014) Hieronim Golczyk et al.   PLANT CELL

Evidence for a single loss of mineralized teeth in the common avian ancestor

(2014) R. W. Meredith et al.   SCIENCE

Complex evolutionary trajectories of sex chromosomes across bird taxa

(2014) Q. Zhou et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Recombination in the Human Pseudoautosomal Region PAR1

(2014) Anjali G. Hinch et al.   PLoS Genetics

Reconstruction of the ancestral marsupial karyotype from comparative gene maps

(2013) Janine E Deakin et al.   BMC EVOLUTIONARY BIOLOGY

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Invited review: Caseins and the casein micelle: Their biological functions, structures, and behavior in foods1

(2013) C. Holt et al.   JOURNAL OF DAIRY SCIENCE

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

ANGES: reconstructing ANcestral GEnomeS maps

(2012) B. R. Jones et al.   BIOINFORMATICS

The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene

(2012) Elizabeth A Pharo et al.   BMC EVOLUTIONARY BIOLOGY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

(2012) Philippe Julien et al.   PLOS BIOLOGY

The Evolution of Milk Casein Genes from Tooth Genes before the Origin of Mammals

(2011) K. Kawasaki et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

PHAST and RPHAST: phylogenetic analysis with space/time models

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

Haptoglobin: Old protein with new functions

(2010) Abdu I. Alayash   CLINICA CHIMICA ACTA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas

(2009) M. J. Phillips et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals

(2009) Christophe M. Lefèvre et al.   REPRODUCTION FERTILITY AND DEVELOPMENT

Analysis of SINE and LINE repeat content of Y chromosomes in the platypus,Ornithorhynchus anatinus

(2009) R. Daniel Kortschak et al.   REPRODUCTION FERTILITY AND DEVELOPMENT

Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

(2008) Zuly E Parra et al.   BMC GENOMICS

Higher-order genome organization in platypus and chicken sperm and repositioning of sex chromosomes during mammalian evolution

(2008) Enkhjargal Tsend-Ayush et al.   CHROMOSOMA

Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes

(2008) F. Veyrunes et al.   GENOME RESEARCH

Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes

(2008) A.-S. Van Laere et al.   GENOME RESEARCH

Defensins and the convergent evolution of platypus and reptile venom genes

(2008) C. M. Whittington et al.   GENOME RESEARCH

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation

(2008) David Brawand et al.   PLOS BIOLOGY

Loss of genes implicated in gastric function during platypus evolution

(2008) Gonzalo R Ordoñez et al.   GENOME BIOLOGY