Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations

Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas

(2017) Yibo Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals

(2016) Zhigang Zhang et al.   CURRENT BIOLOGY

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

Convergent local adaptation to climate in distantly related conifers

(2016) S. Yeaman et al.   SCIENCE

Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude Lizard living in the Qinghai-Tibet Plateau

(2015) Yongzhi Yang et al.   BMC EVOLUTIONARY BIOLOGY

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

Whole-genome sequence of the Tibetan frogNanorana parkeriand the comparative evolution of tetrapod genomes

(2015) Yan-Bo Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis

(2014) Sylvain Aubry et al.   PLoS Genetics

Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons?

(2013) M. dos Reis et al.   GENETICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Draft genome sequence of the Tibetan antelope

(2013) Ri-Li Ge et al.   Nature Communications

HypoxiaDB: a database of hypoxia-regulated proteins

(2013) Pankaj Khurana et al.   Database-The Journal of Biological Databases and Curation

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

The yak genome and adaptation to life at high altitude

(2012) Qiang Qiu et al.   NATURE GENETICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates

(2010) J. F. Storz et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia

(2010) J. Che et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois

(2008) Jing Che et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION