Genome-wide signatures of complex introgression and adaptive evolution in the big cats

The mTOR signalling cascade: paving new roads to cure neurological disease

(2016) Peter B. Crino   Nature Reviews Neurology

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination

(2016) Gang Li et al.   G3-Genes Genomes Genetics

Ocular Features in Alport Syndrome: Pathogenesis and Clinical Significance

(2015) J. Savige et al.   Clinical Journal of the American Society of Nephrology

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

(2015) Gang Li et al.   GENOME RESEARCH

Aberrant Time to Most Recent Common Ancestor as a Signature of Natural Selection

(2015) Haley Hunter-Zinck et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development

(2015) Thomas W Bebee et al.   eLife

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

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Dock-family exchange factors in cell migration and disease

(2014) Gilles Gadea et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Insights into the biological functions of Dock family guanine nucleotide exchange factors

(2014) M. Laurin et al.   GENES & DEVELOPMENT

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Annotated features of domestic cat – Felis catus genome

(2014) Gaik Tamazian et al.   GigaScience

Liprin-α2 promotes the presynaptic recruitment and turnover of RIM1/CASK to facilitate synaptic transmission

(2013) Samantha A. Spangler et al.   JOURNAL OF CELL BIOLOGY

Using Illumina next generation sequencing technologies to sequence multigene families inde novospecies

(2013) Graham M. Hughes et al.   Molecular Ecology Resources

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

(2013) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

The tiger genome and comparative analysis with lion and snow leopard genomes

(2013) Yun Sung Cho et al.   Nature Communications

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Assembly of Lamina-Specific Neuronal Connections by Slit Bound to Type IV Collagen

(2011) Tong Xiao et al.   CELL

Carnivore-Specific SINEs (Can-SINEs): Distribution, Evolution, and Genomic Impact

(2011) K. B. Walters-Conte et al.   JOURNAL OF HEREDITY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Assigning duplication events to relative temporal scales in genome-wide studies

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae)

(2010) Brian W. Davis et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences

(2010) Eduardo Eizirik et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Dock3 induces axonal outgrowth by stimulating membrane recruitment of the WAVE complex

(2010) K. Namekata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Craniodental indicators of prey size preference in the Felidae

(2009) JULIE MEACHEN-SAMUELS et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Basement membranes and human disease

(2009) Tom Van Agtmael et al.   CELL AND TISSUE RESEARCH

Ecological adaptation determines functional mammalian olfactory subgenomes

(2009) S. Hayden et al.   GENOME RESEARCH

ESRP1 and ESRP2 Are Epithelial Cell-Type-Specific Regulators of FGFR2 Splicing

(2009) Claude C. Warzecha et al.   MOLECULAR CELL

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

p53 Regulation of the IGF-1/AKT/mTOR Pathways and the Endosomal Compartment

(2009) Z. Feng   Cold Spring Harbor Perspectives in Biology

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY

Glypicans

(2008) Jorge Filmus et al.   GENOME BIOLOGY