High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl

TimeTree 5: An Expanded Resource for Species Divergence Times

(2022) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity

(2022) Abhisek Chakraborty et al.   iScience

Genomic Insights Into the Molecular Basis of Sexual Selection in Birds

(2021) Shubham K. Jaiswal et al.   Frontiers in Ecology and Evolution

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Genomic Regions Related to White/Black Tail Feather Color in Dwarf Chickens Identified Using a Genome-Wide Association Study

(2021) Changsheng Nie et al.   Frontiers in Genetics

MirGeneDB 2.1: toward a complete sampling of all major animal phyla

(2021) Bastian Fromm et al.   NUCLEIC ACIDS RESEARCH

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata , from Illumina and PacBio sequencing reads

(2020) Wei Li et al.   Plant Genome

Evolution: Brainier Birds

(2020) Peter J. Makovicky et al.   CURRENT BIOLOGY

Evol2Circos: A web-based tool for genome synteny and collinearity analysis and its visualization in fishes

(2020) Manmohan Pandey et al.   JOURNAL OF HEREDITY

Evolution of Flight Muscle Contractility and Energetic Efficiency

(2020) Tianxin Cao et al.   Frontiers in Physiology

Dual-Specificity Phosphatase Regulation in Neurons and Glial Cells

(2019) Pérez-Sen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing

(2019) Ruby Dhar et al.   GigaScience

Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions

(2019) Rei Kajitani et al.   Nature Communications

Exon-Mediated Activation of Transcription Starts

(2019) Ana Fiszbein et al.   CELL

A pair of E3 ubiquitin ligases compete to regulate filopodial dynamics and axon guidance

(2019) Nicholas P. Boyer et al.   JOURNAL OF CELL BIOLOGY

Comparative analysis of corrected tiger genome provides clues to its neuronal evolution

(2019) Parul Mittal et al.   Scientific Reports

Status and distribution changes of the endangered Green Peafowl (Pavo muticus) in China over the past three decades (1990s‒2017)

(2018) Dejun Kong et al.   Avian Research

C-Type Lectin Receptors in Antiviral Immunity and Viral Escape

(2018) Marta Bermejo-Jambrina et al.   Frontiers in Immunology

Revisiting Netrin-1: One Who Guides (Axons)

(2018) Nicholas P. Boyer et al.   Frontiers in Cellular Neuroscience

Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird

(2018) Shubham K. Jaiswal et al.   Frontiers in Genetics

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Selective attention in peacocks during assessment of rival males

(2017) Jessica L. Yorzinski et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The CCR4-NOT complex contributes to repression of Major Histocompatibility Complex class II transcription

(2017) Alfonso Rodríguez-Gil et al.   Scientific Reports

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

(2016) Vagheesh Narasimhan et al.   BIOINFORMATICS

ProteinO-Linked Mannose β-1,4-N-Acetylglucosaminyl-transferase 2 (POMGNT2) Is a Gatekeeper Enzyme for Functional Glycosylation of α-Dystroglycan

(2016) Stephanie M. Halmo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage

(2016) Mahul Chakraborty et al.   NUCLEIC ACIDS RESEARCH

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

AGOUTI: improving genome assembly and annotation using transcriptome data

(2016) Simo V. Zhang et al.   GigaScience

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

(2015) Konstantin Okonechnikov et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Sealer: a scalable gap-closing application for finishing draft genomes

(2015) Daniel Paulino et al.   BMC BIOINFORMATICS

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds

(2015) Rui Borges et al.   BMC GENOMICS

Periostin, a neurite outgrowth-promoting factor, is expressed at high levels in the primate cerebral cortex

(2015) Eiji Matsunaga et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

(2015) Yi Wang et al.   NUCLEIC ACIDS RESEARCH

Sexual selection drives evolution and rapid turnover of male gene expression

(2015) Peter W. Harrison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origins and Impacts of New Mammalian Exons

(2015) Jason J. Merkin et al.   Cell Reports

Chemokines and Chemokine Receptors: Positioning Cells for Host Defense and Immunity

(2014) Jason W. Griffith et al.   Annual Review of Immunology

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

Phosphoinositide turnover in Toll-like receptor signaling and trafficking

(2014) Oanh Thi Tu Le et al.   BMB Reports

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The role of proteases in regulating Eph/ephrin signaling

(2014) Lakmali Atapattu et al.   Cell Adhesion & Migration

Gpr126 Functions in Schwann Cells to Control Differentiation and Myelination via G-Protein Activation

(2013) A. Mogha et al.   JOURNAL OF NEUROSCIENCE

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

TMEM16C facilitates Na+-activated K+ currents in rat sensory neurons and regulates pain processing

(2013) Fen Huang et al.   NATURE NEUROSCIENCE

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

The Collagen Family

(2010) S. Ricard-Blum   Cold Spring Harbor Perspectives in Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evidence for Adaptive Evolution of Olfactory Receptor Genes in 9 Bird Species

(2009) Silke S. Steiger et al.   JOURNAL OF HEREDITY

Multiple Molecular Interactions Implicate the Connectin/Titin N2A Region as a Modulating Scaffold for p94/Calpain 3 Activity in Skeletal Muscle

(2008) Chikako Hayashi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Forkhead box protein 3: Essential immune regulatory role

(2007) Nasim Nik Tavakoli et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY