A new rhesus macaque assembly and annotation for next-generation sequencing analyses

Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data

(2014) Xinxia Peng et al.   JOURNAL OF MEDICAL PRIMATOLOGY

Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression

(2014) Netanya G. Sandler et al.   NATURE

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt et al.   GENOME BIOLOGY

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Improving Genome Assemblies and Annotations for Nonhuman Primates

(2013) R. B. Norgren   ILAR JOURNAL

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Limitations of the rhesus macaque draft genome assembly and annotation

(2012) Xiongfei Zhang et al.   BMC GENOMICS

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RhesusBase: a knowledgebase for the monkey research community

(2012) Shi-Jian Zhang et al.   NUCLEIC ACIDS RESEARCH

Mis-Assembled “Segmental Duplications” in Two Versions of the Bos taurus Genome

(2012) Aleksey V. Zimin et al.   PLoS One

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

(2012) J. Tung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment

(2011) M. Ebeling et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

(2011) Guangmei Yan et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Comparing De Novo Genome Assembly: The Long and Short of It

(2011) Giuseppe Narzisi et al.   PLoS One

Expanding whole exome resequencing into non-human primates

(2011) Eric J Vallender   GENOME BIOLOGY

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors

(2011) Alinda Nagy et al.   Genes

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Bioinformatic approaches to identifying orthologs and assessing evolutionary relationships

(2009) Eric J. Vallender   METHODS

Sim4cc: a cross-species spliced alignment program

(2009) Leming Zhou et al.   NUCLEIC ACIDS RESEARCH

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

(2008) Alinda Nagy et al.   BMC BIOINFORMATICS

Refinement of macaque synteny arrangement with respect to the official rheMac2 macaque sequence assembly

(2008) Roberta Roberto et al.   CHROMOSOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

A high-resolution radiation hybrid map of rhesus macaque chromosome 5 identifies rearrangements in the genome assembly

(2008) Genesio M. Karere et al.   GENOMICS