Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mousePeromyscus eremicus

Natural Genetic Variation Underlying Differences in Peromyscus Repetitive and Social/Aggressive Behaviors

(2014) Kimberly R. Shorter et al.   BEHAVIOR GENETICS

BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads

(2014) Yun Heo et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea

(2014) Facundo M Giorello et al.   BMC GENOMICS

Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq

(2014) Nicholas J. Marra et al.   MOLECULAR ECOLOGY

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

A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads

(2014) Stanley Kimbung Mbandi et al.   Frontiers in Genetics

On the optimal trimming of high-throughput mRNA sequence data

(2014) Matthew D. MacManes   Frontiers in Genetics

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

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

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

The Social Brain: Transcriptome Assembly and Characterization of the Hippocampus from a Social Subterranean Rodent, the Colonial Tuco-Tuco (Ctenomys sociabilis)

(2012) Matthew D. MacManes et al.   PLoS One

Analysis of Expressed Sequence Tags from the Placenta of the Live-Bearing Fish Poeciliopsis (Poeciliidae)

(2011) Tami M. Panhuis et al.   JOURNAL OF HEREDITY

Guidelines of the American Society of Mammalogists for the use of wild mammals in research

(2011) Robert S. Sikes et al.   JOURNAL OF MAMMALOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS