What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes

(2015) Indraneel Mittra et al.   JOURNAL OF BIOSCIENCES

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

(2015) Alastair Crisp et al.   GENOME BIOLOGY

Large scale comparison of non-human sequences in human sequencing data

(2014) Hongseok Tae et al.   GENOMICS

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

(2014) A Gouin et al.   HEREDITY

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Characterization of the Ca2+-Gated and Voltage-Dependent K+-Channel Slo-1 of Nematodes and Its Interaction with Emodepside

(2014) Daniel Kulke et al.   PLoS Neglected Tropical Diseases

Unexpected cross-species contamination in genome sequencing projects

(2014) Samier Merchant et al.   PeerJ

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   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

Characterization of the rat developmental liver transcriptome

(2013) Richard H. Chapple et al.   PHYSIOLOGICAL GENOMICS

The molecular prevalence and MSA-2b gene-based genetic diversity of Babesia bovis in dairy cattle in Thailand

(2013) Pacharathon Simking et al.   VETERINARY PARASITOLOGY

Evolutionary Implications of Horizontal Gene Transfer

(2012) Michael Syvanen   Annual Review of Genetics

Rapid identification of non-human sequences in high-throughput sequencing datasets

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

Molecular and serological prevalence of Babesia bovis and Babesia bigemina in cattle from central region of Syria

(2012) Mohamad Alaa Terkawi et al.   VETERINARY PARASITOLOGY

Pathogen detection using short-RNA deep sequencing subtraction and assembly

(2011) O. Isakov et al.   BIOINFORMATICS

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

Horizontal gene transfer between bacteria and animals

(2011) Julie C. Dunning Hotopp   TRENDS IN GENETICS

bioDBnet: the biological database network

(2009) Uma Mudunuri et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

A whole-genome assembly of the domestic cow, Bos taurus

(2009) Aleksey V Zimin et al.   GENOME BIOLOGY

Molecular detection of Theileria and Babesia infections in cattle

(2008) Kursat Altay et al.   VETERINARY PARASITOLOGY