Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics

NOD1 and NOD2 Regulate Proinflammatory and Prolabor Mediators in Human Fetal Membranes and Myometrium via Nuclear Factor-Kappa B1

(2013) Martha Lappas   BIOLOGY OF REPRODUCTION

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

A zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery

(2013) Wouter J Veneman et al.   BMC GENOMICS

Functional analysis of a zebrafish myd88 mutant identifies key transcriptional components of the innate immune system

(2013) M. van der Vaart et al.   Disease Models & Mechanisms

Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis

(2013) R.A. Scholey et al.   VETERINARY JOURNAL

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

BamView: visualizing and interpretation of next-generation sequencing read alignments

(2012) T. Carver et al.   BRIEFINGS IN BIOINFORMATICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Biomaterial-Associated Infection: Locating the Finish Line in the Race for the Surface

(2012) H. J. Busscher et al.   Science Translational Medicine

Comparison of static immersion and intravenous injection systems for exposure of zebrafish embryos to the natural pathogen Edwardsiella tarda

(2011) Joost J van Soest et al.   BMC IMMUNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

A High-Throughput Screen for Tuberculosis Progression

(2011) Ralph Carvalho et al.   PLoS One

Phosphorylation of the Autophagy Receptor Optineurin Restricts Salmonella Growth

(2011) P. Wild et al.   SCIENCE

Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection

(2010) Anita Ordas et al.   FISH & SHELLFISH IMMUNOLOGY

Host tissue as a niche for biomaterial-associated infection

(2010) SAJ Zaat et al.   Future Microbiology

Alternative Splicing in Development and Function of Chordate Endocrine Systems: A Focus on Pax Genes

(2010) L. Z. Holland et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos

(2010) Oliver W. Stockhammer et al.   MOLECULAR IMMUNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

MapView: visualization of short reads alignment on a desktop computer

(2009) H. Bao et al.   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Tissue around catheters is a niche for bacteria associated with medical device infection

(2009) Corine A. N. Broekhuizen et al.   CRITICAL CARE MEDICINE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH