Comparative RNA-Seq and Microarray Analysis of Gene Expression Changes in B-Cell Lymphomas of Canis familiaris

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

How I treat HIV-associated lymphoma

(2012) K. Dunleavy et al.   BLOOD

Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity

(2011) N. A. Furlotte et al.   BIOINFORMATICS

Functional analysis of expressed sequence tags from the liver and brain of Korean Jindo dogs

(2011) Jae-Young Kim et al.   BMB Reports

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Comparing Next-Generation Sequencing and Microarray Technologies in a Toxicological Study of the Effects of Aristolochic Acid on Rat Kidneys

(2011) Zhenqiang Su et al.   CHEMICAL RESEARCH IN TOXICOLOGY

A systems biology approach to identify molecular pathways altered by HDAC inhibition in osteosarcoma

(2011) Luke A. Wittenburg et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Transcriptomes of the B and T Lineages Compared by Multiplatform Microarray Profiling

(2011) M. W. Painter et al.   JOURNAL OF IMMUNOLOGY

Annotation of the domestic dog genome sequence: finding the missing genes

(2011) Thomas Derrien et al.   MAMMALIAN GENOME

Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods

(2011) Chao Chen et al.   PLoS One

Dog models of naturally occurring cancer

(2011) Jennie L. Rowell et al.   TRENDS IN MOLECULAR MEDICINE

Analysis of gene expression in canine sino-nasal aspergillosis and idiopathic lymphoplasmacytic rhinitis: A transcriptomic analysis

(2011) Morgane Vanherberghen et al.   VETERINARY MICROBIOLOGY

Targeting the PI3K/AKT/mTOR Pathway in Non-Hodgkin’s Lymphoma: Results, Biology, and Development Strategies

(2011) Jonathan H. Schatz   Current Oncology Reports

BioMart: driving a paradigm change in biological data management

(2011) A. Kasprzyk   Database-The Journal of Biological Databases and Curation

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

(2010) James R Bradford et al.   BMC GENOMICS

Leading the way: canine models of genomics and disease

(2010) A. L. Shearin et al.   Disease Models & Mechanisms

A Factor Model Approach to Multiple Testing Under Dependence

(2010) Chloé Friguet et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

The staging and treatment of multicentric high-grade lymphoma in dogs: A review of recent developments and future prospects

(2010) Laura Marconato   VETERINARY JOURNAL

Serological detection of Epstein-Barr virus infection in dogs and cats

(2010) Gemma Milman et al.   VETERINARY MICROBIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Differential efficacy of bortezomib plus chemotherapy within molecular subtypes of diffuse large B-cell lymphoma

(2009) K. Dunleavy et al.   BLOOD

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

(2009) Yan W Asmann et al.   BMC GENOMICS

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

Identifying disease-specific genes based on their topological significance in protein networks

(2009) Zoltán Dezső et al.   BMC Systems Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Evolutionarily conserved cytogenetic changes in hematological malignancies of dogs and humans – man and his best friend share more than companionship

(2008) Matthew Breen et al.   CHROMOSOME RESEARCH

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

A general framework for multiple testing dependence

(2008) J. T. Leek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE