The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

(2012) Brian J Haas et al.   BMC GENOMICS

Single Cell Genomics of the Brain: Focus on Neuronal Diversity and Neuropsychiatric Diseases

(2012) Ivan Y Iourov et al.   CURRENT GENOMICS

Investigating transcriptional states at single-cell-resolution

(2012) Julia Tischler et al.   CURRENT OPINION IN BIOTECHNOLOGY

Transcriptome analysis of Drosophila CNS midline cells reveals diverse peptidergic properties and a role for castor in neuronal differentiation

(2012) Joseph R. Fontana et al.   DEVELOPMENTAL BIOLOGY

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain

(2012) M. E. Hughes et al.   GENOME RESEARCH

Transcriptome comparison between honey bee queen- and worker-destined larvae

(2012) Xuan Chen et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

The physiology of sterol nutrition in the pea aphid Acyrthosiphon pisum

(2012) Sophie Bouvaine et al.   JOURNAL OF INSECT PHYSIOLOGY

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Transcriptomic Analysis of the Salivary Glands of an Invasive Whitefly

(2012) Yun-Lin Su et al.   PLoS One

Complex Modulation of the Aedes aegypti Transcriptome in Response to Dengue Virus Infection

(2012) Mariangela Bonizzoni et al.   PLoS One

Gene expression changes governing extreme dehydration tolerance in an Antarctic insect

(2012) N. M. Teets et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

No-Nonsense Functions for Long Noncoding RNAs

(2011) Takashi Nagano et al.   CELL

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Alternative splicing: global insights

(2010) Martina Hallegger et al.   FEBS Journal

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

De Novo Transcriptome Sequencing in Anopheles funestus Using Illumina RNA-Seq Technology

(2010) Jacob E. Crawford et al.   PLoS One

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Division of labor in honeybees: form, function, and proximate mechanisms

(2009) Brian R. Johnson   BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Experimental approaches for the discovery and characterization of regulatory small RNA

(2009) Cynthia Mira Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Regulation of hypopharyngeal gland activity and oogenesis in honey bee (Apis mellifera) workers

(2009) Jakob Wegener et al.   JOURNAL OF INSECT PHYSIOLOGY

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model

(2008) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic analysis of the honey bee worker venom gland focusing on the mechanisms of protection against tissue damage

(2008) Nico Peiren et al.   TOXICON