EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates

(2011) Alexandre Robert-Seilaniantz et al.   PLANT JOURNAL

Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling

(2011) Felix Krueger et al.   PLoS One

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

(2011) X. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana

(2011) Eric Kemen et al.   PLOS BIOLOGY

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

In-Depth Transcriptome Analysis Reveals Novel TARs and Prevalent Antisense Transcription in Human Cell Lines

(2010) Daniel Klevebring et al.   PLoS One

High-Throughput SuperSAGE for Digital Gene Expression Analysis of Multiple Samples Using Next Generation Sequencing

(2010) Hideo Matsumura et al.   PLoS One

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

De novo sequencing of plant genomes using second-generation technologies

(2009) M. Imelfort et al.   BRIEFINGS IN BIOINFORMATICS

Next-generation tag sequencing for cancer gene expression profiling

(2009) A. S. Morrissy et al.   GENOME RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two Sites in the DNA Target

(2009) Elisabeth Möncke-Buchner et al.   JOURNAL OF MOLECULAR BIOLOGY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

High-Resolution Analysis of the 5′-End Transcriptome Using a Next Generation DNA Sequencer

(2009) Shin-ichi Hashimoto et al.   PLoS One

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription

(2008) Rebecca L Poole et al.   BMC GENOMICS

Activation of Defense Response Pathways by OGs and Flg22 Elicitors in Arabidopsis Seedlings

(2008) Carine Denoux et al.   Molecular Plant

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   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

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

Modeling Transcriptome Based on Transcript-Sampling Data

(2008) Jiang Zhu et al.   PLoS One

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

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE