Annotating genomes with massive-scale RNA sequencing

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1997 • 71,835 citations

Mapping and quantifying mammalian transcriptomes by RNA-Seq

2008 • 12,817 citations

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

2008 • 9,415 citations

<tt>BLAT</tt>—The <tt>BLAST</tt>-Like Alignment Tool

2002 • 8,153 citations

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

2007 • 3,994 citations

Serial Analysis of Gene Expression

1995 • 3,659 citations

The Universal Protein Resource (UniProt)

2004 • 3,591 citations

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

2007 • 3,514 citations

SOAP: short oligonucleotide alignment program

2008 • 3,006 citations

Gene finding in novel genomes

2004 • 2,806 citations

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

2008 • 2,741 citations

Mapping short DNA sequencing reads and calling variants using mapping quality scores

2008 • 2,646 citations

Automated generation of heuristics for biological sequence comparison

2005 • 2,586 citations

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

2008 • 2,448 citations

GeneWise and Genomewise

2004 • 2,406 citations

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

2008 • 2,354 citations

Next-Generation DNA Sequencing Methods

2008 • 2,236 citations

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

2008 • 2,165 citations

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

2003 • 1,841 citations

Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays

2000 • 1,356 citations

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

2008 • 1,270 citations

Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution

2005 • 1,152 citations

Stem cell transcriptome profiling via massive-scale mRNA sequencing

2008 • 1,026 citations

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

2008 • 956 citations

ALLPATHS: De novo assembly of whole-genome shotgun microreads

2008 • 842 citations

The Universal Protein Resource (UniProt)

2007 • 782 citations

A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence

1998 • 745 citations

Genome-wide transcription and the implications for genomic organization

2007 • 701 citations

The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)

2004 • 554 citations

Assembling millions of short DNA sequences using SSAKE

2006 • 502 citations

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

2008 • 468 citations

Whole-genome sequencing and variant discovery in C. elegans

2008 • 413 citations

<tt>GeneID </tt>in Drosophila

2000 • 378 citations

EGASP: the human ENCODE Genome Annotation Assessment Project.

2006 • 338 citations

A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach

2008 • 310 citations

MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries

2008 • 306 citations

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing

2007 • 283 citations

EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA

1997 • 277 citations

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences

2004 • 260 citations

The new paradigm of flow cell sequencing: Table 1.

2008 • 213 citations

ZOOM! Zillions of oligos mapped

2008 • 206 citations

Tag-based approaches for transcriptome research and genome annotation

2005 • 176 citations

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

2008 • 154 citations

Mapping translocation breakpoints by next-generation sequencing

2008 • 138 citations

Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies

2007 • 128 citations

Optimal spliced alignments of short sequence reads

2008 • 117 citations

Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome

2007 • 90 citations

Optimal spliced alignments of short sequence reads

2008 • 87 citations

Whole Genome Sequence Comparisons and “Full-Length” cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation

2004 • 80 citations

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

2006 • 33 citations

ASEtrap: A biological method for speeding up the exploration of spliceomes

2006 • 14 citations