SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

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

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mutation ofFOXL2in Granulosa-Cell Tumors of the Ovary

(2009) Sohrab P. Shah et al.   NEW ENGLAND JOURNAL OF MEDICINE

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

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

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

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

(2008) H. Li et al.   GENOME RESEARCH

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE

Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays

(2008) Shin Lin et al.   GENOME BIOLOGY