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The primary transcriptome of the major human pathogen Helicobacter pylori
Using a novel differential approach (dRNA-seq) selective for the 5′ end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. Expand
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Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
We introduce a matching model for short reads with diverse errors that can, besides mismatches, also cope with indels. Expand
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The African coelacanth genome provides insights into tetrapod evolution.
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looksExpand
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metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.
The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs withinExpand
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A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization orExpand
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Evidence for human microRNA-offset RNAs in small RNA sequencing data
Using short read sequencing data, we show here that moRNAs are also produced from human microRNA precursors, albeit at quite low expression levels. Expand
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The common ancestral core of vertebrate and fungal telomerase RNAs
Telomerase is a ribonucleoprotein with an intrinsic telomerase RNA (TER) component. Within yeasts, TER is remarkably large and presents little similarity in secondary structure to vertebrate orExpand
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DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments
We present DARIO, a free web service that allows to study short read data from small RNA-seq experiments. Expand
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MINCR is a MYC-induced lncRNA able to modulate MYC’s transcriptional network in Burkitt lymphoma cells
Significance Gains of the MYC gene are the most common imbalances in cancer and are associated with poor prognosis, particularly in B-cell lymphoma. Recent advances in DNA sequencing have revealedExpand
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Lacking alignments? The next-generation sequencing mapper segemehl revisited
MOTIVATION Next-generation sequencing has become an important tool in molecular biology. Expand
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