Marcel H. Schulz

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads (2009)

Ye, Kai, Schulz, Marcel H., Long, Quan, Apweiler, Rolf, Ning, Zemin

Motivation: There is a strong demand in the genomic community to develop effective algorithms to reliably identify genomic variants. Indel detection using next-gen data is difficult and...

A short ultraconserved sequence drives transcription from an alternate FBN1 promoter (2008)

Guo, Gao, Bauer, Sebastian, Hecht, Jochen, Schulz, Marcel H., Busche, Andreas, Robinson, Peter N.

FBN1, the gene mutated in Marfan syndrome, encodes fibrillin-1, a large glycoprotein component of the extracellular microfibrils. Human FBN1 has three untranslated upstream exons, and homologous...

The generalised k-Truncated Suffix Tree for time- and space-efficient searches in multiple DNA or protein sequences (2008)

Schulz, Marcel H., Bauer, Sebastian, Robinson, Peter N.

Efficient searching for specific subsequences in a set of longer sequences is an important component of many bioinformatics algorithms. Generalised suffix trees and suffix arrays allow searches for a...

Fast and adaptive variable order Markov chain construction (2008)

Schulz, Marcel H., Weese, David, Rausch, Tobias, Döring, Andreas, Reinert, Knut, Vingron, Martin

Variable order Markov chains (VOMCs) are a flexible class of models that extend the well-known Markov chains. They have been applied to a variety of problems in computational biology, e.g. protein...

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome (2008)

Sultan, Marc, Schulz, Marcel H., Hugues, Richard, Magen, Alon, Klingenhoff, Andreas, Scherf, Matthias, ...

The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. We...

Efficient string mining under constraints via the deferred frequency index (2008)

Weese, David, Schulz, Marcel H.

We propose a general approach for frequency based string mining, which has many applications, e.g. in contrast data mining. Our contribution is a novel algorithm based on a deferred data structure....