Peer Reviewed

2013

Download SEECER and improve your RNA-seq data! [21] H Le, MH Schulz*, BM MCcauley, V Hinman, and Z Bar-Joseph
Probabilistic error correction for RNA sequencing
Nucleic Acids Research [full text]

2012


Details about the new features of DREM 2.0. Check it out! [20] MH Schulz*, WE Devanny*, A Gitter, S Zhong, J Ernst and Z Bar-Joseph
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data
BMC Systems Biology [full text]

An improved method to query for diseases with phenotypes. Test BOQA! [19] S Bauer, S Köhler, MH Schulz and PN Robinson
Bayesian Ontology Querying for Accurate and Noise-Tolerant Semantic Searches
Bioinformatics [full text]

Assemble your Transcriptome with Oases. Subscribe to the mailing list for regular updates. [18] MH Schulz*,DR Zerbino*, M Vingron and E Birney
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
Bioinformatics 28 (8): 1086-1092 [full text]

Fast alignment free similarity computation for DNA sequences with ALF [17] J Göke, MH Schulz, J Lasserre and M Vingron
Estimation of Pairwise Sequence Similarity of Mammalian Enhancers with Word Neighbourhood Counts
Bioinformatics 28 (5): 656-663 [full text]

Sensitive detection of structural variations from resequencing data with SplazerS [16] AK Emde, MH Schulz, D Weese, R and Sun, M Vingron, VM Kalscheuer, SA Haas and K Reinert
Detecting genomic indel variants with exact breakpoints in single-and paired-end sequencing data using SplazerS
Bioinformatics 28 (5): 656-663. [full text]

2011

[15] S Roepcke*, S Stahlberg*, H Klein, MH Schulz, L Theobald, S Gohlke, M Vingron and DJ Walther
A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ
BMC Genomics, 12:624 [full text]


Exact P-values improve similarity searches in ontologies. Maybe for your problem as well? Try here! [14] MH Schulz, S Köhler, S Bauer and PN Robinson
Exact score distribution computation for ontological similarity searches
BMC Bioinformatics, 12:441 [full text]





The software can be downloaded here. [13] P Huggins*, S Zhong*, I Shiff, R Beckerman, O Laptenko, C Prives, MH Schulz , I Simon and
Z Bar-Joseph
DECOD: fast and accurate discriminative DNA motif finding
Bioinformatics, 27 (17):2361-67 [full text]

2010

The first paper to predict enhancer-target associations with up to 2Mb distance to the enhancer [12] C Rödelsperger, G Guo, M Kolanczyk, A Pletschacher, S Köhler, S Bauer, MH Schulz, and
PN Robinson
Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions
Nucleic Acids Research, 40 (7) [full text]

Check out the R package Solas [11] H Richard*, MH Schulz*, M Sultan*, A Nürnberger, S Schrinner, D Balzereit, E Dagand, A Rasche, H Lehrach, M Vingron, SA Haas, and ML Yaspo
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
Nucleic Acids Research, 38 (10):e112 [full text]

2009

Best paper selection IMIA Yearbook of Medical Informatics 2010

[10] S Köhler, MH Schulz, P Krawitz, S Bauer, S Doelken, CE Ott, C Mundlos, D Horn, S Mundlos and PN Robinson
Clinical Diagnostics with Semantic Similarity Searches in Ontologies
The American Journal of Human Genetics, 85 (4):457-64 [full text]

First paper for exact p-value computation in ontology similarity searches. [9] MH Schulz, S Köhler, S Bauer, M Vingron and PN Robinson
Exact Score Distribution Computation for Similarity Searches in Ontologies
Proceedings WABI 2009 , Springer LNCS, Volume 5724, 2009 [full text]

[8] C Rödelsperger, S Köhler, MH Schulz, T Manke, S Bauer and PN Robinson
Short Ultraconserved Promoter Regions Delineate a Class of Ancient, Preferentially Expressed Alternatively Spliced Transcripts
Genomics,94 (5):308-16 [full text]

Best paper award ISMB-SIG Next-Generation Sequencing 2009

[7] K Ye, MH Schulz, Q Long, R Apweiler and Z Ning
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short read data
Bioinformatics, 25 (21):2865-71 [full text]

2008

Reported in Genome News and evaluated by Faculty of 1000 [6] M Sultan*, MH Schulz*, H Richard*, A Magen, A Klingenhoff, M Scherf, M Seifert, T Borodina, A Soldatov, D Parkhomchuk, D Schmidt, S O'Keeffe, S Haas, M Vingron, H Lehrach and ML Yaspo (2008)
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
Science, 321 (5891):956-60 [full text]

Check out the PISA software [5] MH Schulz, D Weese, T Rausch, A Döring, K Reinert and M Vingron
Fast and adaptive variable order Markov chain construction
Proceedings WABI 2008, Springer LNCS, Volume 5251 [full text]

Check out the DFI software [4] D Weese and MH Schulz
Efficient string mining under constraints via the deferred frequency index
Industrial Conference for Data Mining (ICDM 2008), LNAI 5077, pp. 374-388 [full text]

[3] W Chen, V Kalscheu, A Tzschach, C Menzel, R Ullmann, MH Schulz, F Erdogan, N Li, Z Kijas, G Arkesteijn, IL Pajares, M Goetz-Sothmann, U Heinrich, I Rost, A Dufke, U Grasshoff, BG Glaeser, M Vingron and HH Ropers
Mapping translocation breakpoints by next-generation sequencing
Genome Research 18: 1143-1149 [full text]

[2] G Guo, S Bauer, J Hecht, MH Schulz, A Busche and PN Robinson (2008)
A short ultraconserved sequence drives transcription from an alternate FBN1 promoter
The International Journal of Biochemistry & Cell Biology, 40(4):638-50 [full text]

Software maintained by the Robinson Lab [1] MH Schulz*, S Bauer* and PN Robinson (2008)
The generalised k-Truncated Suffix Tree for time- and space- efficient searches in multiple DNA or protein sequences
International Journal of Bioinformatics Research and Applications, 4(1):81-95 [full text]

*shared first authorship

Other

MH Schulz
Data Structures and Algorithms for Analysis of Alternative Splicing with RNA-seq Data (August 2010) [pdf]
Phd thesis at Max Planck Institute for Molecular Genetics (Dep. Computational Molecular Biology) and the Freie Universität Berlin

MH Schulz
Characterisation of Mitochondrial Ribosomal Protein Gene Promoters (2005)
Bachelor's thesis at Max Planck Institute for Molecular Genetics (Dep. Computational Molecular Biology) and the Freie Universität Berlin