High-throughput Genomics & Systems Biology

Publications

Alternative publication profile on google scholar here

    Preprints

    A Dehghani Amirabad, MH Schulz
    Multitask regression for condition-specific prioritization of miRNA targets in transcripts
    PeerJ Preprints, 2016 [full text] presented at GCB 2016, Recomb-CCB 2016


    2016

    [36] F Schmidt , N Gasparoni, G Gasparoni, K Gianmoena, C Cadenas, JK Polansky, P Ebert, KJV Nordström, M Barann, A Sinha, S Fröhler, J Xiong, A Dehghani Amirabad, F Behjati Ardakani, B Hutter, G Zipprich, B Felder, E Jürgen Eils, B Brors, W Chen, JG Hengstler, A Hamann, T Lengauer, P Rosenstiel, J Walter, MH Schulz
    Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction,
    Nucleic Acids Research, 29 November 2016, full text

    ---->The TEPIC software can be downloaded here.

    [35] Durek P, Nordström KJV, Gasparoni G, Kressler C, Almeida M, Salhab A, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Amirabad AD, Ardakani FB, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch CD, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Arrigoni L, Richter AS, Sieverling L, Chang HD, Syrbe U, Manke T, Kalus U, Eils J, Brors B, Ruland J, Lengauer T, Rajewsky N, Chen W, Schulz MH, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schultze JP, Radbruch A, Walter J, Hamann A, Polansky JK
    Epigenetic reprogramming in memory formation of human CD4+ T cells
    Cell Immunity, Volume 45, Issue 5, 15 November 2016, full text

    [34] HG Stunnenberg, The International Human Epigenome Consortium (including F Schmidt, M Schulz), Martin Hirst
    The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery
    Cell, Volume 167, Issue 5, 17 November 2016, full text

    ---->all IHEC papers DEEP press release

    [33] MH Schulz, Z Bar-Joseph
    Probabilistic models for error correction of non-uniform sequencing data
    Algorithms for Next-Generations Sequencing Data: Techniques, Approaches and Applications, in press

    [32] D Weese, MH Schulz, H Richard
    DNA-Seq error correction based on substring indices
    Algorithms for Next-Generations Sequencing Data: Techniques, Approaches and Applications, in press

    [31] D Durai, MH Schulz
    Informed kmer selection for de novo transcriptome assembly
    Bioinformatics, 32 (11): 1670-1677, 2016 [pdf]

    ---->The software can be downloaded here.

    [30] U Götz*, S Marker*, M Cheaib*, K Andresen, S Shrestha, D Durai, KJV Nordström, MH Schulz, M Simon
    Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes
    Nucleic Acids Research,44 (12): 5908-5923, 2016 [pdf]

    [29] D Stöckel*, F Schmidt* , P Trampert, HP Lenhof
    CausalTrail: Testing hypothesis using causal Bayesian networks
    F1000Research 2015, 4(ISCB Comm J):1520 [full text]

    2015

    [28] X He*, AE Cicek*, Y Wang*, MH Schulz , HS Le, Z Bar-Joseph
    De novo ChIP-seq Analysis
    Genome Biology, 16:205 [full text]

    [27] M Cheaib, A Dehghani Amirabad, KJV Nordström, MH Schulz, M Simon
    Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia
    DNA Research, Oxford Journals [full text]

    [26] P Ebert, F Müller, K Nordström, T Lengauer, MH Schulz
    A General Concept for Consistent Documentation of Computational Analyses
    Database, Oxford Journals, 2015 Jun 8 [full text]

    2014

    [25] MH Schulz^,* ,D Weese*, M Holtgrewe*, V Dimitrova,S Niu, K Reinert, H Richard^,*
    Fiona: a parallel and automatic strategy for read error correction
    Bioinformatics 17 (30): i356-i363, ECCB 2014 proceedings [full text]

    ---->Easy to use error correction of genomic reads for indel-prone technologies. Software can be found here .

    [24] MH Schulz
    Letting the data speak for themselves: a fully Bayesian approach to transcriptome assembly
    Genome Biology, 10 15: 498 [full text]

    2013

    [23] T Steijger, JF Abril, PG Engström, F Kokocinski, The RGASP Consortium (including MH Schulz), TJ Hubbard, R Guigó, J Harrow, P Bertone
    Assessment of transcript reconstruction methods for RNA-seq
    Nature Methods [full text]

    [22] MH Schulz, KV Pandit, CL Lino Cardenas, N Ambalavanan, N Kaminski and Z Bar-Joseph
    Reconstructing dynamic microRNA-regulated interaction networks
    PNAS [full text]

    ---->On the PNAS cover with commentary by Uwe Ohler

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

    ---->Download SEECER and improve your RNA-seq data!

    2012

    [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]

    ---->Details about the new features of DREM 2.0. Check it out!

    [19] S Bauer, S Köhler, MH Schulz and PN Robinson
    Bayesian Ontology Querying for Accurate and Noise-Tolerant Semantic Searches
    Bioinformatics [full text]

    ---->An improved method to query for diseases with phenotypes. Test BOQA!

    [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]

    ---->Assemble your Transcriptome with Oases. Subscribe to the mailing list for regular updates. TOP3 most cited in Bioinformatics!

    [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]

    ---->Fast alignment free similarity computation for DNA sequences with ALF

    [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): 619-627. [full text]

    ----> Sensitive detection of structural variations from resequencing data with SplazerS

    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]

    [14] MH Schulz, S Köhler, S Bauer and PN Robinson
    Exact score distribution computation for ontological similarity searches
    BMC Bioinformatics, 12:441 [full text]

    ---->Exact P-values improve similarity searches in ontologies. Maybe for your problem as well? Try 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]

    ---->The software can be downloaded here.

    2010

    [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]

    ---->The first paper to predict enhancer-target associations with up to 2Mb distance to the enhancer

    [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

    [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]

    ---->Best paper selection IMIA Yearbook of Medical Informatics 2010

    [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]

    [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]

    ---->Best paper award ISMB-SIG Next-Generation Sequencing 2009

    2008

    [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]

    ----> Reported in Genome News and evaluated by Faculty of 1000

    [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 PISA 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]

    ---->Check out the DFI software

    [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]

    [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]

    ---->Software maintained by the Robinson Lab

    *shared first authorship