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Items: 45

1.

Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1.

Gier S, Simon M, Nordström K, Khalifa S, Schulz MH, Schmitt MJ, Breinig F.

Front Microbiol. 2019 May 16;10:1102. doi: 10.3389/fmicb.2019.01102. eCollection 2019.

2.

Automated analysis of small RNA datasets with RAPID.

Karunanithi S, Simon M, Schulz MH.

PeerJ. 2019 Apr 10;7:e6710. doi: 10.7717/peerj.6710. eCollection 2019.

3.

Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival.

Kessler SM, Hosseini K, Hussein UK, Kim KM, List M, Schultheiß CS, Schulz MH, Laggai S, Jang KY, Kiemer AK.

Cell Physiol Biochem. 2019;52(4):787-801. doi: 10.33594/000000055.

4.

Improving in-silico normalization using read weights.

Durai DA, Schulz MH.

Sci Rep. 2019 Mar 26;9(1):5133. doi: 10.1038/s41598-019-41502-9.

5.

Identification of transcription factor binding sites using ATAC-seq.

Li Z, Schulz MH, Look T, Begemann M, Zenke M, Costa IG.

Genome Biol. 2019 Feb 26;20(1):45. doi: 10.1186/s13059-019-1642-2.

6.

Analysis of Cell Type-Specific Effects of MicroRNA-92a Provides Novel Insights Into Target Regulation and Mechanism of Action.

Rogg EM, Abplanalp WT, Bischof C, John D, Schulz MH, Krishnan J, Fischer A, Poluzzi C, Schaefer L, Bonauer A, Zeiher AM, Dimmeler S.

Circulation. 2018 Nov 27;138(22):2545-2558. doi: 10.1161/CIRCULATIONAHA.118.034598.

PMID:
30571345
7.

Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency.

Gérard D, Schmidt F, Ginolhac A, Schmitz M, Halder R, Ebert P, Schulz MH, Sauter T, Sinkkonen L.

Nucleic Acids Res. 2019 Feb 20;47(3):1141-1163. doi: 10.1093/nar/gky1240.

8.

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.

Schmidt F, List M, Cukuroglu E, Köhler S, Göke J, Schulz MH.

Bioinformatics. 2018 Sep 1;34(17):i908-i916. doi: 10.1093/bioinformatics/bty553.

9.

Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters.

Behjati Ardakani F, Kattler K, Nordström K, Gasparoni N, Gasparoni G, Fuchs S, Sinha A, Barann M, Ebert P, Fischer J, Hutter B, Zipprich G, Imbusch CD, Felder B, Eils J, Brors B, Lengauer T, Manke T, Rosenstiel P, Walter J, Schulz MH.

Epigenetics Chromatin. 2018 Nov 10;11(1):66. doi: 10.1186/s13072-018-0236-7.

10.

TEPIC 2-an extended framework for transcription factor binding prediction and integrative epigenomic analysis.

Schmidt F, Kern F, Ebert P, Baumgarten N, Schulz MH.

Bioinformatics. 2019 May 1;35(9):1608-1609. doi: 10.1093/bioinformatics/bty856.

11.

On the problem of confounders in modeling gene expression.

Schmidt F, Schulz MH.

Bioinformatics. 2019 Feb 15;35(4):711-719. doi: 10.1093/bioinformatics/bty674.

12.

In silico read normalization using set multi-cover optimization.

Durai DA, Schulz MH.

Bioinformatics. 2018 Oct 1;34(19):3273-3280. doi: 10.1093/bioinformatics/bty307.

13.

Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis.

Dehghani Amirabad A, Ramasamy P, Wierz M, Nordström K, Kessler SM, Schulz MH, Simon M.

Biochim Biophys Acta Mol Basis Dis. 2018 Oct;1864(10):3099-3108. doi: 10.1016/j.bbadis.2018.05.024. Epub 2018 May 30.

PMID:
29859241
14.

JAMI: fast computation of conditional mutual information for ceRNA network analysis.

Hornakova A, List M, Vreeken J, Schulz MH.

Bioinformatics. 2018 Sep 1;34(17):3050-3051. doi: 10.1093/bioinformatics/bty221.

15.

Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation.

Pirritano M, Götz U, Karunanithi S, Nordström K, Schulz MH, Simon M.

Genes (Basel). 2018 Feb 21;9(2). pii: E117. doi: 10.3390/genes9020117.

16.

More than the "Killer Trait": Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host.

Grosser K, Ramasamy P, Amirabad AD, Schulz MH, Gasparoni G, Simon M, Schrallhammer M.

Genome Biol Evol. 2018 Feb 1;10(2):646-656. doi: 10.1093/gbe/evy024.

17.

RegulatorTrail: a web service for the identification of key transcriptional regulators.

Kehl T, Schneider L, Schmidt F, Stöckel D, Gerstner N, Backes C, Meese E, Keller A, Schulz MH, Lenhof HP.

Nucleic Acids Res. 2017 Jul 3;45(W1):W146-W153. doi: 10.1093/nar/gkx350.

18.

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

Schmidt F, Gasparoni N, Gasparoni G, Gianmoena K, Cadenas C, Polansky JK, Ebert P, Nordström K, Barann M, Sinha A, Fröhler S, Xiong J, Dehghani Amirabad A, Behjati Ardakani F, Hutter B, Zipprich G, Felder B, Eils J, Brors B, Chen W, Hengstler JG, Hamann A, Lengauer T, Rosenstiel P, Walter J, Schulz MH.

Nucleic Acids Res. 2017 Jan 9;45(1):54-66. doi: 10.1093/nar/gkw1061. Epub 2016 Nov 29.

19.

Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development.

Durek P, Nordström K, Gasparoni G, Salhab A, Kressler C, de Almeida M, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Arrigoni L, 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, Richter AS, Sieverling L; DEEP Consortium, Chang HD, Syrbe U, Kalus U, Eils J, Brors B, Manke T, Ruland J, Lengauer T, Rajewsky N, Chen W, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schulz MH, Schultze JL, Radbruch A, Walter J, Hamann A, Polansky JK.

Immunity. 2016 Nov 15;45(5):1148-1161. doi: 10.1016/j.immuni.2016.10.022.

20.

Informed kmer selection for de novo transcriptome assembly.

Durai DA, Schulz MH.

Bioinformatics. 2016 Jun 1;32(11):1670-7. doi: 10.1093/bioinformatics/btw217. Epub 2016 Apr 28.

21.

Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes.

Götz U, Marker S, Cheaib M, Andresen K, Shrestha S, Durai DA, Nordström KJ, Schulz MH, Simon M.

Nucleic Acids Res. 2016 Jul 8;44(12):5908-23. doi: 10.1093/nar/gkw267. Epub 2016 Apr 16.

22.

De novo ChIP-seq analysis.

He X, Cicek AE, Wang Y, Schulz MH, Le HS, Bar-Joseph Z.

Genome Biol. 2015 Sep 23;16:205. doi: 10.1186/s13059-015-0756-4.

23.

Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia.

Cheaib M, Dehghani Amirabad A, Nordström KJ, Schulz MH, Simon M.

DNA Res. 2015 Aug;22(4):293-305. doi: 10.1093/dnares/dsv014. Epub 2015 Jul 31.

24.

A general concept for consistent documentation of computational analyses.

Ebert P, Müller F, Nordström K, Lengauer T, Schulz MH.

Database (Oxford). 2015 Jun 8;2015:bav050. doi: 10.1093/database/bav050. Print 2015.

25.

Fiona: a parallel and automatic strategy for read error correction.

Schulz MH, Weese D, Holtgrewe M, Dimitrova V, Niu S, Reinert K, Richard H.

Bioinformatics. 2014 Sep 1;30(17):i356-63. doi: 10.1093/bioinformatics/btu440.

27.

Reconstructing dynamic microRNA-regulated interaction networks.

Schulz MH, Pandit KV, Lino Cardenas CL, Ambalavanan N, Kaminski N, Bar-Joseph Z.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15686-91. doi: 10.1073/pnas.1303236110. Epub 2013 Aug 28.

28.

Probabilistic error correction for RNA sequencing.

Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z.

Nucleic Acids Res. 2013 May 1;41(10):e109. doi: 10.1093/nar/gkt215. Epub 2013 Apr 4.

29.

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.

Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z.

BMC Syst Biol. 2012 Aug 16;6:104. doi: 10.1186/1752-0509-6-104.

30.

Bayesian ontology querying for accurate and noise-tolerant semantic searches.

Bauer S, Köhler S, Schulz MH, Robinson PN.

Bioinformatics. 2012 Oct 1;28(19):2502-8. Epub 2012 Jul 26.

31.

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

Schulz MH, Zerbino DR, Vingron M, Birney E.

Bioinformatics. 2012 Apr 15;28(8):1086-92. doi: 10.1093/bioinformatics/bts094. Epub 2012 Feb 24.

32.

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.

Göke J, Schulz MH, Lasserre J, Vingron M.

Bioinformatics. 2012 Mar 1;28(5):656-63. doi: 10.1093/bioinformatics/bts028. Epub 2012 Jan 12.

33.

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.

Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K.

Bioinformatics. 2012 Mar 1;28(5):619-27. doi: 10.1093/bioinformatics/bts019. Epub 2012 Jan 11.

PMID:
22238266
34.

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.

Roepcke S, Stahlberg S, Klein H, Schulz MH, Theobald L, Gohlke S, Vingron M, Walther DJ.

BMC Genomics. 2011 Dec 20;12:624. doi: 10.1186/1471-2164-12-624.

35.

Exact score distribution computation for ontological similarity searches.

Schulz MH, Köhler S, Bauer S, Robinson PN.

BMC Bioinformatics. 2011 Nov 12;12:441. doi: 10.1186/1471-2105-12-441.

36.

DECOD: fast and accurate discriminative DNA motif finding.

Huggins P, Zhong S, Shiff I, Beckerman R, Laptenko O, Prives C, Schulz MH, Simon I, Bar-Joseph Z.

Bioinformatics. 2011 Sep 1;27(17):2361-7. doi: 10.1093/bioinformatics/btr412. Epub 2011 Jul 12.

37.

Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions.

Rödelsperger C, Guo G, Kolanczyk M, Pletschacher A, Köhler S, Bauer S, Schulz MH, Robinson PN.

Nucleic Acids Res. 2011 Apr;39(7):2492-502. doi: 10.1093/nar/gkq1081. Epub 2010 Nov 24.

38.

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.

Richard H, Schulz MH, Sultan M, Nürnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, Haas SA, Yaspo ML.

Nucleic Acids Res. 2010 Jun;38(10):e112. doi: 10.1093/nar/gkq041. Epub 2010 Feb 11.

39.

Clinical diagnostics in human genetics with semantic similarity searches in ontologies.

Köhler S, Schulz MH, Krawitz P, Bauer S, Dölken S, Ott CE, Mundlos C, Horn D, Mundlos S, Robinson PN.

Am J Hum Genet. 2009 Oct;85(4):457-64. doi: 10.1016/j.ajhg.2009.09.003.

40.

Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts.

Rödelsperger C, Köhler S, Schulz MH, Manke T, Bauer S, Robinson PN.

Genomics. 2009 Nov;94(5):308-16. doi: 10.1016/j.ygeno.2009.07.005. Epub 2009 Aug 4.

41.

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

Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

Bioinformatics. 2009 Nov 1;25(21):2865-71. doi: 10.1093/bioinformatics/btp394. Epub 2009 Jun 26.

42.

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML.

Science. 2008 Aug 15;321(5891):956-60. doi: 10.1126/science.1160342. Epub 2008 Jul 3.

43.

Mapping translocation breakpoints by next-generation sequencing.

Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, Schulz MH, Erdogan F, Li N, Kijas Z, Arkesteijn G, Pajares IL, Goetz-Sothmann M, Heinrich U, Rost I, Dufke A, Grasshoff U, Glaeser B, Vingron M, Ropers HH.

Genome Res. 2008 Jul;18(7):1143-9. doi: 10.1101/gr.076166.108. Epub 2008 Mar 7.

44.

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

Schulz MH, Bauer S, Robinson PN.

Int J Bioinform Res Appl. 2008;4(1):81-95.

PMID:
18283030
45.

A short ultraconserved sequence drives transcription from an alternate FBN1 promoter.

Guo G, Bauer S, Hecht J, Schulz MH, Busche A, Robinson PN.

Int J Biochem Cell Biol. 2008;40(4):638-50. Epub 2007 Oct 2.

PMID:
17996480

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