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Items: 1 to 50 of 251

1.

Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants.

Doncheva NT, Domingues FS, McGivern DR, Shimakami T, Zeuzem S, Lengauer T, Lange CM, Albrecht M, Welsch C.

J Mol Biol. 2019 May 31;431(12):2354-2368. doi: 10.1016/j.jmb.2019.04.034. Epub 2019 Apr 30.

PMID:
31051172
2.

RnBeads 2.0: comprehensive analysis of DNA methylation data.

Müller F, Scherer M, Assenov Y, Lutsik P, Walter J, Lengauer T, Bock C.

Genome Biol. 2019 Mar 14;20(1):55. doi: 10.1186/s13059-019-1664-9.

3.

Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes.

Ahmad M, Helms V, Kalinina OV, Lengauer T.

J Chem Theory Comput. 2019 Apr 9;15(4):2166-2178. doi: 10.1021/acs.jctc.8b01074. Epub 2019 Mar 6.

PMID:
30763093
4.

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.

5.

A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains.

Salhab A, Nordström K, Gasparoni G, Kattler K, Ebert P, Ramirez F, Arrigoni L, Müller F, Polansky JK, Cadenas C, G Hengstler J, Lengauer T, Manke T; DEEP Consortium, Walter J.

Genome Biol. 2018 Sep 28;19(1):150. doi: 10.1186/s13059-018-1510-5.

6.

From hype to reality: data science enabling personalized medicine.

Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B.

BMC Med. 2018 Aug 27;16(1):150. doi: 10.1186/s12916-018-1122-7.

7.

geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.

Döring M, Büch J, Friedrich G, Pironti A, Kalaghatgi P, Knops E, Heger E, Obermeier M, Däumer M, Thielen A, Kaiser R, Lengauer T, Pfeifer N.

Nucleic Acids Res. 2018 Jul 2;46(W1):W271-W277. doi: 10.1093/nar/gky349.

8.

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.

Pan WH, Sommer F, Falk-Paulsen M, Ulas T, Best P, Fazio A, Kachroo P, Luzius A, Jentzsch M, Rehman A, Müller F, Lengauer T, Walter J, Künzel S, Baines JF, Schreiber S, Franke A, Schultze JL, Bäckhed F, Rosenstiel P.

Genome Med. 2018 Apr 13;10(1):27. doi: 10.1186/s13073-018-0534-5.

9.

Results of the first international HIV-1 coreceptor proficiency panel test.

Heger E, Kaiser R, Knops E, Neumann-Fraune M, Schuelter E, Pironti A, Lengauer T, Walter H, Sierra S.

J Clin Virol. 2017 Aug;93:53-56. doi: 10.1016/j.jcv.2017.06.002. Epub 2017 Jun 10.

PMID:
28633097
10.

Using drug exposure for predicting drug resistance - A data-driven genotypic interpretation tool.

Pironti A, Pfeifer N, Walter H, Jensen BO, Zazzi M, Gomes P, Kaiser R, Lengauer T.

PLoS One. 2017 Apr 10;12(4):e0174992. doi: 10.1371/journal.pone.0174992. eCollection 2017.

11.

DeepBlueR: large-scale epigenomic analysis in R.

Albrecht F, List M, Bock C, Lengauer T.

Bioinformatics. 2017 Jul 1;33(13):2063-2064. doi: 10.1093/bioinformatics/btx099.

12.

Elucidating the energetic contributions to the binding free energy.

Ahmad M, Helms V, Kalinina OV, Lengauer T.

J Chem Phys. 2017 Jan 7;146(1):014105. doi: 10.1063/1.4973349.

PMID:
28063433
13.

A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support.

Döring M, Borrego P, Büch J, Martins A, Friedrich G, Camacho RJ, Eberle J, Kaiser R, Lengauer T, Taveira N, Pfeifer N.

Retrovirology. 2016 Dec 20;13(1):85. doi: 10.1186/s12977-016-0320-7.

14.

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.

15.

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation.

Farlik M, Halbritter F, Müller F, Choudry FA, Ebert P, Klughammer J, Farrow S, Santoro A, Ciaurro V, Mathur A, Uppal R, Stunnenberg HG, Ouwehand WH, Laurenti E, Lengauer T, Frontini M, Bock C.

Cell Stem Cell. 2016 Dec 1;19(6):808-822. doi: 10.1016/j.stem.2016.10.019. Epub 2016 Nov 17.

16.

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.

17.

Erratum to: Making sense of big data in health research: towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome Med. 2016 Nov 7;8(1):118. No abstract available.

18.

Determination of Phenotypic Resistance Cutoffs From Routine Clinical Data.

Pironti A, Walter H, Pfeifer N, Knops E, Lübke N, Büch J, Di Giambenedetto S, Kaiser R, Lengauer T; EuResist Network Study Group.

J Acquir Immune Defic Syndr. 2017 Apr 15;74(5):e129-e137. doi: 10.1097/QAI.0000000000001198.

19.

Epigenetic dynamics of monocyte-to-macrophage differentiation.

Wallner S, Schröder C, Leitão E, Berulava T, Haak C, Beißer D, Rahmann S, Richter AS, Manke T, Bönisch U, Arrigoni L, Fröhler S, Klironomos F, Chen W, Rajewsky N, Müller F, Ebert P, Lengauer T, Barann M, Rosenstiel P, Gasparoni G, Nordström K, Walter J, Brors B, Zipprich G, Felder B, Klein-Hitpass L, Attenberger C, Schmitz G, Horsthemke B.

Epigenetics Chromatin. 2016 Jul 29;9:33. doi: 10.1186/s13072-016-0079-z. eCollection 2016.

20.

Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees.

Kalaghatgi P, Pfeifer N, Lengauer T.

Mol Biol Evol. 2016 Oct;33(10):2720-34. doi: 10.1093/molbev/msw123. Epub 2016 Jul 19.

21.

Making sense of big data in health research: Towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome Med. 2016 Jun 23;8(1):71. doi: 10.1186/s13073-016-0323-y. Erratum in: Genome Med. 2016 Nov 7;8(1):118.

22.

Geno2pheno[HCV] - A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents.

Kalaghatgi P, Sikorski AM, Knops E, Rupp D, Sierra S, Heger E, Neumann-Fraune M, Beggel B, Walker A, Timm J, Walter H, Obermeier M, Kaiser R, Bartenschlager R, Lengauer T.

PLoS One. 2016 May 19;11(5):e0155869. doi: 10.1371/journal.pone.0155869. eCollection 2016.

23.

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.

Berger B, Gaasterland T, Lengauer T, Orengo CA, Gaeta B, Markel S, Valencia A.

Bioinformatics. 2017 Sep 15;33(18):2968. doi: 10.1093/bioinformatics/btw090. No abstract available.

24.

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

Albrecht F, List M, Bock C, Lengauer T.

Nucleic Acids Res. 2016 Jul 8;44(W1):W581-6. doi: 10.1093/nar/gkw211. Epub 2016 Apr 15.

25.

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.

Berger B, Gaasterland T, Lengauer T, Orengo C, Gaeta B, Markel S, Valencia A.

PLoS Comput Biol. 2016 Mar 24;12(3):e1004816. doi: 10.1371/journal.pcbi.1004816. eCollection 2016 Mar. No abstract available.

26.

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.

Valencia A, Markel S, Gaeta B, Gaasterland T, Lengauer T, Berger B, Orengo C.

F1000Res. 2016 Feb 11;5. pii: ISCB Comm J-157. doi: 10.12688/f1000research.8051.1. eCollection 2016.

27.

The Role of Conformational Changes in Molecular Recognition.

Ahmad M, Helms V, Kalinina OV, Lengauer T.

J Phys Chem B. 2016 Mar 10;120(9):2138-44. doi: 10.1021/acs.jpcb.5b11593. Epub 2016 Mar 1.

PMID:
26901699
28.

How Molecular Conformational Changes Affect Changes in Free Energy.

Ahmad M, Helms V, Lengauer T, Kalinina OV.

J Chem Theory Comput. 2015 Jul 14;11(7):2945-57. doi: 10.1021/acs.jctc.5b00235.

PMID:
26575732
29.

Enthalpy-Entropy Compensation upon Molecular Conformational Changes.

Ahmad M, Helms V, Lengauer T, Kalinina OV.

J Chem Theory Comput. 2015 Apr 14;11(4):1410-8. doi: 10.1021/ct501161t. Epub 2015 Mar 11.

PMID:
26574352
30.

Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses.

Caprari S, Metzler S, Lengauer T, Kalinina OV.

Viruses. 2015 Oct 19;7(10):5388-409. doi: 10.3390/v7102882.

31.

Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces.

Dietzen M, Kalinina OV, Taškova K, Kneissl B, Hildebrandt AK, Jaenicke E, Decker H, Lengauer T, Hildebrandt A.

Proteins. 2015 Oct;83(10):1887-99. doi: 10.1002/prot.24873. Epub 2015 Aug 24.

32.

Proviral DNA as a Target for HIV-1 Resistance Analysis.

Lübke N, Di Cristanziano V, Sierra S, Knops E, Schülter E, Jensen B, Oette M, Lengauer T, Kaiser R.

Intervirology. 2015;58(3):184-9. doi: 10.1159/000431093. Epub 2015 Jun 27.

33.

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B.

F1000Res. 2015 Jan 15;4:12. doi: 10.12688/f1000research.6038.1. eCollection 2015.

34.

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.

35.

Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc.

Sierra S, Dybowski JN, Pironti A, Heider D, Güney L, Thielen A, Reuter S, Esser S, Fätkenheuer G, Lengauer T, Hoffmann D, Pfister H, Jensen B, Kaiser R.

PLoS One. 2015 May 13;10(5):e0125502. doi: 10.1371/journal.pone.0125502. eCollection 2015.

36.

Effects of sequence alterations on results from genotypic tropism testing.

Pironti A, Sierra S, Kaiser R, Lengauer T, Pfeifer N.

J Clin Virol. 2015 Apr;65:68-73. doi: 10.1016/j.jcv.2015.02.006. Epub 2015 Feb 10.

37.

How to write a presubmission inquiry.

Lengauer T, Nussinov R.

PLoS Comput Biol. 2015 Feb 26;11(2):e1004098. doi: 10.1371/journal.pcbi.1004098. eCollection 2015 Feb. No abstract available.

38.

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.

Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B.

Bioinformatics. 2015 Feb 15;31(4):616-7. doi: 10.1093/bioinformatics/btv019. Epub 2015 Feb 2.

PMID:
25644272
39.

Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences.

Pironti A, Pfeifer N, Kaiser R, Walter H, Lengauer T.

J Int AIDS Soc. 2014 Nov 2;17(4 Suppl 3):19743. doi: 10.7448/IAS.17.4.19743. eCollection 2014.

40.

Comprehensive analysis of DNA methylation data with RnBeads.

Assenov Y, Müller F, Lutsik P, Walter J, Lengauer T, Bock C.

Nat Methods. 2014 Nov;11(11):1138-1140. doi: 10.1038/nmeth.3115. Epub 2014 Sep 28.

41.

Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies.

Pfeifer N, Walter H, Lengauer T.

J Acquir Immune Defic Syndr. 2014 Oct 1;67(2):107-12. doi: 10.1097/QAI.0000000000000283.

42.

BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.

Becker D, Lutsik P, Ebert P, Bock C, Lengauer T, Walter J.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W501-7. doi: 10.1093/nar/gku457. Epub 2014 May 29.

43.

Personalized HIV therapy to control drug resistance.

Lengauer T, Pfeifer N, Kaiser R.

Drug Discov Today Technol. 2014 Mar;11:57-64. doi: 10.1016/j.ddtec.2014.02.004. Review.

44.

Inferring short-range linkage information from sequencing chromatograms.

Beggel B, Neumann-Fraune M, Kaiser R, Verheyen J, Lengauer T.

PLoS One. 2013 Dec 20;8(12):e81687. doi: 10.1371/journal.pone.0081687. eCollection 2013.

45.

Efficient computation of root mean square deviations under rigid transformations.

Hildebrandt AK, Dietzen M, Lengauer T, Lenhof HP, Althaus E, Hildebrandt A.

J Comput Chem. 2014 Apr 15;35(10):765-71. doi: 10.1002/jcc.23513. Epub 2013 Dec 19.

PMID:
24356990
46.

Full genome ultra-deep pyrosequencing associates G-to-A hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B.

Beggel B, Münk C, Däumer M, Hauck K, Häussinger D, Lengauer T, Erhardt A.

J Viral Hepat. 2013 Dec;20(12):882-9. doi: 10.1111/jvh.12110. Epub 2013 Jun 7.

PMID:
24304458
47.

Ambulatory care for HIV-infected patients: differences in outcomes between hospital-based units and private practices: analysis of the RESINA cohort.

Oette M, Reuter S, Kaiser R, Jensen B, Lengauer T, Fätkenheuer G, Knechten H, Hower M, Sagir A, Pfister H, Häussinger D; RESINA study group.

Eur J Med Res. 2013 Nov 21;18:48. doi: 10.1186/2047-783X-18-48.

48.
49.

[Importance of bioinformatics in personalised medicine].

Lengauer T.

Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2013 Nov;56(11):1489-94. doi: 10.1007/s00103-013-1819-x. German.

PMID:
24170077
50.

Sensitive detection of viral transcripts in human tumor transcriptomes.

Schelhorn SE, Fischer M, Tolosi L, Altmüller J, Nürnberg P, Pfister H, Lengauer T, Berthold F.

PLoS Comput Biol. 2013;9(10):e1003228. doi: 10.1371/journal.pcbi.1003228. Epub 2013 Oct 3.

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