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Results: 1 to 20 of 107

1.

Performance studies on distributed virtual screening.

Krüger J, Grunzke R, Herres-Pawlis S, Hoffmann A, de la Garza L, Kohlbacher O, Nagel WE, Gesing S.

Biomed Res Int. 2014;2014:624024. doi: 10.1155/2014/624024. Epub 2014 Jun 17.

PMID:
25032219
[PubMed - in process]
Free PMC Article
2.

The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience.

Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Perez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaino JA, Hermjakob H.

Mol Cell Proteomics. 2014 Jun 30. pii: mcp.O113.036681. [Epub ahead of print]

PMID:
24980485
[PubMed - as supplied by publisher]
Free Article
3.

Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146.

Wagner R, Li J, Kenar E, Kohlbacher O, Machicao F, Häring HU, Fritsche A, Xu G, Lehmann R.

Sci Rep. 2014 Jun 13;4:5296. doi: 10.1038/srep05296.

PMID:
24925104
[PubMed - in process]
Free PMC Article
4.

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaino JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics. 2014 Apr 23. [Epub ahead of print]

PMID:
24760958
[PubMed - as supplied by publisher]
Free Article
5.

In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival.

Menzel M, Meckbach D, Weide B, Toussaint NC, Schilbach K, Noor S, Eigentler T, Ikenberg K, Busch C, Quintanilla-Martinez L, Kohlhofer U, Göke A, Göke F, Handgretinger R, Ottmann C, Bastian BC, Garbe C, Röcken M, Perner S, Kohlbacher O, Bauer J.

Pigment Cell Melanoma Res. 2014 Jul;27(4):671-3. doi: 10.1111/pcmr.12249. Epub 2014 May 6. No abstract available.

PMID:
24703331
[PubMed - in process]
6.

BiNA: a visual analytics tool for biological network data.

Gerasch A, Faber D, Küntzer J, Niermann P, Kohlbacher O, Lenhof HP, Kaufmann M.

PLoS One. 2014 Feb 13;9(2):e87397. doi: 10.1371/journal.pone.0087397. eCollection 2014.

PMID:
24551056
[PubMed - in process]
Free PMC Article
7.

Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways.

Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP.

Blood. 2014 Jan 30;123(5):e1-e10. doi: 10.1182/blood-2013-07-512384. Epub 2013 Dec 9.

PMID:
24324209
[PubMed - indexed for MEDLINE]
8.

On comparison of SimTandem with state-of-the-art peptide identification tools, efficiency of precursor mass filter and dealing with variable modifications.

Novák J, Sachsenberg T, Hoksza D, Skopal T, Kohlbacher O.

J Integr Bioinform. 2013 Nov 14;10(3):228. doi: 10.2390/biecoll-jib-2013-228.

PMID:
24231142
[PubMed - indexed for MEDLINE]
9.

Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data.

Kenar E, Franken H, Forcisi S, Wörmann K, Häring HU, Lehmann R, Schmitt-Kopplin P, Zell A, Kohlbacher O.

Mol Cell Proteomics. 2014 Jan;13(1):348-59. doi: 10.1074/mcp.M113.031278. Epub 2013 Oct 31.

PMID:
24176773
[PubMed - in process]
Free PMC Article
10.

Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays.

Brand LH, Fischer NM, Harter K, Kohlbacher O, Wanke D.

Nucleic Acids Res. 2013 Nov;41(21):9764-78. doi: 10.1093/nar/gkt732. Epub 2013 Aug 23.

PMID:
23975197
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein-protein interactions.

Thiel P, Röglin L, Meissner N, Hennig S, Kohlbacher O, Ottmann C.

Chem Commun (Camb). 2013 Oct 4;49(76):8468-70. doi: 10.1039/c3cc44612c.

PMID:
23939230
[PubMed - indexed for MEDLINE]
12.

Charting a dynamic DNA methylation landscape of the human genome.

Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A.

Nature. 2013 Aug 22;500(7463):477-81. doi: 10.1038/nature12433. Epub 2013 Aug 7.

PMID:
23925113
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A.

Cell. 2013 May 23;153(5):1149-63. doi: 10.1016/j.cell.2013.04.037. Epub 2013 May 9.

PMID:
23664763
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.

Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR.

Mol Cell Proteomics. 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506. Epub 2013 Apr 18.

PMID:
23599424
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Interplay of pH and binding of multivalent metal ions: charge inversion and reentrant condensation in protein solutions.

Roosen-Runge F, Heck BS, Zhang F, Kohlbacher O, Schreiber F.

J Phys Chem B. 2013 May 9;117(18):5777-87. doi: 10.1021/jp401874t. Epub 2013 May 1.

PMID:
23586503
[PubMed - indexed for MEDLINE]
16.

An automated pipeline for high-throughput label-free quantitative proteomics.

Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L.

J Proteome Res. 2013 Apr 5;12(4):1628-44. doi: 10.1021/pr300992u. Epub 2013 Feb 22.

PMID:
23391308
[PubMed - in process]
17.

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.

Perez-Riverol Y, Hermjakob H, Kohlbacher O, Martens L, Creasy D, Cox J, Leprevost F, Shan BP, Pérez-Nueno VI, Blazejczyk M, Punta M, Vierlinger K, Valiente PA, Leon K, Chinea G, Guirola O, Bringas R, Cabrera G, Guillen G, Padron G, Gonzalez LJ, Besada V.

J Proteomics. 2013 Jul 11;87:134-8. doi: 10.1016/j.jprot.2013.01.019. Epub 2013 Jan 29.

PMID:
23376229
[PubMed - indexed for MEDLINE]
18.

PTMeta: increasing identification rates of modified peptides using modification prescanning and meta-analysis.

Nahnsen S, Sachsenberg T, Kohlbacher O.

Proteomics. 2013 Mar;13(6):1042-51. doi: 10.1002/pmic.201200315.

PMID:
23335442
[PubMed - indexed for MEDLINE]
19.

Binding pocket optimization by computational protein design.

Malisi C, Schumann M, Toussaint NC, Kageyama J, Kohlbacher O, Höcker B.

PLoS One. 2012;7(12):e52505. doi: 10.1371/journal.pone.0052505. Epub 2012 Dec 27.

PMID:
23300688
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Tools for label-free peptide quantification.

Nahnsen S, Bielow C, Reinert K, Kohlbacher O.

Mol Cell Proteomics. 2013 Mar;12(3):549-56. doi: 10.1074/mcp.R112.025163. Epub 2012 Dec 17. Review.

PMID:
23250051
[PubMed - indexed for MEDLINE]
Free PMC Article

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