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Results: 1 to 20 of 120

1.

EpiToolKit - A Web-based Workbench for Vaccine Design.

Schubert B, Brachvogel HP, Jürges C, Kohlbacher O.

Bioinformatics. 2015 Feb 20. pii: btv116. [Epub ahead of print]

PMID:
25712691
[PubMed - as supplied by publisher]
Free Article
2.

Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry.

Aiche S, Sachsenberg T, Kenar E, Walzer M, Wiswedel B, Kristl T, Boyles M, Duschl A, Huber CG, Berthold MR, Reinert K, Kohlbacher O.

Proteomics. 2015 Jan 20. doi: 10.1002/pmic.201400391. [Epub ahead of print]

PMID:
25604327
[PubMed - as supplied by publisher]
3.

WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome.

Proikas-Cezanne T, Takacs Z, Dönnes P, Kohlbacher O.

J Cell Sci. 2015 Jan 15;128(2):207-217. Review.

PMID:
25568150
[PubMed - as supplied by publisher]
4.

Dissecting neural differentiation regulatory networks through epigenetic footprinting.

Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A.

Nature. 2015 Feb 19;518(7539):355-9. doi: 10.1038/nature13990. Epub 2014 Dec 24.

PMID:
25533951
[PubMed - in process]
5.

Fluorescence-based imaging of autophagy progression by human WIPI protein detection.

Thost A, Dönnes P, Kohlbacher O, Proikas-Cezanne T.

Methods. 2014 Nov 22. pii: S1046-2023(14)00374-0. doi: 10.1016/j.ymeth.2014.11.011. [Epub ahead of print]

PMID:
25462558
[PubMed - as supplied by publisher]
6.

MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics.

Sachsenberg T, Herbst FA, Taubert M, Kermer R, Jehmlich N, von Bergen M, Seifert J, Kohlbacher O.

J Proteome Res. 2015 Feb 6;14(2):619-27. doi: 10.1021/pr500245w. Epub 2014 Dec 1.

PMID:
25412983
[PubMed - in process]
7.

Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR-domain oligomerization.

Avbelj M, Wolz OO, Fekonja O, Benčina M, Repič M, Mavri J, Krüger J, Schärfe C, Delmiro Garcia M, Panter G, Kohlbacher O, Weber AN, Jerala R.

Blood. 2014 Dec 18;124(26):3896-904. doi: 10.1182/blood-2014-05-573188. Epub 2014 Oct 30.

PMID:
25359991
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Sequence co-evolution gives 3D contacts and structures of protein complexes.

Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS.

Elife. 2014 Sep 25;3. doi: 10.7554/eLife.03430.

PMID:
25255213
[PubMed - in process]
Free Article
9.

ballaxy: web services for structural bioinformatics.

Hildebrandt AK, Stöckel D, Fischer NM, de la Garza L, Krüger J, Nickels S, Röttig M, Schärfe C, Schumann M, Thiel P, Lenhof HP, Kohlbacher O, Hildebrandt A.

Bioinformatics. 2015 Jan 1;31(1):121-2. doi: 10.1093/bioinformatics/btu574. Epub 2014 Sep 2.

PMID:
25183489
[PubMed - in process]
10.

Competing salt effects on phase behavior of protein solutions: tailoring of protein interaction by the binding of multivalent ions and charge screening.

Jordan E, Roosen-Runge F, Leibfarth S, Zhang F, Sztucki M, Hildebrandt A, Kohlbacher O, Schreiber F.

J Phys Chem B. 2014 Sep 25;118(38):11365-74. doi: 10.1021/jp5058622. Epub 2014 Sep 15.

PMID:
25180816
[PubMed - in process]
11.

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins.

Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon KL, Hentze MW, Kohlbacher O, Urlaub H.

Nat Methods. 2014 Oct;11(10):1064-70. doi: 10.1038/nmeth.3092. Epub 2014 Aug 31.

PMID:
25173706
[PubMed - indexed for MEDLINE]
12.

OptiType: precision HLA typing from next-generation sequencing data.

Szolek A, Schubert B, Mohr C, Sturm M, Feldhahn M, Kohlbacher O.

Bioinformatics. 2014 Dec 1;30(23):3310-6. doi: 10.1093/bioinformatics/btu548. Epub 2014 Aug 20.

PMID:
25143287
[PubMed - indexed for MEDLINE]
Free Article
13.

Blocked inverted indices for exact clustering of large chemical spaces.

Thiel P, Sach-Peltason L, Ottmann C, Kohlbacher O.

J Chem Inf Model. 2014 Sep 22;54(9):2395-401. doi: 10.1021/ci500150t. Epub 2014 Sep 2.

PMID:
25136755
[PubMed - in process]
14.

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
15.

The mzTab data exchange format: communicating mass-spectrometry-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, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.

Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.

PMID:
24980485
[PubMed - in process]
Free PMC Article
16.

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
17.

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, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23.

PMID:
24760958
[PubMed - in process]
Free PMC Article
18.

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 - indexed for MEDLINE]
19.

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 - indexed for MEDLINE]
Free PMC Article
20.

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]
Free Article
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