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Results: 1 to 20 of 126

1.

Protein (multi-)location prediction: utilizing interdependencies via a generative model.

Simha R, Briesemeister S, Kohlbacher O, Shatkay H.

Bioinformatics. 2015 Jun 15;31(12):i365-i374. doi: 10.1093/bioinformatics/btv264.

2.

Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry.

Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H.

Methods. 2015 Jun 10. pii: S1046-2023(15)00246-7. doi: 10.1016/j.ymeth.2015.06.005. [Epub ahead of print]

PMID:
26071038
3.

Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High-Performance Liquid Chromatography-Mass Spectrometry-Based Experimental and Computational Pipeline.

Ranninger C, Rurik M, Limonciel A, Ruzek S, Reischl R, Wilmes A, Jennings P, Hewitt P, Dekant W, Kohlbacher O, Huber CG.

J Biol Chem. 2015 Jun 8. pii: jbc.M115.644146. [Epub ahead of print]

4.

Intuitive web-based experimental design for high-throughput biomedical data.

Friedrich A, Kenar E, Kohlbacher O, Nahnsen S.

Biomed Res Int. 2015;2015:958302. doi: 10.1155/2015/958302. Epub 2015 Apr 14.

5.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M.

J Proteome Res. 2015 Jun 10. [Epub ahead of print]

PMID:
25938255
6.

Managing expectations when publishing tools and methods for computational proteomics.

Martens L, Kohlbacher O, Weintraub ST.

J Proteome Res. 2015 May 1;14(5):2002-4. doi: 10.1021/pr501318d. Epub 2015 Apr 22.

7.

EpiToolKit-a web-based workbench for vaccine design.

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

Bioinformatics. 2015 Jul 1;31(13):2211-3. doi: 10.1093/bioinformatics/btv116. Epub 2015 Feb 20.

8.

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 Apr;15(8):1443-7. doi: 10.1002/pmic.201400391. Epub 2015 Feb 14.

9.

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):207-17. doi: 10.1242/jcs.146258.

PMID:
25568150
10.

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
11.

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

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

Methods. 2015 Mar;75:69-78. doi: 10.1016/j.ymeth.2014.11.011. Epub 2014 Nov 22.

PMID:
25462558
12.

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
13.

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.

14.

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.

15.

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
16.

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
17.

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
18.

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.

19.

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
20.

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.

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