Publikationen des QBiC:

2015

  1. Aicheler, F, Li, J, Lehmann, R, Xu, G, and Kohlbacher, O, (2015), Retention Time Prediction Improves Identification in Non-Targeted Lipidomics Approaches. Anal Chem. 87(15):7698-704. PMID 26145158
  2. Friedrich, A, Kenar, E, Kohlbacher, O, and Nahnsen, S, (2015), Intuitive Web-based Experimental Design for High-throughput Biomedical Data. BioMed Res Int, 2015:958302. PMID 25954760
  3. Hildebrandt, AK, Stöckel,D, Fischer, N, de la Garza Trevino, L, Krüger, J, Nickels, S, Röttig, M, Schärfe, C,  Schumann, M, Thiel, P, Lenhof, HP, Kohlbacher, O, and Hildebrandt, A, (2015), ballaxy: web services for structural bioinformatics. Bioinformatics, 31(1):121-2. PMID 25183489
  4. Martens, L, Kohlbacher, O, and Weintraub, ST, (2015), Managing Expectations when Publishing Tools and Methods for Computational Proteomics. J. Proteome Res., 14(5):2002-4. PMID 25764342
  5. Proikas-Cezanne, T, Takacs, Z, Dönnes, P, and Kohlbacher, O (2015). WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome, J. Cell Sci., 128 (2):207-217. PMID 25568150
  6. Ranninger, C, Rurik, M, Limonciel, A, Ruzek, S, Reischl, R, Wilmes, A, Jennings, P, Hewitt, P, Dekant, W, Kohlbacher, O, and Huber, CG (2015). Nephron Toxicity Profiling via Untargeted Metabolome Analysis Emplying a High-Performance Liquid Chromatography-Mass Spectrometry-Based Experimental and Computational Pipeline, J. Biol. Chem., 290(31):19121-32. PMID 26055719
  7. Sachsenberg, T, Herbst, F, Taubert, M, Kermer, R, Jehmlich, N, von Bergen, M, Seifert, J, and Kohlbacher, O (2015). MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics, J. Proteome Res., 14(2):619-27. PMID 25412983
  8. Schubert, B, Brachvogel, H, Jürges, C, and Kohlbacher, O (2015). EpiToolKit - A Web-based Workbench for Vaccine Design. Bioinformatics, 31(13):2211-3. PMID 25712691
  9. Thost, A, Dönnes, P, Kohlbacher, O, and Proikas-Cezanne, T (2015). Fluorescence-based imaging of autophagy progression by human WIPI beta-propeller protein detection in single cells. Methods, 75:69-78. PMID 25462558
  10. 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, and Meissner, A (2015). Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature, 518:355-359. PMID 25533951

 2014

  1. Gerasch, A, Faber, D, Küntzer, J, Niermann, P, Kohlbacher, O, Lenhof, H, and Kaufmann, M (2014), BiNA: a visual analytics tool for biological network data. PLoS ONE, 9(2):e87397. PMID: 24551056
  2. Griss, J, et al., (2014), The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience. Mol. Cell. Prot.:mcp.O113.036681. PMID: 2498048 
  3. Hopf, TA, et al., (2014).  Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife:10.7554/eLife.03430. PMID: 25255213  
  4. Jordan, E, et al., (2014). Competing Salt Effects on Phase Behavior of Protein Solutions: Tailoring of Protein Interaction by the Binding of Multivalent Ions and Charge Screening. J. Phys. Chem. B, 118(38):11365-74. PMID: 2518081
  5. Kenar, E, Franken, H, Forcisi, S, Wörmann, K, Häring, H, Lehmann, R, Schmitt-Kopplin, P, Zell, A, and Kohlbacher, O (2014). Automated Label-Free Quantification of Metabolites from LC-MS Data. Mol. Cell. Prot., 13(1):348-59. PMID: 24176773
  6. Kramer, K, et al., (2014), Photo-cross linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nat. Methods, 11(10):1064-70. PMID: 25173706
  7. Krüger, J, Grunzke, R, Herres-Pawlies, S, de la Garza, L, Kohlbacher, O, Nagel, WE, and Gesing, S (2014), Performance Studies on Distributed Virtual Screening. 2014:624024. PMID: 25032219
  8. Thiel, P, Sach-Peltason, L, Ottmann, C, and Kohlbacher, O (2014), Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces. J. Chem. Inf. Model., 54(9):2395-401. PMID: 25136755
  9. Wagner, R, et al., (2014), Clinical and non-targeted metabolomic profiling of homozygous carries of Transcription Factor 7-like 2 variant rs7903146. Sci. Rep., 4:5296. PMID: 24925104
  10. Walzer, M, et al., (2014), qcML: an exchange format for quality control metrics from mass spectometry experiments. Mol. Cell. Prot., 13(8):1905-13. PMID: 24760958
  11. Szolek A, Schubert B, Mohr C, Sturm M, Feldhahn M, Kohlbacher O, (2014), Opti Type: precision HLA typing from next-generation sequencing data. Bioinformatics. 30 (23):3310-6. PMID: 25143287
  12. Hildebrandt AK, Stöckel D, Fischer NM, de la Garza L, Krüger J, Nickels S, Röttig M, Schärfe C et al., (2014), ballaxy: web services for structural bioinformatics. 31(1):121-2. PMID: 25183489 

2013

  1. Gifford, C.A., et al., Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell, 2013. 153(5): p. 1149-63. PMID:10.1016/j.cell.2013.04.037
  2. Nahnsen, S., T. Sachsenberg, and O. Kohlbacher, PTMeta: Increasing identification rates of modified peptides using modification prescanning and meta-analysis. Proteomics, 2013. 13(6): p. 1042-51. PMID:10.1002/pmic.201200315
  3. Perez-Riverol, Y., et al., Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. J Proteomics, 2013. 87: p. 134-8. PMID: 10.1016/j.jprot.2013.01.019
  4. Roosen-Runge, F., et al., Interplay of pH and binding of multivalent metal ions: charge inversion and reentrant condensation in protein solutions. J Phys Chem B, 2013. 117(18): p. 5777-87. PMID: 10.1021/jp401874t
  5. Thiel, P., et al., Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein-protein interactions. Chem Commun (Camb), 2013. 49(76): p. 8468-70. PMID: 10.1039/c3cc44612c
  6. Walzer, M., et al., The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics, 2013. 12(8): p. 2332-40. PMID: 10.1074/mcp.O113.028506
  7. Ziller, M.J., et al., Charting a dynamic DNA methylation landscape of the human genome. Nature, 2013. 500(7463): p. 477-81. PMID: 10.1038/nature12433
  8. Ahrends, R., et al., Comparison of displacement versus gradient mode for separation of a complex protein mixture by anion-exchange chromatography. J Chromatogr B Analyt Technol Biomed Life Sci, 2012. 901: p. 34-40. PMID: 10.1016/j.jchromb.2012.05.037
  9. Feldhahn, M., et al., miHA-Match: computational detection of tissue-specific minor histocompatibility antigens. J Immunol Methods, 2012. 386(1-2): p. 94-100. PMID: 10.1016/j.jim.2012.09.004
  10. Junker, J., et al., TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J Proteome Res, 2012. 11(7): p. 3914-20. PMID: 10.1021/pr300187f
  11. Nahnsen, S. and O. Kohlbacher, In silico design of targeted SRM-based experiments. BMC Bioinformatics, 2012. 13 Suppl 16: p. S8. PMID: 10.1186/1471-2105-13-S16-S8

2012

  1. Roglin, L., et al., Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 proteins. Proc Natl Acad Sci U S A, 2012. 109(18): p. E1051-3; author reply E1054. PMID: 10.1073/pnas.1116592109