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Oliver Kohlbacher - Publications

Affiliations: 
Eberhard Karls Universität Tübingen, Tübingen, Baden-Württemberg, Germany 
Area:
bioinformatics, computational biology, proteomics, metabolomics, immunology
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Year Citation  Score
2020 Jeong K, Kim J, Gaikwad M, Hidayah SN, Heikaus L, Schlüter H, Kohlbacher O. FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. Cell Systems. PMID 32078799 DOI: 10.1016/J.Cels.2020.01.003  0.317
2020 Wein S, Andrews B, Sachsenberg T, Santos-Rosa H, Kohlbacher O, Kouzarides T, Garcia BA, Weisser H. A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nature Communications. 11: 926. PMID 32066737 DOI: 10.1038/S41467-020-14665-7  0.48
2020 Rurik M, Alka O, Aicheler F, Kohlbacher O. Metabolomics Data Processing Using OpenMS. Methods in Molecular Biology (Clifton, N.J.). 2104: 49-60. PMID 31953812 DOI: 10.1007/978-1-0716-0239-3_4  0.372
2019 Bichmann L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanović S, Rammensee HG, Kohlbacher O. MHCquant: Automated and reproducible data analysis for immunopeptidomics. Journal of Proteome Research. PMID 31589052 DOI: 10.1021/Acs.Jproteome.9B00313  0.371
2019 Fillinger S, de la Garza L, Peltzer A, Kohlbacher O, Nahnsen S. Challenges of big data integration in the life sciences. Analytical and Bioanalytical Chemistry. 411: 6791-6800. PMID 31463515 DOI: 10.1007/S00216-019-02074-9  0.325
2019 Schneider L, Kehl T, Thedinga K, Grammes NL, Backes C, Mohr C, Schubert B, Lenhof K, Gerstner N, Daniel Hartkopf A, Wallwiener M, Kohlbacher O, Keller A, Meese E, Graf N, et al. ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification. Bioinformatics (Oxford, England). PMID 31038669 DOI: 10.1093/Bioinformatics/Btz302  0.539
2018 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, et al. From hype to reality: data science enabling personalized medicine. Bmc Medicine. 16: 150. PMID 30145981 DOI: 10.1186/S12916-018-1122-7  0.305
2018 Löffler MW, Kowalewski DJ, Backert L, Bernhardt J, Adam P, Schuster H, Dengler F, Backes D, Kopp HG, Beckert S, Wagner S, Königsrainer I, Kohlbacher O, Kanz L, Königsrainer A, et al. Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation. Cancer Research. PMID 29789417 DOI: 10.1158/0008-5472.Can-17-1745  0.316
2018 Schubert B, Schärfe C, Dönnes P, Hopf T, Marks D, Kohlbacher O. Population-specific design of de-immunized protein biotherapeutics. Plos Computational Biology. 14: e1005983. PMID 29499035 DOI: 10.1371/Journal.Pcbi.1005983  0.326
2018 Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, ... ... Kohlbacher O, et al. Whither systems medicine? Experimental & Molecular Medicine. 50: e453. PMID 29497170 DOI: 10.1038/Emm.2017.290  0.301
2018 Mohr C, Friedrich A, Wojnar D, Kenar E, Polatkan AC, Codrea MC, Czemmel S, Kohlbacher O, Nahnsen S. qPortal: A platform for data-driven biomedical research. Plos One. 13: e0191603. PMID 29352322 DOI: 10.1371/Journal.Pone.0191603  0.359
2017 Flett FJ, Sachsenberg T, Kohlbacher O, Mackay CL, Interthal H. Differential Enzymatic 16O/18O Labelling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates. Analytical Chemistry. PMID 28885003 DOI: 10.1021/Acs.Analchem.7B01625  0.301
2017 Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, ... ... Kohlbacher O, et al. A community proposal to integrate proteomics activities in ELIXIR. F1000research. 6. PMID 28713550 DOI: 10.12688/F1000Research.11751.1  0.322
2017 Chevrette MG, Aicheler F, Kohlbacher O, Currie CR, Medema MH. SANDPUMA: Ensemble Predictions of Nonribosomal Peptide Chemistry Reveals Biosynthetic Diversity across Actinobacteria. Bioinformatics (Oxford, England). PMID 28633438 DOI: 10.1093/Bioinformatics/Btx400  0.337
2017 Pfeuffer J, Sachsenberg T, Alka O, Walzer M, Fillbrunn A, Nilse L, Schilling O, Reinert K, Kohlbacher O. OpenMS - A platform for reproducible analysis of mass spectrometry data. Journal of Biotechnology. 261: 142-148. PMID 28559010 DOI: 10.1016/J.Jbiotec.2017.05.016  0.34
2017 Vizcaíno JA, Mayer G, Perkins SR, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, et al. The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics : McP. PMID 28515314 DOI: 10.1074/Mcp.M117.068429  0.354
2017 Schubert B, de la Garza L, Mohr C, Walzer M, Kohlbacher O. ImmunoNodes - graphical development of complex immunoinformatics workflows. Bmc Bioinformatics. 18: 242. PMID 28482806 DOI: 10.1186/S12859-017-1667-Z  0.339
2017 Backert L, Kowalewski DJ, Walz S, Schuster H, Berlin C, Neidert MC, Schemionek M, Brümmendorf TH, Vucinic V, Niederwieser D, Kanz L, Salih HR, Kohlbacher O, Weisel K, Rammensee HG, et al. A meta-analysis of HLA peptidome composition in different hematological entities: entity-specific dividing lines and "pan-leukemia" antigens. Oncotarget. 8: 43915-43924. PMID 28159928 DOI: 10.18632/Oncotarget.14918  0.302
2016 Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, ... ... Kohlbacher O, et al. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods. 13: 741-748. PMID 27575624 DOI: 10.1038/Nmeth.3959  0.361
2016 Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of Proteomics. PMID 27498275 DOI: 10.1016/J.Jprot.2016.08.002  0.358
2016 Veit J, Sachsenberg T, Chernev A, Aicheler F, Urlaub H, Kohlbacher O. LFQProfiler and RNP(xl) - Open-source tools for label-free quantification and protein-RNA cross-linking integrated into Proteome Discoverer. Journal of Proteome Research. PMID 27476824 DOI: 10.1021/Acs.Jproteome.6B00407  0.35
2016 Breckels LM, Holden SB, Wojnar D, Mulvey CM, Christoforou A, Groen A, Trotter MW, Kohlbacher O, Lilley KS, Gatto L. Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. Plos Computational Biology. 12: e1004920. PMID 27175778 DOI: 10.1371/Journal.Pcbi.1004920  0.35
2016 Schubert B, Walzer M, Brachvogel HP, Szolek A, Mohr C, Kohlbacher O. FRED 2: an immunoinformatics framework for Python. Bioinformatics (Oxford, England). 32: 2044-6. PMID 27153717 DOI: 10.1093/Bioinformatics/Btw113  0.367
2016 Mueller SC, Backes C, Gress A, Baumgarten N, Kalinina OV, Moll A, Kohlbacher O, Meese E, Keller A. BALL-SNPgp-from genetic variants toward computational diagnostics. Bioinformatics (Oxford, England). PMID 27153685 DOI: 10.1093/Bioinformatics/Btw084  0.343
2016 de la Garza L, Veit J, Szolek A, Röttig M, Aiche S, Gesing S, Reinert K, Kohlbacher O. From the desktop to the grid: scalable bioinformatics via workflow conversion. Bmc Bioinformatics. 17: 127. PMID 26968893 DOI: 10.1186/S12859-016-0978-9  0.327
2016 Krüger J, Kohlbacher O. Containerization and Wrapping of a Mass Spectra Prediction Workflow Peerj. 4. DOI: 10.7287/Peerj.Preprints.2528V1  0.306
2016 Haen SP, Kowalewski DJ, Bernhardt J, Backert L, Backes D, Dengler F, Beckert S, Koenigsrainer I, Kopp H, Kohlbacher O, Koenigsrainer A, Kanz L, Rammensee H, Stevanovic S, Loeffler MW. Unique Alterations in the Immunopeptidome of Colorectal Cancer Reflect Specific Transformations in Cancer-Associated Signaling Pathways and Reveal Tumor-Specific HLA-Ligand Modulations Blood. 128: 862-862. DOI: 10.1182/Blood.V128.22.862.862  0.318
2015 Dammeier S, Nahnsen S, Veit J, Wehner F, Ueffing M, Kohlbacher O. Mass Spectrometry-based Proteomics Reveals Organ-specific Expression Patterns To Be Used as Forensic Evidence. Journal of Proteome Research. PMID 26593679 DOI: 10.1021/Acs.Jproteome.5B00704  0.312
2015 Backert L, Kohlbacher O. Immunoinformatics and epitope prediction in the age of genomic medicine. Genome Medicine. 7: 119. PMID 26589500 DOI: 10.1186/S13073-015-0245-0  0.355
2015 Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A. Testing and validation of computational methods for mass spectrometry. Journal of Proteome Research. PMID 26549429 DOI: 10.1021/Acs.Jproteome.5B00852  0.338
2015 Schneider L, Stöckel D, Kehl T, Gerasch A, Ludwig N, Leidinger P, Huwer H, Tenzer S, Kohlbacher O, Hildebrandt A, Kaufmann M, Gessler M, Keller A, Meese E, Graf N, et al. DrugTargetInspector: An assistance tool for patient treatment stratification. International Journal of Cancer. Journal International Du Cancer. PMID 26501925 DOI: 10.7490/F1000Research.1112901.1  0.588
2015 Zaman U, Richter FM, Hofele R, Kramer K, Sachsenberg T, Kohlbacher O, Lenz C, Urlaub H. Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions. Molecular & Cellular Proteomics : McP. PMID 26450613 DOI: 10.1074/Mcp.M115.052795  0.306
2015 Aicheler F, Li J, Hoene M, Lehmann R, Xu G, Kohlbacher O. Retention Time Prediction Improves Identification in Nontargeted Lipidomics Approaches. Analytical Chemistry. 87: 7698-704. PMID 26145158 DOI: 10.1021/Acs.Analchem.5B01139  0.323
2015 Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H. Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Methods (San Diego, Calif.). PMID 26071038 DOI: 10.1016/J.Ymeth.2015.06.005  0.31
2015 Ranninger C, Rurik M, Limonciel A, Ruzek S, Reischl R, Wilmes A, Jennings P, Hewitt P, Dekant W, Kohlbacher O, Huber CG. Nephron toxicity profiling via untargeted metabolome analysis employing a high performance liquid chromatography-mass spectrometry-based experimental and computational pipeline Journal of Biological Chemistry. 290: 19121-19132. PMID 26055719 DOI: 10.1074/Jbc.M115.644146  0.302
2015 Friedrich A, Kenar E, Kohlbacher O, Nahnsen S. Intuitive web-based experimental design for high-throughput biomedical data. Biomed Research International. 2015: 958302. PMID 25954760 DOI: 10.1155/2015/958302  0.357
2015 Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M. PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface. Journal of Proteome Research. 14: 2988-97. PMID 25938255 DOI: 10.1021/Acs.Jproteome.5B00121  0.337
2015 Martens L, Kohlbacher O, Weintraub ST. Managing expectations when publishing tools and methods for computational proteomics. Journal of Proteome Research. 14: 2002-4. PMID 25764342 DOI: 10.1021/Pr501318D  0.361
2015 Schubert B, Brachvogel HP, Jürges C, Kohlbacher O. EpiToolKit--a web-based workbench for vaccine design. Bioinformatics (Oxford, England). 31: 2211-3. PMID 25712691 DOI: 10.1093/Bioinformatics/Btv116  0.307
2015 Aiche S, Sachsenberg T, Kenar E, Walzer M, Wiswedel B, Kristl T, Boyles M, Duschl A, Huber CG, Berthold MR, Reinert K, Kohlbacher O. Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. Proteomics. 15: 1443-7. PMID 25604327 DOI: 10.1002/Pmic.201400391  0.378
2015 Proikas-Cezanne T, Takacs Z, Dönnes P, Kohlbacher O. WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome. Journal of Cell Science. 128: 207-17. PMID 25568150 DOI: 10.1242/Jcs.146258  0.302
2015 Sachsenberg T, Herbst FA, Taubert M, Kermer R, Jehmlich N, von Bergen M, Seifert J, Kohlbacher O. MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. Journal of Proteome Research. 14: 619-27. PMID 25412983 DOI: 10.1021/Pr500245W  0.361
2015 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. ballaxy: web services for structural bioinformatics. Bioinformatics (Oxford, England). 31: 121-2. PMID 25183489 DOI: 10.1093/Bioinformatics/Btu574  0.569
2015 Gerasch A, Küntzer J, Niermann P, Stöckel D, Kaufmann M, Kohlbacher O, Lenhof H. Network-based interactive navigation and analysis of large biological datasets Information Technology. 57: 37-48. DOI: 10.15496/Publikation-10951  0.57
2015 Haen SP, Kowalewski DJ, Stevanovic S, Backert L, Dengler F, Backes D, Beckert S, Silvia W, Koenigsrainer I, Kopp H, Kohlbacher O, Koenigsrainer A, Kanz L, Rammensee H, Loeffler MW. Interplay Between the Immune System and Colorectal Carcinoma - Towards Tumor-Specific Peptide-Based Vaccination for Any HLA-Type Blood. 126: 1027-1027. DOI: 10.1182/Blood.V126.23.1027.1027  0.306
2014 Krüger J, Grunzke R, Gesing S, Breuers S, Brinkmann A, de la Garza L, Kohlbacher O, Kruse M, Nagel WE, Packschies L, Müller-Pfefferkorn R, Schäfer P, Schärfe C, Steinke T, Schlemmer T, et al. The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations. Journal of Chemical Theory and Computation. 10: 2232-45. PMID 26580747 DOI: 10.1021/Ct500159H  0.303
2014 Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS. Sequence co-evolution gives 3D contacts and structures of protein complexes. Elife. 3. PMID 25255213 DOI: 10.7554/Elife.03430  0.34
2014 Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon KL, Hentze MW, Kohlbacher O, Urlaub H. Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nature Methods. 11: 1064-70. PMID 25173706 DOI: 10.1038/Nmeth.3092  0.307
2014 Szolek A, Schubert B, Mohr C, Sturm M, Feldhahn M, Kohlbacher O. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics. 30: 3310-3316. PMID 25143287 DOI: 10.1093/Bioinformatics/Btu548  0.323
2014 Krüger J, Grunzke R, Herres-Pawlis S, Hoffmann A, de la Garza L, Kohlbacher O, Nagel WE, Gesing S. Performance studies on distributed virtual screening. Biomed Research International. 2014: 624024. PMID 25032219 DOI: 10.1155/2014/624024  0.31
2014 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, ... ... Kohlbacher O, et al. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Molecular & Cellular Proteomics : McP. 13: 2765-75. PMID 24980485 DOI: 10.1074/Mcp.O113.036681  0.357
2014 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, ... ... Kohlbacher O, et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics : McP. 13: 1905-13. PMID 24760958 DOI: 10.1074/Mcp.M113.035907  0.319
2014 Gerasch A, Faber D, Küntzer J, Niermann P, Kohlbacher O, Lenhof HP, Kaufmann M. BiNA: a visual analytics tool for biological network data. Plos One. 9: e87397. PMID 24551056 DOI: 10.1371/Journal.Pone.0087397  0.609
2014 Kenar E, Franken H, Forcisi S, Wörmann K, Häring HU, Lehmann R, Schmitt-Kopplin P, Zell A, Kohlbacher O. Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data. Molecular & Cellular Proteomics : McP. 13: 348-59. PMID 24176773 DOI: 10.1074/Mcp.M113.031278  0.334
2013 Novák J, Sachsenberg T, Hoksza D, Skopal T, Kohlbacher O. On comparison of SimTandem with state-of-the-art peptide identification tools, efficiency of precursor mass filter and dealing with variable modifications. Journal of Integrative Bioinformatics. 10: 228. PMID 24231142 DOI: 10.2390/Biecoll-Jib-2013-228  0.328
2013 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, et al. The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Molecular & Cellular Proteomics : McP. 12: 2332-40. PMID 23599424 DOI: 10.1074/Mcp.O113.028506  0.383
2013 Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L. An automated pipeline for high-throughput label-free quantitative proteomics. Journal of Proteome Research. 12: 1628-44. PMID 23391308 DOI: 10.1021/Pr300992U  0.355
2013 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, et al. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. Journal of Proteomics. 87: 134-8. PMID 23376229 DOI: 10.1016/J.Jprot.2013.01.019  0.39
2013 Nahnsen S, Sachsenberg T, Kohlbacher O. PTMeta: increasing identification rates of modified peptides using modification prescanning and meta-analysis. Proteomics. 13: 1042-1051. PMID 23335442 DOI: 10.1002/Pmic.201200315  0.375
2013 Nahnsen S, Bielow C, Reinert K, Kohlbacher O. Tools for label-free peptide quantification Molecular & Cellular Proteomics. 12: 549-556. PMID 23250051 DOI: 10.1074/Mcp.R112.025163  0.366
2013 Packschies L, Birkenheuer G, Blunk D, Breuers S, Brinkmann A, Vieira IdS, Fels G, Gesing S, Grunzke R, Herres-Pawlis S, Kohlbacher O, Krüger J, Kruse M, Lang U, Müller-Pfefferkorn R, et al. The MoSGrid - e-science gateway: molecular simulations in a distributed computing environment Journal of Cheminformatics. 5: 1-1. DOI: 10.1186/1758-2946-5-S1-O3  0.322
2012 Malisi C, Schumann M, Toussaint NC, Kageyama J, Kohlbacher O, Höcker B. Binding pocket optimization by computational protein design. Plos One. 7: e52505. PMID 23300688 DOI: 10.1371/Journal.Pone.0052505  0.315
2012 Nahnsen S, Kohlbacher O. In silico design of targeted SRM-based experiments Bmc Bioinformatics. 13: 1-9. PMID 23176520 DOI: 10.1186/1471-2105-13-S16-S8  0.352
2012 Feldhahn M, Dönnes P, Schubert B, Schilbach K, Rammensee H, Kohlbacher O. miHA-Match: computational detection of tissue-specific minor histocompatibility antigens. Journal of Immunological Methods. 386: 94-100. PMID 22985828 DOI: 10.1016/J.Jim.2012.09.004  0.32
2012 Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O. TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data Journal of Proteome Research. 11: 3914-3920. PMID 22583024 DOI: 10.1021/Pr300187F  0.386
2012 Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, et al. The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & Cellular Proteomics : McP. 11: M111.014381. PMID 22375074 DOI: 10.1074/Mcp.M111.014381  0.361
2012 Birkenheuer G, Blunk D, Breuers S, Brinkmann A, Vieira IdS, Fels G, Gesing S, Grunzke R, Herres-Pawlis S, Kohlbacher O, Krüger J, Lang U, Packschies L, Müller-Pfefferkorn R, Schäfer P, et al. MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment Journal of Cheminformatics. 4: 21. DOI: 10.1186/1758-2946-4-S1-P21  0.348
2012 Kohlbacher O. CADDSuite – a workflow-enabled suite of open-source tools for drug discovery Journal of Cheminformatics. 4: 1-1. DOI: 10.1186/1758-2946-4-S1-O2  0.368
2011 Tung CW, Ziehm M, Kämper A, Kohlbacher O, Ho SY. POPISK: T-cell reactivity prediction using support vector machines and string kernels. Bmc Bioinformatics. 12: 446. PMID 22085524 DOI: 10.1186/1471-2105-12-446  0.313
2011 Nahnsen S, Bertsch A, Rahnenführer J, Nordheim A, Kohlbacher O. Probabilistic consensus scoring improves tandem mass spectrometry peptide identification. Journal of Proteome Research. 10: 3332-43. PMID 21644507 DOI: 10.1021/Pr2002879  0.306
2011 Bielow C, Gröpl C, Kohlbacher O, Reinert K. Bioinformatics for Qualitative and Quantitative Proteomics Methods of Molecular Biology. 719: 331-349. PMID 21370091 DOI: 10.1007/978-1-61779-027-0_15  0.351
2011 Schumann M, Röttig M, Fischer NM, Kohlbacher O. A framework and workflow system for virtual screening and molecular docking Journal of Cheminformatics. 3: 15. DOI: 10.1186/1758-2946-3-S1-P15  0.357
2011 Birkenheuer G, Blunk D, Breuers S, Brinkmann A, Vieira IdS, Fels G, Gesing S, Grunzke R, Herres-Pawlis S, Kohlbacher O, Kruber N, Krüger J, Lang U, Packschies L, Müller-Pfefferkorn R, et al. MoSGrid – A Molecular Simulation Grid as a new tool in Computational Chemistry, Biology and Material Science Journal of Cheminformatics. 3: 14. DOI: 10.1186/1758-2946-3-S1-P14  0.308
2011 Krüger J, Birkenheuer G, Blunk D, Breuers S, Brinkmann A, Fels G, Gesing S, Grunzke R, Kohlbacher O, Kruber N, Lang U, Packschies L, Müller-Pfefferkorn R, Herres-Pawlis S, Schäfer P, et al. Molecular simulation grid Journal of Cheminformatics. 3: 1-1. DOI: 10.1186/1758-2946-3-S1-O17  0.332
2010 Toussaint NC, Widmer C, Kohlbacher O, Rätsch G. Exploiting physico-chemical properties in string kernels. Bmc Bioinformatics. 11: 1-9. PMID 21034432 DOI: 10.1186/1471-2105-11-S8-S7  0.317
2010 Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, Moll A, Stöckel D, Nickels S, Mueller SC, Lenhof HP, Kohlbacher O. BALL--biochemical algorithms library 1.3. Bmc Bioinformatics. 11: 531. PMID 20973958 DOI: 10.1186/1471-2105-11-531  0.606
2010 Briesemeister S, Rahnenführer J, Kohlbacher O. YLoc--an interpretable web server for predicting subcellular localization. Nucleic Acids Research. 38: W497-502. PMID 20507917 DOI: 10.1093/Nar/Gkq477  0.301
2010 Briesemeister S, Rahnenführer J, Kohlbacher O. Going from where to why--interpretable prediction of protein subcellular localization. Bioinformatics (Oxford, England). 26: 1232-8. PMID 20299325 DOI: 10.1093/Bioinformatics/Btq115  0.329
2010 Bertsch A, Jung S, Zerck A, Pfeifer N, Nahnsen S, Henneges C, Nordheim A, Kohlbacher O. Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics. Journal of Proteome Research. 9: 2696-2704. PMID 20201589 DOI: 10.1021/Pr1001803  0.319
2010 Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nature Methods. 7: S56-68. PMID 20195258 DOI: 10.1038/Nmeth.1436  0.328
2010 Röttig M, Rausch C, Kohlbacher O. Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. Plos Computational Biology. 6. PMID 20072606 DOI: 10.1371/Journal.Pcbi.1000636  0.3
2010 Trusch M, Böhlick A, Hildebrand D, Lichtner B, Bertsch A, Kohlbacher O, Bachmann S, Schlüter H. Application of displacement chromatography for the analysis of a lipid raft proteome. Journal of Chromatography B. 878: 309-314. PMID 20015709 DOI: 10.1016/J.Jchromb.2009.11.035  0.304
2010 Reinert K, Kohlbacher O. OpenMS and TOPP: open source software for LC-MS data analysis. Methods of Molecular Biology. 604: 201-211. PMID 20013373 DOI: 10.1007/978-1-60761-444-9_14  0.377
2010 Ahrends R, Lichtner B, Bertsch A, Kohlbacher O, Hildebrand D, Trusch M, Schlüter H. Application of displacement chromatography for the proteome analysis of a human plasma protein fraction. Journal of Chromatography A. 1217: 3321-3329. PMID 19854443 DOI: 10.1016/J.Chroma.2009.10.028  0.326
2010 Fischer NM, Schneider WM, Kohlbacher O. Rescoring of docking poses using force field-based methods Journal of Cheminformatics. 2: 52. DOI: 10.1186/1758-2946-2-S1-P52  0.342
2009 Toussaint NC, Kohlbacher O. Towards in silico design of epitope-based vaccines. Expert Opinion On Drug Discovery. 4: 1047-1060. PMID 23480396 DOI: 10.1517/17460440903242283  0.311
2009 Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, Elnakady YA, Müller R, Böcker S, Huber CG, Kohlbacher O. De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation Electrophoresis. 30: 3736-3747. PMID 19862751 DOI: 10.1002/Elps.200900332  0.306
2009 Briesemeister S, Blum T, Brady S, Lam Y, Kohlbacher O, Shatkay H. SherLoc2: A High-Accuracy Hybrid Method for Predicting Subcellular Localization of Proteins Journal of Proteome Research. 8: 5363-5366. PMID 19764776 DOI: 10.1021/Pr900665Y  0.333
2009 Blum T, Briesemeister S, Kohlbacher O. MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. Bmc Bioinformatics. 10: 274-274. PMID 19723330 DOI: 10.1186/1471-2105-10-274  0.322
2009 Keller A, Backes C, Gerasch A, Kaufmann M, Kohlbacher O, Meese E, Lenhof H. A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis Bioinformatics. 25: 2787-2794. PMID 19713416 DOI: 10.1093/Bioinformatics/Btp510  0.587
2009 Feldhahn M, Dönnes P, Thiel P, Kohlbacher O. FRED--a framework for T-cell epitope detection. Bioinformatics. 25: 2758-2759. PMID 19578173 DOI: 10.1093/Bioinformatics/Btp409  0.357
2009 Sturm M, Kohlbacher O. TOPPView: An open-source viewer for mass spectrometry data Journal of Proteome Research. 8: 3760-3763. PMID 19425593 DOI: 10.1021/Pr900171M  0.351
2009 Malisi C, Kohlbacher O, Höcker B. Automated scaffold selection for enzyme design. Proteins. 77: 74-83. PMID 19408301 DOI: 10.1002/Prot.22418  0.35
2009 Althaus E, Klau GW, Kohlbacher O, Lenhof H, Reinert K. Integer Linear Programming in Computational Biology Lecture Notes in Computer Science. 5760: 199-218. DOI: 10.1007/978-3-642-03456-5_14  0.566
2008 Toussaint NC, Dönnes P, Kohlbacher O. A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. Plos Computational Biology. 4. PMID 19112482 DOI: 10.1371/Journal.Pcbi.1000246  0.329
2008 Keller A, Backes C, Al-Awadhi M, Gerasch A, Küntzer J, Kohlbacher O, Kaufmann M, Lenhof H. GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. Bmc Bioinformatics. 9: 552-552. PMID 19099609 DOI: 10.1186/1471-2105-9-552  0.607
2008 Timm W, Scherbart A, Böcker S, Kohlbacher O, Nattkemper TW. Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics. Bmc Bioinformatics. 9: 443-443. PMID 18937839 DOI: 10.1186/1471-2105-9-443  0.32
2008 Schulz-Trieglaff O, Pfeifer N, Gröpl C, Kohlbacher O, Reinert K. LC-MSsim – a simulation software for liquid chromatography mass spectrometry data Bmc Bioinformatics. 9: 423-423. PMID 18842122 DOI: 10.1186/1471-2105-9-423  0.349
2008 Kerzmann A, Fuhrmann J, Kohlbacher O, Neumann D. BALLDock/SLICK: a new method for protein-carbohydrate docking. Journal of Chemical Information and Modeling. 48: 1616-25. PMID 18646839 DOI: 10.1021/Ci800103U  0.319
2008 Blum T, Kohlbacher O. MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics. 24: 2108-2109. PMID 18635573 DOI: 10.1093/Bioinformatics/Btn360  0.304
2008 Feldhahn M, Thiel P, Schuler MM, Hillen N, Stevanović S, Rammensee H, Kohlbacher O. EpiToolKit—a web server for computational immunomics Nucleic Acids Research. 36: 519-522. PMID 18440979 DOI: 10.1093/Nar/Gkn229  0.347
2008 Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O. OpenMS - an open-source software framework for mass spectrometry. Bmc Bioinformatics. 9: 163. PMID 18366760 DOI: 10.1186/1471-2105-9-163  0.364
2008 Hildebrandt A, Kohlbacher O, Lenhof HP. Modeling Protein-Protein and Protein-DNA Docking Bioinformatics-From Genomes to Therapies. 2: 601-650. DOI: 10.1002/9783527619368.ch17  0.516
2007 Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O. Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics Bmc Bioinformatics. 8: 468-468. PMID 18053132 DOI: 10.1186/1471-2105-8-468  0.351
2007 Küntzer J, Backes C, Blum T, Gerasch A, Kaufmann M, Kohlbacher O, Lenhof H. BNDB - the Biochemical Network Database. Bmc Bioinformatics. 8: 367-367. PMID 17910766 DOI: 10.1186/1471-2105-8-367  0.624
2007 Sturm M, Quinten S, Huber CG, Kohlbacher O. A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data Nucleic Acids Research. 35: 4195-4202. PMID 17567619 DOI: 10.1093/Nar/Gkm338  0.306
2007 Shatkay H, Höglund A, Brady S, Blum T, Dönnes P, Kohlbacher O. SherLoc: High-accuracy prediction of protein subcellular localization by integrating text and protein sequence data Bioinformatics. 23: 1410-1417. PMID 17392328 DOI: 10.1093/Bioinformatics/Btm115  0.337
2007 Hildebrandt A, Blossey R, Rjasanow S, Kohlbacher O, Lenhof H. Electrostatic potentials of proteins in water: a structured continuum approach Bioinformatics. 23: 99-103. PMID 17237112 DOI: 10.1093/Bioinformatics/Btl312  0.607
2007 Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M. TOPP--the OpenMS proteomics pipeline. Bioinformatics (Oxford, England). 23: e191-7. PMID 17237091 DOI: 10.1093/Bioinformatics/Btl299  0.418
2007 Küntzer J, Kneissl B, Kohlbacher O, Lenhof H. Abstract analysis of pathways using the BN++ software framework Bmc Systems Biology. 1: 24. DOI: 10.1186/1752-0509-1-S1-P24  0.566
2006 Kohlbacher O, Quinten S, Sturm M, Mayr BM, Huber CG. Structure-activity relationships in chromatography: retention prediction of oligonucleotides with support vector regression. Angewandte Chemie. 45: 7009-7012. PMID 17009385 DOI: 10.1002/Anie.200602561  0.36
2006 Kerzmann A, Neumann D, Kohlbacher O. SLICK--scoring and energy functions for protein-carbohydrate interactions. Journal of Chemical Information and Modeling. 46: 1635-42. PMID 16859295 DOI: 10.1021/Ci050422Y  0.307
2006 Dönnes P, Kohlbacher O. SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Research. 34: 194-197. PMID 16844990 DOI: 10.1093/Nar/Gkl284  0.307
2006 Mayr BM, Kohlbacher O, Reinert K, Sturm M, Gröpl C, Lange E, Klein C, Huber CG. Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. Journal of Proteome Research. 5: 414-21. PMID 16457608 DOI: 10.1021/Pr050344U  0.313
2006 Höglund A, Dönnes P, Blum T, Adolph HW, Kohlbacher O. MultiLoc: Prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition Bioinformatics. 22: 1158-1165. PMID 16428265 DOI: 10.1093/Bioinformatics/Btl002  0.323
2006 Moll A, Hildebrandt A, Lenhof H, Kohlbacher O. BALLView: a tool for research and education in molecular modeling Bioinformatics. 22: 365-366. PMID 16332707 DOI: 10.1093/Bioinformatics/Bti818  0.598
2006 Baldes C, Koenig P, Neumann D, Lenhof H-, Kohlbacher O, Lehr C-. Development of a fluorescence-based assay for screening of modulators of human organic anion transporter 1B3 (OATP1B3). European Journal of Pharmaceutics and Biopharmaceutics. 62: 39-43. PMID 16129589 DOI: 10.1016/J.Ejpb.2005.06.001  0.553
2006 Küntzer J, Blum T, Gerasch A, Backes C, Hildebrandt A, Kaufmann M, Kohlbacher O, Lenhof H. BN++ – A Biological Information System Journal of Integrative Bioinformatics. 3: 148-161. DOI: 10.1515/jib-2006-34  0.586
2005 Moll A, Hildebrandt A, Lenhof H, Kohlbacher O. BALLView: an object-oriented molecular visualization and modeling framework. Journal of Computer-Aided Molecular Design. 19: 791-800. PMID 16470421 DOI: 10.1007/S10822-005-9027-X  0.602
2005 Rausch C, Weber T, Kohlbacher O, Wohlleben W, Huson DH. Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Research. 33: 5799-808. PMID 16221976 DOI: 10.1093/Nar/Gki885  0.325
2005 Dönnes P, Kohlbacher O. Integrated modeling of the major events in the MHC class I antigen processing pathway Protein Science. 14: 2132-2140. PMID 15987883 DOI: 10.1110/Ps.051352405  0.306
2005 Gröpl C, Lange E, Reinert K, Kohlbacher O, Sturm M, Huber CG, Mayr BM, Klein CL. Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples Lecture Notes in Computer Science. 151-162. DOI: 10.1007/11560500_14  0.35
2004 Hildebrandt A, Blossey R, Rjasanow S, Kohlbacher O, Lenhof H-. Novel formulation of nonlocal electrostatics. Physical Review Letters. 93: 108104. PMID 15447456 DOI: 10.1103/Physrevlett.93.108104  0.575
2004 Istrail S, Florea L, Halldórsson BV, Kohlbacher O, Schwartz RS, Yap VB, Yewdell JW, Hoffman SL. Comparative immunopeptidomics of humans and their pathogens. Proceedings of the National Academy of Sciences of the United States of America. 101: 13268-72. PMID 15326311 DOI: 10.1073/Pnas.0404740101  0.302
2004 Dönnes P, Höglund A, Sturm M, Comtesse N, Backes C, Meese E, Kohlbacher O, Lenhof HP. Integrative analysis of cancer-related data using CAP Faseb Journal. 18: 1465-1467. PMID 15231723 DOI: 10.1096/Fj.04-1797Fje  0.579
2004 Neumann D, Lehr C, Lenhof H, Kohlbacher O. Computational modeling of the sugar–lectin interaction Advanced Drug Delivery Reviews. 56: 437-457. PMID 14969752 DOI: 10.1016/J.Addr.2003.10.019  0.603
2002 Sirava M, Schäfer T, Eiglsperger M, Kaufmann M, Kohlbacher O, Bornberg-Bauer E, Lenhof HP. BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics (Oxford, England). 18: S219-30. PMID 12386006 DOI: 10.1093/BIOINFORMATICS/18.SUPPL_2.S219  0.552
2002 Althaus E, Kohlbacher O, Lenhof H, Müller P. A combinatorial approach to protein docking with flexible side chains. Journal of Computational Biology. 9: 597-612. PMID 12323095 DOI: 10.1089/106652702760277336  0.594
2002 Neumann D, Kohlbacher O, Lenhof H, Lehr C. Lectin-sugar interaction. Calculated versus experimental binding energies. Febs Journal. 269: 1518-1524. PMID 11874467 DOI: 10.1046/J.1432-1033.2002.02800.X  0.572
2001 Kohlbacher O, Burchardt A, Moll A, Hildebrandt A, Bayer P, Lenhof H. Structure prediction of protein complexes by an NMR-based protein docking algorithm. Journal of Biomolecular Nmr. 20: 15-21. PMID 11430751 DOI: 10.1023/A:1011216130486  0.599
2001 Kohlbacher O, Lenhof HP. BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library. Bioinformatics (Oxford, England). 16: 815-24. PMID 11108704 DOI: 10.1093/bioinformatics/16.9.815  0.557
2000 Boghossian NP, Kohlbacher O, Lenhof HP. Rapid software prototyping in molecular modeling using the biochemical algorithms library (BALL) Acm Journal of Experimental Algorithms. 5: 16. DOI: 10.1145/351827.384258  0.612
1999 Boghossian N, Kohlbacher O, Lenhof H. BALL: Biochemical Algorithms Library Lecture Notes in Computer Science. 330-344. DOI: 10.1007/3-540-48318-7_26  0.61
Low-probability matches (unlikely to be authored by this person)
2006 Neumann D, Kohlbacher O, Merkwirth C, Lengauer T. A fully computational model for predicting percutaneous drug absorption. Journal of Chemical Information and Modeling. 46: 424-9. PMID 16426076 DOI: 10.1021/Ci050332T  0.298
2015 Simha R, Briesemeister S, Kohlbacher O, Shatkay H. Protein (multi-)location prediction: utilizing interdependencies via a generative model. Bioinformatics (Oxford, England). 31: i365-74. PMID 26072505 DOI: 10.1093/Bioinformatics/Btv264  0.298
2018 Bilich T, Nelde A, Bichmann L, Roerden M, Salih HR, Kowalewski DJ, Schuster H, Tsou CC, Marcu A, Neidert MC, Lübke M, Rieth J, Schemionek M, Brümmendorf TH, Vucinic V, ... ... Kohlbacher O, et al. The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy. Blood. PMID 30530751 DOI: 10.1182/Blood-2018-07-866830  0.298
2009 Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O. Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach. Journal of Proteome Research. 8: 4109-4115. PMID 19492844 DOI: 10.1021/Pr900064B  0.297
2010 Trusch M, Ehlert S, Bertsch A, Kohlbacher O, Hildebrand D, Schlüter H, Tallarek U. Improved particle‐packed HPLC/MS microchips for proteomic analysis Ieee Journal of Solid-State Circuits. 33: 3283-3291. PMID 21049518 DOI: 10.1002/Jssc.201000474  0.296
2018 Prasser F, Kohlbacher O, Mansmann U, Bauer B, Kuhn KA. Data Integration for Future Medicine (DIFUTURE). Methods of Information in Medicine. 57: e57-e65. PMID 30016812 DOI: 10.3414/Me17-02-0022  0.295
2010 Zhang F, Weggler S, Ziller MJ, Ianeselli L, Heck BS, Hildebrandt A, Kohlbacher O, Skoda MW, Jacobs RM, Schreiber F. Universality of protein reentrant condensation in solution induced by multivalent metal ions. Proteins. 78: 3450-7. PMID 20872851 DOI: 10.1002/Prot.22852  0.294
2012 Ahrends R, Lichtner B, Buck F, Hildebrand D, Kotasinska M, Kohlbacher O, Kwiatkowski M, Wagner M, Trusch M, Schlüter H. Comparison of displacement versus gradient mode for separation of a complex protein mixture by anion-exchange chromatography. Journal of Chromatography B. 901: 34-40. PMID 22727752 DOI: 10.1016/J.Jchromb.2012.05.037  0.294
2012 Röglin L, Thiel P, Kohlbacher O, Ottmann C. Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 proteins Proceedings of the National Academy of Sciences of the United States of America. 109: 201116592. PMID 22532669 DOI: 10.1073/Pnas.1116592109  0.293
2015 Walz S, Stickel JS, Kowalewski DJ, Schuster H, Weisel K, Backert L, Kahn S, Nelde A, Stroh T, Handel M, Kohlbacher O, Kanz L, Salih HR, Rammensee HG, Stevanović S. The antigenic landscape of multiple myeloma: mass spectrometry (re)defines targets for T-cell-based immunotherapy. Blood. 126: 1203-13. PMID 26138685 DOI: 10.1182/Blood-2015-04-640532  0.293
2015 de Lange O, Wolf C, Thiel P, Krüger J, Kleusch C, Kohlbacher O, Lahaye T. DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats. Nucleic Acids Research. PMID 26481363 DOI: 10.1093/Nar/Gkv1053  0.292
2009 Toussaint NC, Kohlbacher O. OptiTope—a web server for the selection of an optimal set of peptides for epitope-based vaccines Nucleic Acids Research. 37: 617-622. PMID 19420066 DOI: 10.1093/Nar/Gkp293  0.291
2013 Thiel P, Röglin L, Meissner N, Hennig S, Kohlbacher O, Ottmann C. Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein-protein interactions Chemical Communications. 49: 8468-8470. PMID 23939230 DOI: 10.1039/C3Cc44612C  0.291
2017 van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, ... ... Kohlbacher O, et al. The future of metabolomics in ELIXIR. F1000research. 6. PMID 29043062 DOI: 10.12688/F1000Research.12342.2  0.29
2012 Herres-Pawlis S, Birkenheuer G, Brinkmann A, Gesing S, Grunzke R, Jäkel R, Kohlbacher O, Krüger J, Vieira IDS. Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway Studies in Health Technology and Informatics. 175: 142-151. DOI: 10.3233/978-1-61499-054-3-142  0.29
2016 Rabsteyn A, Kyzirakos C, Schröder C, Sturm M, Mohr C, Walzer M, Pflückhahn U, Walter M, Feldhahn M, Laske K, Bonin M, Ebinger M, Stevanovic S, Bauer P, Kohlbacher O, et al. Abstract A113: iVacALL: A personalized peptide-vaccination design platform for pediatric acute lymphoblastic leukemia patients based on patient-individual tumor-specific variants Cancer Immunology Research. 4. DOI: 10.1158/2326-6074.Cricimteatiaacr15-A113  0.289
2009 Mitschke J, Fuss J, Blum T, Höglund A, Reski R, Kohlbacher O, Rensing SA. Prediction of dual protein targeting to plant organelles: Methods New Phytologist. 183: 224-236. PMID 19368670 DOI: 10.1111/J.1469-8137.2009.02832.X  0.289
2016 Kowalewski DJ, Walz S, Backert L, Schuster H, Kohlbacher O, Kanz L, Salih HR, Rammensee H, Stevanovic S, Stickel JS. Abstract A112: Mapping the impact of proteasome inhibitor therapy on the antigenic landscape of multiple myeloma: Identifying robust targets for T cell immunotherapy Cancer Immunology Research. 4. DOI: 10.1158/2326-6074.Cricimteatiaacr15-A112  0.288
2011 Röttig M, Medema MH, Blin K, Weber T, Rausch C, Kohlbacher O. NRPSpredictor2-a web server for predicting NRPS adenylation domain specificity Nucleic Acids Research. 39: 362-367. PMID 21558170 DOI: 10.1093/Nar/Gkr323  0.287
2016 Dietsche T, Tesfazgi Mebrhatu M, Brunner MJ, Abrusci P, Yan J, Franz-Wachtel M, Schärfe C, Zilkenat S, Grin I, Galán JE, Kohlbacher O, Lea S, Macek B, Marlovits TC, Robinson CV, et al. Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus. Plos Pathogens. 12: e1006071. PMID 27977800 DOI: 10.1371/Journal.Ppat.1006071  0.286
2009 Schultheiss SJ, Busch W, Lohmann JU, Kohlbacher O, Rätsch G. KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics (Oxford, England). 25: 2126-33. PMID 19389732 DOI: 10.1093/Bioinformatics/Btp278  0.284
2005 Schuler MM, Dönnes P, Nastke M, Kohlbacher O, Rammensee H, Stevanovic S. SNEP: SNP-derived epitope prediction program for minor H antigens. Immunogenetics. 57: 816-820. PMID 16341860 DOI: 10.1007/S00251-005-0054-5  0.284
2004 Kohlbacher O, Reinert K. Differenzielle Proteomanalyse – Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges) Information Technology. 46: 31-38. DOI: 10.1524/Itit.46.1.31.26506  0.283
2023 Kontou EE, Walter A, Alka O, Pfeuffer J, Sachsenberg T, Mohite OS, Nuhamunada M, Kohlbacher O, Weber T. UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. Journal of Cheminformatics. 15: 52. PMID 37173725 DOI: 10.1186/s13321-023-00724-w  0.282
2012 Trusch M, Tillack K, Kwiatkowski M, Bertsch A, Ahrends R, Kohlbacher O, Martin R, Sospedra M, Schlüter H. Displacement chromatography as first separating step in online two-dimensional liquid chromatography coupled to mass spectrometry analysis of a complex protein sample--the proteome of neutrophils. Journal of Chromatography A. 1232: 288-294. PMID 22391494 DOI: 10.1016/J.Chroma.2012.02.029  0.282
2018 Creydt M, Hudzik D, Rurik M, Kohlbacher O, Fischer M. Food Authentication: Small Molecule Profiling as a Tool for the Geographic Discrimination of German White Asparagus. Journal of Agricultural and Food Chemistry. PMID 30472843 DOI: 10.1021/Acs.Jafc.8B05791  0.281
2013 Thiel P, Peltason L, Ottmann C, Kohlbacher O. Deterministic clustering of the available chemical space Journal of Cheminformatics. 5: 53. DOI: 10.1186/1758-2946-5-S1-P53  0.281
2017 Schuster H, Peper JK, Bösmüller HC, Röhle K, Backert L, Bilich T, Ney B, Löffler MW, Kowalewski DJ, Trautwein N, Rabsteyn A, Engler T, Braun S, Haen SP, Walz JS, ... ... Kohlbacher O, et al. The immunopeptidomic landscape of ovarian carcinomas. Proceedings of the National Academy of Sciences of the United States of America. PMID 29093164 DOI: 10.1073/Pnas.1707658114  0.28
2011 Gesing S, Hemert Jv, Kacsuk P, Kohlbacher O. Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools Concurrency and Computation: Practice and Experience. 23: 223-234. DOI: 10.1002/Cpe.1687  0.279
2016 Hong HS, Koch SD, Scheel B, Gnad-Vogt U, Schröder A, Kallen KJ, Wiegand V, Backert L, Kohlbacher O, Hoerr I, Fotin-Mleczek M, Billingsley JM. Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy. Oncoimmunology. 5: e1249560. PMID 28123889 DOI: 10.1080/2162402X.2016.1249560  0.278
2013 Brand LH, Fischer NM, Harter K, Kohlbacher O, Wanke D. Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Research. 41: 9764-78. PMID 23975197 DOI: 10.1093/Nar/Gkt732  0.276
2018 Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell. PMID 30078747 DOI: 10.1016/J.Ccell.2018.07.001  0.276
2014 Thiel P, Sach-Peltason L, Ottmann C, Kohlbacher O. Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces Journal of Chemical Information and Modeling. 54: 2395-2401. PMID 25136755 DOI: 10.1021/Ci500150T  0.275
2014 Jordan E, Roosen-Runge F, Leibfarth S, Zhang F, Sztucki M, Hildebrandt A, Kohlbacher O, Schreiber F. Competing salt effects on phase behavior of protein solutions: tailoring of protein interaction by the binding of multivalent ions and charge screening. The Journal of Physical Chemistry. B. 118: 11365-74. PMID 25180816 DOI: 10.1021/Jp5058622  0.275
2018 Nelde A, Kowalewski DJ, Backert L, Schuster H, Werner JO, Klein R, Kohlbacher O, Kanz L, Salih HR, Rammensee HG, Stevanović S, Walz JS. HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell-based immunotherapy. Oncoimmunology. 7: e1316438. PMID 29632711 DOI: 10.1080/2162402X.2017.1316438  0.274
2009 Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, Oldiges M, Kohlbacher O, Zell A. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. Bmc Systems Biology. 3: 5. PMID 19144170 DOI: 10.1186/1752-0509-3-5  0.273
2012 Briesemeister S, Rahnenführer J, Kohlbacher O. No longer confidential: estimating the confidence of individual regression predictions. Plos One. 7: e48723. PMID 23166592 DOI: 10.1371/Journal.Pone.0048723  0.273
2013 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. Charting a dynamic DNA methylation landscape of the human genome. Nature. 500: 477-81. PMID 23925113 DOI: 10.1038/Nature12433  0.272
2008 Blum T, Kohlbacher O. Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks. Journal of Computational Biology. 15: 565-576. PMID 18631021 DOI: 10.1089/Cmb.2008.0044  0.271
2019 Ali M, Foldvari Z, Giannakopoulou E, Böschen ML, Strønen E, Yang W, Toebes M, Schubert B, Kohlbacher O, Schumacher TN, Olweus J. Induction of neoantigen-reactive T cells from healthy donors. Nature Protocols. PMID 31101906 DOI: 10.1038/S41596-019-0170-6  0.27
2014 Hopf TA, Schärfe CPI, Rodrigues JPGLM, Green AG, Kohlbacher O, Sander C, Bonvin AMJJ, Marks DS. Author response: Sequence co-evolution gives 3D contacts and structures of protein complexes Elife. DOI: 10.7554/Elife.03430.032  0.27
2016 Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. Nature Methods. 13: 651-656. PMID 27493588 DOI: 10.1038/Nmeth.3902  0.27
2015 Thost AK, Dönnes P, Kohlbacher O, Proikas-Cezanne T. Fluorescence-based imaging of autophagy progression by human WIPI protein detection. Methods (San Diego, Calif.). 75: 69-78. PMID 25462558 DOI: 10.1016/J.Ymeth.2014.11.011  0.269
2016 Löffler MW, Chandran PA, Laske K, Schroeder C, Bonzheim I, Walzer M, Hilke FJ, Trautwein N, Kowalewski DJ, Schuster H, Günder M, Carcamo Yañez VA, Mohr C, Sturm M, Nguyen HP, ... ... Kohlbacher O, et al. Erratum to "Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient". Journal of Hepatology. PMID 27863814 DOI: 10.1016/J.Jhep.2016.10.021  0.268
2019 Licha D, Vidali S, Aminzadeh-Gohari S, Alka O, Breitkreuz L, Kohlbacher O, Reischl RJ, Feichtinger RG, Kofler B, Huber CG. Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models. International Journal of Molecular Sciences. 20. PMID 31398922 DOI: 10.3390/Ijms20163873  0.267
2016 Ranninger C, Schmidt LE, Rurik M, Limonciel A, Jennings P, Kohlbacher O, Huber CG. Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry. Analytica Chimica Acta. 930: 13-22. PMID 27265900 DOI: 10.1016/J.Aca.2016.05.017  0.266
2019 Cain N, Alka O, Segelke T, von Wuthenau K, Kohlbacher O, Fischer M. Food fingerprinting: Mass spectrometric determination of the cocoa shell content (Theobroma cacao L.) in cocoa products by HPLC-QTOF-MS. Food Chemistry. 298: 125013. PMID 31260999 DOI: 10.1016/J.Foodchem.2019.125013  0.265
2013 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, ... ... Kohlbacher O, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 153: 1149-63. PMID 23664763 DOI: 10.1016/J.Cell.2013.04.037  0.264
2009 Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D. Simultaneous alignment of short reads against multiple genomes. Genome Biology. 10: R98. PMID 19761611 DOI: 10.1186/Gb-2009-10-9-R98  0.264
2013 Schärfe CP, Taeger J, Reuter P, Fischer NM, Krüger J, Wissinger B, Kohlbacher O. Development of a pharmacorphore model for pharmacological chaperones targeting mutant trafficking-deficient CNG channels. Journal of Cheminformatics. 5: 1-2. DOI: 10.1186/1758-2946-5-S1-O18  0.263
2018 Domingo-Calap P, Schubert B, Joly M, Solis M, Untrau M, Carapito R, Georgel P, Caillard S, Fafi-Kremer S, Paul N, Kohlbacher O, González-Candelas F, Bahram S. An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides. Plos Pathogens. 14: e1007368. PMID 30335851 DOI: 10.1371/Journal.Ppat.1007368  0.262
2010 Kirchler T, Briesemeister S, Singer M, Schütze K, Keinath M, Kohlbacher O, Vicente-Carbajosa J, Teige M, Harter K, Chaban C. The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. European Journal of Cell Biology. 89: 175-183. PMID 20047775 DOI: 10.1016/J.Ejcb.2009.11.023  0.262
2016 Schubert B, Kohlbacher O. Designing string-of-beads vaccines with optimal spacers. Genome Medicine. 8: 9. PMID 26813686 DOI: 10.1186/S13073-016-0263-6  0.262
2021 Bichmann L, Gupta S, Rosenberger G, Kuchenbecker L, Sachsenberg T, Ewels P, Alka O, Pfeuffer J, Kohlbacher O, Röst H. DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics. Journal of Proteome Research. PMID 34153189 DOI: 10.1021/acs.jproteome.1c00123  0.262
2015 Lange Od, Wolf C, Thiel P, Krüger J, Kohlbacher O, Lahaye T. DNA-binding proteins from marine bacteria expand the sequence diversity of known TALE-like repeats Nucleic Acids Research. 43. DOI: 10.15496/Publikation-10911  0.259
2013 Sturm M, Kohlbacher O, Handgretinger R, Rammensee H, Kyzirakos C, Pflückhahn U, Schroeder C, Bauer P, Walter M, Feldhahn M, Walzer M, Mohr C, Szolek A, Bonin M, Ebinger M, et al. iVacALL: utilizing next-generation sequencing for the establishment of an individual peptide vaccination approach for paediatric acute lymphoblastic leukaemia Bone Marrow Transplantation. 48. DOI: 10.15496/Publikation-3782  0.259
2011 Bertsch A, Gröpl C, Reinert K, Kohlbacher O. OpenMS and TOPP: open source software for LC-MS data analysis. Methods in Molecular Biology (Clifton, N.J.). 696: 353-67. PMID 21063960 DOI: 10.1007/978-1-60761-987-1_23  0.256
2012 Michta E, Schad K, Blin K, Ort-Winklbauer R, Röttig M, Kohlbacher O, Wohlleben W, Schinko E, Mast Y. The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494 Environmental Microbiology. 14: 3203-3219. PMID 23116164 DOI: 10.1111/1462-2920.12006  0.255
2011 Zhang GL, Ansari HR, Bradley P, Cawley GC, Hertz T, Hu X, Jojic N, Kim Y, Kohlbacher O, Lund O, Lundegaard C, Magaret CA, Nielsen M, Papadopoulos H, Raghava GP, et al. Machine learning competition in immunology - Prediction of HLA class I binding peptides. Journal of Immunological Methods. 374: 1-4. PMID 21986107 DOI: 10.1016/J.Jim.2011.09.010  0.254
2013 Roosen-Runge F, Heck BS, Zhang F, Kohlbacher O, Schreiber F. Interplay of pH and binding of multivalent metal ions: charge inversion and reentrant condensation in protein solutions. The Journal of Physical Chemistry. B. 117: 5777-87. PMID 23586503 DOI: 10.1021/Jp401874T  0.252
2020 Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O. EPIFANY - A method for efficient high-confidence protein inference. Journal of Proteome Research. PMID 31975601 DOI: 10.1021/acs.jproteome.9b00566  0.252
2011 Toussaint NC, Maman Y, Kohlbacher O, Louzoun Y. Universal peptide vaccines - optimal peptide vaccine design based on viral sequence conservation. Vaccine. 29: 8745-8753. PMID 21875632 DOI: 10.1016/J.Vaccine.2011.07.132  0.25
2015 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, ... ... Kohlbacher O, et al. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 518: 355-9. PMID 25533951 DOI: 10.1038/Nature13990  0.25
2016 Kohlbacher O, Vitek O, Weintraub ST. Challenges in Large-Scale Computational Mass Spectrometry and Multiomics. Journal of Proteome Research. 15: 681-2. PMID 26939758 DOI: 10.1021/Acs.Jproteome.6B00067  0.249
2016 Kyzirakos C, Mohr C, Armeanu-Ebinger S, Feldhahn M, Hadaschik D, Walzer M, Döcker D, Menzel M, Nahnsen S, Kohlbacher O, Biskup S. Optimized neoantigen selection based on tumor exome data Annals of Oncology. 27. DOI: 10.1093/Annonc/Mdw378.51  0.249
2016 Boyles MS, Ranninger C, Reischl R, Rurik M, Tessadri R, Kohlbacher O, Duschl A, Huber CG. Copper oxide nanoparticle toxicity profiling using untargeted metabolomics. Particle and Fibre Toxicology. 13: 49. PMID 27609141 DOI: 10.1186/S12989-016-0160-6  0.248
2020 Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, Allen-Vercoe E, von Bergen M. Corrigendum to Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics. 224: 103829. PMID 32467047 DOI: 10.1016/J.Jprot.2020.103829  0.244
2022 Jeong K, Babović M, Gorshkov V, Kim J, Jensen ON, Kohlbacher O. FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts. Nature Communications. 13: 4407. PMID 35906205 DOI: 10.1038/s41467-022-31922-z  0.243
2008 Zhang F, Skoda MW, Jacobs RM, Zorn S, Martin RA, Martin CM, Clark GF, Weggler S, Hildebrandt A, Kohlbacher O, Schreiber F. Reentrant condensation of proteins in solution induced by multivalent counterions. Physical Review Letters. 101: 148101. PMID 18851577 DOI: 10.1103/Physrevlett.101.148101  0.242
2018 Walz JS, Kowalewski DJ, Backert L, Nelde A, Kohlbacher O, Weide B, Kanz L, Salih HR, Rammensee HG, Stevanović S. Favorable immune signature in CLL patients, defined by antigen-specific T-cell responses, might prevent second skin cancers. Leukemia & Lymphoma. 59: 1949-1958. PMID 29295645 DOI: 10.1080/10428194.2017.1403022  0.241
2011 Feldhahn M, Menzel M, Weide B, Bauer P, Meckbach D, Garbe C, Kohlbacher O, Bauer J. No evidence of viral genomes in whole‐transcriptome sequencing of three melanoma metastases Experimental Dermatology. 20: 766-768. PMID 21672032 DOI: 10.1111/J.1600-0625.2011.01312.X  0.24
2017 Armeanu-Ebinger S, Hadaschik D, Kyzirakos C, Mohr C, Battke F, Kohlbacher O, Nahnsen S, Biskup S. 29Number of predicted tumour-neoantigens as biomarker for cancer immunotherapies Annals of Oncology. 28. DOI: 10.1093/Annonc/Mdx509  0.237
2012 Wörmann K, Lucio M, Forcisi S, Heinzmann SS, Kenar E, Franken H, Rosenbaum L, Schmitt-Kopplin P, Kohlbacher O, Zell A, Häring HU, Lehmann R. Metabolomics in diabetes research | "metabolomics" in der Diabetesforschung Diabetologe. 8: 42-48. DOI: 10.1007/S11428-011-0778-9  0.235
2014 Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP. Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways. Blood. 123: e1-e10. PMID 24324209 DOI: 10.1182/Blood-2013-07-512384  0.232
2008 Peifer C, Urich R, Schattel V, Abadleh M, Röttig M, Kohlbacher O, Laufer S. Implications for selectivity of 3,4-diarylquinolinones as p38αMAP kinase inhibitors Bioorganic & Medicinal Chemistry Letters. 18: 1431-1435. PMID 18207396 DOI: 10.1016/J.Bmcl.2007.12.073  0.23
2019 Löffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, Mühlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, ... ... Kohlbacher O, et al. Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma. Genome Medicine. 11: 28. PMID 31039795 DOI: 10.1186/S13073-019-0636-8  0.228
2007 Höglund A, Blum T, Brady S, Dönnes P, Miguel JS, Rocheford M, Kohlbacher O, Shatkay H. Significantly improved prediction of subcellular localization by integrating text and protein sequence data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 16-27. PMID 17094224  0.227
2015 Venturelli S, Belz RG, Kämper A, Berger A, von Horn K, Wegner A, Böcker A, Zabulon G, Langenecker T, Kohlbacher O, Barneche F, Weigel D, Lauer UM, Bitzer M, Becker C. Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors. The Plant Cell. PMID 26530086 DOI: 10.1105/Tpc.15.00585  0.226
2004 Höglund A, Kohlbacher O. From sequence to structure and back again: approaches for predicting protein-DNA binding. Proteome Science. 2: 3. PMID 15202939 DOI: 10.1186/1477-5956-2-3  0.226
2004 Höglund A, Kohlbacher O. From sequence to structure and back again: approaches for predicting protein-DNA binding. Proteome Science. 2: 3. PMID 15202939 DOI: 10.1186/1477-5956-2-3  0.226
2020 Netz E, Dijkstra TMH, Sachsenberg T, Zimmermann L, Walzer M, Monecke T, Ficner R, Dybkov O, Urlaub H, Kohlbacher O. OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS. Molecular & Cellular Proteomics : McP. PMID 33067342 DOI: 10.1074/mcp.TIR120.002186  0.224
2006 Kohlbacher O, Quinten S, Sturm M, Mayr BM, Huber CG. Struktur‐Aktivitäts‐Beziehungen in der Chromatographie: Retentionsvorhersage für Oligonucleotide mit Supportvektorregression Angewandte Chemie. 118: 7166-7169. DOI: 10.1002/Ange.200602561  0.22
2022 Alka O, Shanthamoorthy P, Witting M, Kleigrewe K, Kohlbacher O, Röst HL. DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics. Nature Communications. 13: 1347. PMID 35292629 DOI: 10.1038/s41467-022-29006-z  0.218
2014 Wagner R, Li J, Kenar E, Kohlbacher O, Machicao F, Häring HU, Fritsche A, Xu G, Lehmann R. Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146. Scientific Reports. 4: 5296. PMID 24925104 DOI: 10.1038/Srep05296  0.216
2001 Turner RJ, Chaturvedi K, Edwards NJ, Fasulo D, Halpern AL, Huson DH, Kohlbacher O, Miller JR, Reinert K, Remington KA, Schwartz R, Walenz B, Yooseph S, Istrail S. Visualization challenges for a new cyber-pharmaceutical computing paradigm Proceedings - Ieee 2001 Symposium On Parallel and Large-Data Visualization and Graphics. 7-18. DOI: 10.1109/PVGS.2001.964398  0.21
2014 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. Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR-domain oligomerization. Blood. 124: 3896-904. PMID 25359991 DOI: 10.1182/Blood-2014-05-573188  0.21
2021 Bandeira N, Deutsch EW, Kohlbacher O, Martens L, Vizcaíno JA. Data management of sensitive human proteomics data: current practices, recommendations and perspectives for the future. Molecular & Cellular Proteomics : McP. 100071. PMID 33711481 DOI: 10.1016/j.mcpro.2021.100071  0.206
2022 Elhabashy H, Merino F, Alva V, Kohlbacher O, Lupas AN. Exploring protein-protein interactions at the proteome level. Structure (London, England : 1993). 30: 462-475. PMID 35219399 DOI: 10.1016/j.str.2022.02.004  0.204
2021 Green AG, Elhabashy H, Brock KP, Maddamsetti R, Kohlbacher O, Marks DS. Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences. Nature Communications. 12: 1396. PMID 33654096 DOI: 10.1038/s41467-021-21636-z  0.204
2021 Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, ... ... Kohlbacher O, et al. A proteomics sample metadata representation for multiomics integration and big data analysis. Nature Communications. 12: 5854. PMID 34615866 DOI: 10.1038/s41467-021-26111-3  0.201
2012 Venturelli S, Berger A, Weiland T, Smirnow I, Schenk A, Horn Kv, Leischner C, Weiss T, Kämper A, Kohlbacher O, Böcker A, Eickhoff H, Wiesmüller K, Lauer U, Bitzer M. Entwicklung, Charakterisierung und Evaluierung neuartiger auf Naturstoffen basierender Histondeacetylase-Inhibitoren für die Therapie solider Tumore Zeitschrift Fur Gastroenterologie. 50. DOI: 10.1055/S-0032-1324018  0.199
2017 Schärfe CPI, Tremmel R, Schwab M, Kohlbacher O, Marks DS. Genetic variation in human drug-related genes. Genome Medicine. 9: 117. PMID 29273096 DOI: 10.1186/S13073-017-0502-5  0.197
2003 Florea L, Halldórsson B, Kohlbacher O, Schwartz R, Hoffman S, Istrail S. Epitope prediction algorithms for peptide-based vaccine design. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 2: 17-26. PMID 16826643 DOI: 10.1109/CSB.2003.1227293  0.194
2009 Venturelli S, Horn Kv, Berger A, Weiland T, Smirnow I, Schenk A, Weiss T, Kämper A, Kohlbacher O, Gregor M, Lauer U, Bitzer M. Identifikation und präklinische Charakterisierung neuartiger epigenetischer Wirkstoffe zur Behandlung therapieresistenter Tumore am Beispiel des Hepatozellulären Karzinoms Zeitschrift Fur Gastroenterologie. 47. DOI: 10.1055/S-0029-1225688  0.192
2014 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, ... ... Kohlbacher O, et al. In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival. Pigment Cell & Melanoma Research. 27: 671-3. PMID 24703331 DOI: 10.1111/Pcmr.12249  0.191
2010 Widmer C, Toussaint NC, Altun Y, Kohlbacher O, Rätsch G. Novel machine learning methods for MHC class I binding prediction Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6282: 98-109. DOI: 10.1007/978-3-642-16001-1_9  0.188
2017 Nieselt K, Pfeifer N, Lupas AN, Kohlbacher O. Poster abstracts of the 25th German Conference on Bioinformatics Peerj. DOI: 10.7287/Peerj.Preprints.3268V1  0.188
2022 Prokosch HU, Bahls T, Bialke M, Eils J, Fegeler C, Gruendner J, Haarbrandt B, Hampf C, Hoffmann W, Hund H, Kampf M, Kapsner LA, Kasprzak P, Kohlbacher O, Krefting D, et al. The COVID-19 Data Exchange Platform of the German University Medicine. Studies in Health Technology and Informatics. 294: 674-678. PMID 35612174 DOI: 10.3233/SHTI220554  0.182
2020 Kutuzova S, Colaianni P, Röst H, Sachsenberg T, Alka O, Kohlbacher O, Burla B, Torta F, Schrübbers L, Kristensen M, Nielsen L, Herrgård MJ, McCloskey D. SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing. Analytical Chemistry. PMID 33269929 DOI: 10.1021/acs.analchem.0c03421  0.178
2022 Winkler S, Winkler I, Figaschewski M, Tiede T, Nordheim A, Kohlbacher O. De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet. Bmc Bioinformatics. 23: 139. PMID 35439941 DOI: 10.1186/s12859-022-04670-6  0.177
2020 Marcu A, Bichmann L, Kuchenbecker L, Backert L, Kowalewski DJ, Freudenmann L, Löffler MW, Lübke M, Walz J, Velz J, Moch H, Regli L, Silginer M, Weller M, Schlosser A, ... Kohlbacher O, et al. The HLA Ligand Atlas: A novel immuno-oncology resource for T-cell antigen discovery. Journal of Clinical Oncology. 38: 3128-3128. DOI: 10.1200/jco.2020.38.15_suppl.3128  0.177
2023 Jeong K, Kaulich PT, Jung W, Kim J, Tholey A, Kohlbacher O. Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top-down proteomics. Proteomics. e2300068. PMID 37997224 DOI: 10.1002/pmic.202300068  0.175
2016 Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, ... ... Kohlbacher O, et al. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. Journal of Cheminformatics. 8: 18. PMID 29270804 DOI: 10.1186/S13321-016-0119-5  0.174
2022 Singh J, Elhabashy H, Muthukottiappan P, Stepath M, Eisenacher M, Kohlbacher O, Gieselmann V, Winter D. Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo. Nature Communications. 13: 6212. PMID 36266287 DOI: 10.1038/s41467-022-33951-0  0.172
2020 Samonig L, Loipetzberger A, Blöchl C, Rurik M, Kohlbacher O, Aberger F, Huber CG. Proteins and Molecular Pathways Relevant for the Malignant Properties of Tumor-Initiating Pancreatic Cancer Cells. Cells. 9. PMID 32503348 DOI: 10.3390/cells9061397  0.172
2020 Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, ... ... Kohlbacher O, et al. Feature-based molecular networking in the GNPS analysis environment. Nature Methods. PMID 32839597 DOI: 10.1038/S41592-020-0933-6  0.171
2014 Roberts JC, Yang J, Kohlbacher O, Ward MO, Zhou MX. Novel visual metaphors for multivariate networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8380: 127-150. DOI: 10.1007/978-3-319-06793-3_7  0.168
2020 Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, ... ... Kohlbacher O, et al. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure (London, England : 1993). PMID 33065067 DOI: 10.1016/j.str.2020.09.011  0.167
2023 Figaschewski M, Sürün B, Tiede T, Kohlbacher O. The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards. Bmc Bioinformatics. 24: 88. PMID 36890446 DOI: 10.1186/s12859-023-05194-3  0.166
2020 Beyan O, Choudhury A, van Soest J, Kohlbacher O, Zimmermann L, Stenzhorn H, Karim MR, Dumontier M, Decker S, da Silva Santos LOB, Dekker A. Distributed Analytics on Sensitive Medical Data: The Personal Health Train Data Intelligence. 2: 96-107. DOI: 10.1162/dint_a_00032  0.164
2020 Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H. Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature Communications. 11: 5250. PMID 33067435 DOI: 10.1038/s41467-020-19047-7  0.163
2022 Kubiniok P, Marcu A, Bichmann L, Kuchenbecker L, Schuster H, Hamelin DJ, Duquette JD, Kovalchik KA, Wessling L, Kohlbacher O, Rammensee HG, Neidert MC, Sirois I, Caron E. Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues. Iscience. 25: 103768. PMID 35141507 DOI: 10.1016/j.isci.2022.103768  0.152
2012 Herres-Pawlis S, Birkenheuer G, Brinkmann A, Gesing S, Grunzke R, Jäkel R, Kohlbacher O, Krüger J, Dos Santos Vieira I. Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway. Studies in Health Technology and Informatics. 175: 142-51. PMID 22942005  0.152
2020 Gleim LC, Karim MR, Zimmermann L, Kohlbacher O, Stenzhorn H, Decker S, Beyan O. Enabling ad-hoc reuse of private data repositories through schema extraction. Journal of Biomedical Semantics. 11: 6. PMID 32641124 DOI: 10.1186/s13326-020-00223-z  0.151
2020 Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, Allen-Vercoe E, von Bergen M. Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics. 222: 103791. PMID 32335296 DOI: 10.1016/J.Jprot.2020.103791  0.149
2020 Akgün M, Ünal AB, Ergüner B, Pfeifer N, Kohlbacher O. Identifying Disease-Causing Mutations with Privacy Protection. Bioinformatics (Oxford, England). PMID 32683440 DOI: 10.1093/bioinformatics/btaa641  0.149
2016 Kowalewski DJ, Walz S, Backert L, Schuster H, Kohlbacher O, Weisel K, Rittig SM, Kanz L, Salih HR, Rammensee HG, Stevanović S, Stickel JS. Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini. Blood Cancer Journal. 6: e411. PMID 27058226 DOI: 10.1038/bcj.2016.14  0.144
2022 Palmblad M, Böcker S, Degroeve S, Kohlbacher O, Käll L, Noble WS, Wilhelm M. Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics. Journal of Proteome Research. PMID 35119864 DOI: 10.1021/acs.jproteome.1c00900  0.144
2024 Pfeuffer J, Bielow C, Wein S, Jeong K, Netz E, Walter A, Alka O, Nilse L, Colaianni PD, McCloskey D, Kim J, Rosenberger G, Bichmann L, Walzer M, Veit J, ... ... Kohlbacher O, et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nature Methods. PMID 38366242 DOI: 10.1038/s41592-024-02197-7  0.142
2022 Akgün M, Pfeifer N, Kohlbacher O. Efficient Privacy-Preserving Whole Genome Variant Queries. Bioinformatics (Oxford, England). PMID 35150254 DOI: 10.1093/bioinformatics/btac070  0.141
2006 Lange E, Gröpl C, Reinert K, Kohlbacher O, Hildebrandt A. High-accuracy peak picking of proteomics data using wavelet techniques. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 243-54. PMID 17094243  0.141
2022 Jeong K, Kim J, Kohlbacher O. Mass Deconvolution of Top-Down Mass Spectrometry Datasets by FLASHDeconv. Methods in Molecular Biology (Clifton, N.J.). 2500: 145-157. PMID 35657592 DOI: 10.1007/978-1-0716-2325-1_11  0.138
2020 Hentrich T, Koch A, Weber N, Kilzheimer A, Maia A, Burkhardt S, Rall K, Casadei N, Kohlbacher O, Riess O, Schulze-Hentrich JM, Brucker SY. The Endometrial Transcription Landscape of MRKH Syndrome. Frontiers in Cell and Developmental Biology. 8: 572281. PMID 33072755 DOI: 10.3389/fcell.2020.572281  0.134
2020 Sürün B, Schärfe CPI, Divine MR, Heinrich J, Toussaint NC, Zimmermann L, Beha J, Kohlbacher O. ClinVAP: a reporting strategy from variants to therapeutic options. Bioinformatics (Oxford, England). 36: 2316-2317. PMID 31830259 DOI: 10.1093/bioinformatics/btz924  0.133
2021 Marcu A, Bichmann L, Kuchenbecker L, Kowalewski DJ, Freudenmann LK, Backert L, Mühlenbruch L, Szolek A, Lübke M, Wagner P, Engler T, Matovina S, Wang J, Hauri-Hohl M, Martin R, ... ... Kohlbacher O, et al. HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. Journal For Immunotherapy of Cancer. 9. PMID 33858848 DOI: 10.1136/jitc-2020-002071  0.133
2020 Lübke M, Spalt S, Kowalewski DJ, Zimmermann C, Bauersfeld L, Nelde A, Bichmann L, Marcu A, Peper JK, Kohlbacher O, Walz JS, Le-Trilling VTK, Hengel H, Rammensee HG, Stevanović S, et al. Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models. The Journal of Experimental Medicine. 217. PMID 31869419 DOI: 10.1084/jem.20191164  0.126
2006 Peifer C, Krasowski A, Hämmerle N, Kohlbacher O, Dannhardt G, Totzke F, Schächtele C, Laufer S. Profile and Molecular Modeling of 3-(Indole-3-yl)-4-(3,4,5-trimethoxyphenyl)-1H-pyrrole-2,5dione (1) as a Highly Selective VEGF-R2/3 Inhibitor Journal of Medicinal Chemistry. 49: 7549-7553. PMID 17149885 DOI: 10.1021/Jm0609871  0.124
2016 Ranninger C, Schmidt LE, Rurik M, Limonciel A, Jennings P, Kohlbacher O, Huber CG. Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry Analytica Chimica Acta. DOI: 10.1016/j.aca.2016.05.017  0.123
2022 Childebayeva A, Rohrlach AB, Barquera R, Rivollat M, Aron F, Szolek A, Kohlbacher O, Nicklisch N, Alt KW, Gronenborn D, Meller H, Friederich S, Prüfer K, Deguilloux MF, Krause J, et al. Population Genetics and Signatures of Selection in Early Neolithic European Farmers. Molecular Biology and Evolution. PMID 35578825 DOI: 10.1093/molbev/msac108  0.123
2019 Richter B, Rurik M, Gurk S, Kohlbacher O, Fischer M. Food monitoring: Screening of the geographical origin of white asparagus using FT-NIR and machine learning Food Control. 104: 318-325. DOI: 10.1016/J.Foodcont.2019.04.032  0.122
2024 Röhl A, Netz E, Kohlbacher O, Elhabashy H. CLAUDIO: automated structural analysis of cross-linking data. Bioinformatics (Oxford, England). 40. PMID 38498849 DOI: 10.1093/bioinformatics/btae146  0.12
2016 Löffler MW, Anoop Chandran P, Laske K, Schroeder C, Bonzheim I, Walzer M, Hilke FJ, Trautwein N, Kowalewski DJ, Schuster H, Günder M, Carcamo Yañez VA, Mohr C, Sturm M, Nguyen HP, ... ... Kohlbacher O, et al. Personalized peptide vaccine induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient. Journal of Hepatology. PMID 27397612 DOI: 10.1016/j.jhep.2016.06.027  0.119
2020 Arndt M, Rurik M, Drees A, Bigdowski K, Kohlbacher O, Fischer M. Comparison of different sample preparation techniques for NIR screening and their influence on the geographical origin determination of almonds (Prunus dulcis MILL.) Food Control. 115: 107302. DOI: 10.1016/J.Foodcont.2020.107302  0.116
2020 Klare J, Rurik M, Rottmann E, Bollen A, Kohlbacher O, Fischer M, Hackl T. Determination of the Geographical Origin of L. by H NMR Spectroscopy. Journal of Agricultural and Food Chemistry. PMID 33103896 DOI: 10.1021/acs.jafc.0c05642  0.113
2024 Bayas A, Mansmann U, Ön BI, Hoffmann VS, Berthele A, Mühlau M, Kowarik MC, Krumbholz M, Senel M, Steuerwald V, Naumann M, Hartberger J, Kerschensteiner M, Oswald E, Ruschil C, ... ... Kohlbacher O, et al. Prospective study validating a multidimensional treatment decision score predicting the 24-month outcome in untreated patients with clinically isolated syndrome and early relapsing-remitting multiple sclerosis, the ProVal-MS study. Neurological Research and Practice. 6: 15. PMID 38449051 DOI: 10.1186/s42466-024-00310-x  0.105
2020 Nelde A, Bilich T, Heitmann JS, Maringer Y, Salih HR, Roerden M, Lübke M, Bauer J, Rieth J, Wacker M, Peter A, Hörber S, Traenkle B, Kaiser PD, Rothbauer U, ... ... Kohlbacher O, et al. SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. Nature Immunology. PMID 32999467 DOI: 10.1038/s41590-020-00808-x  0.104
2022 Buchert R, Schenk E, Hentrich T, Weber N, Rall K, Sturm M, Kohlbacher O, Koch A, Riess O, Brucker SY, Schulze-Hentrich JM. Genome Sequencing and Transcriptome Profiling in Twins Discordant for Mayer-Rokitansky-Küster-Hauser Syndrome. Journal of Clinical Medicine. 11. PMID 36233463 DOI: 10.3390/jcm11195598  0.1
2021 Kittner M, Lamping M, Rieke DT, Götze J, Bajwa B, Jelas I, Rüter G, Hautow H, Sänger M, Habibi M, Zettwitz M, de Bortoli T, Ostermann L, Ševa J, Starlinger J, ... Kohlbacher O, et al. Annotation and initial evaluation of a large annotated German oncological corpus. Jamia Open. 4: ooab025. PMID 33898938 DOI: 10.1093/jamiaopen/ooab025  0.097
2021 Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, Bos KI, Forrest S, Hernández-Zaragoza DI, Sauter J, Solloch U, ... ... Kohlbacher O, et al. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Molecular Biology and Evolution. PMID 34002224 DOI: 10.1093/molbev/msab147  0.095
2008 Zhang F, Skoda MWA, Jacobs RMJ, Zorn S, Martin RA, Martin CM, Clark GF, Weggler S, Hildebrandt A, Kohlbacher O, Schreiber F. Reentrant condensation of proteins in solution induced by multivalent counterions Physical Review Letters. 101. DOI: 10.1103/PhysRevLett.101.148101  0.093
2021 Immel A, Pierini F, Rinne C, Meadows J, Barquera R, Szolek A, Susat J, Böhme L, Dose J, Bonczarowska J, Drummer C, Fuchs K, Ellinghaus D, Kässens JC, Furholt M, ... Kohlbacher O, et al. Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry. Communications Biology. 4: 113. PMID 33495542 DOI: 10.1038/s42003-020-01627-4  0.092
2019 Zhang L, Winkler S, Schlottmann FP, Kohlbacher O, Elias JE, Skotheim JM, Ewald JC. Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast. Frontiers in Cell and Developmental Biology. 7: 338. PMID 31921850 DOI: 10.3389/Fcell.2019.00338  0.081
2009 Schultheiss SJ, Busch W, Lohmann J, Kohlbacher O, Rätsch G. Abstracts from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology. June 27, 2009. Stockholm, Sweden. Bmc Bioinformatics. I1, O1-7, P1-7. PMID 19856525 DOI: 10.1186/1471-2105-10-s13-o1  0.079
2008 Reinert K, Conrad T, Kohlbacher O. Bioinformatics: Bioinformatics Support for Mass Spectrometric Quality Control Proteomics Sample Preparation. 423-432. DOI: 10.1002/9783527622832.ch13  0.079
2020 Scheidt T, Alka O, Gonczarowska-Jorge H, Gruber W, Rathje F, Dell'Aica M, Rurik M, Kohlbacher O, Zahedi RP, Aberger F, Huber CG. Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells. Cell Communication and Signaling : Ccs. 18: 99. PMID 32576205 DOI: 10.1186/s12964-020-00591-0  0.077
2021 Magunia H, Lederer S, Verbuecheln R, Gilot BJ, Koeppen M, Haeberle HA, Mirakaj V, Hofmann P, Marx G, Bickenbach J, Nohe B, Lay M, Spies C, Edel A, Schiefenhövel F, ... ... Kohlbacher O, et al. Machine learning identifies ICU outcome predictors in a multicenter COVID-19 cohort. Critical Care (London, England). 25: 295. PMID 34404458 DOI: 10.1186/s13054-021-03720-4  0.077
2012 Gesing S, Grunzke R, Krüger J, Birkenheuer G, Wewior M, Schäfer P, Schuller B, Schuster J, Herres-Pawlis S, Breuers S, Balaskó Á, Kozlovszky M, Fabri AS, Packschies L, Kacsuk P, ... ... Kohlbacher O, et al. A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics Journal of Grid Computing. 10: 769-790. DOI: 10.1007/s10723-012-9247-y  0.075
2011 Toussaint NC, Feldhahn M, Ziehm M, Stevanović S, Kohlbacher O. T-cell epitope prediction based on self-tolerance 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 584-588. DOI: 10.1145/2147805.2147905  0.072
2023 Mühlenbruch L, Abou-Kors T, Dubbelaar ML, Bichmann L, Kohlbacher O, Bens M, Thomas J, Ezić J, Kraus JM, Kestler HA, von Witzleben A, Mytilineos J, Fürst D, Engelhardt D, Doescher J, et al. The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination. British Journal of Cancer. 1-11. PMID 36823366 DOI: 10.1038/s41416-023-02197-y  0.068
2023 Renovanz M, Kurz SC, Rieger J, Walter B, Becker H, Hille H, Bombach P, Rieger D, Grosse L, Häusser L, Skardelly M, Merk DJ, Paulsen F, Hoffmann E, Gani C, ... ... Kohlbacher O, et al. Clinical outcome of biomarker-guided therapies in adult patients with tumors of the nervous system. Neuro-Oncology Advances. 5: vdad012. PMID 36915613 DOI: 10.1093/noajnl/vdad012  0.066
2023 Schönecker S, Hoffmann V, Albashiti F, Thasler R, Hagedorn M, Louiset ML, Kopczak A, Rösler J, Baki E, Wunderlich S, Kohlmayer F, Kuhn K, Boeker M, Tünnerhoff J, Poli S, ... ... Kohlbacher O, et al. PREDICT-juvenile-stroke: PRospective evaluation of a prediction score determining individual clinical outcome three months after ischemic stroke in young adults - a study protocol. Bmc Neurology. 23: 2. PMID 36597038 DOI: 10.1186/s12883-022-03003-7  0.065
2019 Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, ... Kohlbacher O, et al. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000research. 8. PMID 33163154 DOI: 10.12688/f1000research.20244.2  0.065
2021 Völkel G, Fürstberger A, Schwab JD, Werle SD, Ikonomi N, Gscheidmeier T, Kraus JM, Groß A, Holderried M, Balig J, Jobst F, Kuhn P, Kuhn KA, Kohlbacher O, Kaisers UX, et al. Patient empowerment during the COVID-19 pandemic: Ensuring safe and fast communication of test results. Journal of Medical Internet Research. PMID 33999836 DOI: 10.2196/27348  0.064
2006 Kerzmann A, Neumann D, Kohlbacher O. SLICK — Scoring and Energy Functions for Protein—Carbohydrate Interactions. Cheminform. 37. DOI: 10.1002/CHIN.200641209  0.064
2020 Kapsner LA, Kampf MO, Seuchter SA, Gruendner J, Gulden C, Mate S, Mang JM, Schüttler C, Deppenwiese N, Krause L, Zöller D, Balig J, Fuchs T, Fischer P, Haverkamp C, ... ... Kohlbacher O, et al. Reduced Rate of Inpatient Hospital Admissions in 18 German University Hospitals During the COVID-19 Lockdown. Frontiers in Public Health. 8: 594117. PMID 33520914 DOI: 10.3389/fpubh.2020.594117  0.058
2021 Völkel G, Fürstberger A, Schwab JD, Werle SD, Ikonomi N, Gscheidmeier T, Kraus JM, Groß A, Holderried M, Balig J, Jobst F, Kuhn P, Kuhn KA, Kohlbacher O, Kaisers UX, et al. Metadata Correction: Patient Empowerment During the COVID-19 Pandemic by Ensuring Safe and Fast Communication of Test Results: Implementation and Performance of a Tracking System. Journal of Medical Internet Research. 23: e31253. PMID 34152993 DOI: 10.2196/31253  0.051
2014 Kohlbacher O, Schreiber F, Ward MO. Multivariate networks in the life sciences Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8380: 61-73. DOI: 10.1007/978-3-319-06793-3_4  0.048
2021 Lang C, Weber N, Möller M, Schramm L, Schelm S, Kohlbacher O, Fischer M. Genetic authentication: Differentiation of hazelnut cultivars using polymorphic sites of the chloroplast genome Food Control. 130: 108344. DOI: 10.1016/J.FOODCONT.2021.108344  0.047
2022 Blum C, Baur D, Achauer LC, Berens P, Biergans S, Erb M, Hömberg V, Huang Z, Kohlbacher O, Liepert J, Lindig T, Lohmann G, Macke JH, Römhild J, Rösinger-Hein C, et al. Personalized neurorehabilitative precision medicine: from data to therapies (MWKNeuroReha) - a multi-centre prospective observational clinical trial to predict long-term outcome of patients with acute motor stroke. Bmc Neurology. 22: 238. PMID 35773640 DOI: 10.1186/s12883-022-02759-2  0.045
2019 Winkler I, Bitter C, Winkler S, Weichenhan D, Thavamani A, Hengstler JG, Borkham-Kamphorst E, Kohlbacher O, Plass C, Geffers R, Weiskirchen R, Nordheim A. Identification of Ppar-modulated miRNA hubs that target the fibrotic tumor microenvironment. Proceedings of the National Academy of Sciences of the United States of America. PMID 31871210 DOI: 10.1073/Pnas.1909145117  0.044
2021 Arndt M, Rurik M, Drees A, Ahlers C, Feldmann S, Kohlbacher O, Fischer M. Food authentication: Determination of the geographical origin of almonds (Prunus dulcis Mill.) via near-infrared spectroscopy Microchemical Journal. 160: 105702. DOI: 10.1016/j.microc.2020.105702  0.021
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