| 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 |
|
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