Publications

297 entries « 2 of 6 »

Griss, Johannes; Perez-Riverol, Yasset; Lewis, Steve; Tabb, David L; Dianes, José A; del-Toro, Noemi; Rurik, Marc; Walzer, Mathias M; Kohlbacher, Oliver; Hermjakob, Henning; Wang, Rui; Vizcaíno, Juan Antonio

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

Nat. Methods, 13 (8), pp. 651-656, 2016.

(Abstract | Links | BibTeX)

Ranninger, Christina; Schmidt, Lukas E; Rurik, Marc; Limonciel, Alice; Jennings, Paul; Kohlbacher, Oliver; Huber, Christian G

Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry

Anal. Chim. Acta, 930 , pp. 13-22, 2016.

(Abstract | Links | BibTeX)

Perez-Riverol, Yasset; Gatto, Laurent; Wang, Rui; Sachsenberg, Timo; Uszkoreit, Julian; Leprevost, Felipe; Fufezan, Christian; Ternent, Tobias; Eglen, Stephen J; Katz, Daniel S S; Pollard, Tom J; Konovalov, Alexander; Flight, Robert M; Blin, Kai; Vizcaino, Juan Antonio

Ten Simple Rules for Taking Advantage of git and GitHub

bioRxiv, 2016.

(Abstract | Links | BibTeX)

Löffler, Markus; Chandra, Anoop P; Laske, Karoline; Schroeder, Christopher; Bonzheim, Irina; Hilke, Franz J; Kowalewski, Daniel J; Trautwein, Nico; Schuster, Heiko; Gründer, Marc; Walzer, Mathias; Mohr, Christopher; Nguyen, Huu-Phuc; Riess, Olaf; Bauer, Peter; Nahnsen, Sven; Königsrainer, Alfred; Nadalina, Silvio; Zieker, Derek; Glatzle, Jörg; Thiel, Karolin; Clasen, Stephan; Bösmüller, Hans; Fend, Falko; Kohlbacher, Oliver; Gouttefangeas, Cecile; Stevanovic, Stefan; Rammensee, Hans-Georg

Personalized peptide vaccine induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient

J. Hepatol., 65 (4), pp. 849-55, 2016.

(Abstract | Links | BibTeX)

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

OpenMS: A flexible open-source software platform for mass spectrometry data analysis

Nat. Methods, 13 (9), pp. 741-748, 2016.

(Abstract | Links | BibTeX)

Veit, Johannes; Sachsenberg, Timo; Chernev, Alexsandr; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver

LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer

J. Proteome Res., 15 (9), pp. 3441-8., 2016.

(Abstract | Links | BibTeX)

Boyles, Matthe; Ranninger, Christina; Reischl, Roland; Rurik, Marc; Tessadri, Richard; Kohlbacher, Oliver; Duschl, Albert; Huber, Christian

Copper oxide nanoparticle toxicity profiling using untargeted metabolomics

Part. Fiber Toxicol., 13 , pp. 49, 2016.

(Abstract | Links | BibTeX)

Nicoludis, John M; Vogt, Bennett E; Green, Anna G; Schärfe, Charlotta PI; Marks, Debora S; Gaudet, Rachelle

Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4

eLife, 5 , pp. e18449, 2016.

(Abstract | Links | BibTeX)

Krüger, Jens; Thiel, Philipp; Merelli, Ivan; Grunzke, Richard; Gesing, Sandra

Portals and Web-based Resources for Virtual Screening.

Curr Drug Targets, 2016, (automatic medline import).

(Abstract | Links | BibTeX)

Hong, Henoch S; Koch, Sven D; Scheel, Birgit; Gnad-Vogt, Ulrike; Schröder, Andreas; Kallen, Karl-Josef; Wiegand, Volker; Backert, Linus; Kohlbacher, Oliver; Hoerr, Ingmar; Fotin-Mleczek, Mariola; Billingsley, James M

Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy

Oncoimmunol., 5 (12), pp. e1249560., 2016.

(Abstract | Links | BibTeX)

Thijssen, Bram; Dijkstra, Tjeerd; Heskes, Tom; Wessels, Lodewyk

BCM: toolkit for Bayesian analysis of Computational Models using samplers

BMC Systems Biology, 10:100 , 2016.

(Abstract | Links | BibTeX)

Dietsche, Tobias; Mebrhatu, Mehari Tesfazgi; Brunner, Matthias J; Abrusci, Patrizia; Yan, Jun; Franz-Wachtel, Mirita; Schärfe, Charlotta; Zilkenat, Susann; Grin, Iwan; Galán, Jorge E; Kohlbacher, Oliver; Lea, Susan; Macek, Boris; Marlovits, Thomas C; Robinson, Carol; Wagner, Samuel

Structural and functional characterization of the bacterial type III secretion export apparatus

PLoS Pathogens, 12 (12), pp. e1006071., 2016.

(Abstract | Links | BibTeX)

Krüger, Jens; Kohlbacher, Oliver

Containerization and wrapping of a mass spectra prediction workflow

2016.

(Abstract | Links | BibTeX)

Aebersold, Rudolf; Kohlbacher, Oliver; Vitek, Olga

Computational Mass Spectrometry (Dagstuhl Seminar 15351)

Dagstuhl Reports, 5 (8), pp. 9–33, 2016, ISSN: 2192-5283.

(Links | BibTeX)

Hildebrandt, Anna Katharina; Stöckel, Daniel; Fischer, Nina; de la Trevino, Luis Garza; Krüger, Jens; Nickels, Stefan; Röttig, Marc; Schärfe, Charlotta; Schumann, Marcel; Thiel, Philipp; Lenhof, Hans-Peter; Kohlbacher, Oliver; Hildebrandt, Andreas

ballaxy: web services for structural bioinformatics

Bioinformatics, 31 (1), pp. 121-2, 2015.

(Abstract | Links | BibTeX)

Proikas-Cezanne, Tassula; Takacs, Zsuzsanna; Dönnes, Pierre; Kohlbacher, Oliver

WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome

J. Cell Sci., 128 (2), pp. 207-217, 2015.

(Abstract | Links | BibTeX)

Thost, Ann-Kathrin; Dönnes, Pierre; Kohlbacher, Oliver; Proikas-Cezanne, Tassula

Fluorescence-based imaging of autophagy progression by human WIPI beta-propeller protein detection in single cells

Methods, 75 , pp. 69-78, 2015.

(Abstract | Links | BibTeX)

Sachsenberg, Timo; Herbst, Florian-Alexander; Taubert, Martin; Kermer, René; Jehmlich, Nico; von Bergen, Martin; Seifert, Jana; Kohlbacher, Oliver

MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

J. Proteome Res., 14 (2), pp. 619-27, 2015.

(Abstract | Links | BibTeX)

Gerasch, Andreas; Küntzer, Jan; Niermann, Peter; Stöckel, Daniel; Kohlbacher, Oliver; Lenhof, Hans-Peter

Network-based interactive navigation and analysis of large biological datasets

it - Information Technology, 57 (1), pp. 37-48, 2015.

(Abstract | Links | BibTeX)

Ziller, Michael J; Edri, Reuven; Yaffe, Yakey; Donaghey, Julie; Pop, Ramona; Mallard, William; Issner, Robbyn; Gifford, Casey A; Goren, Alon; Xing, Jeffrey; Gu, Hongcang; Cacchiarelli, Davide; Tsankov, Alexander M; Epstein, Charles; Rinn, John L; Mikkelsen, Tarjei S; Kohlbacher, Oliver; Gnirke, Andreas; Bernstein, Bradley E; Elkabetz, Yechiel; Meissner, Alexander

Dissecting neural differentiation regulatory networks through epigenetic footprinting.

Nature, 518 , pp. 355-359, 2015.

(Abstract | Links | BibTeX)

Aiche, Stephan; Sachsenberg, Timo; Kenar, Erhan; Walzer, Mathias; Wiswedel, Bernd; Kristl, Theresa; Boyles, Matthew; Duschl, Albert; Huber, Christian; Berthold, Michael; Reinert, Knut; Kohlbacher, Oliver

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

Proteomics, 15 (8), pp. 1443-7, 2015.

(Abstract | Links | BibTeX)

Schubert, Benjamin; Brachvogel, Hans-Philipp; Jürges, Christopher; Kohlbacher, Oliver

EpiToolKit – A Web-based Workbench for Vaccine Design

Bioinformatics, 31 (13), pp. 2211-3, 2015.

(Abstract | Links | BibTeX)

Friedrich, Andreas; Kenar, Erhan; Kohlbacher, Oliver; Nahnsen, Sven

Intuitive Web-based Experimental Design for High-throughput Biomedical Data

BioMed Res Int, 2015 , pp. 958302, 2015.

(Abstract | Links | BibTeX)

Martens, Lennart; Kohlbacher, Oliver; Weintraub, Susan T

Managing Expectations when Publishing Tools and Methods for Computational Proteomics

J. Proteome Res., 14 (5), pp. 2002-4, 2015.

(Abstract | Links | BibTeX)

Uszkoreit, Julian; Maerkens, Alexandra; Perez-Riverol, Yasset; Meyer, Helmut E; Marcus, Katrin; Stephan, Christian; Kohlbacher, Oliver; Eisenacher, Martin

PIA - An intuitive protein inference engine with a web-based user interface

J. Proteome Res., 14 (7), pp. 2988-97, 2015.

(Abstract | Links | BibTeX)

Sharma, Kundan; Hrle, Ajla; Kramer, Katharina; Sachsenberg, Timo; Staals, Raymond H J; Randau, Lennart; Marchfelder, Anita; van der Oost, John; Kohlbacher, Oliver; Conti, Elena; Urlaub, Henning

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

Methods, pp. S1046-2023(15)00246-7, 2015.

(Abstract | Links | BibTeX)

Ranninger, Christina; Rurik, Marc; Limonciel, Alice; Ruzek, Silke; Reischl, Roland; Wilmes, Anja; Jennings, Paul; Hewitt, Philip; Dekant, Wolfgang; Kohlbacher, Oliver; Huber, Christian G

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

J. Biol. Chem., 290 (31), pp. 19121-32, 2015.

(Abstract | Links | BibTeX)

Simha, Ramanuja; Briesemeister, Sebastian; Kohlbacher, Oliver; Shatkay, Hagit

Protein (Multi-)Location Prediction: Utilizing Interdependencies via a Generative Model

Bioinformatics, 31 (12), pp. i365-i374, 2015.

(Abstract | Links | BibTeX)

Walz, Simon; Stickel, Juliane Sarah; Kowalewski, Daniel Johannes; Schuster, Heiko; Weisel, Katja; Backert, Linus; Kahn, Stefan; Nelde, Annika; Stroh, Tatjana; Handel, Martina; Kohlbacher, Oliver; Kanz, Lothar; Salih, Helmut Rainer; Rammensee, Hans-Georg; Stevanovic, Stefan

The antigenic landscape of multiple myeloma: mass spectrometry (re-)defines targets for T-cell based immunotherapy

Blood, 126 (10), pp. 1203-13, 2015.

(Abstract | Links | BibTeX)

Aicheler, Fabian; Li, Jia; Lehmann, Rainer; Xu, Guowang; Kohlbacher, Oliver

Retention Time Prediction Improves Identification in Non-Targeted Lipidomics Approaches

Anal. Chem., 87 (15), pp. 7698-704, 2015.

(Abstract | Links | BibTeX)

de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

DNA-binding proteins from marine bacteria expand the sequence diversity of known TALE-like repeats

Nucl. Acids Res, 43 (20), pp. 10065-80, 2015.

(Abstract | Links | BibTeX)

Venturelli, Sascha; Belz, Regina G; Kämper, Andreas; Berger, Alexandra; von Horn, Kyra; Wegner, André; Böcker, Alexander; Zabulon, Gérald; Langenecker, Tobias; Kohlbacher, Oliver; Barneche, Fredy; Weigel, Detlef; Lauer, Ulrich M; Bitzer, Michael; Becker, Claude

Plants release precursors of potent histone deacetylase inhibitors to suppress growth of competitors

Plant Cell, 27 (11), pp. 3175-89., 2015.

(Abstract | Links | BibTeX)

Zaman, Uzma; Richter, Florian M; Hofele, Romina; Kramer, Katharina; Sachsenberg, Timo; Lenz, Christof; Urlaub, Henning

Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions

Mol. Cell. Prot., 14 (12), pp. 3196-210, 2015.

(Abstract | Links | BibTeX)

Backert, Linus; Kohlbacher, Oliver

Immunoinformatics and epitope prediction in the age of genomic medicine

Genome Med., 7 (1), pp. 119, 2015.

(Abstract | Links | BibTeX)

Kowalewski, Daniel J; Schuster, Heiko; Backert, Linus; Berlin, Claudia; Kahn, Stefan; Kanz, Lothar; Salih, Helmut R; Rammensee, Hans-Georg; Stevanovic, Stefan; Stickel, Juliane Sarah

HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)

Proceedings of the National Academy of Sciences of the United States of America, 112 (2), pp. E166–E175, 2015.

(Abstract | Links | BibTeX)

Bier, David; Thiel, Philipp; Briels, Jeroen; Ottmann, Christian

Stabilization of Protein-Protein Interactions in chemical biology and drug discovery.

Prog Biophys Mol Biol, 119 (1), pp. 10-9, 2015, (automatic medline import).

(Abstract | Links | BibTeX)

Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P.I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity

Structure, 23 (11), pp. 2087 - 2098, 2015.

(Abstract | Links | BibTeX)

Kenar, Erhan; Franken, Holger; Forcisi, Sara; Wörmann, Kilian; Häring, Hans-Ulrich; Lehmann, Rainer; Schmitt-Kopplin, Philippe; Zell, Andreas; Kohlbacher, Oliver

Automated Label-Free Quantification of Metabolites from LC-MS Data

Mol. Cell. Prot., 13 (1), pp. 348-59, 2014.

(Abstract | Links | BibTeX)

Beck, Florian; Geiger, Jörg; Gambaryan, Stepan; Veit, Johannes; Vaudel, Marc; Nollau, Peter; Kohlbacher, Oliver; Martens, Lennart; Walter, Ulrich; Sickmann, Albert; Zahedi, René P

Time-resolved characterization of cAMP/PKA-dependant signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways

Blood, 123 (4), pp. e1-e10, 2014.

(Abstract | Links | BibTeX)

Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver

Rebuilding KEGG Maps - An integrative approach for visual analytics of metabolic networks

Pacific Visualization Symposium (PacificVis), 2014 IEEE, pp. 97-104, IEEE 2014.

(Abstract | Links | BibTeX)

Gerasch, Andreas; Faber, Daniel; Küntzer, Jan; Niermann, Peter; Kohlbacher, Oliver; Lenhof, Hans-Peter; Kaufmann, Michael

BiNA: a visual analytics tool for biological network data

PLoS ONE, 9 (2), pp. e87397, 2014.

(Abstract | Links | BibTeX)

Kohlbacher, Oliver; Schreiber, Falk; Ward, Matthew O

Multivariate Networks in the Life Sciences

Multivariate Network Visualization 2013, Chapter 4, pp. 61-73, Springer, 2014.

(Links | BibTeX)

Roberts, Jonathan C; Yang, Jing; Kohlbacher, Oliver; Ward, Matthew O; Zhou, Michelle X

Novel Visual Metaphors for Multivariate Networks

Multivariate Network Visualization 2013, Chapter 7, pp. 127-147, Springer, 2014.

(Links | BibTeX)

Aebersold, Rudolph; Kohlbacher, Oliver; Vitek, Olga (Ed.)

Report from Dagstuhl Seminar 13491 Computational Mass Spectrometry

Dagstuhl Publishing, Dagstuhl, Germany, 3 (12), 2014.

(Abstract | Links | BibTeX)

Menzel, Moritz; Meckbach, Diana; Weide, Benjamin; Toussaint, Nora C; Schilbach, Karin; Noor, Seema; Eigentler, Thomas; Ikenberg, Kristian; Busch, Christian; Qunitanilla-Martinez, Leticia; Göke, Antonia; Göke, Friederike; Handgretinger, Rupert; Ottmann, Christian; Bastian, Boris; Garbe, Claus; Röcken, Martin; Perner, Sven; Kohlbacher, Oliver; Bauer, Jürgen

In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival

Pigment Cell Melanoma Res., 23 (3), pp. E45, 2014.

(Abstract | Links | BibTeX)

Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper Velgaard; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaino, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

qcML: an exchange format for quality control metrics from mass spectrometry experiments

Mol. Cell. Prot., 13 (8), pp. 1905-13, 2014.

(Abstract | Links | BibTeX)

Krüger, Jens; Grunzke, Richard; Gesing, Sandra; Breuers, Sebastian; Brinkmann, André; de la Garza, Luis; Kohlbacher, Oliver; Kruse, Martin; Nagel, Wolfgang; Packschies, Lars; Müller-Pfefferkorn, Ralph; Schärfe, Charlotta; Steinke, Thomas; Schlemmer, Tobias; Warzecha, Klaus; Zink, Andreas; Herres-Pawlis, Sonja

The MoSGrid Science Gateway – A Complete Solution for Molecular Simulations

J. Chem. Theor. Comput., 10 (6), pp. 2232-2245, 2014.

(Abstract | Links | BibTeX)

Wagner, Robert; Li, Jia; Kenar, Erhan; Kohlbacher, Oliver; Machicao, Fausto; Häring, Hans-Ulrich; Fritsche, Andreas; Xu, Guowang; Lehmann, Rainer

Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146

Sci. Rep., 4 , pp. 5296, 2014.

(Abstract | Links | BibTeX)

Krüger, Jens; Grunzke, Richard; Herres-Pawlies, Sonja; de la Garza, Luis; Kohlbacher, Oliver; Nagel, Wolfgang E; Gesing, Sandra

Performance Studies on Distributed Virtual Screening

Biomed Res Int, 2014 , pp. 624024, 2014.

(Abstract | Links | BibTeX)

Griss, Johannes; Jones, Andrew R; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G; Salek, Reza M; Steinbeck, Christhop; Neuhauser, Nadin; Cox, Jürgen; Neumann, Steffen; Fan, Jun; Reisinger, Florian; Xu, Qing-Wei; Bandeira, Nuno; Xenarios, Ioannis; Kohlbacher, Oliver; Vizcaino, Juan Antonio; Hermjakob, Henning

The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience

Mol. Cell. Prot., pp. mcp.O113.036681, 2014.

(Abstract | Links | BibTeX)

297 entries « 2 of 6 »
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