Publications

320 entries « 1 of 7 »

Identifying Đisease-Causing Mutations with Privacy Protection

Bioinformatics, 2020.

(Abstract | BibTeX)

Gleim, L C; Karim, M R; Zimmermann, L; Kohlbacher, O; Stenzhorn, H; Decker, S; Beyan, O

Enabling ad-hoc reuse of private data repositories through schema extraction

J Biomed Semantics, 11 (1), pp. 6, 2020.

(Abstract | BibTeX)

Starke, R; Oliphant, K; Jehmlich, N; Sch?pe, S S; Sachsenberg, T; Kohlbacher, O; Allen-Vercoe, E; von Bergen, M

Corrigendum to Ŧracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities

J Proteomics, 224 , pp. 103829, 2020.

(BibTeX)

Scheidt, T; Alka, O; Gonczarowska-Jorge, H; Gruber, W; Rathje, F; DellÁica, M; Rurik, M; Kohlbacher, O; Zahedi, R P; Aberger, F; Huber, C G

Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells

Cell Commun. Signal, 18 (1), pp. 99, 2020.

(Abstract | BibTeX)

Samonig, L; Loipetzberger, A; Bl?chl, C; Rurik, M; Kohlbacher, O; Aberger, F; Huber, C G

Proteins and Molecular Pathways Relevant for the Malignant Properties of Ŧumor-Initiating Pancreatic Cancer Cells

Cells, 9 (6), 2020.

(Abstract | BibTeX)

Starke, R; Oliphant, K; Jehmlich, N; Sch?pe, S S; Sachsenberg, T; Kohlbacher, O; Allen-Vercoe, E; von Bergen, M

Ŧracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities

J Proteomics, 222 , pp. 103791, 2020.

(Abstract | BibTeX)

Pfeuffer Julianus; Sachsenberg, Timo; Dijkstra Tjeerd Serang Oliver; Reinert Knut; Kohlbacher Oliver M H ;

EPIFANY - A method for efficient high-confidence protein inference

J. Proteome Res., 2020.

(Abstract | Links | BibTeX)

Hentrich, T; Koch, A; Weber, N; Kilzheimer, A; Burkhardt, S; Rall, K; Casadei, N; Kohlbacher, O; Riess, O; Schulze-Hentrich, JM; Brucker, SY

The endometrial transcription landscape of MRKH syndrome

bioRxiv, 2020.

(Abstract | Links | BibTeX)

Voelkel, Gunnar; Fuerstberger, Axel; Schwab, Julian D; Kuehlwein, Silke D; Gscheidmeier, Thomas; Kraus, Johann M; Gross, Alexander; Kohlmayer, Florian; Kuhn, Peter; Kuhn, Klaus A; Kohlbacher, Oliver; Seufferlein, Thomas; Kestler, Hans A

A secure and rapid query-software for COVID-19 test results that can easily be integrated into the clinical workflow to avoid communication overload

medRxiv, 2020.

(Abstract | Links | BibTeX)

Nothias, L F; Petras, D; Schmid, R; D?hrkop, K; Rainer, J; Sarvepalli, A; Protsyuk, I; Ernst, M; Tsugawa, H; Fleischauer, M; Aicheler, F; Aksenov, A A; Alka, O; Allard, P M; Barsch, A; Cachet, X; Caraballo-Rodriguez, A M; Silva, Da R R; Dang, T; Garg, N; Gauglitz, J M; Gurevich, A; Isaac, G; Jarmusch, A K; Kamen?k, Z; Kang, K B; Kessler, N; Koester, I; Korf, A; Gouellec, Le A; Ludwig, M; H, Martin C; McCall, L I; McSayles, J; Meyer, S W; Mohimani, H; Morsy, M; Moyne, O; Neumann, S; Neuweger, H; Nguyen, N H; Nothias-Esposito, M; Paolini, J; Phelan, V V; Pluskal, T; Quinn, R A; Rogers, S; Shrestha, B; Tripathi, A; van der Hooft, J J J; Vargas, F; Weldon, K C; Witting, M; Yang, H; Zhang, Z; Zubeil, F; Kohlbacher, O; B?cker, S; Alexandrov, T; Bandeira, N; Wang, M; Dorrestein, P C

Feature-based molecular networking in the GNPS analysis environment

Nat. Methods, 2020.

(Abstract | BibTeX)

Jeong, K; Kim, J; Gaikwad, M; Hidayah, S N; Heikaus, L; Schl?ter, H; Kohlbacher, O

FLASĦĐeconv: Ultrafast, Ħigh-Quality Feature Đeconvolution for Ŧop-Đown Proteomics

Cell Syst, 10 (2), pp. 213–218, 2020.

(Abstract | BibTeX)

Wein, S; Andrews, B; Sachsenberg, T; Santos-Rosa, H; Kohlbacher, O; Kouzarides, T; Garcia, B A; Weisser, H

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Nat Commun, 11 (1), pp. 926, 2020.

(Abstract | BibTeX)

Lichao Zhang Sebastian Winkler, Fabian Schlottmann Oliver Kohlbacher Josh Elias Jan Skotheim Jennifer Ewald P E M C

Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast

Front. Cell Dev. Biol., 2019.

(Abstract | Links | BibTeX)

Bilich, Tatjana; Nelde, Annika; Bichmann, Leon; Roerden, Malte; Salih, Helmut R; Kowalewski, Daniel J; Schuster, Heiko; Tsou, Chih-Chiang; Marcu, Ana; Neidert, Marian C; Lübke, Maren; Rieth, Jonas; Schemionek, Mirle; Brümmendorf, Tim H; Vucinic, Vladan; Niederwieser, Dietger; Bauer, Jens; Märklin, Melanie; Peper, Janet K; Klein, Reinhild; Kanz, Lothar; Rammensee, Hans-Georg; Stevanovic, Stefan; Walz, Juliane S

The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy

Blood, 133 (6), pp. 550-565, 2019.

(Abstract | Links | BibTeX)

Löffler, Markus W; Mohr, Christopher; Bichmann, Leon; Freudenmann, Lena Katharina; Walzer, Mathias; Schroeder, Christopher W; Trautwein, Nico; Hilke, Franz J; Zinser, Raphael S; Mühlenbruch, Lena; Kowalewski, Daniel J; Schuster, Heiko; Sturm, Marc; Matthes, Jakob; Riess, Olaf; Czemmel, Stefan; Nahnsen, Sven; Königsrainer, Ingmar; Thiel, Karolin; Nadalin, Silvio; Beckert, Stefan; Bösmüller, Hans; Fend, Falko; Velic, Ana; Macek, Boris; Haen, Sebastian P; Buonaguro, Luigi; Kohlbacher, Oliver; Königsrainer, Alfred; Rammensee, Hans-Georg; Consortium, The HepaVac

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

Genome Med., Forthcoming.

(Abstract | BibTeX)

Ali, Muhammed; Foldvari, Zsofia; Giannakopoulou, Eirini; Böschen, Maxi-Lu; Strønen, Erlend; Yang, Weiwen; Toebes, Mireille; Schubert, Benjamin; Kohlbacher, Oliver; Schumacher, Ton N; Olweus, Johanna

Induction Of Neoantigen Reactive T Cells From Healthy Donors

Nat. Protocols, Forthcoming.

(Abstract | Links | BibTeX)

Alka, Oliver; Sachsenberg, Timo; Bichmann, Leon; Pfeuffer, Julianus; Weisser, Hendrik; Wein, Samuel; Netz, Eugen; Rurik, Marc; Kohlbacher, Oliver; Rost, Hannes

OpenMS for open source analysis of mass spectrometric data

PeerJ Preprints, 7 , pp. e27766v1, 2019, ISSN: 2167-9843.

(Links | BibTeX)

Cain, Nicolas; Alka, Oliver; Segelke, Torben; von Wuthenau, Kristian; Kohlbacher, Oliver; Fischer, Markus

Food fingerprinting: Mass spectrometric determination of the cocoa shell content (Theobroma cacao L.) in cocoa products by HPLC-QTOF-MS

Food Chemistry, 298 , pp. 125013, 2019, ISSN: 0308-8146.

(Abstract | Links | BibTeX)

Licha, David; Vidali, Silvia; Aminzadeh-Gohari, Sepideh; Alka, Oliver; Breitkreuz, Leander; Kohlbacher, Oliver; Reischl, Roland J; Feichtinger, René G; Kofler, Barbara; Huber, Christian G

Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models

International Journal of Molecular Sciences, 20 (16), 2019, ISSN: 1422-0067.

(Abstract | Links | BibTeX)

Bichmann, Leon; Nelde, Annika; Ghosh, Michael; Heumos, Lukas; Mohr, Christopher; Peltzer, Alexander; Kuchenbecker, Leon; Sachsenberg, Timo; Walz, Juliane S; Stevanović, Stefan; Rammensee, Hans-Georg; Kohlbacher, Oliver

MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics

Journal of Proteome Research, 18 (11), pp. 3876-3884, 2019, (PMID: 31589052).

(Links | BibTeX)

Sürün, Bilge; Schärfe, Charlotta P I; Divine, Mathew R; Heinrich, Julian; Toussaint, Nora C; Zimmermann, Lukas; Beha, Janina; Kohlbacher, Oliver

ClinVAP: A reporting strategy from variants to therapeutic options

Bioinformatics, 2019, ISSN: 1367-4803, (btz924).

(Abstract | Links | BibTeX)

Lübke, Maren; Spalt, Stefanie; Kowalewski, Daniel J; Zimmermann, Cosima; Bauersfeld, Liane; Nelde, Annika; Bichmann, Leon; Marcu, Ana; Peper, Janet Kerstin; Kohlbacher, Oliver; Walz, Juliane S; Le-Trilling, Vu Thuy Khanh; Hengel, Hartmut; Rammensee, Hans-Georg; Stevanović, Stefan; Halenius, Anne

Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models

The Journal of Experimental Medicine, 217 (3), 2019, ISSN: 0022-1007, (e20191164).

(Abstract | Links | BibTeX)

Creydt, Marina; Hudzik, Daria; Rurik, Marc; Kohlbacher, Oliver; Fischer, Markus

Food Authentication: Small Molecule Profiling as a Tool for the Geographic Discrimination of German White Asparagus

J. Agric. Food Chem., 66 (50), pp. 13328-13339, 2018.

(Abstract | Links | BibTeX)

Rehm, Markus; Apweiler, Rolf; Beissbarth, Tim; Berthold, Michael; Blüthgen, Nils; Burmeister, Yvonne; Dammann, Olaf; Deutsch, Andreas; Feuerhake, Friederike; Franke, Andre; Hasenauer, Jan; Hoffmann, Steve; Höfer, Thomas; Jansen, Peter; Kaderali, Lars; Klingmüller, Ursula; Koch, Ina; Kohlbacher, Oliver; Kuepfer, Lars; Lammert, Frank; Maier, Dieter; Pfeifer, Nico; Radde, Nicole; Roeder, Ingo; Saez-Rodriguez, Julio; Sax, Ulrich; Schmeck, Bernd; Schuppert, Andreas; Seilheimer, Bernd; Theis, Fabian; Vera-Gonzáles, Julio; Wolkenhauer, Olaf

Whither Systems Medicine?

Exp. Mol. Med., 50 (3), pp. e453, 2018.

(Abstract | Links | BibTeX)

Schubert, Benjamin; Schärfe, Charlotta; Dönnes, Pierre; Hopf, Thomas; Marks, Debora; Kohlbacher, Oliver

Population-specific design of de-immunized protein biotherapeutics

PLoS Comput Biol, 14 (3), pp. (3):e1005983, 2018.

(Abstract | Links | BibTeX)

Mohr, Christopher; Friedrich, Andreas; Wojnar, David; Kenar, Erhan; Polatkan, Aydin-Can; Codrea, Marius Cosmin; Czemmel, Stefan; Kohlbacher, Oliver; Nahnsen, Sven

qPortal: A platform for data-driven biomedical research

PLoS ONE, 13 (1), pp. e0191603, 2018.

(Abstract | Links | BibTeX)

Choobdar, Sarvenaz; Ahsen, Mehmet E; Crawford, Jake; Tomasoni, Mattia; Lamparter, David; Lin, Junyuan; Hescott, Benjamin; Hu, Xiaozhe; Mercer, Johnathan; Natoli, Ted; Narayan, Rajiv; Aravind, ; Subramanian, ; Stolovitzky, Gustavo; Kutalik, Zoltán; Lage, Kasper; Slonim, Donna K; Saez-Rodriguez, Julio; Cowen, Lenore J; Bergmann, Sven; Marbach, Daniel

Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases

bioRxiv, 2018.

(Abstract | Links | BibTeX)

Brunk, Elizabeth; Sahoo, Swagatika; Zielinski, Daniel C; Altunkaya, Ali; Dräger, Andreas; Mih, Nathan; Gatto, Francesco; Nilsson, Avlant; Gonzalez, German Andres Preciat; Aurich, Maike Kathrin; Prlić, Andreas; Sastry, Anand; Danielsdottir, Anna D; Heinken, Almut; Noronha, Alberto; Rose, Peter W; Burley, Stephen K; Fleming, Ronan M T; Nielsen, Jens; Thiele, Ines; Palsson, Bernhard O

Recon3D enables a three-dimensional view of gene variation in human metabolism

Nature Biotechnology, 2018.

(Abstract | Links | BibTeX)

Thijssen, Bram; Dijkstra, Tjeerd M H; Heskes, Tom; Wessels, Lodewyk F A

Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates

Bioinformatics, 34 (5), pp. 803-811, 2018.

(Abstract | Links | BibTeX)

Lederer, Simone; Dijkstra, Tjeerd M H; Heskes, Tom

Additive Dose Response Models: Explicit Formulation and the Loewe Additivity Consistency Condition

Frontiers in Pharmacology, 9 (31), 2018.

(Abstract | Links | BibTeX)

Löffler, Markus W; Kowalewski, Daniel J; Backert, Linus; Bernhardt, Jörg; Adam, Patrick; Schuster, Heiko; Dengler, Florian; Backes, Daniel; Kopp, Hans-Georg; Beckert, Stefan; Wagner, Silvia; Königsrainer, Ingmar; Kohlbacher, Oliver; Kanz, Lothar; Königsrainer, Alfred; Rammensee, Hans-Georg; Stevanovic, Stefan; Haen, Sebastian P

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

Cancer Res., 78 (16), pp. 4627-4641, 2018.

(Abstract | Links | BibTeX)

Kahles, André; Lehmann, Kjong-Van; Toussaint, Nora C; Hüser, Matthias; Stark, Stefan; Sachsenberg, Timo; Stegle, Oliver; Kohlbacher, Oliver; Sander, Chris; Network, Gunnar TCGA PanCanAtlas; Rätsch,

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

Cancer Cell, 34 (2), pp. 211-224, 2018.

(Abstract | Links | BibTeX)

Fröhlich, Holger; Balling, Rudi; Beerenwinkel, Niko; Kohlbacher, Oliver; Kumar, Santosh; Lengauer, Thomas; Maathuis, Marloes; Moreau, Yves; Murphy, Susan; Przytycka, Teresa; Röst, Hannes; Rebhan, Michael; Schuppert, Andreas; Schwab, Matthias; Spang, Rainer; Stekhoven, Daniel; Sun, Jimeng; Ziemek, Daniel; Zupan, Blaz

From Hype to Reality: Data Science enabling Personalized Medicine

BMC Medicine, 16 , pp. 150, 2018.

(Abstract | Links | BibTeX)

Prasser, Fabian; Kohlbacher, Oliver; Mansmann, Ulrich; Bauer, Bernhard; Kuhn, Klaus A

Data Integration for Future Medicine (DIFUTURE) - An Architectural and Methodological Overview

Methods Inf Med, 57 (S01), pp. e57-r65, 2018.

(Abstract | Links | BibTeX)

Gleim, Lars Christoph; Karim, Md. Rezaul; Zimmermann, Lukas; Stenzhorn, Holger; Decker, Stefan; Beyan, Oya

Schema Extraction for Privacy Preserving Processing of Sensitive Data

MEPDaW-SeWeBMeDA-SWeTI 2018 Joint Proceedings of MEPDaW, SeWeBMeDA and SWeTI 2018, 2112 , CEUR Workshop Proceedings 2018.

(Abstract | Links | BibTeX)

Domingo-Calap, Pilar; Schubert, Benjamin; Joly, Mélanie; Solis, Morgane; Untrau, Meiggie; Carapito, Raphael; Georgel, Philippe; Caillard, Sophie; Fafi-Kremer, Samira; Paul, Nicodème; Kohlbacher, Oliver; González-Candelas, Fernando; Bahram, Seiamak

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

PLoS Pathogens, 14 (10), pp. e1007368, 2018.

(Abstract | Links | BibTeX)

Deutsch, Eric; Perez-Riverol, Yasset; Chalkley, Robert; Wilhelm, Mathias; Tate, Stephen; Sachsenberg, Timo; Walzer, Mathias; Käll, Lukas; Delanghe, Bernard; Böcker, Sebastian; Schymanski, Emma; Wilmes, Paul; Dorfer, Viktoria; Kuster, Bernhard; Volders, Pieter-Jan; Jehmlich, Nico; Vissers, Johannes; Wolan, Dennis; Wang, Ana; Mendoza, Luis; Shofstahl, Jim; Dowsey, Andrew; Griss, Johannes; Salek, Reza; Neumann, Steffen; Binz, Pierre-Alain; Lam, Henry; Vizcaíno, Juan; Bandeira, Nuno; Röst, Hannes

Expanding the use of spectral libraries in proteomics

Journal of Proteome Research, 2018.

(Abstract | Links | BibTeX)

Karim, Md. Rezaul; Nguyen, Binh-Phi; Zimmermann, Lukas; Kirsten, Toralf; Löbe, Matthias; Meineke, Frank; Stenzhorn, Holger; Kohlbacher, Oliver; Decker, Stefan; Beyan, Oya (Ed.)

A Distributed Analytics Platform to Execute FHIR based Phenotyping Algorithms

2018.

(BibTeX)

Wein, Samuel; Andrews, Byron; Sachsenberg, Timo; Santos-Rosa, Helena; Kohlbacher, Oliver; Kouzarides, Tony; Garcia, Benjamin A; Weisser, Hendrik

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

bioRxiv, 2018.

(Abstract | Links | BibTeX)

Halfmann, Marc; Stenzhorn, Holger; Gerjets, Peter; Kohlbacher, Oliver; Oestermeier, Uwe

User-Driven Development of a Novel Molecular Tumor Board Support Tool

Vidal, Sören AuerMaria-Esther (Ed.): DILS 2018: Data Integration in the Life Sciences, pp. 195-199, Springer, 2018.

(Abstract | Links | BibTeX)

Friedrich, Andreas; de la Garza, Luis; Kohlbacher, Oliver; Nahnsen, Sven

Interactive Visualization for Large-Scale Multi-factorial Research Designs

Auer, Maria-Esther Vidal Sören (Ed.): DILS 2018: Data Integration in the Life Sciences, pp. 75-84, 2018.

(Abstract | Links | BibTeX)

Audain, Enrique; Uszkoreit, Julian; Sachsenberg, Timo; Pfeuffer, Julianus; Liang, Xiao; Hermjakob, Henning; Sanchez, Aniel; Eisenacher, Martin; Reinert, Knut; Tabb, David L; Kohlbacher, Oliver; Perez-Riverol, Yasset

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics

J. Proteomics, 150 , pp. 170–182, 2017.

(Abstract | Links | BibTeX)

Backert, Linus; Kowalewski, Daniel; Walz, Simon; Schuster, Heiko; Berlin, Claudia; Neidert, Marian; Schemionek, Mirle; Brümmendorf, Tim Hendrik; Vicinic, Vladan; Niederwieser, Dietger; Kanz, Lothar; Salih, Helmut Rainer; Kohlbacher, Oliver; Weisel, Katja; Rammensee, Hans-Georg; Stevanovic, Stefan; Walz, Juliana Sarah

A meta-analysis of HLA peptidome composition in different hematological entities: Entity-specific dividing lines and

Oncotarget, 8 (27), pp. 43915-43924., 2017.

(Abstract | Links | BibTeX)

Haen, Sebastian P; Groh, Christiane; Schumm, Michael; Backert, Linus; Löffler, Markus W; Federmann, Birgit; Faul, Christoph; Dörfel, Daniela; Vogel, Wichard; Handgretinger, Rupert; Kanz, Lothar; Bethge, Wolfgang A

Haploidentical hematopoietic cell transplantation using in vitro T cell depleted grafts as salvage therapy in patients with disease relapse after prior allogeneic transplantation

Annals of Hematology, pp. 1-11, 2017.

(Abstract | Links | BibTeX)

Nelde, Annika; Kowalewski, Daniel J; Backert, Linus; Schuster, Heiko; Werner, Jan-Ole; Klein, Reinhild; Kohlbacher, Oliver; Kanz, Lothar; Salih, Helmut R; Rammensee, Hans-Georg; Stevanović, Stefan; Stickel, Juliane S

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

OncoImmunol., 5 (12), pp. e1249560, 2017.

(Abstract | Links | BibTeX)

Heimgärtner, Florian; Hettich, Stefan; Kohlbacher, Oliver; Menth, Michael

Scaling Home Automation to Public Buildings: A Distributed Multiuser Setup for OpenHAB 2

Global Internet of Things Summit (GIoTS) 2017, 2017.

(Abstract | Links | BibTeX)

Schubert, Benjamin; de la Garza, Luis; Mohr, Christopher; Walzer, Mathias; Kohlbacher, Oliver

ImmunoNodes - Graphical Development of Complex Immunoinformatics Workflows

BMC Bioinformatics, 18 (1), pp. 242, 2017.

(Abstract | Links | BibTeX)

Vizcaino, Juan Antonio; Mayer, Gerhard; Perkins, Simon R; Barnsnes, Harald; Vaudel, Marc; Perez-Riverol, Yasset; Ternent, Tobias; Uszkoreit, Julian; Eisenacher, Martin; Fischer, Lutz; Rappsilber, Juri; Netz, Eugen; Walzer, Mathias; Kohlbacher, Oliver; Leitner, Alexander; Chalkley, Robert J; Ghali, Fawaz; Martínez-Bartolomé, Salvador; Deutsch, Eric W; Jones, Andrew R

The mzIdentML data standard version 1.2, supporting advances in proteome informatics

Mol. Cell. Prot., 16 (7), pp. 1275-1285, 2017.

(Abstract | Links | BibTeX)

Pfeuffer, Julianus U; Sachsenberg, Timo; Alka, Oliver; Walzer, Mathias; Fillbrunn, Alexander; Nilse, Lars; Schilling, Oliver; Reinert, Knut; Kohlbacher, Oliver

OpenMS - A platform for reproducible analysis of mass spectrometry data

J. Biotechnol., pp. S0168-1656(17)30251-1, 2017.

(Abstract | Links | BibTeX)

Chevrette, Marc G; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R; Medema, Marnix H

SANDPUMA: Ensemble Predictions of Nonribosomal Peptide Chemistry Reveals Biosynthetic Diversity across Actinobacteria

Bioinformatics, 33 (20), pp. 3202-3210, 2017.

(Abstract | Links | BibTeX)

320 entries « 1 of 7 »

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