Bioinformatics

2024

MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0

Buur, L. M., Declercq, A., Strobl, M. T., Bouwmeester, R., Degroeve, S., Martens, L., Dorfer, V. & Gabriels, R., 16 Mar 2024, In: Journal of Proteome Research. 23, 8, p. 3200-3207 8 p.

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Ontology-based Multi-Perspective Process Mining in Laboratories: A Case Study

Mayrhuber, E. M., Helm, E. & Ehrlinger, L., 13 Apr 2024.

Research output: Contribution to conference › Paper › peer-review

Single molecule studies of dynamic platelet interactions with endothelial cells

Hauser, F., Naderer, C., Priglinger, E., Peterbauer, A., Fischer, M., Redl, H. & Jacak, J., 2024, In: Frontiers in Bioengineering and Biotechnology. 12, 1372807.

Research output: Contribution to journal › Article › peer-review

Open Access

2023

Amino Acid-Based Polyphosphorodiamidates with Hydrolytically Labile Bonds for Degradation-Tuned Photopolymers

Haudum, S., Lenhart, S., Müller, S. M., Tupe, D., Naderer, C., Dehne, T., Sittinger, M., Major, Z., Griesser, T., Brüggemann, O., Jacak, J. & Teasdale, I., 20 Jun 2023, In: ACS Macro Letters. 12, 6, p. 673-678 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Citations (Scopus)

Analysis of Extracellular Vesicle Data on Fluorescence and Atomic Force Microscopy Images

Janout, H., Schurr, J., Haghofer, A., Hauser, F., Jacak, J. & Winkler, S., 2023, Biomedical Engineering Systems and Technologies - 15th International Joint Conference, BIOSTEC 2022, Revised Selected Papers. Roque, A. C. A., Gracanin, D., Lorenz, R., Tsanas, A., Bier, N., Fred, A. & Gamboa, H. (eds.). Springer, p. 16-33 18 p. (Communications in Computer and Information Science; vol. 1814 CCIS).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Automated Data Adaptation for the Segmentation of Blood Vessels

Haghofer, A., Ebner, T., Kainz, P., Weißensteiner, M., Ghaffari-Tabrizi-Wizsy, N., Hatab, I., Scharinger, J. & Winkler, S., 2023, Biomedical Engineering Systems and Technologies - 15th International Joint Conference, BIOSTEC 2022, Revised Selected Papers. Roque, A. C. A., Gracanin, D., Lorenz, R., Tsanas, A., Bier, N., Fred, A. & Gamboa, H. (eds.). Springer, p. 53-72 20 p. (Communications in Computer and Information Science; vol. 1814 CCIS).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Automated Segmentation of Patterned Cells in Micropatterning Microscopy Images

Schurr, J., Haghofer, A., Lanzerstorfer, P. & Winkler, S., 2023, Biomedical Engineering Systems and Technologies - 15th International Joint Conference, BIOSTEC 2022, Revised Selected Papers. Roque, A. C. A., Gracanin, D., Lorenz, R., Tsanas, A., Bier, N., Fred, A. & Gamboa, H. (eds.). Springer, p. 34-52 19 p. (Communications in Computer and Information Science; vol. 1814 CCIS).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Biological image analysis using deep learning

Hauser, F., 7 Jan 2023.

Research output: Contribution to conference › Poster

Evaluating Machine Learning and Heuristic Optimization Based Surrogates as a Replacement for a Complex Building Simulation Model

Kefer, K., Haijes, S., Mörth, M., Heimrath, R., Mach, T., Kaisermayer, V., Zemann, C., Muschick, D., Burlacu, B., Winkler, S. & Affenzeller, M., 2023, 11th International Workshop on Simulation for Energy, Sustainable Development and Environment, SESDE 2023. Bruzzone, A. G., Janosy, J. S., Nicoletti, L. & Zacharewicz, G. (eds.). Cal-Tek srl, (Proceedings of the International Workshop on Simulation for Energy, Sustainable Development and Environment, SESDE; vol. 2023-September).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Open Access

Evolutionary Algorithms for Segment Optimization in Vectorial GP

Fleck, P., Silva, S., Winkler, S., Vanneschi, L., Kommenda, M. & Affenzeller, M., 15 Jul 2023, GECCO 2023 Companion - Proceedings of the 2023 Genetic and Evolutionary Computation Conference Companion. Association for Computing Machinery, Inc, p. 439-442 4 p. (GECCO 2023 Companion - Proceedings of the 2023 Genetic and Evolutionary Computation Conference Companion).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Open Access

From Authoring to Evaluating an Electronic Health Quality Measure: Applying Logic to FHIR® with CQL for Calculating Immunization Coverage

Lin, A. M., Schwab, A., Abolhassni, R. & Winkler, S., 2 May 2023, dHealth 2023: Proceedings of the 17th Health Informatics Meets Digital Health Conference. 301 ed. IOS Press, Vol. 301. p. 12-17 6 p. (Studies in health technology and informatics).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Open Access

2 Citations (Scopus)

Histological classification of canine and feline lymphoma using a modular approach based on deep learning and advanced image processing

Haghofer, A., Fuchs-Baumgartinger, A., Lipnik, K., Klopfleisch, R., Aubreville, M., Scharinger, J., Weissenböck, H., Winkler, S. M. & Bertram, C. A., 9 Nov 2023, In: Scientific Reports. 13, 1, p. 1-15 15 p., 19436.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Citations (Scopus)

Improvements and applications of quantitative single molecule localization microscopy

Hauser, F., 11 Apr 2023, 114 p.

Research output: Types of Theses › Doctoral Thesis

Open Access

In Vitro Quantification of Cellular Spheroids in Patterned Petri Dishes

Schurr, J., Haghofer, A., Fürsatz, M., Janout, H., Nürnberg, S. & Winkler, S., 2023.

Research output: Contribution to conference › Paper › peer-review

Live Cell Imaging and in vivo Cell Tracking in Tissues

Naderer, C., Hauser, F., Hochreiner, A., Axmann, M. & Jacak, J., 2023, Bioimaging in Tissue Engineering and Regeneration: Advanced Microscopy and Preclinical Imaging. Springer

Research output: Chapter in Book/Report/Conference proceedings › Chapter › peer-review

Open Access

Low-Fluorescence Starter for Optical 3D Lithography of Sub-40 nm Structures

Gvindzhiliia, G., Sivun, D., Naderer, C., Jacak, J. & Klar, T. A., 26 May 2023, In: ACS Applied Optical Materials. 1, 5, p. 945-951 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Citations (Scopus)

MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search

Dorl, S., Winkler, S., Mechtler, K. & Dorfer, V., 3 Feb 2023, In: Journal of Proteome Research. 22, 2, p. 462-470 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Citations (Scopus)

MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity

Birklbauer, M. J., Matzinger, M., Müller, F., Mechtler, K. & Dorfer, V., 1 Sept 2023, In: Journal of Proteome Research. 22, 9, p. 3009-3021 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Citation (Scopus)

New buffer systems for photopainting of single biomolecules

Naderer, C., Krobath, H., Sivun, D., Gvindzhiliia, G., Klar, T. A. & Jacak, J., 2023, In: RSC Applied Interfaces. 1, 1, p. 110-121 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Nuclear Morphometry using a Deep Learning-based Algorithm has Prognostic Relevance for Canine Cutaneous Mast Cell Tumors

Haghofer, A., Parlak, E., Bartel, A., Donovan, T. A., Assenmacher, C.-A., Bolfa, P., Dark, M. J., Fuchs-Baumgartinger, A., Klang, A., Jäger, K., Klopfleisch, R., Merz, S., Richter, B., Schulman, F. Y., Ganz, J., Scharinger, J., Aubreville, M., Winkler, S. M., Kiupel, M. & Bertram, C. A., 26 Sept 2023.

Research output: Working paper › Preprint

File

40 Downloads (Pure)

Ontology-based Dynamic Event Log Generation for Semantic Process Mining

Mayrhuber, E. M., Jul 2023

Research output: Types of Theses › Master's Thesis / Diploma Thesis

Prediction of Patients' Length of Stay after Surgery using Multi-Model-Ensembles

Vetter, J., Strobl, M. T., Halmerbauer, G. & Winkler, S., 2023.

Research output: Contribution to conference › Poster › peer-review

Purification Analysis, Intracellular Tracking, and Colocalization of Extracellular Vesicles Using Atomic Force and 3D Single-Molecule Localization Microscopy

Puthukodan, S., Hofmann, M., Mairhofer, M., Janout, H., Schurr, J., Hauser, F., Naderer, C., Preiner, J., Winkler, S., Sivun, D. & Jacak, J., 11 Apr 2023, In: Analytical Chemistry. 95, 14, p. 6061-6070 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Citation (Scopus)

Symbolic Regression in Materials Science: Discovering Interatomic Potentials from Data

Burlacu, B., Kommenda, M., Kronberger, G., Winkler, S. M. & Affenzeller, M., 2023, Genetic Programming Theory and Practice XIX. Trujillo, L., Winkler, S. M., Silva, S. & Banzhaf, W. (eds.). Singapore: Springer Nature Singapore, p. 1-30 30 p.

Research output: Chapter in Book/Report/Conference proceedings › Chapter › peer-review

The Class IIA Histone Deacetylase (HDAC) Inhibitor TMP269 Downregulates Ribosomal Proteins and Has Anti-Proliferative and Pro-Apoptotic Effects on AML Cells

Urwanisch, L., Unger, M. S., Sieberer, H., Dang, H.-H., Neuper, T., Regl, C., Vetter, J., Schaller, S., Winkler, S., Kerschbamer, E., Weichenberger, C., Krenn, P., Luciano, M., Pleyer, L., Greil, R., Huber, C., Aberger, F. & Horejs-Hoeck, J., 7 Feb 2023, In: Cancers. 15, 4, 1039.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Citations (Scopus)

Toward an Integrated Machine Learning Model of a Proteomics Experiment

Neely, B. A., Dorfer, V., Martens, L., Bludau, I., Bouwmeester, R., Degroeve, S., Deutsch, E. W., Gessulat, S., Käll, L., Palczynski, P., Payne, S. H., Rehfeldt, T. G., Schmidt, T., Schwämmle, V., Uszkoreit, J., Vizcaíno, J. A., Wilhelm, M. & Palmblad, M., 3 Mar 2023, In: Journal of Proteome Research. 22, 3, p. 681-696 16 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

17 Citations (Scopus)

Using Explainable Artificial Intelligence for Data Based Detection of Complications in Records of Patient Treatments

Strobl, M. T., Vetter, J., Halmerbauer, G., Königswieser, T. & Winkler, S., 10 Feb 2023, Computer Aided Systems Theory – EUROCAST 2022 - 18th International Conference, Revised Selected Papers: 18th International Conference, Las Palmas de Gran Canaria, Spain, February 20–25, 2022, Revised Selected Papers. Moreno-Díaz, R., Pichler, F. & Quesada-Arencibia, A. (eds.). Springer, p. 173-180 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13789 LNCS).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Vectorial Genetic Programming - Optimizing Segments for Feature Extraction

Fleck, P., Winkler, S., Kommenda, M. & Affenzeller, M., 3 Mar 2023.

Research output: Working paper › Preprint

File

45 Downloads (Pure)

2022

ADHERENCE TO GUIDELINE IN PATIENTS WITH HERNIA REPAIR IN EIGHT UPPER AUSTRIAN HOSPITALS.

Scheidleder, N., Halmerbauer, G., Strobl, M. T. & Königswieser, T., 2022.

Research output: Contribution to conference › Poster › peer-review

Analysis of Cell Viability in Microfluidic Spheroid Arrays by Image Analysis and Neural Networks

Schurr, J., Eilenberger, C., Selinger, F., Ertl, P., Scharinger, J. & Winkler, S., 2022, In: International Journal of Practical Healthcare Innovation and Management Techniques. 2022, vol. 9, no. 2, p. 1 - 22

Research output: Contribution to journal › Article › peer-review

A Simplified and Robust Activation Procedure of Glass Surfaces for Printing Proteins and Subcellular Micropatterning Experiments

Karimian, T., Hager, R., Karner, A., Weghuber, J. & Lanzerstorfer, P., 25 Feb 2022, In: Biosensors. 12, 3, 140.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Citations (Scopus)

Automated Cell Segmentation for Micropatterning Microscopy Image

Schurr, J., 2022, BIOSTEC 15th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOIMAGING).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Data Platform for the Unification and Analysis of Extracellular Vesicle Data

Janout, H., 2022, 15th International Joint Conference on Biomedical Engineering Systems and Technologies.

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Differential effects of glucose-dependent insulinotropic polypeptide receptor/glucagon-like peptide-1 receptor heteromerization on cell signaling when expressed in HEK-293 cells

Al-Zaid, B., Chacko, S., Ezeamuzie, C. I., Bünemann, M., Krasel, C., Karimian, T., Lanzerstorfer, P. & Al-Sabah, S., Oct 2022, In: Pharmacology Research and Perspectives. 10, 5, e01013.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Citations (Scopus)

Dissociation of β2m from MHC class I triggers formation of noncovalent transient heavy chain dimers: Dissociation of β2m from MHC class I triggers formation of noncovalent transient heavy chain dimers

Dirscherl, C., Löchte, S., Hein, Z., Kopicki, J.-D., Harders, A. R., Linden, N., Karner, A., Preiner, J., Weghuber, J., Garcia-Alai, M., Uetrecht, C., Zacharias, M., Piehler, J., Lanzerstorfer, P. & Springer, S., May 2022, In: Journal of Cell Science. 135, 9, jcs259498.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Citations (Scopus)

Dynamic in Situ Confinement Triggers Ligand-Free Neuropeptide Receptor Signaling

Sànchez, F. M., Dietz, M. S., Müller, U., Weghuber, J., Gatterdam, K., Wieneke, R., Heilemann, M., Lanzerstorfer, P. & Tampé, R., 26 Oct 2022, In: Nano Letters. 22, 20, p. 8363-8371 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Citations (Scopus)

Fluorescence Microscopy-Based Quantitation of GLUT4 Translocation

Heckmann, M., Klanert, G., Sandner, G. P., Lanzerstorfer, P., Auer, M. & Weghuber, J., 21 Jan 2022, In: Methods and Applications in Fluorescence. 10, 2, 022001.

Research output: Contribution to journal › Review article › peer-review

Open Access

6 Citations (Scopus)

Grammar-Based Vectorial Genetic Programming for Symbolic Regression

Fleck, P., Winkler, S., Kommenda, M. & Affenzeller, M., 11 Feb 2022, Genetic Programming Theory and Practice XVIII. Springer, Vol. XVIII. p. 21-43 23 p.

Research output: Chapter in Book/Report/Conference proceedings › Chapter › peer-review

Identification of Similarities and Clusters of Bread Baking Recipes Based on Data of Ingredients

Anlauf, S., Lasslberger, M., Grassmann, R., Himmelbauer, J. & Winkler, S., 2022, 8th International Food Operations and Processing Simulation Workshop, FoodOPS 2022. Bruzzone, A. G., Longo, F. & Vignali, G. (eds.). DIME UNIVERSITY OF GENOA, 002. (8th International Food Operations and Processing Simulation Workshop, FoodOPS 2022).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Identification of Surrogate Models for the Prediction of Degrees of Freedom within a Tolerance Chain

Janout, H., Paier, T., Ringelhahn, C., Heckmann, M. K., Haghofer, A., Kronberger, G. & Winkler, S., 2022, International Conference on Industry 4.0 and Smart Manufacturing.

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

Identification of Surrogate Models for the Prediction of Degrees of Freedom within a Tolerance Chain

Janout, H., Paier, T., Ringelhahn, C., Heckmann, M., Haghofer, A., Kronberger, G. & Winkler, S., 2022, In: Procedia Computer Science. 217, p. 796-805 10 p.

Research output: Contribution to journal › Conference article › peer-review

Open Access

Identifying Differential Equations for the Prediction of Blood Glucose using Sparse Identification of Nonlinear Systems.

Joedicke, D., Parra, D., Kronberger, G. & Winkler, S. M., 2022, Computer Aided Systems Theory – EUROCAST 2022 - 18th International Conference, Revised Selected Papers. Moreno-Díaz, R., Pichler, F. & Quesada-Arencibia, A. (eds.). p. 181-188 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13789 LNCS).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

1 Citation (Scopus)

ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data

Vetter, J., Schaller, S., Heinzel, A., Aschauer, C., Reindl-Schwaighofer, R., Jelencsics, K., Hu, K., Oberbauer, R. & Winkler, S., 6 Jan 2022, In: BMC Bioinformatics. 23, 1, p. 21 21.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Citation (Scopus)

Linker Engineering of Ligand-Decorated DNA Origami Nanostructures Affects Biological Activity

Domínguez, C. M., García-Chamé, M., Müller, U., Kraus, A., Gordiyenko, K., Itani, A., Haschke, H., Lanzerstorfer, P., Rabe, K. S. & Niemeyer, C. M., 1 Sept 2022, In: Small. 18, 35, 2202704.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Citations (Scopus)

Microcontact Printing of Biomolecules on Various Polymeric Substrates: Limitations and Applicability for Fluorescence Microscopy and Subcellular Micropatterning Assays

Hager, R., Forsich, C., Duchoslav, J., Burgstaller, C., Stifter, D., Weghuber, J. & Lanzerstorfer, P., 2022, In: ACS Applied Polymer Materials. 4, 10, p. 6887-6896 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Citations (Scopus)

Multi-Level Analysis of Adipose Tissue Reveals the Relevance of Perivascular Subpopulations and an Increased Endothelial Permeability in Early-Stage Lipedema

Strohmeier, K., Hofmann, M., Jacak, J., Narzt, M. S., Wahlmueller, M., Mairhofer, M., Schaedl, B., Holnthoner, W., Barsch, M., Sandhofer, M., Wolbank, S. & Priglinger, E., 18 May 2022, In: Biomedicines. 10, 5, 1163.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Citations (Scopus)

Prädiktion der postoperativen Verweildauer auf Basis von präoperativen Routinedaten in Krankenhäusern mittels Multi-Model-Ensembles

Vetter, J., Strobl, M. T., Halmerbauer, G., Hochstrasser, T., Guttmann, J., Königswieser, T. & Winkler, S., 17 Jun 2022.

Research output: Contribution to conference › Poster › peer-review

Shapley Value Based Variable Interaction Networks for Data Stream Analysis.

Zenisek, J., Dorl, S., Falkner, D., Gaisberger, L., Winkler, S. M. & Affenzeller, M., 2022, Computer Aided Systems Theory – EUROCAST 2022 - 18th International Conference, Revised Selected Papers. Moreno-Díaz, R., Pichler, F. & Quesada-Arencibia, A. (eds.). p. 130-138 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13789 LNCS).

Research output: Chapter in Book/Report/Conference proceedings › Conference contribution › peer-review

1 Citation (Scopus)

Simulation-Based Optimization of Residential Energy Flows Using White Box Modeling by Genetic Programming

Kefer, K., Hanghofer, R., Kefer, P., Stöger, M., Hofer, B., Affenzeller, M. & Winkler, S., 1 Mar 2022, In: ENERGY AND BUILDINGS. 258, 111829.

Research output: Contribution to journal › Article › peer-review

10 Citations (Scopus)

Symbolic Regression in Materials Science: Discovering Interatomic Potentials from Data

Burlacu, B., Kommenda, M., Kronberger, G., Winkler, S. & Affenzeller, M., 13 Jun 2022, arXiv.

Research output: Working paper › Preprint

File

100 Downloads (Pure)

Bioinformatics

Research output

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