Research Group Bioinformatics and Computational Biology

Publications

Publications per year 2006 2013 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024

• 164 Article
• 9 Contribution to proceedings
• 6 Chapter
• 4 Paper
• 8 More
  • 4 Meeting abstract/Conference paper
  • 3 Review
  • 1 Preprint

Publications per year

Publications per year

Search results

• 2024

  3D feasibility of 2D RNA-RNA interaction paths by stepwise folding simulations

  Beckmann-Schneider, I. K., Waldl, M., Will, S. & Hofacker, I. L., Feb 2024, In: RNA. 30, 2, p. 113-123 11 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

  • Stereospecificity 100%
  • Documentation 100%

• A framework for automated scalable designation of viral pathogen lineages from genomic data

  McBroome, J., de Bernardi Schneider, A., Roemer, C., Wolfinger, M. T., Hinrichs, A. S., O’Toole, A. N., Ruis, C., Turakhia, Y., Rambaut, A. & Corbett-Detig, R., Feb 2024, In: Nature Microbiology. 9, 2, p. 550-560 11 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Antibody-ligand interactions on a high-capacity staphylococcal protein A resin

  Tscheliessnig, R., Silva, G. L., Plewka, J., Jakob, L. A., Lichtenegger, H., Jungbauer, A. & Dias-Cabral, A. C., 16 Aug 2024, In: Journal of Chromatography A. 1730, 465102.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction

  von Löhneysen, S., Spicher, T., Varenyk, Y., Yao, H. T., Lorenz, R., Hofacker, I. & Stadler, P. F., 1 Jun 2024, In: Journal of computational biology : a journal of computational molecular cell biology. 31, 6, p. 549-563 15 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data

  Thiel, B. C., Bussi, G., Poblete, S. & Hofacker, I. L., 9 Sep 2024, In: Nucleic Acids Research. 52, 16, p. e73

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework

  Popitsch, N., Neumann, T., von Haeseler, A. & Ameres, S. L., 25 Jun 2024, In: Genome Biology. 25, 1, 19 p., 166.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• The 3' terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17

  Gemmill, D. L., Nelson, C. R., Badmalia, M. D., Pereira, H. S., Kerr, L., Wolfinger, M. T. & Patel, T. R., Feb 2024, In: Biochemistry and Cell Biology. 102, 1, p. 96-105 10 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

  • RNA Virus 100%
  • RNA 28%
  • Virus Replication 28%
  • Liquid 28%
  • Antibody 14%

• tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development

  Rappol, T., Waldl, M., Chugunova, A., Hofacker, I. L., Pauli, A. & Vilardo, E., 23 Sep 2024, In: Nucleic Acids Research. 52, 17, p. 10575-10594 20 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Xinyang flavivirus, from Haemaphysalis flava ticks in Henan Province, China, defines a basal, likely tick-only Orthoflavivirus clade

  Wang, L. L., Cheng, Q., Newton, N. D., Wolfinger, M. T., Morgan, M. S., Slonchak, A., Khromykh, A. A., Cheng, T. Y. & Parry, R. H., 2024, In: Journal of General Virology. 105, 5, 001991.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2023

  A Structural Refinement Technique for Protein-RNA Complexes Based on a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein

  Darai, N., Hengphasatporn, K., Wolschann, P., Wolfinger, M. T., Shigeta, Y., Rungrotmongkol, T. & Harada, R., 2023, In: Bulletin of the Chemical Society of Japan. 96, 7, p. 677-685 9 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment

  Farman, M. R., Petrackova, D., Kumar, D., Drzmisek, J., Saha, A., Curnova, I., Capek, J., Hejnarova, V., Amman, F., Hofacker, I. & Vecerek, B., 31 Dec 2023, In: Emerging microbes & infections. 12, 1, 16 p., e2146536.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model

  Badelt, S., Lorenz, R. & Hofacker, I. L., 1 Jan 2023, In: Bioinformatics (Oxford, England). 39, 1, btad034.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

  • Energy 100%
  • Transcription 100%
  • RNA Folding 100%
  • Heuristics 100%
  • RNA 50%

• Investigating RNA-RNA interactions through computational and biophysical analysis

  Mrozowich, T., Park, S. M., Waldl, M., Henrickson, A., Tersteeg, S., Nelson, C. R., De Klerk, A., Demeler, B., Hofacker, I. L., Wolfinger, M. T. & Patel, T. R., 22 May 2023, In: Nucleic Acids Research. 51, 9, p. 4588-4601 14 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

  • RNA 100%
  • Japanese Encephalitis Virus Group 20%
  • Cyclization 13%
  • Virus 13%
  • X Ray 6%

• Local RNA folding revisited

  Waldl, M., Spicher, T., Lorenz, R., Beckmann, I. K., Hofacker, I. L., Von Löhneysen, S. & Stadler, P. F., 1 Aug 2023, In: Journal of Bioinformatics and Computational Biology. 21, 4, 2350016.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

  • Accuracy 100%
  • RNA 100%
  • RNA Folding 100%
  • Structure Prediction 100%
  • Sample 50%

• Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes

  Weiszmann, J., Walther, D., Clauw, P., Back, G., Gunis, J., Reichardt, I., Koemeda, S., Jez, J., Nordborg, M., Schwarzerova, J., Pierides, I., Nägele, T. & Weckwerth, W., Oct 2023, In: Plant Physiology. 193, 2, p. 980-1000 21 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

  • Cold Acclimatization 100%
  • Acclimatization 20%
  • DNA Methylation 20%

• ModelRevelator: Fast phylogenetic model estimation via deep learning

  Burgstaller-Muehlbacher, S., Crotty, S. M., Schmidt, H. A., Reden, F., Drucks, T. & von Haeseler, A., Nov 2023, In: Molecular Phylogenetics and Evolution. 188, 107905.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Modified RNAs and predictions with the ViennaRNA Package

  Varenyk, Y., Spicher, T., Hofacker, I. L. & Lorenz, R., 1 Nov 2023, In: Bioinformatics. 39, 11, btad696.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package

  Yao, H. T., Lorenz, R., Hofacker, I. L. & Stadler, P. F., Dec 2023, In: Algorithms for Molecular Biology. 18, 1, 8.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• SVhound: detection of regions that harbor yet undetected structural variation

  Paulin, L. F., Raveendran, M., Harris, R. A., Rogers, J., von Haeseler, A. & Sedlazeck, F. J., 20 Jan 2023, In: BMC Bioinformatics. 24, 1, 23.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

  • Rhesus Monkey 100%
  • 1000 Genomes Project 100%
• 2022

  Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats

  D'Souza, M. H., Mrozowich, T., Badmalia, M. D., Geeraert, M., Frederickson, A., Henrickson, A., Demeler, B., Wolfinger, M. T. & Patel, T. R., 10 Jun 2022, In: Nucleic Acids Research. 50, 10, p. 5881-5898 18 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction

  Flamm, C., Wielach, J., Wolfinger, M. T., Badelt, S., Lorenz, R. & Hofacker, I. L., 11 Jul 2022, In: Frontiers in bioinformatics. 2, 7 p., 835422.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?

  Crotty, S. M. & Holland, B. R., Nov 2022, In: Systematic Biology. 71, 6, p. 1541-1548 8 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Comprehensive Analysis of Nasal Polyps Reveals a More Pronounced Type 2 Transcriptomic Profile of Epithelial Cells and Mast Cells in Aspirin-Exacerbated Respiratory Disease

  Bangert, C., Villazala-Merino, S., Fahrenberger, M., Krausgruber, T., Bauer, W. M., Stanek, V., Campion, N. J., Bartosik, T., Quint, T., Regelsberger, G., Niederberger-Leppin, V., Bock, C., Schneider, S. & Eckl-Dorna, J., 28 Mar 2022, In: Frontiers in Immunology. 13, 16 p., 850494.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology

  Kutschera, L. S. & Wolfinger, M. T., 2 Jul 2022, In: Virus Evolution. 8, 1, 11 p., veac051.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus internal Ribosome Entry Site

  Gosavi, D., Wower, I., Beckmann-Schneider, I. K., Hofacker, I. L., Wower, J., Wolfinger, M. T. & Sztuba-Solinska, J., 31 Dec 2022, In: RNA Biology. 19, 1, p. 496-506 11 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Melanopsin elevates locomotor activity during the wake state of the diurnal zebrafish

  Dekens, M. P. S., Fontinha, B. M., Gallach, M., Pflügler, S. & Tessmar-Raible, K., May 2022, In: EMBO Reports. 23, 5, e51528.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes

  Gornik, S. G., Flores, V., Reinhardt, F., Erber, L., Salas-Leiva, D. E., Douvropoulou, O., Lassadi, I., Einarsson, E., Mörl, M., Git, A., Stadler, P. F., Pain, A. & Waller, R. F., 1 Oct 2022, In: Molecular Biology and Evolution. 39, 10, 16 p., msac191.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Molecular archaeology of human cognitive traits

  Kaczanowska, J., Ganglberger, F., Chernomor, O., Kargl, D., Galik, B., Hess, A., Moodley, Y., von Haeseler, A., Bühler, K. & Haubensak, W., 30 Aug 2022, In: Cell Reports. 40, 9, 111287.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation

  Huth, M., Santini, L., Galimberti, E., Ramesmayer, J., Titz-Teixeira, F., Sehlke, R., Oberhuemer, M., Stummer, S., Herzog, V., Garmhausen, M., Romeike, M., Chugunova, A., Leesch, F., Holcik, L., Weipoltshammer, K., Lackner, A., Schoefer, C., von Haeseler, A., Bücker, C., Pauli, A., & 4 othersAmeres, S. L., Smith, A., Beyer, A. & Leeb, M., 3 Mar 2022, In: Genes & Development. 36, 5-6, p. 348-367 20 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Rewiring of Gene Expression in Pseudomonas aeruginosa During Diauxic Growth Reveals an Indirect Regulation of the MexGHI-OpmD Efflux Pump by Hfq

  Rozner, M., Nukarinen, E., Wolfinger, M. T., Amman, F., Weckwerth, W., Bläsi, U. & Sonnleitner, E., 23 Jun 2022, In: Frontiers in Microbiology. 13, 12 p., 919539.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein

  Darai, N., Mahalapbutr, P., Wolschann, P., Lee, V. S., Wolfinger, M. T. & Rungrotmongkol, T., 15 Jul 2022, In: Scientific Reports. 12, 1, 12 p., 12137.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2021

  An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3 '-untranslated region

  Harima, H., Orba, Y., Torii, S., Qiu, Y., Kajihara, M., Eto, Y., Matsuta, N., Hang'ombe, B. M., Eshita, Y., Uemura, K., Matsuno, K., Sasaki, M., Yoshii, K., Nakao, R., Hall, W. W., Takada, A., Abe, T., Wolfinger, M. T., Simuunza, M. & Sawa, H., 1 Mar 2021, In: Scientific Reports. 11, 1, 15 p., 4883.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• ATM controls meiotic DNA double-strand break formation and recombination and affects synaptonemal complex organization in plants

  Kurzbauer, M-T., Janisiw, M. P., Paulin, L. F., Prusén Mota, I., Tomanov, K., Krsicka, O., Haeseler, A. V., Schubert, V. & Schlögelhofer, P., May 2021, In: The Plant Cell. 33, 5, p. 1633–1656 24 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Complex evolution of light-dependent protochlorophyllide oxidoreductases in aerobic anoxygenic phototrophs: origin, phylogeny and function

  Chernomor, O., Peters, L., Schneidewind, J., Loeschcke, A., Knieps-Grünhagen, E., Schmitz, F., von Lieres, E., Kutta, R. J., Svensson, V., Jaeger, K-E., Drepper, T., von Haeseler, A. & Krauss, U., Mar 2021, In: Molecular Biology and Evolution. 38, 3, p. 819–837 19 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Culture-free detection of antibiotic resistance markers from native patient samples by hybridization capture sequencing

  Ferreira, I., Lepuschitz, S., Beisken, S., Fiume, G., Mrazek, K., Frank, B. J. H., Huber, S., Knoll, M. A., von Haeseler, A., Materna, A., Hofstaetter, J. G., Posch, A. E. & Weinberger, J., Aug 2021, In: Microorganisms. 9, 8, 13 p., 1672.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

  Spicher, T., Delitz, M., Schneider, A. D. B. & Wolfinger, M. T., Feb 2021, In: Genes. 12, 2, p. 1-17 17 p., 239.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence-An Experimental Study of the Human Voltage-Dependent Anion Channel

  Zayni, S., Damiati, S., Moreno-Flores, S., Amman, F., Hofacker, I., Jin, D. & Ehmoser, E-K., Oct 2021, In: Membranes. 11, 10, 11 p., 741.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin

  Cianciulli Sesso, A., Lilic, B., Amman, F., Wolfinger, M. T., Sonnleitner, E. & Blasi, U., 30 Apr 2021, In: Frontiers in Microbiology. 12, 19 p., 626715.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Rna secondary structures with limited base pair span: Exact backtracking and an application

  Lorenz, R. & Stadler, P. F., Jan 2021, In: Genes. 12, 1, p. 1-9 9 p., 14.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes

  Entzian, G., Hofacker, I. L., Ponty, Y., Lorenz, R. & Tanzer, A., 1 Aug 2021, In: Bioinformatics. 37, 15, p. 2126-2133 8 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Sequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants

  Sims, J., Sestini, G., Elgert, C., von Haeseler, A. & Schlögelhofer, P., 15 Jan 2021, In: Nature Communications. 12, 1, 13 p., 387.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Timing strains of the marine insect Clunio marinus diverged and persist with gene flow

  Kaiser, T. S., von Haeseler, A., Tessmar-Raible, K. & Heckel, D. G., Mar 2021, In: Molecular Ecology. 30, 5, p. 1264-1280 17 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• TMT-Opsins differentially modulate medaka brain function in a context-dependent manner

  Fontinha, B. M., Zekoll, T., Al-Rawi, M., Gallach, M., Reithofer, F., Barker, A. J., Hofbauer, M., Fischer, R. M., Von Haeseler, A., Baier, H. & Tessmar-Raible, K., 7 Jan 2021, In: PLoS Biology. 19, 1, 31 p., e3001012.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2020

  A compendium of genome-wide sequence reads from NBS (nucleotide binding site) domains of resistance genes in the common potato

  Prakash, C., Trognitz, F. C., Venhuizen, P., von Haeseler, A. & Trognitz, B., 9 Jul 2020, In: Scientific Reports. 10, 1, 21 p., 11392.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• A human tissue screen identifies a regulator of ER secretion as a brain-size determinant

  Esk, C., Lindenhofer, D., Haendeler, S., Wester, R. A., Pflug, F., Schroeder, B., Bagley, J. A., Elling, U., Zuber, J., von Haeseler, A. & Knoblich, J. A., 20 Nov 2020, In: Science. 370, 6519, p. 935-941 7 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals

  Popitsch, N., Huber, C. D., Buchumenski, I., Eisenberg, E., Jantsch, M., von Haeseler, A. & Gallach, M., 1 Apr 2020, In: Genome Biology and Evolution. 12, 4, p. 345-357 13 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia

  Wastika, C. E., Harima, H., Sasaki, M., Hang'ombe, B. M., Eshita, Y., Qiu, Y., Hall, W. W., Wolfinger, M. T., Sawa, H. & Orba, Y., Sep 2020, In: Viruses. 12, 9, 21 p., 1017.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing

  Riva, L., Yuan, S., Yin, X., Martin-Sancho, L., Matsunaga, N., Pache, L., Burgstaller-Muehlbacher, S., De Jesus, P. D., Teriete, P., Hull, M. V., Chang, M. W., Chan, J. F-W., Cao, J., Poon, V. K-M., Herbert, K. M., Cheng, K., Nguyen, T-T. H., Rubanov, A., Pu, Y., Nguyen, C., & 25 othersChoi, A., Rathnasinghe, R., Schotsaert, M., Miorin, L., Dejosez, M., Zwaka, T. P., Sit, K-Y., Martinez-Sobrido, L., Liu, W-C., White, K. M., Chapman, M. E., Lendy, E. K., Glynne, R. J., Albrecht, R., Ruppin, E., Mesecar, A. D., Johnson, J. R., Benner, C., Sun, R., Schultz, P. G., Su, A. I., García-Sastre, A., Chatterjee, A. K., Yuen, K-Y. & Chanda, S. K., 24 Jul 2020, In: Nature. 586, 7827, p. 113-119 7 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq

  Sonnleitner, E., Pusic, P., Wolfinger, M. T. & Bläsi, U., 26 May 2020, In: Frontiers in Microbiology. 11, 13 p., 1001.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Distinguishing Felsenstein zone from Farris zone using neural networks

  Leuchtenberger, A. F., Crotty, S. M., Drucks, T., Schmidt, H. A., Burgstaller-Muehlbacher, S. & von Haeseler, A., Dec 2020, In: Molecular Biology and Evolution. 37, 12, p. 3632–3641 10 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access