Publications

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2024

24-001
Tom Rappol, Maria Waldl, Anastasia Chugunova, Ivo L Hofacker, Andrea Pauli, and Elisa Vilardo
tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development
Nucleic Acids Research, 52(17):10575–10594, 07 2024, doi:10.1093/nar/gkae595

24-002
Bernhard C Thiel, Giovanni Bussi, Simón Poblete, and Ivo L Hofacker
Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data
Nucleic Acids Research, 52(16):e73–e73, 2024, doi:10.1093/nar/gkae602

24-003
Maria Waldl, Hua-Ting Yao, and Ivo L Hofacker
Sequence design for RNA-RNA interactions
In RNA Design: Methods and Protocols, Methods in Molecular Biology, pages 1–16. Springer, 2024, doi:10.1007/978-1-0716-4079-1_1

24-004
Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo Hofacker, and Peter F Stadler
Phylogenetic and chemical probing information as soft constraints in RNA secondary structure prediction
Journal of Computational Biology, 31(6):549–563, 2024, doi:10.1089/cmb.2024.0519

24-005
Irene K Beckmann, Maria Waldl, Sebastian Will, and Ivo L Hofacker
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations
RNA, 30(2):113–123, 2024, doi:10.1261/rna.079756.123

24-006
Iuliia Ozerova, Jorg Fallmann, Mario Morl, Matthias Bernt, Sonja J. Prohaska, and Peter F. Stadler
Aberrant mitochondrial tRNA genes appear frequently in animal evolution
Genome Biol. Evol., 16(11):evae232, 2024, doi:10.1093/gbe/evae232

24-007
Marcos E González Laffitte, Klaus Weinbauer, Tieu-Long Phan, Nora Beier, Nico Domschke, Christoph Flamm, Thomas Gatter, Daniel Merkle, Peter F. Stadler
Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions
Symmetry, 16:1217, 2024, doi:10.3390/sym16091217

24-008
Benoit Besson, Gijs J. Overheul, Michael T. Wolfinger, Sandra Junglen, Ronald P. van Rij
Pan-flavivirus analysis reveals sfRNA-independent, 3’UTR-biased siRNA production from an Insect-Specific Flavivirus
J. Virol. e01215-24 (2024), doi:10.1128/jvi.01215-24

24-009
Yasuda, N., Ali, S., Aman, A., Krusong, K., Herfindo, N., Chavasiri, W., Choowongkomon, K., Wolschann, P., Mahalapbutr, P., Rungrotmongkol, T., & Hannongbua, S.
In vitro and in silico studies of the inclusion complexation of 8-bromobaicalein with β-cyclodextrins
Journal of Molecular Graphics and Modelling, 132, Artikel 108840, doi:10.1016/j.jmgm.2024.108840

24-010
Aman, A., Ali, S., Oopkaew, L., Mahalapbutr, P., Ismail, A., Krusong, K., Wolschann, P., & Rungrotmongkol, T.
Inclusion complexes of regorafenib with beta- and gamma-cyclodextrin derivatives: In silico and in vitro studies
Journal of Molecular Liquids, 411, Artikel 125645, doi:10.1016/j.molliq.2024.125645

24-011
Ali, S., Aman, A., Hengphasatporn, K., Oopkaew, L., Todee, B., Fujiki, R., Harada, R., Shigeta, Y., Krusong, K., Choowongkomon, K., Chavasiri, W., Wolschann, P., Mahalapbutr, P., & Rungrotmongkol, T.
Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation
Computational Biology and Chemistry, 112, Artikel 108111, doi:10.1016/j.compbiolchem.2024.108111

24-012
Pojtanadithee, P., Isswanich, K., Buaban, K., Chamni, S., Wilasluck, P., Deetanya, P., Wangkanont, K., Langer, T., Wolschann, P., Sanachai, K., & Rungrotmongkol, T.
A combination of structure-based virtual screening and experimental strategies to identify the potency of caffeic acid ester derivatives as SARS-CoV-2 3CLpro inhibitor from an in-house database
Biophysical Chemistry, 304, Artikel 107125, doi:10.1016/j.bpc.2023.107125

24-013
Ali, S., Saokaew, P., Aman, A., Todsaporn, D., Sanachai, K., Krusong, K., Hannongbua, S., Wolschann, P., Mahalapbutr, P., & Rungrotmongkol, T.
Enhancing solubility and stability of piperine using β-cyclodextrin derivatives: computational and experimental investigations
Journal of Biomolecular Structure and Dynamics, doi:10.1080/07391102.2024.2305696

24-014
Boonpalit, K., Chuntakaruk, H., Kinchagawat, J., Wolschann, P., Hannongbua, S., Rungrotmongkol, T., & Nutanong, S.
Pre-training strategy for antiviral drug screening with low-data graph neural network: A case study in HIV-1 K103N reverse transcriptase
Journal of Computational Chemistry, doi:10.1002/jcc.27514

24-015
Tscheliessnig, R., Silva, G. L., Plewka, J., Jakob, L. A., Lichtenegger, H., Jungbauer, A., & Dias-Cabral, A. C.
Antibody-ligand interactions on a high-capacity staphylococcal protein A resin
Journal of Chromatography A, 1730, Artikel 465102, doi:10.1016/j.chroma.2024.465102

24-016
Varenyk, Y., Theodorakis, P. E., Pham, D. Q. H., Li, M. S., & Krupa, P.
Exploring Structural Insights of Aβ42 and α-Synuclein Monomers and Heterodimer:A Comparative Study Using Implicit and Explicit Solvent Simulations
Journal of Physical Chemistry B, 128(19), 4655-4669, doi:10.1021/acs.jpcb.4c00503

24-017
Yao, H. T., Marchand, B., Berkemer, S. J., Ponty, Y., & Will, S.
Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms for Molecular Biology, 19(1), Artikel 13, doi:10.1186/s13015-024-00258-2

24-018
iLan-Lan Wang, Qia Cheng, Natalee D. Newton, Michael T. Wolfinger, Mahali S. Morgan, Andrii Slonchak, Alexander A. Khromykh, Tian-Yin Cheng, Rhys H. Parry
Xinyang flavivirus, from Haemaphysalis flava ticks in Henan province, China, defines a basal, likely tick-only flavivirus clade
J. Gen. Virol. 105(5) (2024), doi:10.1099/jgv.0.001991

24-019
Jakob McBroome, Adriano de Bernardi Schneider, Cornelius Roemer, Michael T. Wolfinger, Angie S. Hinrichs, Aine N. O’Toole, Chris Ruis, Yatish Turakhia, Andrew Rambaut, and Russell Corbett-Detig
A framework for automated scalable designation of viral pathogen lineages from genomic data
,Nature Microbiol. 9:550–560 (2024) doi:10.1038/s41564-023-01587-5

24-020
Danielle L. Gemmill, Corey R. Nelson, Maulik D. Badmalia, Higor S. Pereira, Michael T. Wolfinger, and Trushar Patel
The 3’ terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17
,Biochem. Cell Biol. 102(1):96–105 (2024) doi:10.1139/bcb-2023-0036

24-021
Ameera Vaheeda Shanavas, Manoj Changat, Marc Hellmuth, and Peter F. Stadler
Unique least common ancestors and clusters in directed acyclic graphs
In S. Kalyanasundaram and A. Maheshwari, editors, Algorithms and Discrete Applied Mathematics. CALDAM 2024, volume 14508 of Lect. Notes Comp. Sci., pages 148–161, Cham, 2024. Springer

24-022
Ulisses Nunes da Rocha, Jonas Coelho Kasmanas, Rene Kallies, Joao Pedro Saraiva, Rodolfo Brizola Toscan, Polanca Stefanic, Marcos Fleming Bicalho, Felipe Borim Correa, Merve Nida Basturk, Efthymios Fousekis, Luiz Miguel Viana Barbosa, Julia Plewka, Alexander J Probst, Petr Baldrian, Peter F. Stadler, and CLUE-TERRA Consortium
MuDoGeR: Multi-domain genome recovery from metagenomes made easy
Mol. Ecol. Resources, 24:e13904, 2024, doi:10.1101/2022.06.21.496983

24-023
Grover E. C. Guzman, Peter F. Stadler, and Andre Fujita
Cavity approach for the ap-proximation of spectral density of with heterogeneous structures
Phys. Rev. E, 109:034303, 2024, doi:10.1103/PhysRevE.109.034303

24-024
Peter F Stadler, Sarah von Lohneysen, and Mario Morl
Limits of experimental evidence in rna secondary structure prediction
Frontiers Bioinf., 4:1346779, 2024, doi:10.3389/fbinf.2024.1346779

24-025
Nicola Vassena and Peter F. Stadler
Unstable cores are the source of instability in chemical reaction networks
Proc. Roy. Soc. A, 480:20230694, 2024, doi:10.1098/rspa.2023.0694

24-026
Marcos E. Gonzalez Laﬃtte and Peter F. Stadler
Progressive multiple alignment of graphs
Algorithms, 17(3):116, 2024, doi:10.3390/a17030116

24-027
Jos´e Antonio Ramırez-Rafael, Annachiara Korchmaros, Katia Avina-Padilla, Alitzel Lopez Sanchez, Andrea Arlette Espana-Tinajero, Marc Hellmuth, Peter F. Stadler, and Maribel Hernandez-Rosales
REvolutionH-tl: Reconstruction of evolutionary histories tool
In Celine Scornavacca and Maribel Hern´andez-Rosales, editors, Comparative Genomics, volume 14616 of Lect. Notes Comp. Sci., pages 89–109, Cham, 2024. Springer Nature Switzerland

24-028
Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, and Peter F. Stadler
Comparative RNA geGenomics
Comparative Genomics, New York, 2nd edition, 2024. update of [539], doi:10.1007/978-1-0716-3838-5_12

24-029
Marc Hellmuth and Peter F. Stadler
The theory of gene family histories
In Joao C. Setubal, Peter F. Stadler, and Jens Stoye, editors, Comparative Genomics, volume 2802 of Methods in Molecular Biology, pages 1–32. Springer Nature, Humana, New York, 2nd edition, 2024

24-030
Felix Kuhnl, Peter F. Stadler, and Sven Findeiß
Assessing the quality of cotranscriptional folding simulations
In Ronny Lorenz, editor, RNA Folding: Methods and Protocols, volume 2726 of Methods in Molecular Biology, pages 347–376. Springer Nature, Humana, New York, doi:10.1101/2020.01.06.895607

24-031
Angel Garcia-Chung, Marisol Bermudez-Montana, Peter F. Stadler, Jurgen Jost, and Guillermo Restrepo
Chemically inspired Erdos-Renyi hypergraphs
J. Math. Chem., 62:1357–1383, 2024, doi:10.1007/s10910-024-01595-8

24-032
Manoj Changat, Ameera Vaheeda Shanavas, and Peter F. Stadler
Transit functions and pyramid-like binary clustering systems
Discr. Appl. Math., 357:365–384, 2024, doi:10.1016/j.dam.2024.06.032

24-033
Tieu-Long Phan, Klaus Weinbauer, Thomas Gartner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, and Peter F. Stadler
Reaction rebalancing: A novel approach to curating reaction databases
J. Cheminf., 16:82, 2024, doi:10.1186/s13321-024-00875-4

24-034
Bruno J. Schmidt, Tom Hartmann, and Peter F. Stadler
Sorting signed permutations by tandem duplication random loss and inverse tandem duplication random loss
Adv. Appl. Math., 161:102757, 2024, doi:10.1016/j.aam.2024.102757

24-035
Franziska Reinhardt, Anette Kaiser, Simone Promel, and Peter F. Stadler
Evolution of neuropeptide Y/RFamide-like receptors in nematodes
Heliyon, 10(14):e34473, 2024, doi:10.1016/j.heliyon.2024.e34473

24-036
Anne Hoffmann, Christian Lorenz, Jorg Fallmann, Philippe Wolff, Anthony Lechner, Heike Betat, Mario Morl, and Peter F. Stadler
Temperature-dependent tRNA modifications in Bacillales
Int. J. Mol. Sci., 25:8823, 2024, doi:10.3390/ijms25168823

24-037
Eugenio Llanos Ballestas, Wilmer Leal, Andres Bernal, Jost Jurgen, and Peter F. Stadler
Are the chemical families still there? Formal structure of similarity of elements and its thermochemical domain
Proc. Roy. Soc. A, 480(2298):20240165, 2024, doi:10.1098/rspa.2024.0165

24-038
Anahy Santiago Arguello, Guillaume E. Scholz, and Peter F. Stadler
Core potentials: The consensus segmentation conjecture
Math. Comp. Sci., 18:19, 2024, doi:10.1007/s11786-024-00593-y

24-039
Yingjie Pan, Yifan Liu, Tieu Long Phan, Jialun Gao, Yong Wang, Hao Fang
Biomanufacturing of Inositol from Corn Stover with Biological Pretreatment by an In Vitro Synthetic Biology Platform
ACS Sustainable Chem. Eng. 2024, doi:10.1021/acssuschemeng.4c08006

2023

23-001
Farman, M. R., Petrackova, D., Kumar, D., Drzmisek, J., Saha, A., Curnova, I., Capek, J., Hejnarova, V., Amman, F., Hofacker, I. & Vecerek, B.
Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment
Emerging microbes & infections. 12, 1, 16 p., 2146536, doi:10.1080/22221751.2022.2146536

23-002
Chonnikan Hanpaibool, Natharin Ngamwongsatit, Puey Ounjai, Sirilata Yotphan, Peter Wolschann, Adrian J. Mulholland, James Spencer, and Thanyada Rungrotmongkol
Pyrazolones Potentiate Colistin Activity against MCR-1-Producing Resistant Bacteria: Computational and Microbiological Study
ACS Omega 2023, 8, 9, 8366-8376 (Article), doi:10.1021/acsomega.2c07165

23-003
Stefan Badelt, Ronny Lorenz, Ivo L Hofacker
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model
Bioinformatics, Volume 39, Issue 1, January 2023, btad034, doi:10.1093/bioinformatics/btad034

23-004
Roman Ochsenreiter and Michael T. Wolfinger
Strukturierte RNAs in Viren (in German)
BIOspektrum 02.23:156 (2023), doi:10.1007/s12268-023-1907-x

23-005
Tyler Mrozowich, Sean Park, Maria Waldl, Amy Henrickson, Scott Tersteeg, Corey R. Nelson, Anneke Deklerk, Borries Demeler, Ivo L. Hofacker, Michael T. Wolfinger, Trushar R. Patel
Investigating RMA-RNA interactiona through computational and biophysical analysis
Nucleic Acids Res. (2023), doi:10.1093/nar/gkad223

23-006
Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol and Ryuhei Harada
A Structural Refinement Technique for Protein-RNA Complexes Using Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein
Bulletin of the Chemical Society of Japan, doi:10.1246/bcsj.20230092

23-007
Phoomintara Longsompurana, Thanyada Rungrotmongkol, Nongluk Plongthongkum, Kittikhun Wangkanont, Peter Wolschann, Rungtiva P. Poo-arporn
Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2
PLoS ONE 18(10): e0293263., doi:10.1371/journal.pone.0293263

23-008
Malinee Promkatkaew, Pornthip Boonsri, Songwut Suramitr, Thitinun Karpkird, Peter Wolschann, Supa Hannongbua
Stability improvement of UV-filter between methoxy cinnamic acid derivatives and cyclodextrins inclusion complexes based on DFT and TD-DFT investigations
Journal of Molecular Graphics and Modelling 125 (2023) 108619, doi:10.1016/j.jmgm.2023.108619

23-009
P. Pojtanadithee, K. Hengphasatporn, A. Suroengrit, S. Boonyasuppayakorn, P. Wilasluck, P. Deetanya, K. Wangkanont, I.P. Sukanadi, W. Chavasiri, P. Wolschann, Th. Langer, Y. Shigeta, Ph. Maitarad, K. Sanachai, Th. Rungrotmongkol
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 ECLpro through Structure-Based Virtual Screning and Experimental Approaches
J Chem Inf Model 63, 5244-5258 (2023), doi:10.1021/acs.jcim.3c00663

23-010
Siriluk Rattanabunyong, Khuanjarat Choengpanya, Chonticha Suwattanasophon, Duangnapa Kiriwan, Peter Wolschann, Thomanai Lamtha, Abdul Rajjak Shaikh, Jatuporn Rattanasrisomporn, and Kiattawee Choowongkomon
Biochemical and structural comparisons of non-nucleoside reverse transcriptase inhibitors against feline immunodeficiency virus and human immunodeficiency virus
J Vet Sci. 2023;24:e67, doi:10.4142/jvs.22326

23-011
Aamir Aman, Saba Ali, Panupong Mahalapbutr, Kuakarun Krusong, Peter Wolschann and Thanyada Rungrotmongkol
Enhancing solubility and stability of sorafenib through cyclodextrin-based inclusion complexation: in silico and in vitro studies
RSC Adv., 2023, 13, 27244, doi:10.1039/d3ra03867j

23-012
Piyatida Pojtanadithee, Kulpornsorn Isswanich, Koonchira Buaban, Supakarn Chamni, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Thierry Langer, Peter Wolschann, Kamonpan Sanachai, Thanyada Rungrotmongkol
A combination of structure-based virtual screening and experimentali strategies to identify the potency of caffeic acid ester derivatives as SARS-CoV-2 3CLpro inhibitor from an in-house database
Biophysical Chemistry 304 (2024) 107125, doi:10.1016/j.bpc.2023.107125

23-013
Mariam R Farman, Denisa Petráčková, Dilip Kumar, Jakub Držmıšek, Argha Saha, Ivana Čurnová, Jan Čapek, Václava Hejnarová, Fabian Amman, Ivo L. Hofacker, and Branislav Vevcerek
Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment
Emerging Microbes & Infections, 12:e2146536, 2023, doi:10.1080/22221751.2022.2146536

23-014
Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K Beckmann, Ivo L Hofacker, Sarah Von Lohneysen, and Peter F Stadler
Local RNA folding revisisted
Journal of Bioinformatics and Computational Biology, 2023, doi:10.1142/S0219720023500166

23-015
Anda Ramona Tanasie, Peter Kerpedjiev, Stefan Hammer, Stefan Badelt
DrForna: visualization of cotranscriptional folding
Bioinformatics, 2023, 39(9), doi:10.1093/bioinformatics/btad555

23-016
Jakob L Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F Stadler
On the Realisability of Chemical Pathways
LNBI 14348, pp 409-419, 2023, doi:10.1007/978-981-99-7074-2_32

23-017
Sven Findeiß, Christoph Flamm, Yann Ponty
Rational Design of RiboNucleic Acids
Dagstuhl Reports, 12(9):121–149, 2023, doi:10.4230/DagRep.12.9.121

23-018
Nino Lauber, Ondřej Ticháček, Rudra Bose, Christoph Flamm, Luca Leuzzi, T-Y Dora Tang, Kepa Ruiz-Mirazo, Daniele De Martino
Statistical mechanics of biomolecular condensates via cavity methods
iScience 26:106300, 2023, doi:10.1016/j.isci.2023.106300

23-019
Badelt S, Lorenz R
A guide to computational cotranscriptional folding featuring the SRP RNA
bioRxiv (2023) page(s): 2023--06

23-020
Yao, H. T., Lorenz, R., Hofacker, I. L. & Stadler, P. F.
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
Biology. 18, 1, 8, doi:10.1186/s13015-023-00236-0

23-021
Darren Gemmill, Corey Nelson, Maulik Badmalia, Higor Pereira, Michael T. Wolfinger, and Trushar Patel
The 3’ terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17
Biochem. Cell Biol (2023), doi:10.1139/bcb-2023-0036

23-022
Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
A Structural Refinement Technique for Protein-RNA Complexes Using a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein
B. Chem. Soc. Jpn. 96(7):677–685 (2023), doi:10.1246/bcsj.20230092

23-023
Gemmill, D. L., Pereira, H. S., Badmalia, M. D., Nelson, C. R., Wolfinger, M. T. & Patel, T. R.
Identification and characterisation of G-quadruplexes from viral genomes
Biophysical Journal. 122, 3, S. 444A-444A Meeting Abstract: 2159-Plat

23-024
Fiedler, L., Bernt, M., Middendorf, M. & Stadler, P. F.
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs
BMC Bioinformatics. 24, 1, 235, doi:10.1186/s12859-023-05371-4

23-025
Avila Santos, A. P., Kabiru Nata’ala, M., Kasmanas, J. C., Bartholomäus, A., Keller-Costa, T., Jurburg, S. D., Tal, T., Camarinha-Silva, A., Saraiva, J. P., Ponce de Leon Ferreira de Carvalho, A. C., Stadler, P. F., Sipoli Sanches, D. & Rocha, U.
The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes
Animal Microbiome. 5, 1, 48, doi:10.1186/s42523-023-00267-3

23-026
Hellmuth, M., Schaller, D. & Stadler, P. F
Clustering systems of phylogenetic networks
Theory in Biosciences. 142, 4, S. 301-358 58 S, doi:10.1007/s12064-023-00398-w

23-027
Klapproth, C., Zötzsche, S., Kühnl, F., Fallmann, J., Stadler, P. F. & Findeiß, S., Sep. 2023
Tailored machine learning models for functional RNA detection in genome-wide screens
NAR: Genomics and Bioinformatics. 5, 3, S. lqad072 lqad072, doi:10.1093/nargab/lqad072

23-028
Hellmuth, M., Huber, K. T., Moulton, V., Scholz, G. E. & Stadler, P. F.
Injective Split Systems
Graphs and Combinatorics. 39, 4, 65, doi:10.1007/s00373-023-02660-w

23-029
Schaller, D., Geiss, M., Hellmuth, M. & Stadler, P. F.
Best Match Graphs with Binary Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics. 20, 3, S. 1679-1690, doi:10.1109/TCBB.2022.3143870

23-030
Kolberg, T., von Löhneysen, S., Ozerova, I., Wellner, K., Hartmann, R. K., Stadler, P. F. & Mörl, M.
Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA
Nucleic Acids Research. 51, 11, S. e63-e63, doi:10.1093/nar/gkad312

23-031
Seemann, C. R., Moulton, V., Stadler, P. F. & Hellmuth, M.
Planar median graphs and cubesquare-graphs
Discrete Applied Mathematics. 331, S. 38-58 21 S, doi:10.1016/j.dam.2023.01.022

23-032
Korchmaros, A., Schaller, D., Hellmuth, M. & Stadler, P. F.
Quasi-best match graphs
Discrete Applied Mathematics. 331, S. 104-125 22 S, doi:10.1016/j.dam.2023.01.015

23-033
Bran, A. M., Stadler, P. F., Jost, J. & Restrepo, G.
The six stages of the convergence of the periodic system to its final structure
Communications Chemistry. 6, 1, 87, doi:10.1038/s42004-023-00883-9

23-034
Santiago Arguello, A., Montellano-Ballesteros, J. J. & Stadler, P. F.
Hamiltonicity in power graphs of a class of abelian groups
Journal of Algebraic Combinatorics. 57, 1, S. 313-328 16 S, doi:10.1007/s10801-022-01172-9

23-035
González Laffitte, M. E., Beier, N., Domschke, N. & Stadler, P. F.
Comparison of Atom Maps
Match. 90, 1, S. 75-102 28 S, doi:10.46793/match.90-1.075G

23-036
Schaller, D., Hellmuth, M. & Stadler, P.
ORIENTATION OF FITCH GRAPHS AND RECONCILIATION-FREE INFERENCE OF HORIZONTAL GENE TRANSFER IN GENE TREES
SIAM Journal on Discrete Mathematics. 37, 3, S. 2172-2207

23-037
Domingo, E., Schuster, P., Elena, S. F. & Perales, C.
Viral Fitness and Evolution
Band 439. S. 341-344 (Current Topics in Microbiology and Immunology)

23-038
Schuster, P. & Stadler, P.
Virus Evolution on Fitness Landscapes
Band 439. S. 1-94 (Current Topics in Microbiology and Immunology)

23-039
Sangkhawasi, M., Kerdpol, K., Ismail, A., Nutho, B., Hanpiboon, C., Wolschann, P., Krusong, K., Rungrotmongkol, T. & Hannongbua, S.
In Vitro and In Silico Study on the Molecular Encapsulation of α-Tocopherol in a Large-Ring Cyclodextrin
International Journal of Molecular Sciences. 24, 5, 4425, doi:10.3390/ijms24054425

23-040
Avila Santos, A. P., Kabiru Nata’ala, M., Kasmanas, J. C., Bartholomäus, A., Keller-Costa, T., Jurburg, S. D., Tal, T., Camarinha-Silva, A., Saraiva, J. P., Ponce de Leon Ferreira de Carvalho, A. C., Stadler, P. F., Sipoli Sanches, D., Rocha, U.
The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes
Animal Microbiome. 5, 1, 48., doi:10.1186/s42523-023-00267-3

23-041
Klapproth, C., Zötzsche, S., Kühnl, F., Fallmann, J., Stadler, P. F. & Findeiß, S.
Tailored machine learning models for functional RNA detection in genome-wide screens
NAR: Genomics and Bioinformatics. 5, 3, S. lqad072 lqad072, doi:10.1093/nargab/lqad072

23-042
Anders, J. & Stadler, P. F.
RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions
Journal of Integrative Bioinformatics. 20, 3, 20220046, doi:10.1515/jib-2022-0046

23-043
Rocha, U., Coelho Kasmanas, J., Kallies, R., Saraiva, J. P., Toscan, R. B., Štefanič, P., Bicalho, M. F., Borim Correa, F., Baştürk, M. N., Fousekis, E., Viana Barbosa, L. M., Plewka, J., Probst, A. J., Baldrian, P. & Stadler, P. F.
MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy
Molecular Ecology Resources, doi:10.1111/1755-0998.13904

2022

22-001
Suriyan Thengyai, Yuewei Guo, Khanit Suwanborirux, Heinz Berner, Helmut Spreitzer, Peter Wolschann, Supa Hannongbua and Anuchit Plubrukarn
2D‐QSAR and CoMFA Models for Antitubercular Activity of Scalarane‐Type Sesterterpenes
Sci. Pharm. 2022, 90, 47, doi:10.3390/scipharm90030047

22-002
Amy Oo, Panupong Mahalapbutr, Kuakarun Krusong, Ponsiri Liangsakul, Sariyarach Thanasansurapong, Vichai Reutrakul, Chutima Kuhakarn, Phornphimon Maitarad, Atit Silsirivanit, Peter Wolschann, Siyaporn Putthisen, Khanittha Kerdpol, Thanyada Rungrotmongkol
Inclusion complexation of emodin with various b-cyclodextrin derivatives: Preparation, characterization, molecular docking, and anticancer activity
Journal of Molecular Liquids Volume 367, Part A, 1 December 2022, 120314, doi:10.1016/j.molliq.2022.120314

22-003
Stadler, P. F., & Will, S.
Bi-alignments with affine gaps costs.
Algorithms for Molecular Biology, 17(1), [10], doi:10.1186/s13015-022-00219-7

22-004
D'Souza, M. H., Mrozowich, T., Badmalia, M. D., Geeraert, M., Frederickson, A., Henrickson, A., Demeler, B., Wolfinger,M. T., & Patel, T. R.
Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats.
Nucleic Acids Research, 50(10), 5881-5898, doi:10.1093/nar/gkac414

22-005
Wortz, J., Smith, V., Fallmann, J., Koenig, S., Thuraisingam, T., Walther, P., Urlaub, H., Stadler, P. F., Allers, T., Hille, F., & Marchfelder, A.
Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair.
Frontiers in Microbiology, 13, [822304], doi:10.3389/fmicb.2022.822304

22-006
Engelhardt, J., Scheer, O., Stadler, P. F., & Prohaska, S. J.
Evolution of DNA Methylation Across Ecdysozoa.
Journal of Molecular Evolution, 90(1), 56-72, doi:10.1007/s00239-021-10042-0

22-007
Reinhardt, F., & Stadler, P. F.
ExceS-A: an exon-centric split aligner.
Journal of Integrative Bioinformatics, 19(1), doi:10.1515/jib-2021-0040

22-008
Flamm, C., Hellmuth, M., Merkle, D., Nojgaard, N., & Stadler, P. F.
Generic Context-Aware Group Contributions.
I E E E - A C M Transactions on Computational Biology and Bioinformatics, 19(1), 429-442, doi:10.1109/TCBB.2020.2998948

22-009
Gosavi, D., Wower, I., Beckmann, I. K., Hofacker, I. L., Wower, J., Wolfinger, M. T., & Sztuba-Solinska, J.
Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus internal Ribosome Entry Site.
RNA Biology, 19 (1), 496-506, doi:10.1080/15476286.2022.2058818

22-010
Ender, A., Grafl, N., Kolberg, T., Findeiss, S., Stadler, P. F., & Moerl, M.
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes.
RNA, 28(4), 551-567, doi:10.1261/rna.078814.121

22-011
Mrozowich, T., Park, S. M., Wolfinger, M. T., & Patel, T. R.
Investigating flaviviral genomic cyclization.
Biophysical Journal, 121(3), 311A-311A, doi:10.1016/j.bpj.2021.11.1203

22-012
Park, S. M., Mrozowich, T., Wolfinger, M. T., & Patel, T. R.
Investigating Japanese encephalitis virus long-range terminal region interactions.
Biophysical Journal, 121(3), 206A-206A, doi:10.1016/j.bpj.2021.11.1703

22-013
Kamonpan Sanachai, Tuanjai Somboon, Patcharin Wilasluck, Peerapon Deetanya, Peter Wolschann, Thierry Langer, Vannajan Sanghiran Lee, Kittikhun Wangkanont, Thanyada Rungrotmongkol, Supot Hannongbua
Identification of repurposing therapeutics toward SARS-CoV-2 main protease by virtual screening
PLoS ONE 17(6): e0269563, doi:10.1371/journal.pone.0269563

22-014
Anderson, J. L., Fagerberg, R., Flamm, C., Fontana, W., Kolcak, J., Laurent, C. V. F. P., Merkle, D. & Nojgaard, N.
Representing Catalytic Mechanisms with Rule Composition
Journal of Chemical Information and Modeling. 62, 22, S. 5513-5524 12 S., doi:10.1021/acs.jcim.2c00426

22-015
Müller, S., Flamm, C. & Stadler, P. F.
What makes a reaction network "chemical"?
Journal of Cheminformatics. 14, 1, 24 S., 63, doi:10.1186/s13321-022-00621-8

22-016
Hartman, T., Bannach, M., Middendorf, M., Stadler, P., Wieseke, N. & Hellmuth, M.
Complete edge-colored permutation graphs
Advances in Applied Mathematics. 139, 34 S., 102377., doi:10.1016/j.aam.2022.102377

22-017
Hellmuth, M., Schaller, D. & Stadler, P. F.
Compatibility of partitions with trees, hierarchies, and split systems
Discrete Applied Mathematics. 314, S. 265-283 19 S., doi:10.1016/j.dam.2022.03.014

22-018
Bruckmann, C., Stadler, P. F. & Hellmuth, M.
From modular decomposition trees to rooted median graphs
Discrete Applied Mathematics. 310, S. 1-9 9 S., doi:10.1016/j.dam.2021.12.017

22-019
Christoph Flamm, Julia Wielach, Michael T Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L Hofacker
Caveats to deep learning approaches to RNA secondary structure prediction.
Front Bioinf 2:835422, 2022 , doi:10.3389/fbinf.2022.835422

22-020
Nitchakan Darai, Panupong Mahalapbutr, Peter Wolschann, Vannajan Sanghiran Lee, Michael T. Wolﬁnger, Thanyada Rungrotmongkol
Theoretical studies on RNA recognition by Musashi 1 RNA–binding protein
Sci. Rep. 12:12137 (2022), doi:10.1038/s41598-022-16252-w

22-021
Marlena Rozner, Ella Nukarinen, Michael T. Wolfinger, Fabian Amman, Wolfram Weckwerth, Udo Blaesi, Elisabeth Sonnleitner
Rewiring of Gene Expression in Pseudomonas aeruginosa During Diauxic Growth Reveals an Indirect Regulation of the MexGHI-OpmD Efflux Pump by Hfq
Front. Microbiol. 13:919539 (2022), doi:10.3389/fmicb.2022.919539

22-022
Lena S. Kutschera, Michael T. Wolfinger
Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology
Virus Evol. (8):1 veac051 (2022), doi:10.1093/ve/veac051

22-023
Guzman, G. E. C., Stadler, P. F. & Fujita, A.
Efficient eigenvalue counts for tree-like networks
Journal of complex networks. 10, 5, 15 S., 040., doi:10.1093/comnet/cnac040

22-024
Santiago Arguello, A., Montellano-Ballesteros, J. J. & Stadler, P. F.
Hamiltonicity in power graphs of a class of abelian groups
Journal of Algebraic Combinatorics, doi:10.1007/s10801-022-01172-9

22-025
Nunn, A., Otto, C., Fasold, M., Stadler, P. F. & Langenberger, D.
Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches
BMC Genomics. 23, 1, 10 S., 477, doi:10.1186/s12864-022-08691-6

22-026
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.
Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes
Molecular Biology and Evolution. 39, 10, msac191, doi:10.1093/molbev/msac191

22-027
Sanachai, K., Mahalapbutr, P., Hengphasatporn, K., Shigeta, Y., Seetaha, S., Tabtimmai, L., Langer, T., Wolschann, P., Kittikool, T., Yotphan, S., Choowongkomon, K. & Rungrotmongkol, T.
Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus Kinases
ACS Omega. 7, 37, S. 33548-33559 12 S, doi:10.1021/acsomega.2c0453533548ACS

2021

21-001
S Zayni, S Damiati, S Moreno-Flores, F Amman, I Hofacker, D Jin, ...
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
Membranes 11 (10), 741, doi:10.3390/membranes11100741

21-002
MT Wolfinger, R Ochsenreiter, IL Hofacker
Functional RNA Structures in the 3′ UTR of Mosquito-Borne Flaviviruses
Virus Bioinformatics, 65-100, doi:10.1201/9781003097679-5

21-003
G Entzian, IL Hofacker, Y Ponty, R Lorenz, A Tanzer
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes
Bioinformatics 37 (15), 2126-2133, doi:10.1093/bioinformatics/btab066

21-004
Devadatta Gosavi, Iwona Wower, Irene K Beckmann, Ivo L Hofacker, Jacek Wower, Michael T Wolfinger, Joanna Sztuba-Solinska
Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
bioRxiv 2021.05.13.444024, doi:10.1101/2021.05.13.444024

21-005
Anastasia Cianciulli Sesso, Branislav Lilić, Fabian Amman, Michael T. Wolfinger, Elisabeth Sonnleitner, Udo Bläsi
Gene Expression Profiling of Pseudomonas Aeruginosa Upon Exposure to Colistin and Tobramycin
Front. Microbiol. 12:937 (2021), doi:10.3389/fmicb.2021.626715

21-006
Hayato Harima, Yasuko Orba, Shiho Torii, Yongjin Qiu, Masahiro Kajihara, Yoshiki Eto, Naoya Matsuta, Bernard M. Hang’ombe, Yuki Eshita, Kentaro Uemura, Keita Matsuno, Michihito Sasaki, Kentaro Yoshii, Ryo Nakao, William W. Hall, Ayato Takada, Takashi Abe, Michael T. Wolfinger, Martin Simuunza, Hirofumi Sawa
An African Tick Flavivirus Forming an Independent Clade Exhibits Unique Exoribonuclease-Resistant RNA Structures in the Genomic 3’-Untranslated Region
Sci. Rep. 11:4883 (2021), doi: 10.1038/s41598-021-84365-9

21-007
Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider, Michael T. Wolfinger
Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus
Genes 12 (2):239 (2021), doi:10.3390/genes12020239

21-008
Esther Heid, Samuel Goldman, Karthik Sankaranarayanan, Connor W Coley, Christoph Flamm, William H Green
EHreact: Extended Hasse diagrams for the extraction and scoring of enzymatic reaction templates
J Chem Inf Model Publication Date:September 29, 2021 Online ahead of print, doi:10.1021/acs.jcim.1c00921

21-009
Jakob L Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolčák, Christophe VFP Laurent, Daniel Merkle and Nikolai Nøjgaard
Graph Transformation for Enzymatic Mechanisms
Bioinformatics 37(1):i392-i400 2021, doi:10.1093/bioinformatics/btab296

21-010
Nino Lauber, Christoph Flamm, Kepa Ruiz-Mirazo
Minimal metabolism: a key concept to investigate the origins and nature of biological systems
BioEssays, 2021:2100201, doi:10.1002/bies.202100103

21-011
Ronny Lorenz, Christoph Flamm, Ivo L Hofacker Peter F Stadler
Efficient Algorithms for Co-folding of Multiple RNAs.
In: Ye X. et al. (eds) Biomedical Engeneering Systems and Technologies. BIOSTEC 2020. Communications in Computer and Information Science, vol 1400, pp 193-214, 2021 ISBN: 978-3-030-72378-1, doi:10.1007/978-3-030-72379-8_10

21-012
Kerdpol, K., Daengngern, R., Sattayanon, C., Namuangruk, S., Rungrotmongkol, T., Wolschann, P., Kungwan, N., Hannongbua, S.
Effect of Water Microsolvation on the Excited-State Proton Transfer of 3-Hydroxyflavone Enclosed in gamma-Cyclodextrin
Molecules, 26(4), [843], doi:10.3390/molecules26040843

21-013
Dienstbier, A., Amman, F., Petrackova, D., Stipl, D., Capek, J., Zavadilova, J., Fabianova, K., Drzmisek, J., Kumar, D., Wildung, M., Pouchnik, D., Vecerek, B.
Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution
Emerging infectious diseases, 27(1), 57-68, doi:10.3201/eid2701.191541

21-014
Lorenz, R., Stadler, P. F.
Rna secondary structures with limited base pair span: Exact backtracking and an application
Genes, 12(1), 1-9. [14], doi:10.3390/genes12010014

21-015
Ponty, Y., Hammer, S., Yao, H. T., Will, S.
Advanced Design of Structural RNAs Using RNARedPrint
in Methods in Molecular Biology (Band 2284, S. 1-15). Springer-Nature. Methods in Molecular Biology Band 2284, doi:10.1007/978-1-0716-1307-8_1

21-016
Anders, J., Petruschke, H., Jehmlich, N., Haange, S-B., von Bergen, M., Stadler, P. F.
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations
BMC Bioinformatics, 22 (1), [277], doi:10.1186/s12859-021-04159-8

21-017
Kolora, S. R. R., Gysi, D. M., Schaffer, S., Grimm-Seyfarth, A., Szabolcs, M., Faria, R., Henle, K., Stadler, P. F., Schlegel, M., Nowick, K.
Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards
Genome Biology and Evolution, 13(8), [109], doi:10.1093/gbe/evab109

21-018
Stadler, P. F.
Alignments of biomolecular contact maps
Interface Focus, 11(4), [20200066], doi:10.1098/rsfs.2020.0066

21-019
Vieira, L. M., Jorge, N. A. N., de Sousa, J. B., Setubal, J. C., Stadler, P. F., Walter, M. E. M. T.
Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction
Frontiers in Oncology , 11, [681579], doi:10.3389/fonc.2021.681579

21-020
Schaller, D., Geiss, M., Stadler, P. F., Hellmuth, M.
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs
Journal of Mathematical Biology, 82(3), [20], doi:10.1007/s00285-021-01564-8

21-021
Schaller, D., Stadler, P. F., Hellmuth, M.
Complexity of modification problems for best match graphs
Theoretical Computer Science, 865, 63-84, doi:10.1016/j.tcs.2021.02.037

21-022
Lipaeva, P., Vereshchagina, K., Drozdova, P., Jakob, L., Kondrateva, E., Lucassen, M., Bedulina, D., Timofeyev, M., Stadler, P., Luckenbach, T.
Different ways to play it cool: Transcriptomic analysis sheds light on different activity patterns of three amphipod species under long-term cold exposure
Molecular Ecology, doi:10.1111/mec.16164

21-023
Yaskolka Meir, A., Keller, M., Mueller, L., Bernhart, S. H., Tsaban, G., Zelicha, H., Rinott, E., Kaplan, A., Gepner, Y., Shelef, I., Schwarzfuchs, D., Ceglarek, U., Stadler, P., Blueher, M., Stumvoll, M., Kovacs, P., Shai, I.
Effects of lifestyle interventions on epigenetic signatures of liver fat: Central randomized controlled trial
Liver international, doi:10.1111/liv.14916

21-024
Leal, W., Restrepo, G., Stadler, P. F., Jost, J.
FORMAN-RICCI CURVATURE FOR HYPERGRAPHS
Advances in Complex Systems, 24(01), [2150003], doi:10.1142/S021952592150003X

21-025
Hellmuth, M., Seemann, C. R., Stadler, P. F.
Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees
Discrete mathematics and theoretical computer science, 23(1), [13], doi:10.46298/dmtcs.6040

21-026
Schaller, D., Geiss, M., Hellmuth, M., & Stadler, P. F.
Heuristic algorithms for best match graph editing
Algorithms for Molecular Biology, 16(1), [19], doi:10.1186/s13015-021-00196-3

21-027
Doncheva, N. T., Palasca, O., Yarani, R., Litman, T., Anthon, C., Groenen, M. A. M., Stadler, P. F., Pociot, F., Jensen, L. J.,Gorodkin, J.
Human pathways in animal models: possibilities and limitations
Nucleic Acids Research, 49(4), 1859-1871, doi:10.1093/nar/gkab012

21-028
Schaller, D., Lafond, M., Stadler, P. F., Wieseke, N., Hellmuth, M
Indirect identification of horizontal gene transfer
Journal of Mathematical Biology, 83(1), [10], doi:10.1007/s00285-021-01631-0

21-029
Gatter, T., von Loehneysen, S., Fallmann, J., Drozdova, P., Hartmann, T., Stadler, P. F
LazyB: fast and cheap genome assembly
Algorithms for Molecular Biology, 16(1), [8], doi:10.1186/s13015-021-00186-5

21-030
Yaskolka Meir, A., Keller, M., Bernhart, S. H., Rinott, E., Tsaban, G., Zelicha, H., Kaplan, A., Schwarzfuchs, D., Shelef, I., Gepner, Y., Li, J., Lin, Y., Blueher, M., Ceglarek, U., Stumvoll, M., Stadler, P. F., Stampfer, M. J., Kovacs, P., Liang, L., Shai, I.
Lifestyle weight-loss intervention may attenuate methylation aging: the CENTRAL MRI randomized controlled trial
Clinical epigenetics, 13(1), [48], doi:10.1186/s13148-021-01038-0

21-031
Ender, A., Etzel, M., Hammer, S., Findeiss, S., Stadler, P., Moerl, M.
Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch
Nucleic Acids Research, 49(3), 1784-1800, doi:10.1093/nar/gkaa1282

21-032
Velandia-Huerto, C. A., Fallmann, J., Stadler, P. F.
miRNAture-Computational Detection of microRNA Candidates
Genes, 12(3), [348], doi:10.3390/genes12030348

21-033
Bedulina, D., Drozdova, P., Gurkov, A., von Bergen, M., Stadler, P. F., Luckenbach, T., Timofeyev, M., Kalkhof, S.
Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus cyaneus
Science of the Total Environment, 763, [143008], doi:10.1016/j.scitotenv.2020.143008

21-034
Jakob, L., Vereshchagina, K. P., Tillmann, A., Rivarola-Duarte, L., Axenov-Gribanov, D., Bedulina, D. S., Gurkov, A. N., Drozdova, P., Timofeyev, M. A., Stadler, P. F., Luckenbach, T., Poertner, H-O., Sartoris, F. J., Lucassen, M.
Thermal reaction norms of key metabolic enzymes reflect divergent physiological and behavioral adaptations of closely related amphipod species
Scientific Reports, 11(1), [4562], doi:10.1038/s41598-021-83748-2

21-035
Schaller, D., Geiss, M., Chavez, E., Gonzalez Laffitte, M., Lopez Sanchez, A., Stadler, B. M. R., Valdivia, D. I., Hellmuth, M., Hernandez Rosales, M., Stadler, P. F.
Best match graphs (vol 78, 2015, 2019)
Journal of Mathematical Biology, 82(6), [47], doi:10.1007/s00285-021-01601-6

2020

20-001
Doo Nam Kim, Bernhard C. Thiel, Tyler Mrozowich, Scott P. Hennelly, Ivo L. Hofacker, Trushar R. Patel, Karissa Y. Sanbonmatsu
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution
Nature Communications volume 11, Article number: 148 (2020), doi:10.1038/s41467-019-13942-4

20-002
Kamonpan Sanachai, Panupong Mahalapbutr, Kiattawee Choowongkomon, Rungtiva P. Poo-arporn, Peter Wolschann, Thanyada Rungrotmongko
Insights into the Binding Recognition and Susceptibility of Tofacitinib toward Janus Kinases
ACS Omega 2020, 5, 1, 369-377, 2020, doi:10.1021/acsomega.9b0280076

20-003
Helmut Viernstein, Peter Wolschann
Cyclodextrin inclusion complexation and pharmaceutical applications
ScienceAsia 46 (2020): 254–262, doi:10.2306/scienceasia1513-1874.2020.048

20-004
Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, and Rolf Backofen
The locality dilemma of Sankoff-like RNA alignments
Bioinformatics, 36:i242–i250, 2020, doi:10.1093/bioinformatics/btaa431

20-005
Denisa Petrácková, Mariam R Farman, Fabian Amman, Irena Linhartová, Ana Dienstbier, Dilip Kumar, Jakub Drzmísek, Ivo L. Hofacker, Maria Eugenia Rodriguez, and Branislav Vecerek
Transcriptional profiling of human macrophages during infection with bordetella pertussis
RNA biology, 17:731–742, 2020, doi:10.1080/15476286.2020.1727694

20-006
Keating, Sarah M et al (+140 Coauthors)
SBML Level 3: an extensible format for the exchange and reuse of biological models
Mol Sys Biol 16(8):e9110 (2020), doi:10.15252/msb.20199110

20-007
Ronny Lorenz Christoph Flamm, Ivo L Hofacker Peter F Stadler
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) Vol 3, pp 23-31, 2020, ISBN: 978-989-758-398-8, doi:10.5220/0008916600230031

20-008
Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F Stadler
Generic Context-Aware Group Contributions
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2020, doi:10.1109/TCBB.2020.2998948

20-009
Christida E. Wastika, Hayato Harima, Michihito Sasaki, Bernard M. Hang'ombe, Yuki Eshita, Yongjin Qiu, William W. Hall, Michael T. Wolfinger, Hirofumi Sawa, Yasuko Orba
Discoveries of exoribonuclease-resistant structures of insect-specific flaviviruses isolated in Zambia
Viruses 12(9):1017 (2020), doi:10.3390/v12091017

20-010
Elisabeth Sonnleitner, Petra Pusic, Michael T. Wolfinger, Udo Bläsi
Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq
Front. Microbiol. 11:1001 (2020), doi:10.3389/fmicb.2020.01001

20-011
Balogh, G., Bernhart, S. H., Stadler, P. F. & Schor, J.
A probabilistic version of Sankoff's maximum parsimony algorithm
Journal of Bioinformatics and Computational Biology (JBCB). 18, 1, 19 S., 2050004, doi:10.1142/S0219720020500043

20-012
Nitsche, A., Arnold, C., Ueberham, U., Reiche, K., Fallmann, J., Hackermueller, J., Horn, F., Stadler, P. F. & Arendt, T.
Alzheimer-related genes show accelerated evolution
Molecular Psychiatry. 7 S., doi:10.1038/s41380-020-0680-1

20-013
Hordijk, W., Kauffman, S. A. & Stadler, P. F.
Average Fitness Differences on NK Landscapes
Theory in Biosciences. 139, 1, S. 1-7 7 S., doi:10.1007/s12064-019-00296-0

20-014
Geiss, M., Gonzalez Laffitte, M. E., Lopez Sanchez, A., Valdivia, D. I., Hellmuth, M., Hernandez Rosales, M. & Stadler, P. F.
Best match graphs and reconciliation of gene trees with species trees
Journal of Mathematical Biology. 37 S., doi:10.1007/s00285-020-01469-y

20-015
Hellmuth, M., Geiss, M. & Stadler, P. F.
Complexity of modification problems for reciprocal best match graphs
Theoretical Computer Science. 809, S. 384-393 10 S., doi:10.1016/j.tcs.2019.12.033

20-016
Hotarat, W., Nutho, B., Wolschann, P., Rungrotmongkol, T. & Hannongbua, S.
Delivery of Alpha-Mangostin Using Cyclodextrins through a Biological Membrane: Molecular Dynamics Simulation
Molecules. 25, 11, 17 S., 2532, doi:10.3390/molecules25112532

20-017
Breitfeld, J., Kehr, S., Mueller, L., Stadler, P. F., Boettcher, Y., Blueher, M., Stumvoll, M. & Kovacs, P.
Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity
Frontiers in Endocrinology. 11, 18 S., 138, doi:10.3389/fendo.2020.00138

20-018
Long, Y. & Stadler, P.
Exact-2-relation graphs
Discrete Applied Mathematics. 285, S. 212-226 15 S., doi:10.1016/j.dam.2020.05.015

20-019
Stadler, P. F., Geiss, M., Schaller, D., Sanchez, A. L., Laffitte, M. G., Valdivia, D. I., Hellmuth, M. & Rosales, M. H.
From pairs of most similar sequences to phylogenetic best matches
Algorithms for Molecular Biology. 15, 1, 20 S., 5., doi:10.1186/s13015-020-00165-2

20-020
Vilardo, E., Amman, F., Toth, U., Kotter, A., Helm, M. & Rossmanith, W.
Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B
Nucleic Acids Research. 48, 11, S. 6157-6169 13 S., doi:10.1093/nar/gkaa353

20-021
Hellmuth, M., Seemann, C. R. & Stadler, P. F.
Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees
Discrete Applied Mathematics. 283, S. 495-511 17 S, doi:10.1016/j.dam.2020.01.036

20-022
Berkemer, S. J., Maier, L-K., Amman, F., Bernhart, S. H., Woertz, J., Maerkle, P., Pfeiffer, F., Stadler, P. F. & Marchfelder, A.
Identification of RNA 3 ' ends and termination sites in Haloferax volcanii
RNA Biology. 14 S., doi:10.1080/15476286.2020.1723328

20-023
Binder, S., Zipfel, I., Friedrich, M., Riedel, D., Ende, S., Kaempf, C., Wiedemann, K., Buschmann, T., Puppel, S-H., Reiche, K., Stadler, P. F. & Horn, F.
Master and servant: LINC00152-a STAT3-induced long noncoding RNA regulates STAT3 in a positive feedback in human multiple myeloma
Bmc medical genomics. 13, 1, 13 S., doi:10.1186/s12920-020-0692-3

20-024
Entzian, G. & Raden, M.
pourRNA-a time- and memory-efficient approach for the guided exploration of RNA energy landscapes
Bioinformatics. 36, 2, S. 462-469 8 S., doi:10.1093/bioinformatics/btz583

20-025
Antonio Corona-Gomez, J., Jair Garcia-Lopez, I., Stadler, P. F. & Fernandez-Valverde, S. L.
Splicing conservation signals in plant long noncoding RNAs
RNA. 26, 7, S. 784-793 10 S., doi:10.1261/rna.074393.119

20-026
Kammarabutr, J., Mahalapbutr, P., Okumura, H., Wolschann, P. & Rungrotmongkol, T.
Structural dynamics and susceptibility of anti-HIV drugs against HBV reverse transcriptase
Journal of biomolecular structure & dynamics. 10 S., doi:10.1080/07391102.2020.1751715

20-027
Shatilina, Z., Drozdova, P., Bedulina, D., Rivarola-Duarte, L., Schreiber, S., Otto, C., Juehling, F., Aulhorn, S., Busch, W., Lubyaga, Y., Kondrateva, E., Pobezhimova, T., Jakob, L., Lucassen, M., Sartoris, F. J., Hackermueller, J., Poertner, H-O., Stadler, P. F., Luckenbach, T. & Timofeyev, M.
Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species
Comparative biochemistry and physiology d-Genomics & proteomics. 33, 7 S., 100630., doi:10.1016/j.cbd.2019.100630

20-028
Erber, L., Hoffmann, A., Fallmann, J., Hagedorn, M., Hammann, C., Stadler, P. F., Betat, H., Prohaska, S. & Moerl, M.
Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes inDictyostelium discoideum
International Journal of Molecular Sciences. 21, 15, 16 S., 5210, doi:10.3390/ijms21155210

20-029
Seal, R. L., Chen, L-L., Griffiths-Jones, S., Lowe, T. M., Mathews, M. B., O'Reilly, D., Pierce, A. J., Stadler, P. F., Ulitsky, I., Wolin, S. L. & Bruford, E. A.
A guide to naming human non-coding RNA genes
MBO Journal. 39, 6, 18 S., 103777, doi:10.15252/embj.2019103777

20-030
Alexandra Popa, Jakob-Wendelin Genger, Michael Nicholson, Thomas Penz, Daniela Schmid, Stephan W Aberle, Benedikt Agerer, Alexander Lercher, Lukas Endler, Henrique Colaco, Mark Smyth, Michael Schuster, Miguel L. Grau, Francisco Martinez-Jimenez, Oriol Pich, Wegene Borena, Erich Pawelka, Zsofia Keszei, Martin Senekowitsch, Jan Laine, Judith H Aberle, Monika Redlberger-Fritz, Mario Karolyi, Alexander Zoufaly, Sabine Maritschnik, Martin Borkovec, Peter Hufnagl, Manfred Nairz, Günter Weiss, Michael T. Wolfinger, Dorothee von Laer, Giulio Superti-Furga, Nuria Lopez-Bigas, Elisabeth Puchhammer-Stöckl, Franz Allerberger, Franziska Michor, Christoph Bock, Andreas Bergthaler
Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2
Sci. Transl. Med. eabe2555 (2020), doi:10.1126/scitranslmed.abe2555

20-031
Waldl M., Will S., Wolfinger M.T., Hofacker I.L., Stadler P.F.
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2019. Lecture Notes in Computer Science, vol 12313. Springer, Cham., doi:10.1007/978-3-030-63061-4_15

20-032
Sen, R., Fallmann, J., Walter, M. E. M. T. & Stadler, P. F.
Are spliced ncRNA host genes distinct classes of lncRNAs?
Theory in Biosciences. 11 S., doi:10.1007/s12064-020-00330-6

20-033
Guenzel, C., Kuehnl, F., Arnold, K., Findeiss, S., Weinberg, C. E., Stadler, P. F. & Moerl, M.
Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches
RNA Biology. 11 S., doi:10.1080/15476286.2020.1816336

20-034
Keller, M., Yaskolka Meir, A., Bernhart, S. H., Gepner, Y., Shelef, I., Schwarzfuchs, D., Tsaban, G., Zelicha, H., Hopp, L., Mueller, L., Rohde, K., Boettcher, Y., Stadler, P. F., Stumvoll, M., Blueher, M., Kovacs, P. & Shai, I.
DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial
Genome Medicine. 12, 1, 18 S., 97., doi:10.1186/s13073-020-00794-7

20-035
Miladi, M., Raden, M., Will, S. & Backofen, R.
Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains
Algorithms for Molecular Biology. 15, 1, 11 S., 19., doi:10.1186/s13015-020-00179-w

20-036
Schwarz, T. S., Berkemer, S. J., Bernhart, S. H., Weiss, M., Ferreira-Cerca, S., Stadler, P. F. & Marchfelder, A.
Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea
Frontiers in Microbiology. 11, 15 S., 594838., doi:10.3389/fmicb.2020.594838