Works by Stadler, Peter F.

Results: 309

Crossover operators for molecular graphs with an application to virtual drug screening.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00958-w

By:

Domschke, Nico;
Schmidt, Bruno J.;
Gatter, Thomas;
Golnik, Richard;
Eisenhuth, Paul;
Liessmann, Fabian;
Meiler, Jens;
Stadler, Peter F.

Publication type:

Article

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs.

Published in:

Human Mutation, 2013, v. 34, n. 6, p. 925, doi. 10.1002/humu.22323

By:

Sabarinathan, Radhakrishnan;
Tafer, Hakim;
Seemann, Stefan E.;
Hofacker, Ivo L.;
Stadler, Peter F.;
Gorodkin, Jan

Publication type:

Article

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs.

Published in:

Human Mutation, 2013, v. 34, n. 4, p. 546, doi. 10.1002/humu.22273

By:

Sabarinathan, Radhakrishnan;
Tafer, Hakim;
Seemann, Stefan E.;
Hofacker, Ivo L.;
Stadler, Peter F.;
Gorodkin, Jan

Publication type:

Article

Computational design of RNAs with complex energy landscapes.

Published in:

Biopolymers, 2013, v. 99, n. 12, p. 1124, doi. 10.1002/bip.22337

By:

Höner zu Siederdissen, Christian;
Hammer, Stefan;
Abfalter, Ingrid;
Hofacker, Ivo L.;
Flamm, Christoph;
Stadler, Peter F.

Publication type:

Article

Combinatorial vector fields and the valley structure of fitness landscapes.

Published in:

Journal of Mathematical Biology, 2010, v. 61, n. 6, p. 877, doi. 10.1007/s00285-010-0326-z

By:

Stadler, Bärbel M. R.;
Stadler, Peter F.

Publication type:

Article

Pseudoknots in RNA folding landscapes.

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 187, doi. 10.1093/bioinformatics/btv572

By:

Kucharík, Marcel;
Hofacker, Ivo L.;
Stadler, Peter F.;
Jing Qin

Publication type:

Article

SHAPE directed RNA folding.

Published in:

Bioinformatics, 2016, v. 32, n. 1, p. 145, doi. 10.1093/bioinformatics/btv523

By:

Lorenz, Ronny;
Luntzer, Dominik;
Hofacker, Ivo L.;
Stadler, Peter F.;
Wolfinger, Michael T.

Publication type:

Article

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.

Published in:

Bioinformatics, 2014, v. 30, n. 14, p. 2009

By:

Kucharík, Marcel;
Hofacker, Ivo L.;
Stadler, Peter F.;
Qin, Jing

Publication type:

Article

Lacking alignments? The next-generation sequencing mapper segemehl revisited.

Published in:

Bioinformatics, 2014, v. 30, n. 13, p. 1837, doi. 10.1093/bioinformatics/btu146

By:

Otto, Christian;
Stadler, Peter F.;
Hoffmann, Steve

Publication type:

Article

Challenges in RNA virus bioinformatics.

Published in:

Bioinformatics, 2014, v. 30, n. 13, p. 1793, doi. 10.1093/bioinformatics/btu105

By:

Marz, Manja;
Beerenwinkel, Niko;
Drosten, Christian;
Fricke, Markus;
Frishman, Dmitrij;
Hofacker, Ivo L.;
Hoffmann, Dieter;
Middendorf, Martin;
Rattei, Thomas;
Stadler, Peter F.;
Töpfer, Armin

Publication type:

Article

snoStrip: a snoRNA annotation pipeline.

Published in:

Bioinformatics, 2014, v. 30, n. 1, p. 115, doi. 10.1093/bioinformatics/btt604

By:

Bartschat, Sebastian;
Kehr, Stephanie;
Tafer, Hakim;
Stadler, Peter F.;
Hertel, Jana

Publication type:

Article

Fast and sensitive mapping of bisulfite-treated sequencing data.

Published in:

Bioinformatics, 2012, v. 28, n. 13, p. 1698, doi. 10.1093/bioinformatics/bts254

By:

Otto, Christian;
Stadler, Peter F.;
Hoffmann, Steve

Publication type:

Article

Addendum: topology and prediction of RNA pseudoknots.

Published in:

Bioinformatics, 2012, v. 28, n. 2, p. 300, doi. 10.1093/bioinformatics/btr643

By:

Reidys, Christian M.;
Huang, Fenix W. D.;
Andersen, Jørgen E.;
Penner, Robert C.;
Stadler, Peter F.;
Nebel, Markus E.

Publication type:

Article

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

Published in:

Bioinformatics, 2012, v. 28, n. 1, p. 17, doi. 10.1093/bioinformatics/btr598

By:

Langenberger, David;
Pundhir, Sachin;
Ekstrøm, Claus T.;
Stadler, Peter F.;
Hoffmann, Steve;
Gorodkin, Jan

Publication type:

Article

Fast accessibility-based prediction of RNA–RNA interactions.

Published in:

Bioinformatics, 2011, v. 27, n. 14, p. 1934, doi. 10.1093/bioinformatics/btr281

By:

Tafer, Hakim;
Amman, Fabian;
Eggenhofer, Florian;
Stadler, Peter F.;
Hofacker, Ivo L.

Publication type:

Article

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

Published in:

Bioinformatics, 2011, v. 27, n. 14, p. 1894, doi. 10.1093/bioinformatics/btr314

By:

Rose, Dominic;
Hiller, Michael;
Schutt, Katharina;
Hackermüller, Jörg;
Backofen, Rolf;
Stadler, Peter F.

Publication type:

Article

A folding algorithm for extended RNA secondary structures.

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. i129, doi. 10.1093/bioinformatics/btr220

By:

zu Siederdissen, Christian Höner;
Bernhart, Stephan H.;
Stadler, Peter F.;
Hofacker, Ivo L.

Publication type:

Article

Topology and prediction of RNA pseudoknots.

Published in:

Bioinformatics, 2011, v. 27, n. 8, p. 1076, doi. 10.1093/bioinformatics/btr090

By:

Reidys, Christian M.;
Huang, Fenix W. D.;
Andersen, Jørgen E.;
Penner, Robert C.;
Stadler, Peter F.;
Nebel, Markus E.

Publication type:

Article

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.

Published in:

Bioinformatics, 2011, v. 27, n. 3, p. 317, doi. 10.1093/bioinformatics/btq651

By:

Menzel, Peter;
Stadler, Peter F.;
Gorodkin, Jan

Publication type:

Article

PLEXY: efficient target prediction for box C/D snoRNAs.

Published in:

Bioinformatics, 2011, v. 27, n. 2, p. 279, doi. 10.1093/bioinformatics/btq642

By:

Kehr, Stephanie;
Bartschat, Sebastian;
Stadler, Peter F.;
Tafer, Hakim

Publication type:

Article

RNAsnoop: efficient target prediction for H/ACA snoRNAs.

Published in:

Bioinformatics, 2010, v. 26, n. 5, p. 610, doi. 10.1093/bioinformatics/btp680

By:

Tafer, Hakim;
Kehr, Stephanie;
Hertel, Jana;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

Target prediction and a statistical sampling algorithm for RNA–RNA interaction.

Published in:

Bioinformatics, 2010, v. 26, n. 2, p. 175, doi. 10.1093/bioinformatics/btp635

By:

Huang, Fenix W. D.;
Jing Qin;
Reidys, Christian M.;
Stadler, Peter F.

Publication type:

Article

Partition function and base pairing probabilities for RNA–RNA interaction prediction.

Published in:

Bioinformatics, 2009, v. 25, n. 20, p. 2646, doi. 10.1093/bioinformatics/btp481

By:

Huang, Fenix W. D.;
Qin, Jing;
Reidys, Christian M.;
Stadler, Peter F.

Publication type:

Article

Evidence for human microRNA-offset RNAs in small RNA sequencing data.

Published in:

Bioinformatics, 2009, v. 25, n. 18, p. 2298, doi. 10.1093/bioinformatics/btp419

By:

Langenberger, David;
Bermudez-Santana, Clara;
Hertel, Jana;
Hoffmann, Steve;
Khaitovich, Philipp;
Stadler, Peter F.

Publication type:

Article

Structural profiles of human miRNA families from pairwise clustering.

Published in:

Bioinformatics, 2009, v. 25, n. 3, p. 291, doi. 10.1093/bioinformatics/btn628

By:

Bogumil Kaczkowski;
Elfar Torarinsson;
Kristin Reiche;
Jakob Hull Havgaard;
Peter F. Stadler;
Jan Gorodkin

Publication type:

Article

SnoReport: computational identification of snoRNAs with unknown targets.

Published in:

Bioinformatics, 2008, v. 24, n. 2, p. 158, doi. 10.1093/bioinformatics/btm464

By:

Jana Hertel;
Ivo L. Hofacker;
Peter F. Stadler

Publication type:

Article

CREx: inferring genomic rearrangements based on common intervals.

Published in:

Bioinformatics, 2007, v. 23, n. 21, p. 2957, doi. 10.1093/bioinformatics/btm468

By:

Matthias Bernt;
Daniel Merkle;
Kai Ramsch;
Guido Fritzsch;
Marleen Perseke;
Detlef Bernhard;
Martin Schlegel;
Peter F. Stadler;
Martin Middendorf

Publication type:

Article

Thermodynamics of RNA–RNA binding.

Published in:

Bioinformatics, 2006, v. 22, n. 10, p. 1177, doi. 10.1093/bioinformatics/btl024

By:

Ulrike Mückstein;
Hakim Tafer;
Jörg Hackermüller;
Stephan H. Bernhart;
Peter F. Stadler;
Ivo L. Hofacker

Publication type:

Article

Memory efficient folding algorithms for circular RNA secondary structures.

Published in:

Bioinformatics, 2006, v. 22, n. 10, p. 1172, doi. 10.1093/bioinformatics/btl023

By:

Ivo L. Hofacker;
Peter F. Stadler

Publication type:

Article

Local RNA base pairing probabilities in large sequences.

Published in:

Bioinformatics, 2006, v. 22, n. 5, p. 614, doi. 10.1093/bioinformatics/btk014

By:

Stephan H. Bernhart;
Ivo L. Hofacker;
Peter F. Stadler

Publication type:

Article

Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-29400-y

By:

Kamm, Kai;
Osigus, Hans-Jürgen;
Stadler, Peter F.;
DeSalle, Rob;
Schierwater, Bernd

Publication type:

Article

Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair.

Published in:

Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.822304

By:

Wörtz, Julia;
Smith, Victoria;
Fallmann, Jörg;
König, Sabine;
Thuraisingam, Tharani;
Walther, Paul;
Urlaub, Henning;
Stadler, Peter F.;
Allers, Thorsten;
Hille, Frank;
Marchfelder, Anita

Publication type:

Article

Inferring chemical reaction patterns using rule composition in graph grammars.

Published in:

Journal of Systems Chemistry, 2013, v. 4, n. 1, p. 1, doi. 10.1186/1759-2208-4-4

By:

Andersen, Jakob L.;
Flamm, Christoph;
Merkle, Daniel;
Stadler, Peter F.

Publication type:

Article

Evolution of metabolic networks: a computational frame-work.

Published in:

Journal of Systems Chemistry, 2010, v. 1, n. 1, p. 1, doi. 10.1186/1759-2208-1-4

By:

Flamm, Christoph;
Ullrich, Alexander;
Ekker, Heinz;
Mann, Martin;
Högerl, Daniel;
Rohrschneider, Markus;
Sauer, Sebastian;
Scheuermann, Gerik;
Klemm, Konstantin;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

miRNAture —Computational Detection of microRNA Candidates.

Published in:

Genes, 2021, v. 12, n. 3, p. 348, doi. 10.3390/genes12030348

By:

Velandia-Huerto, Cristian A.;
Fallmann, Jörg;
Stadler, Peter F.;
Bortoluzzi, Stefania

Publication type:

Article

RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application.

Published in:

Genes, 2021, v. 12, n. 1, p. 14, doi. 10.3390/genes12010014

By:

Lorenz, Ronny;
Stadler, Peter F.

Publication type:

Article

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes.

Published in:

Genes, 2018, v. 9, n. 8, p. 372, doi. 10.3390/genes9080372

By:

Waldl, Maria;
Thiel, Bernhard C.;
Ochsenreiter, Roman;
Wolfinger, Michael T.;
Stadler, Peter F.;
Holzenleiter, Alexander;
de Araujo Oliveira, João Victor;
Walter, Maria Emília M. T.

Publication type:

Article

Clustering Rfam 10.1: Clans, Families, and Classes.

Published in:

Genes, 2012, v. 3, n. 3, p. 378, doi. 10.3390/genes3030378

By:

Lessa, Felipe A.;
Raiol, Tainá;
Brigido, Marcelo M.;
Martins Neto, Daniele S. B.;
Walter, Maria Emíilia M. T.;
Stadler, Peter F.

Publication type:

Article

Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions.

Published in:

Genes, 2011, v. 2, n. 4, p. 912, doi. 10.3390/genes2040912

By:

Parikesit, Arli A.;
Stadler, Peter F.;
Prohaska, Sonja J.

Publication type:

Article

Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02199-6

By:

Hoser, Simon M.;
Hoffmann, Anne;
Meindl, Andreas;
Gamper, Maximilian;
Fallmann, Jörg;
Bernhart, Stephan H.;
Müller, Lisa;
Ploner, Melanie;
Misslinger, Matthias;
Kremser, Leopold;
Lindner, Herbert;
Geley, Stephan;
Schaal, Heiner;
Stadler, Peter F.;
Huettenhofer, Alexander

Publication type:

Article

Finding the <italic>K</italic> best synthesis plans.

Published in:

Journal of Cheminformatics, 2018, v. 10, n. 1, p. 1, doi. 10.1186/s13321-018-0273-z

By:

Fagerberg, Rolf;
Flamm, Christoph;
Kianian, Rojin;
Merkle, Daniel;
Stadler, Peter F.

Publication type:

Article

Convexity Deficit of Benzenoids.

Published in:

Croatica Chemica Acta, 2019, v. 92, n. 4, p. 457, doi. 10.5562/cca3602

By:

Bašić, Nino;
Berkemer, Sarah J.;
Fallmann, Jörg;
Fowler, Patrick W.;
Gatter, Thomas;
Pisanski, Tomaž;
Retzlaff, Nancy;
Stadler, Peter F.;
Zemljič, Sara Sabrina

Publication type:

Article

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control.

Published in:

Nature Genetics, 2015, v. 47, n. 11, p. 1316, doi. 10.1038/ng.3413

By:

Kretzmer, Helene;
Bernhart, Stephan H;
Bergmann, Anke K;
Doose, Gero;
Jühling, Frank;
Otto, Christian;
Eberth, Sonja;
Eils, Roland;
Stadler, Peter F;
Hoffmann, Steve;
Wang, Wei;
Hovestadt, Volker;
Picelli, Simone;
Lichter, Peter;
Radlwimmer, Bernhard;
Drexler, Hans G;
MacLeod, Roderick A F;
Flicek, Paul;
Haas, Siegfried;
Hummel, Michael

Publication type:

Article

Bcheck: a wrapper tool for detecting RNase P RNA genes.

Published in:

BMC Genomics, 2010, v. 11, p. 432, doi. 10.1186/1471-2164-11-432

By:

Yusuf, Dilmurat;
Marz, Manja;
Stadler, Peter F.;
Hofacker, Ivo L.

Publication type:

Article

Genomic organization of eukaryotic tRNAs.

Published in:

BMC Genomics, 2010, v. 11, p. 270, doi. 10.1186/1471-2164-11-270

By:

Bermudez-Santana, Clara;
Attolini, Camille Stephan-Otto;
Kirsten, Toralf;
Engelhardt, Jan;
Prohaska, Sonja J.;
Steigele, Stephan;
Stadler, Peter F.

Publication type:

Article

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum.

Published in:

BMC Genomics, 2009, v. 10, p. 464, doi. 10.1186/1471-2164-10-464

By:

Copeland, Claudia C.;
Marz, Manja;
Rose, Dominic;
Hertel, Jana;
Brindley, Paul J.;
Santana, Clara Bermudez;
Kehr, Stephanie;
Attolini, Camille Stephan-Otto;
Stadler, Peter F.

Publication type:

Article

Comparative promoter region analysis powered by CORG.

Published in:

BMC Genomics, 2005, v. 6, p. 24, doi. 10.1186/1471-2164-6-24

By:

Dieterich, Christoph;
Grossmann, Steffen;
Tanzer, Andrea;
Röpcke, Stefan;
Arndt, Peter F;
Stadler, Peter F.;
Vingron, Martin

Publication type:

Article

Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05371-4

By:

Fiedler, Lisa;
Bernt, Matthias;
Middendorf, Martin;
Stadler, Peter F.

Publication type:

Article

Non-coding RNAs in Ciona intestinalis.

Published in:

Bioinformatics, 2005, v. 21, p. ii77, doi. 10.1093/bioinformatics/bti1113

By:

Missal, Kristin;
Rose, Dominic;
Stadler, Peter F.

Publication type:

Article

Multiple sequence alignment with user-defined constraints at GOBICS.

Published in:

Bioinformatics, 2005, v. 21, n. 7, p. 1271, doi. 10.1093/bioinformatics/bti142

By:

Burkhard Morgenstern;
Nadine Werner;
Sonja J. Prohaska;
Rasmus Steinkamp;
Isabelle Schneider;
Amarendran R. Subramanian;
Peter F. Stadler;
Jan Weyer-Menkhoff

Publication type:

Article