Publications by authors named "Peter F Stadler"

100Publications

Beyond Plug and Pray: Context Sensitivity and Design of Artificial Neomycin Riboswitches.

RNA Biol 2020 Sep 3. Epub 2020 Sep 3.

Institute for Biochemistry, Leipzig University , Brüderstraße 34, D-04103 Leipzig, Germany.

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http://dx.doi.org/10.1080/15476286.2020.1816336DOI Listing
September 2020

MCPIP1 ribonuclease can bind and cleave mRNA in -amplified neuroblastoma cells.

RNA Biol 2020 Aug 20:1-13. Epub 2020 Aug 20.

Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Kraków, Poland.

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http://dx.doi.org/10.1080/15476286.2020.1804698DOI Listing
August 2020

Generic Context-Aware Group Contributions.

IEEE/ACM Trans Comput Biol Bioinform 2020 Jun 1;PP. Epub 2020 Jun 1.

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http://dx.doi.org/10.1109/TCBB.2020.2998948DOI Listing
June 2020

Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in .

Int J Mol Sci 2020 Jul 23;21(15). Epub 2020 Jul 23.

Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany.

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http://dx.doi.org/10.3390/ijms21155210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7432833PMC
July 2020

Distinct abdominal and gluteal adipose tissue transcriptome signatures are altered by exercise training in African women with obesity.

Sci Rep 2020 Jun 24;10(1):10240. Epub 2020 Jun 24.

Division of Exercise Science and Sports Medicine, Department of Human Biology, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1038/s41598-020-66868-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314771PMC
June 2020

A probabilistic version of Sankoff's maximum parsimony algorithm.

J Bioinform Comput Biol 2020 02;18(1):2050004

Young Investigators Group Bioinformatics and Transcriptomics, Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, D-04318 Leipzig, Germany.

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http://dx.doi.org/10.1142/S0219720020500043DOI Listing
February 2020

From pairs of most similar sequences to phylogenetic best matches.

Algorithms Mol Biol 2020 9;15. Epub 2020 Apr 9.

CONACYT-Instituto de Matemáticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230 Juriquilla, Querétaro, QRO México.

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http://dx.doi.org/10.1186/s13015-020-00165-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147060PMC
April 2020

Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity.

Front Endocrinol (Lausanne) 2020 26;11:138. Epub 2020 Mar 26.

University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.3389/fendo.2020.00138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115744PMC
March 2020

Splicing conservation signals in plant long noncoding RNAs.

RNA 2020 Jul 2;26(7):784-793. Epub 2020 Apr 2.

Unidad de Genómica Avanzada, Langebio, Cinvestav, 36821 Irapuato, Guanajuato, Mexico.

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http://dx.doi.org/10.1261/rna.074393.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297117PMC
July 2020

Alzheimer-related genes show accelerated evolution.

Mol Psychiatry 2020 Mar 13. Epub 2020 Mar 13.

Paul Flechsig Institute of Brain Research, Liebigstraße 19, 04103, Leipzig, Germany.

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http://dx.doi.org/10.1038/s41380-020-0680-1DOI Listing
March 2020

A guide to naming human non-coding RNA genes.

EMBO J 2020 Mar 24;39(6):e103777. Epub 2020 Feb 24.

Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.

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http://dx.doi.org/10.15252/embj.2019103777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073466PMC
March 2020

Best match graphs and reconciliation of gene trees with species trees.

J Math Biol 2020 04 30;80(5):1459-1495. Epub 2020 Jan 30.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.

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http://dx.doi.org/10.1007/s00285-020-01469-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052050PMC
April 2020

Enrichment and identification of small proteins in a simplified human gut microbiome.

J Proteomics 2020 02 10;213:103604. Epub 2019 Dec 10.

Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Systems Biology, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2019.103604DOI Listing
February 2020

flowEMMi: an automated model-based clustering tool for microbial cytometric data.

BMC Bioinformatics 2019 Dec 9;20(1):643. Epub 2019 Dec 9.

Department of Environmental Microbiology, Research Group Flow Cytometry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, 04318, Germany.

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http://dx.doi.org/10.1186/s12859-019-3152-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6902487PMC
December 2019

Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits.

Sci Rep 2019 11 26;9(1):17561. Epub 2019 Nov 26.

University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany.

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http://dx.doi.org/10.1038/s41598-019-54037-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879607PMC
November 2019

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.

Nucleic Acids Res 2020 01;48(D1):D626-D632

Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Saxony 04318, Germany.

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http://dx.doi.org/10.1093/nar/gkz994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145636PMC
January 2020

Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species.

Comp Biochem Physiol Part D Genomics Proteomics 2020 03 31;33:100630. Epub 2019 Oct 31.

Institute of Biology, Irkutsk State University, Lenin str. 3, RUS-664003 Irkutsk, Russia; Baikal Research Centre, Lenin str. 21, RUS-664003 Irkutsk, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.cbd.2019.100630DOI Listing
March 2020

Reciprocal best match graphs.

J Math Biol 2020 02 30;80(3):865-953. Epub 2019 Oct 30.

Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany.

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http://dx.doi.org/10.1007/s00285-019-01444-2DOI Listing
February 2020

Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.

Nucleic Acids Res 2019 11;47(20):10543-10552

Swarm Intelligence and Complex Systems, Department of Computer Science, Universität Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.

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http://dx.doi.org/10.1093/nar/gkz833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6847864PMC
November 2019

Selection Pressures on RNA Sequences and Structures.

Evol Bioinform Online 2019 29;15:1176934319871919. Epub 2019 Aug 29.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany.

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http://journals.sagepub.com/doi/10.1177/1176934319871919
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http://dx.doi.org/10.1177/1176934319871919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6716170PMC
August 2019

A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking .

Biotechniques 2019 10 29;67(4):178-183. Epub 2019 Aug 29.

Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany.

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http://dx.doi.org/10.2144/btn-2019-0047DOI Listing
October 2019

DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation.

Nucleic Acids Res 2019 09;47(17):9087-9103

Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany.

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http://dx.doi.org/10.1093/nar/gkz635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753476PMC
September 2019

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species.

BMC Evol Biol 2019 07 8;19(1):138. Epub 2019 Jul 8.

Department of Bioanalytical Ecotoxicology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318, Leipzig, Germany.

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http://dx.doi.org/10.1186/s12862-019-1470-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6613252PMC
July 2019

Average Fitness Differences on NK Landscapes.

Theory Biosci 2020 Feb 18;139(1):1-7. Epub 2019 Jun 18.

Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany.

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http://dx.doi.org/10.1007/s12064-019-00296-0DOI Listing
February 2020

Exploration of the chemical space and its three historical regimes.

Proc Natl Acad Sci U S A 2019 06 11;116(26):12660-12665. Epub 2019 Jun 11.

Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany;

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http://dx.doi.org/10.1073/pnas.1816039116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600933PMC
June 2019

The RNA workbench 2.0: next generation RNA data analysis.

Nucleic Acids Res 2019 07;47(W1):W511-W515

Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany.

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http://dx.doi.org/10.1093/nar/gkz353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602469PMC
July 2019

Automatic curation of large comparative animal MicroRNA datasets.

Bioinformatics 2019 11;35(22):4553-4559

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz271DOI Listing
November 2019

Ryūtō: network-flow based transcriptome reconstruction.

BMC Bioinformatics 2019 Apr 16;20(1):190. Epub 2019 Apr 16.

Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-019-2786-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469118PMC
April 2019

Best match graphs.

J Math Biol 2019 06 9;78(7):2015-2057. Epub 2019 Apr 9.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.

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http://dx.doi.org/10.1007/s00285-019-01332-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534531PMC
June 2019

SSS-test: a novel test for detecting positive selection on RNA secondary structure.

BMC Bioinformatics 2019 Mar 21;20(1):151. Epub 2019 Mar 21.

Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, Königin-Luise-Straße 1-3, Berlin, 14195, Germany.

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http://dx.doi.org/10.1186/s12859-019-2711-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429701PMC
March 2019

Identification and characterization of novel conserved RNA structures in Drosophila.

BMC Genomics 2018 Dec 11;19(1):899. Epub 2018 Dec 11.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870, Denmark.

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http://dx.doi.org/10.1186/s12864-018-5234-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288889PMC
December 2018

Superbubbles revisited.

Algorithms Mol Biol 2018 1;13:16. Epub 2018 Dec 1.

1Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Universität Leipzig, Augustusplatz 12, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/s13015-018-0134-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6271648PMC
December 2018

Patterning the insect eye: From stochastic to deterministic mechanisms.

PLoS Comput Biol 2018 11 15;14(11):e1006363. Epub 2018 Nov 15.

Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.

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http://dx.plos.org/10.1371/journal.pcbi.1006363
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http://dx.doi.org/10.1371/journal.pcbi.1006363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6264902PMC
November 2018

Coordinate systems for supergenomes.

Algorithms Mol Biol 2018 24;13:15. Epub 2018 Sep 24.

1Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Universität Leipzig, Augustusplatz 12, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/s13015-018-0133-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151955PMC
September 2018

RNApuzzler: efficient outerplanar drawing of RNA-secondary structures.

Bioinformatics 2019 04;35(8):1342-1349

Image and Signal Processing Group, Department of Computer Science, Leipzig University, Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty817DOI Listing
April 2019

Noncoding RNA Transcripts during Differentiation of Induced Pluripotent Stem Cells into Hepatocytes.

Stem Cells Int 2018 19;2018:5692840. Epub 2018 Aug 19.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstr. 1618, 04107 Leipzig, Germany.

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https://www.hindawi.com/journals/sci/2018/5692840/
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http://dx.doi.org/10.1155/2018/5692840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120260PMC
August 2018

Nonprotein-Coding RNAs as Regulators of Development in Tunicates.

Results Probl Cell Differ 2018;65:197-225

Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.

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http://dx.doi.org/10.1007/978-3-319-92486-1_11DOI Listing
July 2019

The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments.

BMC Res Notes 2018 Jul 28;11(1):512. Epub 2018 Jul 28.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.

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http://dx.doi.org/10.1186/s13104-018-3633-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6064048PMC
July 2018

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes.

Genes (Basel) 2018 Jul 26;9(8). Epub 2018 Jul 26.

Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.3390/genes9080372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6115765PMC
July 2018

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

Sci Rep 2018 07 24;8(1):11168. Epub 2018 Jul 24.

University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany.

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http://dx.doi.org/10.1038/s41598-018-29400-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057997PMC
July 2018

Split-inducing indels in phylogenomic analysis.

Algorithms Mol Biol 2018 16;13:12. Epub 2018 Jul 16.

2Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/s13015-018-0130-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047143PMC
July 2018

Chemical Transformation Motifs-Modelling Pathways as Integer Hyperflows.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar-Apr;16(2):510-523. Epub 2017 Dec 11.

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http://dx.doi.org/10.1109/TCBB.2017.2781724DOI Listing
January 2020

Reconstructing gene trees from Fitch's xenology relation.

J Math Biol 2018 11 27;77(5):1459-1491. Epub 2018 Jun 27.

Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany.

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http://dx.doi.org/10.1007/s00285-018-1260-8DOI Listing
November 2018

Cover-Encodings of Fitness Landscapes.

Bull Math Biol 2018 08 12;80(8):2154-2176. Epub 2018 Jun 12.

Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 04103, Leipzig, Germany.

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http://dx.doi.org/10.1007/s11538-018-0451-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061522PMC
August 2018

Phylogenetics beyond biology.

Theory Biosci 2018 Nov 21;137(2):133-143. Epub 2018 Jun 21.

Max-Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany.

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http://dx.doi.org/10.1007/s12064-018-0264-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208858PMC
November 2018

Rare Splice Variants in Long Non-Coding RNAs.

Noncoding RNA 2017 Jul 5;3(3). Epub 2017 Jul 5.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.3390/ncrna3030023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831916PMC
July 2017

Finding the K best synthesis plans.

J Cheminform 2018 Apr 5;10(1):19. Epub 2018 Apr 5.

Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090, Vienna, Austria.

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http://dx.doi.org/10.1186/s13321-018-0273-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5887019PMC
April 2018

Time-consistent reconciliation maps and forbidden time travel.

Algorithms Mol Biol 2018 6;13. Epub 2018 Feb 6.

1Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Strasse 47, 17487 Greifswald, Germany.

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http://dx.doi.org/10.1186/s13015-018-0121-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5800358PMC
February 2018

Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration.

J Exp Zool B Mol Dev Evol 2018 01 22;330(1):5-14. Epub 2018 Jan 22.

Santa Fe Institute, Santa Fe, New Mexico.

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http://dx.doi.org/10.1002/jez.b.22785DOI Listing
January 2018

Comparative RNA Genomics.

Methods Mol Biol 2018 ;1704:363-400

Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://link.springer.com/10.1007/978-1-4939-7463-4_14
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http://dx.doi.org/10.1007/978-1-4939-7463-4_14DOI Listing
December 2018

Gene Phylogenies and Orthologous Groups.

Methods Mol Biol 2018 ;1704:1-28

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.

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http://dx.doi.org/10.1007/978-1-4939-7463-4_1DOI Listing
August 2018

Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem.

J Math Biol 2018 08 19;77(2):313-341. Epub 2017 Dec 19.

Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany.

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http://dx.doi.org/10.1007/s00285-017-1197-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060901PMC
August 2018

Accurate mapping of tRNA reads.

Bioinformatics 2018 04;34(7):1116-1124

Department of Theoretical Chemistry of the University of Vienna, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btx756DOI Listing
April 2018

Detailed secondary structure models of invertebrate 7SK RNAs.

RNA Biol 2018 02 21;15(2):158-164. Epub 2017 Dec 21.

a Bioinformatics Group, Department of Computer Science , Leipzig University , Härtelstraße 16-18, Leipzig , Germany.

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http://dx.doi.org/10.1080/15476286.2017.1412913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798955PMC
February 2018

Inferring phylogenetic trees from the knowledge of rare evolutionary events.

J Math Biol 2018 06 7;76(7):1623-1653. Epub 2017 Dec 7.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center of Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany.

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http://dx.doi.org/10.1007/s00285-017-1194-6DOI Listing
June 2018

The fungal snoRNAome.

RNA 2018 03 1;24(3):342-360. Epub 2017 Dec 1.

Young Investigators Group Bioinformatics and Transcriptomics, Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ, D-04318 Leipzig, Germany.

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http://dx.doi.org/10.1261/rna.062778.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5824354PMC
March 2018

Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1.

J Theor Biol 2018 02 23;438:143-150. Epub 2017 Nov 23.

TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, Leipzig, D-04107, Germany; Paul-Flechsig-Institute for Brain Research, University of Leipzig, Jahnallee 59, Leipzig, D-04109, Germany; Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, 04107, Germany; Bioinformatics, Faculty of Agricultural Sciences, Institute of Animal Science, University of Hohenheim, Garbenstrasse 13, Stuttgart, 70593, Germany; Freie Universität Berlin, Faculty for Biology, Chemistry, and Pharmacy, Institute for Biology, Königin-Luise-Strasse 1-3, Berlin, 14195, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2017.11.015DOI Listing
February 2018

An intermediate level of abstraction for computational systems chemistry.

Philos Trans A Math Phys Eng Sci 2017 Dec;375(2109)

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig D-04107, Germany.

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http://dx.doi.org/10.1098/rsta.2016.0354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5686410PMC
December 2017

SMORE: Synteny Modulator of Repetitive Elements.

Life (Basel) 2017 Oct 31;7(4). Epub 2017 Oct 31.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.3390/life7040042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745555PMC
October 2017

Keeping it complicated: Mitochondrial genome plasticity across diplonemids.

Sci Rep 2017 10 26;7(1):14166. Epub 2017 Oct 26.

Department of biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, 2900 Edouard-Montpetit, Montreal, H3T 1J4, QC, Canada.

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http://dx.doi.org/10.1038/s41598-017-14286-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658414PMC
October 2017

Tractable RNA-ligand interaction kinetics.

BMC Bioinformatics 2017 Oct 16;18(Suppl 12):424. Epub 2017 Oct 16.

Department of Computer Science and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstr. 16-18, Leipzig, D-04107, Germany.

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http://dx.doi.org/10.1186/s12859-017-1823-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657077PMC
October 2017

A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts.

BMC Genomics 2017 Oct 18;18(1):804. Epub 2017 Oct 18.

Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Hartelstrasse 16-18, Leipzig, D-04107, Germany.

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http://dx.doi.org/10.1186/s12864-017-4178-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5648457PMC
October 2017

Similarity-Based Segmentation of Multi-Dimensional Signals.

Sci Rep 2017 09 27;7(1):12355. Epub 2017 Sep 27.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig, Härtelstrasse 16-18, D-04107, Leipzig, Germany.

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http://dx.doi.org/10.1038/s41598-017-12401-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617875PMC
September 2017

Design of Artificial Riboswitches as Biosensors.

Sensors (Basel) 2017 Aug 30;17(9). Epub 2017 Aug 30.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.

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http://dx.doi.org/10.3390/s17091990DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5621056PMC
August 2017

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements.

Algorithms Mol Biol 2017 23;12:22. Epub 2017 Aug 23.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/s13015-017-0113-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569537PMC
August 2017

Recent advances in RNA folding.

J Biotechnol 2017 Nov 8;261:97-104. Epub 2017 Jul 8.

Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria; RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany; Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jbiotec.2017.07.007DOI Listing
November 2017

Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes.

BMC Evol Biol 2017 07 6;17(1):163. Epub 2017 Jul 6.

Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.

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http://dx.doi.org/10.1186/s12862-017-1001-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501109PMC
July 2017

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation.

J Biotechnol 2017 Nov 26;261:76-84. Epub 2017 May 26.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria; RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany; Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA.

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http://dx.doi.org/10.1016/j.jbiotec.2017.05.019DOI Listing
November 2017

Molecular Phylogenetics 2016.

Biomed Res Int 2016 29;2016:9029306. Epub 2016 Dec 29.

Bioinformatics, Institute for Informatics, Leipzig University, Leipzig, Germany.

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http://dx.doi.org/10.1155/2016/9029306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5227124PMC
February 2017

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.

Nucleic Acids Res 2017 05;45(8):e60

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkw1325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416843PMC
May 2017

Evolution of Fungal U3 snoRNAs: Structural Variation and Introns.

Noncoding RNA 2017 Jan 5;3(1). Epub 2017 Jan 5.

Helmholtz Centre for Environmental Research-UFZ, Young Investigators Group Bioinformatics and Transcriptomics Permoserstraße 15, D-04318 Leipzig, Germany.

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http://dx.doi.org/10.3390/ncrna3010003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832005PMC
January 2017

Applicability of a computational design approach for synthetic riboswitches.

Nucleic Acids Res 2017 04;45(7):4108-4119

Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany.

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http://dx.doi.org/10.1093/nar/gkw1267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397205PMC
April 2017

The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations.

J Math Biol 2017 07 30;75(1):199-237. Epub 2016 Nov 30.

Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Johannisgasse 26, 04103 , Leipzig, Germany.

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http://dx.doi.org/10.1007/s00285-016-1084-3DOI Listing
July 2017

Phylogenetic distribution of plant snoRNA families.

BMC Genomics 2016 11 24;17(1):969. Epub 2016 Nov 24.

Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany.

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http://dx.doi.org/10.1186/s12864-016-3301-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5122169PMC
November 2016

Design specifications for cellular regulation.

Theory Biosci 2016 Dec 18;135(4):231-240. Epub 2016 Nov 18.

Bioinformatics Group at the Department of Computer Science, Interdisciplinary Center for Bioinformatics, ScaDS, Competence Center for Scalable Data services and Solutions, and German Center for Integrative Biodiversity Research, University Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany.

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http://dx.doi.org/10.1007/s12064-016-0239-5DOI Listing
December 2016

Accurate annotation of protein-coding genes in mitochondrial genomes.

Mol Phylogenet Evol 2017 01 28;106:209-216. Epub 2016 Sep 28.

Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04103 Leipzig, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2016.09.024DOI Listing
January 2017

Sound-meaning association biases evidenced across thousands of languages.

Proc Natl Acad Sci U S A 2016 09 12;113(39):10818-23. Epub 2016 Sep 12.

Department of Psychology, Cornell University, Ithaca, NY 14853; Interacting Minds Centre, Aarhus University, 8000 Aarhus C, Denmark.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047153PMC
http://dx.doi.org/10.1073/pnas.1605782113DOI Listing
September 2016

Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum.

BMC Genomics 2016 08 30;17:691. Epub 2016 Aug 30.

Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C, Colombia.

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http://dx.doi.org/10.1186/s12864-016-2934-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006418PMC
August 2016