Paper Review Records
All Paper Review Records
10 valid samples · Newest publication first
Review days = acceptance date − received date. PDF, DOI, and publisher-page sources are retained.
Extension of partial atom-to-atom maps: uniqueness and algorithms
AuthorsMarcos E. González Laffitte; Tieu-Long Phan; Peter F. Stadler
Affiliations1. Center for Scalable Data Analytics and Artificial Intelligence Dresden-Leipzig (ScaDS.AI), Leipzig University, Leipzig, Germany; 2. Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Leipzig, Germany; 3. Department of Mathematics and Computer Science, University of Southern Denmark, Funen, Odense, Denmark; 4. Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; 5. Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; 6. Facultad de Ciencias, Universidad National de Colombia, Bogotá, Colombia; 7. Santa Fe Institute, Santa Fe, USA
Lossless pangenome indexing using tag arrays
AuthorsParsa Eskandar; Benedict Paten; Jouni Sirén
Affiliations1. UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
Dolphyin: a combinatorial algorithm for identifying 1-Dollo phylogenies in cancer
AuthorsDaniel W. Feng; Mohammed El-Kebir
Affiliations1. Department of Biomedical Informatics, Harvard Medical School, Boston, USA; 2. Siebel School of Computing and Data Science, University of Illinois Urbana-Champaign, Urbana, USA; 3. Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, USA
Probing transcription factor subsets in gene regulatory networks
AuthorsLukas Geis; Dennis Hecker; Martin Hoefer; Ulrich Meyer; Marcel H. Schulz
Affiliations1. Institute of Computer Science, Goethe University Frankfurt, Frankfurt am Main, Germany; 2. Institute for Computational Genomic Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany; 3. Department of Computer Science, RWTH Aachen, Aachen, Germany
Comparing the ability of embedding methods on metabolic hypergraphs for capturing taxonomy-based features
AuthorsMattia Cervellini; Blerina Sinaimeri; Catherine Matias; Alessio Martino
Affiliations1. Department of AI, Data and Decision Sciences, LUISS University, Rome, Italy; 2. Laboratoire de Probabilités, Statistique et Modélisation, Sorbonne Université, Paris, France; 3. Université de Paris Cité, Paris, France; 4. Centre National de la Recherche Scientifique, Paris, France
Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs
AuthorsRocco Ascone; Giulia Bernardini; Alessio Conte; Massimo Equi; Esteban Gabory; Roberto Grossi; Nadia Pisanti
Affiliations1. University of Trieste, Trieste , Italy; 2. University of Milan, Milan , Italy; 3. University of Pisa, Pisa , Italy; 4. University of Helsinki, Helsinki , Finland; 5. CWI Amsterdam, Amsterdam, Netherlands; 6. University of Palermo, Palermo, Italy
An efficient algorithm for exploring RNA branching conformations under the nearest-neighbor thermodynamic model
AuthorsSvetlana Poznanović; Owen Cardwell; Christine Heitsch
Affiliations1. School of Mathematical and Statistical Sciences, Clemson University, Clemson, USA; 2. Department of Mathematics, University of Bonn, Bonn, Germany; 3. School of Mathematics, Georgia Institute of Technology, Atlanta, USA
Inferring and summarizing tumor phylogenies from bulk DNA data
AuthorsYuanyuan Qi; Henri Schmidt; Mohammed El-Kebir
Affiliations1. Siebel School of Computing and Data Science, University of Illinois Urbana-Champaign, Urbana, USA; 2. Department of Computer Science, Princeton University, Princeton, USA; 3. Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, USA
Orientability of undirected phylogenetic networks to a desired class: practical algorithms and application to tree-child orientation
AuthorsTsuyoshi Urata; Manato Yokoyama; Haruki Miyaji; Momoko Hayamizu
Affiliations1. Department of Pure and Applied Mathematics, Graduate School of Fundamental Science and Engineering, Waseda University, Tokyo, Japan; 2. Department of Applied Mathematics, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
Computing double-pushout graph transformation rules and atom-to-atom maps from KEGG RCLASS data
AuthorsNora Beier; Thomas Gatter; Jakob L. Andersen; Peter F. Stadler
Affiliations1. Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany; 2. Department of Mathematics and Computer Science, University of Southern Denmark, Odense M, Denmark; 3. Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; 4. Department of Theoretical Chemistry, University of Vienna, Vienna, Austria; 5. Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia; 6. Santa Fe Institute, Santa Fe, USA; 7. Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
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