@Proceedings{belazzougui_et_al:LIPIcs.WABI.2023,
title = {{LIPIcs, Volume 273, WABI 2023, Complete Volume}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {1--400},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023},
URN = {urn:nbn:de:0030-drops-186250},
doi = {10.4230/LIPIcs.WABI.2023},
annote = {Keywords: LIPIcs, Volume 273, WABI 2023, Complete Volume}
}
@InProceedings{belazzougui_et_al:LIPIcs.WABI.2023.0,
author = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
title = {{Front Matter, Table of Contents, Preface, Conference Organization}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {0:i--0:xiv},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.0},
URN = {urn:nbn:de:0030-drops-186267},
doi = {10.4230/LIPIcs.WABI.2023.0},
annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
@InProceedings{przytycka:LIPIcs.WABI.2023.1,
author = {Przytycka, Teresa M.},
title = {{Algorithmic Approaches to Study Mutational Processes in Cancer}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {1:1--1:2},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.1},
URN = {urn:nbn:de:0030-drops-186278},
doi = {10.4230/LIPIcs.WABI.2023.1},
annote = {Keywords: Biological Networks, Cancer, Mutational Signatures, DNA Damage, DNA Repair}
}
@InProceedings{shen_et_al:LIPIcs.WABI.2023.2,
author = {Shen, Chengze and Liu, Baqiao and Williams, Kelly P. and Warnow, Tandy},
title = {{EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {2:1--2:2},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.2},
URN = {urn:nbn:de:0030-drops-186285},
doi = {10.4230/LIPIcs.WABI.2023.2},
annote = {Keywords: Multiple sequence alignment, constraint alignment, MAFFT}
}
@InProceedings{wedell_et_al:LIPIcs.WABI.2023.3,
author = {Wedell, Eleanor and Shen, Chengze and Warnow, Tandy},
title = {{BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {3:1--3:2},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.3},
URN = {urn:nbn:de:0030-drops-186296},
doi = {10.4230/LIPIcs.WABI.2023.3},
annote = {Keywords: Phylogenetic Placement, EPA-ng, Phylogenetics}
}
@InProceedings{arasti_et_al:LIPIcs.WABI.2023.4,
author = {Arasti, Shayesteh and Mirarab, Siavash},
title = {{Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {4:1--4:20},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.4},
URN = {urn:nbn:de:0030-drops-186309},
doi = {10.4230/LIPIcs.WABI.2023.4},
annote = {Keywords: Phylogenetics, Gene tree discordance, Quartet score, Quartet distance, Subtree prune and regraft, Tree search, ASTRAL}
}
@InProceedings{dai_et_al:LIPIcs.WABI.2023.5,
author = {Dai, Junyan and Rubel, Tobias and Han, Yunheng and Molloy, Erin K.},
title = {{Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {5:1--5:23},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.5},
URN = {urn:nbn:de:0030-drops-186312},
doi = {10.4230/LIPIcs.WABI.2023.5},
annote = {Keywords: phylogenetics, parsimony, Dollo, Camin-Sokal, dynamic programming, constraints}
}
@InProceedings{gorecki_et_al:LIPIcs.WABI.2023.6,
author = {G\'{o}recki, Pawe{\l} and Rutecka, Natalia and Mykowiecka, Agnieszka and Paszek, Jaros{\l}aw},
title = {{Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {6:1--6:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.6},
URN = {urn:nbn:de:0030-drops-186329},
doi = {10.4230/LIPIcs.WABI.2023.6},
annote = {Keywords: Genomic Duplication, Gene-Species Mapping, Duplication Episode, Gene Tree, Species Tree}
}
@InProceedings{vaniersel_et_al:LIPIcs.WABI.2023.7,
author = {van Iersel, Leo and Jones, Mark and Julien, Esther and Murakami, Yukihiro},
title = {{Making a Network Orchard by Adding Leaves}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {7:1--7:20},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.7},
URN = {urn:nbn:de:0030-drops-186333},
doi = {10.4230/LIPIcs.WABI.2023.7},
annote = {Keywords: Phylogenetics, Network, Orchard Networks, Proximity Measures, NP-hardness}
}
@InProceedings{han_et_al:LIPIcs.WABI.2023.8,
author = {Han, Yunheng and Molloy, Erin K.},
title = {{Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {8:1--8:2},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.8},
URN = {urn:nbn:de:0030-drops-186347},
doi = {10.4230/LIPIcs.WABI.2023.8},
annote = {Keywords: Tumor Phylogenetics, Cell Lineage Trees, Quartets, Supertrees, ASTRAL}
}
@InProceedings{roddur_et_al:LIPIcs.WABI.2023.9,
author = {Roddur, Mrinmoy Saha and Snir, Sagi and El-Kebir, Mohammed},
title = {{Inferring Temporally Consistent Migration Histories}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {9:1--9:22},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.9},
URN = {urn:nbn:de:0030-drops-186357},
doi = {10.4230/LIPIcs.WABI.2023.9},
annote = {Keywords: Metastasis, Migration, Integer Linear Programming, Maximum parsimony}
}
@InProceedings{rizzo_et_al:LIPIcs.WABI.2023.10,
author = {Rizzo, Nicola and C\'{a}ceres, Manuel and M\"{a}kinen, Veli},
title = {{Finding Maximal Exact Matches in Graphs}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {10:1--10:17},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.10},
URN = {urn:nbn:de:0030-drops-186364},
doi = {10.4230/LIPIcs.WABI.2023.10},
annote = {Keywords: Sequence to graph alignment, bidirectional BWT, r-index, suffix tree, founder graphs}
}
@InProceedings{qiu_et_al:LIPIcs.WABI.2023.11,
author = {Qiu, Yutong and Shen, Yihang and Kingsford, Carl},
title = {{Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {11:1--11:22},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.11},
URN = {urn:nbn:de:0030-drops-186374},
doi = {10.4230/LIPIcs.WABI.2023.11},
annote = {Keywords: Integer Linear Programming, Genome Graphs, Flow Network, Graph Comparison}
}
@InProceedings{rajput_et_al:LIPIcs.WABI.2023.12,
author = {Rajput, Jyotshna and Chandra, Ghanshyam and Jain, Chirag},
title = {{Co-Linear Chaining on Pangenome Graphs}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {12:1--12:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.12},
URN = {urn:nbn:de:0030-drops-186389},
doi = {10.4230/LIPIcs.WABI.2023.12},
annote = {Keywords: Sequence alignment, variation graph, genome sequencing, path cover}
}
@InProceedings{hong_et_al:LIPIcs.WABI.2023.13,
author = {Hong, Aaron and Oliva, Marco and K\"{o}ppl, Dominik and Bannai, Hideo and Boucher, Christina and Gagie, Travis},
title = {{Acceleration of FM-Index Queries Through Prefix-Free Parsing}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {13:1--13:16},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.13},
URN = {urn:nbn:de:0030-drops-186390},
doi = {10.4230/LIPIcs.WABI.2023.13},
annote = {Keywords: FM-index, pangenomics, scalability, word-based indexing, random access}
}
@InProceedings{schulz_et_al:LIPIcs.WABI.2023.14,
author = {Schulz, Tizian and Medvedev, Paul},
title = {{Exact Sketch-Based Read Mapping}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {14:1--14:19},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.14},
URN = {urn:nbn:de:0030-drops-186403},
doi = {10.4230/LIPIcs.WABI.2023.14},
annote = {Keywords: Sequence Sketching, Long-read Mapping, Exact Algorithm, Dynamic Programming}
}
@InProceedings{rouze_et_al:LIPIcs.WABI.2023.15,
author = {Rouz\'{e}, Timoth\'{e} and Martayan, Igor and Marchet, Camille and Limasset, Antoine},
title = {{Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {15:1--15:27},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.15},
URN = {urn:nbn:de:0030-drops-186414},
doi = {10.4230/LIPIcs.WABI.2023.15},
annote = {Keywords: k-mer, subsampling, sketching, Jaccard, containment, metagenomics}
}
@InProceedings{khan_et_al:LIPIcs.WABI.2023.16,
author = {Khan, Jamshed and Rubel, Tobias and Dhulipala, Laxman and Molloy, Erin and Patro, Rob},
title = {{Fast, Parallel, and Cache-Friendly Suffix Array Construction}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {16:1--16:21},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.16},
URN = {urn:nbn:de:0030-drops-186424},
doi = {10.4230/LIPIcs.WABI.2023.16},
annote = {Keywords: Suffix Array, Longest Common Prefix, Data Structures, Indexing, Parallel Algorithms}
}
@InProceedings{rahman_et_al:LIPIcs.WABI.2023.17,
author = {Rahman, Amatur and Dufresne, Yoann and Medvedev, Paul},
title = {{Compression Algorithm for Colored de Bruijn Graphs}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {17:1--17:14},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.17},
URN = {urn:nbn:de:0030-drops-186434},
doi = {10.4230/LIPIcs.WABI.2023.17},
annote = {Keywords: colored de Bruijn graphs, disk compression, k-mer sets, simplitigs, spectrum-preserving string sets}
}
@InProceedings{fan_et_al:LIPIcs.WABI.2023.18,
author = {Fan, Jason and Singh, Noor Pratap and Khan, Jamshed and Pibiri, Giulio Ermanno and Patro, Rob},
title = {{Fulgor: A Fast and Compact \{k-mer\} Index for Large-Scale Matching and Color Queries}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {18:1--18:21},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.18},
URN = {urn:nbn:de:0030-drops-186446},
doi = {10.4230/LIPIcs.WABI.2023.18},
annote = {Keywords: k-mers, Colored de Bruijn Graph, Compression, Read-mapping}
}
@InProceedings{gray_et_al:LIPIcs.WABI.2023.19,
author = {Gray, Mateo and Will, Sebastian and Jabbari, Hosna},
title = {{SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {19:1--19:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.19},
URN = {urn:nbn:de:0030-drops-186454},
doi = {10.4230/LIPIcs.WABI.2023.19},
annote = {Keywords: RNA, MFE, Secondary Structure Prediction, Dangle, Sparsification, Space Complexity, Time Complexity}
}
@InProceedings{boury_et_al:LIPIcs.WABI.2023.20,
author = {Boury, Th\'{e}o and Ponty, Yann and Reinharz, Vladimir},
title = {{Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {20:1--20:22},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.20},
URN = {urn:nbn:de:0030-drops-186460},
doi = {10.4230/LIPIcs.WABI.2023.20},
annote = {Keywords: Subgraph Isomorphism, 3D RNA, Parameterized Complexity, Tree Decomposition, Boltzmann sampling, Neighborhood metrics, Kink-Turn family}
}
@InProceedings{gu_et_al:LIPIcs.WABI.2023.21,
author = {Gu, Xinyu and Qi, Yuanyuan and El-Kebir, Mohammed},
title = {{Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {21:1--21:20},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.21},
URN = {urn:nbn:de:0030-drops-186479},
doi = {10.4230/LIPIcs.WABI.2023.21},
annote = {Keywords: Multi-objective optimization, dynamic programming, RNA sequence design, reverse translation, mRNA vaccine design}
}
@InProceedings{bohnenkamper:LIPIcs.WABI.2023.22,
author = {Bohnenk\"{a}mper, Leonard},
title = {{Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {22:1--22:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.22},
URN = {urn:nbn:de:0030-drops-186484},
doi = {10.4230/LIPIcs.WABI.2023.22},
annote = {Keywords: Comparative Genomics, Genome Rearrangement, Double-Cut-And-Join, Indels, Integer Linear Programming, Capping}
}
@InProceedings{ferdosi_et_al:LIPIcs.WABI.2023.23,
author = {Ferdosi, Mohsen and Ge, Yuejun and Kingsford, Carl},
title = {{Reinforcement Learning for Robotic Liquid Handler Planning}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {23:1--23:16},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.23},
URN = {urn:nbn:de:0030-drops-186494},
doi = {10.4230/LIPIcs.WABI.2023.23},
annote = {Keywords: Liquid Handler, Reinforcement Learning, Planning}
}
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