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ORCIDAlgorithms for Molecular Biology, Volume 16
Volume 16, Number 1, December 2021
- Peter Røgen
:
Quantifying steric hindrance and topological obstruction to protein structure superposition. 1 - Jens Zentgraf, Sven Rahmann:
Fast lightweight accurate xenograft sorting. 2 - Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin:
Improving metagenomic binning results with overlapped bins using assembly graphs. 3 - Diego P. Rubert, Fábio Viduani Martinez, Marília D. V. Braga:
Natural family-free genomic distance. 4 - Cong Ma, Hongyu Zheng, Carl Kingsford:
Exact transcript quantification over splice graphs. 5 - Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher:
Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. 6 - Fenix W. D. Huang, Christopher L. Barrett, Christian M. Reidys:
The energy-spectrum of bicompatible sequences. 7 - Thomas Gatter, Sarah von Löhneysen, Jörg Fallmann, Polina Drozdova, Tom Hartmann, Peter F. Stadler:
LazyB: fast and cheap genome assembly. 8 - Katharina Jahn, Niko Beerenwinkel, Louxin Zhang:
The Bourque distances for mutation trees of cancers. 9 - Amatur Rahman, Rayan Chikhi, Paul Medvedev:
Disk compression of k-mer sets. 10 - Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger, Gunnar W. Klau:
Using the longest run subsequence problem within homology-based scaffolding. 11 - Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy J. Warnow:
Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation. 12 - Trevor S. Frisby, Christopher James Langmead:
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution. 13 - Leah L. Weber, Mohammed El-Kebir:
Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors. 14 - Leonie Selbach, Tobias Kowalski, Klaus Gerwert, Maike Buchin, Axel Mosig:
Shape decomposition algorithms for laser capture microdissection. 15 - Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson:
Approximate search for known gene clusters in new genomes using PQ-trees. 16 - Hooman Zabeti, Nick C. Dexter, Amir Hosein Safari, Nafiseh Sedaghat, Maxwell W. Libbrecht, Leonid Chindelevitch:
INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis. 17 - Naveed Ahmed Azam, Jianshen Zhu, Yanming Sun, Yu Shi, Aleksandar Shurbevski, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming. 18 - David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Heuristic algorithms for best match graph editing. 19 - Fabian Hausmann, Stefan Kurtz:
DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention. 20 - Gabriel Siqueira, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Zanoni Dias:
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions. 21 - David Fernández-Baca, Lei Liu:
Testing the agreement of trees with internal labels. 22 - David Schaller, Marc Hellmuth, Peter F. Stadler:
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set. 23 - Klairton Lima Brito, Andre Rodrigues Oliveira, Alexsandro Oliveira Alexandrino, Ulisses Dias, Zanoni Dias:
An improved approximation algorithm for the reversal and transposition distance considering gene order and intergenic sizes. 24 - Tim Anderson, Travis J. Wheeler:
An optimized FM-index library for nucleotide and amino acid search. 25
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