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Algorithms for Molecular Biology, Volume 11
Volume 11, 2016
- Henrike Indrischek
, Nicolas Wieseke, Peter F. Stadler
The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. 1 - Jean P. Zukurov, Sieberth do Nascimento-Brito, Angela C. Volpini
Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage. 2 - Guillaume Holley, Roland Wittler, Jens Stoye
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage. 3 - Manuel Lafond, Riccardo Dondi, Nadia El-Mabrouk:
The link between orthology relations and gene trees: a correction perspective. 4 - Thomas D. Wu:
Bitpacking techniques for indexing genomes: I. Hash tables. 5 - Cinzia Pizzi
MissMax: alignment-free sequence comparison with mismatches through filtering and heuristics. 6 - Sebastian Will, Hosna Jabbari:
Sparse RNA folding revisited: space-efficient minimum free energy structure prediction. 7 - Ronny Lorenz
RNA folding with hard and soft constraints. 8 - Thomas D. Wu:
Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays. 9 - Giles Miclotte
Jabba: hybrid error correction for long sequencing reads. 10 - Songjian Lu, Gunasheil Mandava, Gaibo Yan, Xinghua Lu:
An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem. 11 - Roberto Grossi, Costas S. Iliopoulos, Robert Mercas
Circular sequence comparison: algorithms and applications. 12 - Krister M. Swenson, Pijus Simonaitis
Models and algorithms for genome rearrangement with positional constraints. 13 - Rui Henriques
BicNET: Flexible module discovery in large-scale biological networks using biclustering. 14 - Benjamin Drinkwater, Michael A. Charleston
Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem. 15 - Prabina Kumar Meher
Identification of donor splice sites using support vector machine: a computational approach based on positional, compositional and dependency features. 16 - William R. Taylor:
An algorithm to parse segment packing in predicted protein contact maps. 17 - Jianbo Lu, Guoliang Xu, Shihua Zhang, Benzhuo Lu:
An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data. 18 - Elizabeth T. Hobbs, Talmo Pereira
A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. 19 - Timo Beller, Enno Ohlebusch:
A representation of a compressed de Bruijn graph for pan-genome analysis that enables search. 20 - Roberto Grossi, Costas S. Iliopoulos, Robert Mercas, Nadia Pisanti, Solon P. Pissis
Erratum to: Circular sequence comparison: algorithms and applications. 21 - Yelena Frid, Dan Gusfield:
An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding. 22 - Rui Henriques
BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge. 23 - Jérôme Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, Anne-France Dekairelle, Jean-Luc Gala:
Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis. 24 - Ricardo Andrade, Martin Wannagat, Cecilia Coimbra Klein, Vicente Acuña, Alberto Marchetti-Spaccamela
Enumeration of minimal stoichiometric precursor sets in metabolic networks. 25 - Jun Zhou, Yu Lin
Analysis of gene copy number changes in tumor phylogenetics. 26 - Sudhir Srivastava, Shashi Bhushan Lal, Dwijesh Chandra Mishra, Ulavappa B. Angadi, K. K. Chaturvedi, Shesh N. Rai, Anil Rai
An efficient algorithm for protein structure comparison using elastic shape analysis. 27 - Timo Beller, Enno Ohlebusch:
Erratum to: A representation of a compressed de Bruijn graph for pan-genome analysis that enables search. 28:1-28:2
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