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ORCIDAlgorithms for Molecular Biology, Volume 12
Volume 12, Number 1, December 2017
- Laurent Noé
:
Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds. 1:1-1:16 - Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Hélène Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix:
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. 2:1-2:19 - Diego P. Rubert, Pedro Feijão, Marília Dias Vieira Braga, Jens Stoye, Fábio Viduani Martinez:
Approximating the DCJ distance of balanced genomes in linear time. 3:1-3:13 - Riccardo Dondi, Manuel Lafond, Nadia El-Mabrouk:
Approximating the correction of weighted and unweighted orthology and paralogy relations. 4:1-4:15 - Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas S. Iliopoulos, Manal Mohamed, Solon P. Pissis, Dimitris Polychronopoulos:
On avoided words, absent words, and their application to biological sequence analysis. 5:1-5:12 - Daniel Bork, Ricson Cheng, Jincheng Wang, Jean Sung, Ran Libeskind-Hadas:
On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model. 6:1-6:12 - Yun Deng, David Fernández-Baca:
An efficient algorithm for testing the compatibility of phylogenies with nested taxa. 7:1-7:12 - Raghuram Thiagarajan, Amir Alavi, Jagdeep T. Podichetty, Jason N. Bazil, Daniel A. Beard:
The feasibility of genome-scale biological network inference using Graphics Processing Units. 8:1-8:13 - Marius Erbert, Steffen Rechner, Matthias Müller-Hannemann:
Gerbil: a fast and memory-efficient k-mer counter with GPU-support. 9:1-9:12 - Safa Jammali, Esaie Kuitche, Ayoub Rachati, François Bélanger, Michelle S. Scott, Aïda Ouangraoua:
Aligning coding sequences with frameshift extension penalties. 10:1-10:18 - Dan F. DeBlasio, John D. Kececioglu:
Core column prediction for protein multiple sequence alignments. 11:1-11:16 - Thomas Tschager, Simon Rösch, Ludovic Gillet, Peter Widmayer:
A better scoring model for de novo peptide sequencing: the symmetric difference between explained and measured masses. 12:1-12:13 - Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira:
Complexity and algorithms for copy-number evolution problems. 13:1-13:11 - Daniel Doerr, Metin Balaban, Pedro Feijão, Cédric Chauve:
The gene family-free median of three. 14:1-14:14 - Sven Jager, Benjamin Schiller, Philipp Babel, Malte Blumenroth, Thorsten Strufe, Kay Hamacher:
StreAM-Tg: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs. 15:1-15:16 - Guillaume Fertin, Géraldine Jean, Eric Tannier:
Algorithms for computing the double cut and join distance on both gene order and intergenic sizes. 16:1-16:11 - Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar:
Isometric gene tree reconciliation revisited. 17:1-17:16 - Adam M. Novak, Erik Garrison, Benedict Paten:
A graph extension of the positional Burrows-Wheeler transform and its applications. 18:1-18:12 - Louis Fippo Fitime, Olivier F. Roux, Carito Guziolowski, Loïc Paulevé:
Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming. 19:1-19:14 - Emna Ben Abdallah, Maxime Folschette, Olivier F. Roux, Morgan Magnin:
ASP-based method for the enumeration of attractors in non-deterministic synchronous and asynchronous multi-valued networks. 20:1-20:23 - Christopher Schröder, Sven Rahmann:
A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification. 21:1-21:12 - Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout, Peter F. Stadler:
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements. 22:1-22:11 - Marc Hellmuth:
Biologically feasible gene trees, reconciliation maps and informative triples. 23:1-23:16 - William R. Taylor:
Algorithms for matching partially labelled sequence graphs. 24:1-24:22 - Shixiang Wan, Quan Zou:
HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing. 25:1-25:10 - Felipe A. Louza, Guilherme P. Telles, Steve Hoffmann, Cristina Dutra de Aguiar Ciferri:
Generalized enhanced suffix array construction in external memory. 26:1-26:16 - Burkhard Morgenstern, Svenja Schöbel, Chris-André Leimeister:
Phylogeny reconstruction based on the length distribution of k-mismatch common substrings. 27:1-27:12
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