Journal: Algorithms for Molecular Biology

Volume 12, Issue 1

0 -- 0Diego P. Rubert, Pedro Feijão, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez. Approximating the DCJ distance of balanced genomes in linear time
0 -- 0Daniel 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
0 -- 0Raghuram Thiagarajan, Amir Alavi, Jagdeep T. Podichetty, Jason N. Bazil, Daniel A. Beard. The feasibility of genome-scale biological network inference using Graphics Processing Units
0 -- 0Marius Erbert, Steffen Rechner, Matthias Müller-Hannemann. Gerbil: a fast and memory-efficient k-mer counter with GPU-support
0 -- 0Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira. Complexity and algorithms for copy-number evolution problems
0 -- 0Yun Deng, David Fernández-Baca. An efficient algorithm for testing the compatibility of phylogenies with nested taxa
0 -- 0Felipe Alves da Louza, Guilherme P. Telles, Steve Hoffmann, Cristina Dutra de Aguiar Ciferri. Generalized enhanced suffix array construction in external memory
0 -- 0Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene 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
0 -- 0Sven Jager, Benjamin Schiller, Philipp Babel, Malte Blumenroth, Thorsten Strufe, Kay Hamacher. g: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs
0 -- 0Shixiang Wan, Quan Zou. HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing
0 -- 0Thomas Tschager, Simon Rösch, Ludovic Gillet, Peter Widmayer. A better scoring model for de novo peptide sequencing: the symmetric difference between explained and measured masses
0 -- 0Laurent Noé. Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds
0 -- 0Riccardo Dondi, Manuel Lafond, Nadia El-Mabrouk. Approximating the correction of weighted and unweighted orthology and paralogy relations
0 -- 0Guillaume Fertin, Géraldine Jean, Eric Tannier. Algorithms for computing the double cut and join distance on both gene order and intergenic sizes
0 -- 0Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar. Isometric gene tree reconciliation revisited
0 -- 0Christopher Schröder, Sven Rahmann. A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification
0 -- 0Marwa 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
0 -- 0Marc Hellmuth. Biologically feasible gene trees, reconciliation maps and informative triples
0 -- 0Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, Loïc Paulevé. Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming
0 -- 0Dan F. DeBlasio, John D. Kececioglu. Core column prediction for protein multiple sequence alignments
0 -- 0Yannis 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
0 -- 0Safa Jammali, Esaie Kuitche, Ayoub Rachati, François Bélanger, Michelle Scott, Aïda Ouangraoua. Aligning coding sequences with frameshift extension penalties
0 -- 0Burkhard Morgenstern, Svenja Schöbel, Chris-Andre Leimeister. Phylogeny reconstruction based on the length distribution of k-mismatch common substrings
0 -- 0Daniel Doerr, Metin Balaban, Pedro Feijão, Cédric Chauve. The gene family-free median of three
0 -- 0Adam M. Novak, Erik Garrison, Benedict Paten. A graph extension of the positional Burrows-Wheeler transform and its applications
0 -- 0William R. Taylor. Algorithms for matching partially labelled sequence graphs
0 -- 0Emna 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