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Algorithms for Molecular Biology, Volume 10
Volume 10, 2015
- Yaron A. B. Goldstein, Alexander Bockmayr
:
Double and multiple knockout simulations for genome-scale metabolic network reconstructions. 1 - Le Vinh, Tran Lang, Le Binh, Tran Hoai:
A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads. 2 - Beatrice Donati, Christian Baudet
, Blerina Sinaimeri
, Pierluigi Crescenzi
, Marie-France Sagot:
EUCALYPT: efficient tree reconciliation enumerator. 3 - Matteo Comin
, Andrea Leoni, Michele Schimd
:
Clustering of reads with alignment-free measures and quality values. 4 - Burkhard Morgenstern, Binyao Zhu, Sebastian Horwege, Chris Leimeister:
Estimating evolutionary distances between genomic sequences from spaced-word matches. 5 - Sandeep Amberkar
, Lars Kaderali
:
An integrative approach for a network based meta-analysis of viral RNAi screens. 6 - Tristan Aumentado-Armstrong
, Bogdan Istrate, Robert A. Murgita:
Algorithmic approaches to protein-protein interaction site prediction. 7 - Junfeng Gu, Xu Yang, Ling Kang, Jinying Wu, Xicheng Wang:
MoDock: A multi-objective strategy improves the accuracy for molecular docking. 8 - Ludwig Krippahl
, Pedro Barahona
:
Protein docking with predicted constraints. 9 - Steve Hoffmann, Peter F. Stadler
, Korbinian Strimmer
:
A simple data-adaptive probabilistic variant calling model. 10 - Luis C. González, Hui Wang, Dennis R. Livesay, Donald J. Jacobs:
A virtual pebble game to ensemble average graph rigidity. 11 - Gustavo Rodrigues Galvão
, Orlando Lee, Zanoni Dias:
Sorting signed permutations by short operations. 12 - Fábio Viduani Martinez
, Pedro Feijão, Marília D. V. Braga, Jens Stoye
:
On the family-free DCJ distance and similarity. 13 - Duc-Hau Le:
A novel method for identifying disease associated protein complexes based on functional similarity protein complex networks. 14 - Wim Hordijk, Joshua I. Smith, Mike A. Steel
:
Algorithms for detecting and analysing autocatalytic sets. 15 - Sharon Bruckner, Falk Hüffner
, Christian Komusiewicz:
A graph modification approach for finding core-periphery structures in protein interaction networks. 16 - Dominik Kopczynski
, Sven Rahmann
:
An online peak extraction algorithm for ion mobility spectrometry data. 17 - Vladimír Boza
, Brona Brejová
, Tomás Vinar
:
GAML: genome assembly by maximum likelihood. 18 - Joseph Crawford, Yihan Sun, Tijana Milenkovic:
Fair evaluation of global network aligners. 19 - Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot:
A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs. 20 - Wei Peng, Jianxin Wang, Fang-Xiang Wu
, Yi Pan
:
Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison. 21 - Cédric Saule, Robert Giegerich:
Pareto optimization in algebraic dynamic programming. 22 - Pegah Khosravi
, Vahid H. Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei, Gary D. Bader
:
Inferring interaction type in gene regulatory networks using co-expression data. 23 - Sanghamitra Bandyopadhyay, Sumanta Ray
, Anirban Mukhopadhyay
, Ujjwal Maulik
:
A multiobjective approach for identifying protein complexes and studying their association in multiple disorders. 24 - Pegah Khosravi
, Vahid H. Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Gary D. Bader
, Bahram Goliaei:
Erratum to: Inferring interaction type in gene regulatory networks using co-expression data. 25 - Kieran Boyce
, Fabian Sievers, Desmond G. Higgins:
Instability in progressive multiple sequence alignment algorithms. 26 - Aleksandar Poleksic:
A polynomial time algorithm for computing the area under a GDT curve. 27 - Gabriel Cardona
, Joan Carles Pons, Francesc Rosselló
:
A reconstruction problem for a class of phylogenetic networks with lateral gene transfers. 28 - Govind Nair
, Christian Jungreuthmayer, Michael Hanscho, Jürgen Zanghellini
:
Designing minimal microbial strains of desired functionality using a genetic algorithm. 29 - Jongpill Choi, Kiejung Park, Seong Beom Cho, Myungguen Chung:
HIA: a genome mapper using hybrid index-based sequence alignment. 30 - Katja Reichel
, Valentin Bahier, Cédric Midoux
, Nicolas Parisey, Jean-Pierre Masson, Solenn Stoeckel
:
Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics. 31
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