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ORCIDAlgorithms 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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