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  1. Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in seq...

    Authors: Roberto Grossi, Costas S. Iliopoulos, Robert Mercas, Nadia Pisanti, Solon P. Pissis, Ahmad Retha and Fatima Vayani

    Citation: Algorithms for Molecular Biology 2016 11:12

    Content type: Research

    Published on:

    The Erratum to this article has been published in Algorithms for Molecular Biology 2016 11:21

  2. The mutual exclusivity of somatic genome alterations (SGAs), such as somatic mutations and copy number alterations, is an important observation of tumors and is widely used to search for cancer signaling pathw...

    Authors: Songjian Lu, Gunasheil Mandava, Gaibo Yan and Xinghua Lu

    Citation: Algorithms for Molecular Biology 2016 11:11

    Content type: Research

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  3. Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, un...

    Authors: Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert and Jan Fostier

    Citation: Algorithms for Molecular Biology 2016 11:10

    Content type: Software article

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  4. A large class of RNA secondary structure prediction programs uses an elaborate energy model grounded in extensive thermodynamic measurements and exact dynamic programming algorithms. External experimental evid...

    Authors: Ronny Lorenz, Ivo L. Hofacker and Peter F. Stadler

    Citation: Algorithms for Molecular Biology 2016 11:8

    Content type: Research

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  5. Hash tables constitute a widely used data structure for indexing genomes that provides a list of genomic positions for each possible oligomer of a given size. The offset array in a hash table grows exponential...

    Authors: Thomas D. Wu

    Citation: Algorithms for Molecular Biology 2016 11:5

    Content type: Research

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  6. In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motiva...

    Authors: Jean P. Zukurov, Sieberth do Nascimento-Brito, Angela C. Volpini, Guilherme C. Oliveira, Luiz Mario R. Janini and Fernando Antoneli

    Citation: Algorithms for Molecular Biology 2016 11:2

    Content type: Software article

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  7. The accurate annotation of genes in newly sequenced genomes remains a challenge. Although sophisticated comparative pipelines are available, computationally derived gene models are often less than perfect. Thi...

    Authors: Henrike Indrischek, Nicolas Wieseke, Peter F. Stadler and Sonja J. Prohaska

    Citation: Algorithms for Molecular Biology 2016 11:1

    Content type: Research

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  8. Markov chains are a common framework for individual-based state and time discrete models in evolution. Though they played an important role in the development of basic population genetic theory, the analysis o...

    Authors: Katja Reichel, Valentin Bahier, Cédric Midoux, Nicolas Parisey, Jean-Pierre Masson and Solenn Stoeckel

    Citation: Algorithms for Molecular Biology 2015 10:31

    Content type: Software article

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  9. A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapid...

    Authors: Jongpill Choi, Kiejung Park, Seong Beom Cho and Myungguen Chung

    Citation: Algorithms for Molecular Biology 2015 10:30

    Content type: Software article

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  10. The rational, in silico prediction of gene-knockouts to turn organisms into efficient cell factories is an essential and computationally challenging task in metabolic engineering. Elementary flux mode analys...

    Authors: Govind Nair, Christian Jungreuthmayer, Michael Hanscho and Jürgen Zanghellini

    Citation: Algorithms for Molecular Biology 2015 10:29

    Content type: Research

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  11. Lateral, or Horizontal, Gene Transfers are a type of asymmetric evolutionary events where genetic material is transferred from one species to another. In this paper we consider LGT networks, a general model of p...

    Authors: Gabriel Cardona, Joan Carles Pons and Francesc Rosselló

    Citation: Algorithms for Molecular Biology 2015 10:28

    Content type: Research

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  12. Detecting protein complexes within protein–protein interaction (PPI) networks is a major step toward the analysis of biological processes and pathways. Identification and characterization of protein complexes ...

    Authors: Sanghamitra Bandyopadhyay, Sumanta Ray, Anirban Mukhopadhyay and Ujjwal Maulik

    Citation: Algorithms for Molecular Biology 2015 10:24

    Content type: Research

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  13. Knowledge of interaction types in biological networks is important for understanding the functional organization of the cell. Currently information-based approaches are widely used for inferring gene regulator...

    Authors: Pegah Khosravi, Vahid H Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei and Gary D Bader

    Citation: Algorithms for Molecular Biology 2015 10:23

    Content type: Research

    Published on:

    The Erratum to this article has been published in Algorithms for Molecular Biology 2015 10:25

  14. Pareto optimization combines independent objectives by computing the Pareto front of its search space, defined as the set of all solutions for which no other candidate solution scores better under all objectives....

    Authors: Cédric Saule and Robert Giegerich

    Citation: Algorithms for Molecular Biology 2015 10:22

    Content type: Research

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  15. The increase of protein–protein interaction (PPI) data of different species makes it possible to identify common subnetworks (conserved protein complexes) across species via local alignment of their PPI networ...

    Authors: Wei Peng, Jianxin Wang, Fangxiang Wu and Pan Yi

    Citation: Algorithms for Molecular Biology 2015 10:21

    Content type: Research

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  16. The problem of enumerating bubbles with length constraints in directed graphs arises in transcriptomics where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced ...

    Authors: Gustavo Sacomoto, Vincent Lacroix and Marie-France Sagot

    Citation: Algorithms for Molecular Biology 2015 10:20

    Content type: Research

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  17. Analogous to genomic sequence alignment, biological network alignment identifies conserved regions between networks of different species. Then, function can be transferred from well- to poorly-annotated specie...

    Authors: Joseph Crawford, Yihan Sun and Tijana Milenković

    Citation: Algorithms for Molecular Biology 2015 10:19

    Content type: Research

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  18. Resolution of repeats and scaffolding of shorter contigs are critical parts of genome assembly. Modern assemblers usually perform such steps by heuristics, often tailored to a particular technology for produci...

    Authors: Vladimír Boža, Broňa Brejová and Tomáš Vinař

    Citation: Algorithms for Molecular Biology 2015 10:18

    Content type: Research

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  19. The core–periphery model for protein interaction (PPI) networks assumes that protein complexes in these networks consist of a dense core and a possibly sparse periphery that is adjacent to vertices in the core...

    Authors: Sharon Bruckner, Falk Hüffner and Christian Komusiewicz

    Citation: Algorithms for Molecular Biology 2015 10:16

    Content type: Research

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  20. Autocatalytic sets are considered to be fundamental to the origin of life. Prior theoretical and computational work on the existence and properties of these sets has relied on a fast algorithm for detectingsel...

    Authors: Wim Hordijk, Joshua I Smith and Mike Steel

    Citation: Algorithms for Molecular Biology 2015 10:15

    Content type: Research

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  21. Structural variation in genomes can be revealed by many (dis)similarity measures. Rearrangement operations, such as the so called double-cut-and-join (DCJ), are large-scale mutations that can create complex ch...

    Authors: Fábio V Martinez, Pedro Feijão, Marília DV Braga and Jens Stoye

    Citation: Algorithms for Molecular Biology 2015 10:13

    Content type: Research

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  22. During evolution, global mutations may alter the order and the orientation of the genes in a genome. Such mutations are referred to as rearrangement events, or simply operations. In unichromosomal genomes, the...

    Authors: Gustavo Rodrigues Galvão, Orlando Lee and Zanoni Dias

    Citation: Algorithms for Molecular Biology 2015 10:12

    Content type: Research

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  23. The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensembl...

    Authors: Luis C González, Hui Wang, Dennis R Livesay and Donald J Jacobs

    Citation: Algorithms for Molecular Biology 2015 10:11

    Content type: Research

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  24. Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing ...

    Authors: Steve Hoffmann, Peter F Stadler and Korbinian Strimmer

    Citation: Algorithms for Molecular Biology 2015 10:10

    Content type: Research

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  25. This paper presents a constraint-based method for improving protein docking results. Efficient constraint propagation cuts over 95% of the search time for finding the configurations with the largest contact su...

    Authors: Ludwig Krippahl and Pedro Barahona

    Citation: Algorithms for Molecular Biology 2015 10:9

    Content type: Research

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  26. Interaction sites on protein surfaces mediate virtually all biological activities, and their identification holds promise for disease treatment and drug design. Novel algorithmic approaches for the prediction ...

    Authors: Tristan T Aumentado-Armstrong, Bogdan Istrate and Robert A Murgita

    Citation: Algorithms for Molecular Biology 2015 10:7

    Content type: Review article

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  27. Alignment-free methods are increasingly used to calculate evolutionary distances between DNA and protein sequences as a basis of phylogeny reconstruction. Most of these methods, however, use heuristic distance...

    Authors: Burkhard Morgenstern, Bingyao Zhu, Sebastian Horwege and Chris André Leimeister

    Citation: Algorithms for Molecular Biology 2015 10:5

    Content type: Research

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  28. The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an...

    Authors: Matteo Comin, Andrea Leoni and Michele Schimd

    Citation: Algorithms for Molecular Biology 2015 10:4

    Content type: Research

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  29. Phylogenetic tree reconciliation is the approach of choice for investigating the coevolution of sets of organisms such as hosts and parasites. It consists in a mapping between the parasite tree and the host tr...

    Authors: Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi and Marie-France Sagot

    Citation: Algorithms for Molecular Biology 2015 10:3

    Content type: SOFTWARE ARTICLE

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  30. Metagenomics is the study of genetic materials derived directly from complex microbial samples, instead of from culture. One of the crucial steps in metagenomic analysis, referred to as “binning”, is to separa...

    Authors: Le Van Vinh, Tran Van Lang, Le Thanh Binh and Tran Van Hoai

    Citation: Algorithms for Molecular Biology 2015 10:2

    Content type: Research

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  31. The universal pacemaker (UPM) model extends the classical molecular clock (MC) model, by allowing each gene, in addition to its individual intrinsic rate as in the MC, to accelerate or decelerate according to ...

    Authors: Sagi Snir

    Citation: Algorithms for Molecular Biology 2014 9:26

    Content type: Research

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  32. Biclustering, the discovery of sets of objects with a coherent pattern across a subset of conditions, is a critical task to study a wide-set of biomedical problems, where molecular units or patients are meanin...

    Authors: Rui Henriques and Sara C Madeira

    Citation: Algorithms for Molecular Biology 2014 9:27

    Content type: Research

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  33. Finding new functional fragments in biological sequences is a challenging problem. Methods addressing this problem commonly search for clusters of pattern occurrences that are statistically significant. A meas...

    Authors: Mireille Régnier, Evgenia Furletova, Victor Yakovlev and Mikhail Roytberg

    Citation: Algorithms for Molecular Biology 2014 9:25

    Content type: Research

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  34. Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms...

    Authors: Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F Stadler and Christoph Flamm

    Citation: Algorithms for Molecular Biology 2014 9:23

    Content type: Research

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  35. Sets of sequence data used in phylogenetic analysis are often plagued by both random noise and systematic biases. Since the commonly used methods of phylogenetic reconstruction are designed to produce trees it...

    Authors: Bernhard Misof, Karen Meusemann, Björn M von Reumont, Patrick Kück, Sonja J Prohaska and Peter F Stadler

    Citation: Algorithms for Molecular Biology 2014 9:22

    Content type: Review article

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  36. Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splic...

    Authors: Jing Qin, Markus Fricke, Manja Marz, Peter F Stadler and Rolf Backofen

    Citation: Algorithms for Molecular Biology 2014 9:19

    Content type: Research

    Published on: