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  1. Content type: Research

    Analysis of elementary modes (EMs) is proven to be a powerful constraint-based method in the study of metabolic networks. However, enumeration of EMs is a hard computational task. Additionally, due to their la...

    Authors: Sayed-Amir Marashi, Laszlo David and Alexander Bockmayr

    Citation: Algorithms for Molecular Biology 2012 7:17

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  2. Content type: Research

    For many predictive applications a large number of models is generated and later clustered in subsets based on structure similarity. In most clustering algorithms an all-vs-all root mean square deviation (RMSD...

    Authors: Federico Fogolari, Alessandra Corazza, Paolo Viglino and Gennaro Esposito

    Citation: Algorithms for Molecular Biology 2012 7:16

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  3. Content type: Research

    There are several common ways to encode a tree as a matrix, such as the adjacency matrix, the Laplacian matrix (that is, the infinitesimal generator of the natural random walk), and the matrix of pairwise dist...

    Authors: Frederick A Matsen and Steven N Evans

    Citation: Algorithms for Molecular Biology 2012 7:14

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  4. Content type: Research

    The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics ...

    Authors: Jonas S Almeida, Alexander Grüneberg, Wolfgang Maass and Susana Vinga

    Citation: Algorithms for Molecular Biology 2012 7:12

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  5. Content type: Research

    Through the wealth of information contained within them, genome-wide association studies (GWAS) have the potential to provide researchers with a systematic means of associating genetic variants with a wide var...

    Authors: Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski and Tero Aittokallio

    Citation: Algorithms for Molecular Biology 2012 7:11

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  6. Content type: Research

    Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses ...

    Authors: Susana Vinga, Alexandra M Carvalho, Alexandre P Francisco, Luís MS Russo and Jonas S Almeida

    Citation: Algorithms for Molecular Biology 2012 7:10

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  7. Content type: Research

    Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing p...

    Authors: Lavanya Kannan and Ward C Wheeler

    Citation: Algorithms for Molecular Biology 2012 7:9

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  8. Content type: Research

    We present optimal linear time algorithms for computing the Shapley values and 'heightened evolutionary distinctiveness' (HED) scores for the set of taxa in a phylogenetic tree. We demonstrate the efficiency o...

    Authors: Iain Martyn, Tyler S Kuhn, Arne O Mooers, Vincent Moulton and Andreas Spillner

    Citation: Algorithms for Molecular Biology 2012 7:6

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  9. Content type: Research

    High-throughput sequencing, such as ribonucleic acid sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) analyses, enables various features of organisms to be compared through tag coun...

    Authors: Koji Kadota, Tomoaki Nishiyama and Kentaro Shimizu

    Citation: Algorithms for Molecular Biology 2012 7:5

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  10. Content type: Research

    Supertree methods combine trees on subsets of the full taxon set together to produce a tree on the entire set of taxa. Of the many supertree methods, the most popular is MRP (Matrix Representation with Parsimo...

    Authors: Nam Nguyen, Siavash Mirarab and Tandy Warnow

    Citation: Algorithms for Molecular Biology 2012 7:3

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  11. Content type: Research

    High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e.g. repetitive reg...

    Authors: Stefan Enroth, Claes R Andersson, Robin Andersson, Claes Wadelius, Mats G Gustafsson and Jan Komorowski

    Citation: Algorithms for Molecular Biology 2012 7:2

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  12. Content type: Research

    A combined quantitative trait loci (QTL) and microarray-based approach is commonly used to find differentially expressed genes which are then identified based on the known function of a gene in the biological ...

    Authors: Hirokazu Matsuda, Yukio Taniguchi and Hiroaki Iwaisaki

    Citation: Algorithms for Molecular Biology 2012 7:1

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  13. Content type: Research

    In genomics, a commonly encountered problem is to extract a subset of variables out of a large set of explanatory variables associated with one or several quantitative or qualitative response variables. An exa...

    Authors: Tahir Mehmood, Harald Martens, Solve Sæbø, Jonas Warringer and Lars Snipen

    Citation: Algorithms for Molecular Biology 2011 6:27

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  14. Content type: Software article

    Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely use...

    Authors: Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler and Ivo L Hofacker

    Citation: Algorithms for Molecular Biology 2011 6:26

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  15. Content type: Research

    Algorithms of sequence alignment are the key instruments for computer-assisted studies of biopolymers. Obviously, it is important to take into account the "quality" of the obtained alignments, i.e. how closely...

    Authors: Valery O Polyanovsky, Mikhail A Roytberg and Vladimir G Tumanyan

    Citation: Algorithms for Molecular Biology 2011 6:25

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  16. Content type: Research

    Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowled...

    Authors: Stelios P Pavlidis, Annette M Payne and Stephen M Swift

    Citation: Algorithms for Molecular Biology 2011 6:22

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  17. Content type: Research

    We consider the following problem: Given an undirected network and a set of sender–receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting ...

    Authors: Britta Dorn, Falk Hüffner, Dominikus Krüger, Rolf Niedermeier and Johannes Uhlmann

    Citation: Algorithms for Molecular Biology 2011 6:21

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  18. Content type: Research

    The MatrixMatchMaker algorithm was recently introduced to detect the similarity between phylogenetic trees and thus the coevolution between proteins. MMM finds the largest common submatrices between pairs of p...

    Authors: Alex Rodionov, Alexandr Bezginov, Jonathan Rose and Elisabeth RM Tillier

    Citation: Algorithms for Molecular Biology 2011 6:17

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  19. Content type: Research

    When inferring phylogenetic trees different algorithms may give different trees. To study such effects a measure for the distance between two trees is useful. Quartet distance is one such measure, and is the n...

    Authors: Jesper Nielsen, Anders K Kristensen, Thomas Mailund and Christian NS Pedersen

    Citation: Algorithms for Molecular Biology 2011 6:15

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  20. Content type: Research

    Clustering is a widely used technique for analysis of gene expression data. Most clustering methods group genes based on the distances, while few methods group genes according to the similarities of the distri...

    Authors: Huakun Wang, Zhenzhen Wang, Xia Li, Binsheng Gong, Lixin Feng and Ying Zhou

    Citation: Algorithms for Molecular Biology 2011 6:14

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  21. Content type: Research

    Proteins are dynamic molecules that exhibit a wide range of motions; often these conformational changes are important for protein function. Determining biologically relevant conformational changes, or true var...

    Authors: Raghavendra Hosur, Rohit Singh and Bonnie Berger

    Citation: Algorithms for Molecular Biology 2011 6:12

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  22. Content type: Research

    We describe an average-case O(n2) algorithm to list all reversals on a signed permutation π that, when applied to π, produce a permutation that is closer to the identity. This algorithm is optimal in the sense th...

    Authors: Krister M Swenson, Ghada Badr and David Sankoff

    Citation: Algorithms for Molecular Biology 2011 6:11

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  23. Content type: Research

    Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysi...

    Authors: Bonnie B Kirkpatrick

    Citation: Algorithms for Molecular Biology 2011 6:10

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  24. Content type: Research

    Massively parallel whole transcriptome sequencing, commonly referred as RNA-Seq, is quickly becoming the technology of choice for gene expression profiling. However, due to the short read length delivered by c...

    Authors: Marius Nicolae, Serghei Mangul, Ion I Măndoiu and Alex Zelikovsky

    Citation: Algorithms for Molecular Biology 2011 6:9

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  25. Content type: Research

    Supertree methods represent one of the major ways by which the Tree of Life can be estimated, but despite many recent algorithmic innovations, matrix representation with parsimony (MRP) remains the main algori...

    Authors: M Shel Swenson, Rahul Suri, C Randal Linder and Tandy Warnow

    Citation: Algorithms for Molecular Biology 2011 6:7

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  26. Content type: Research

    Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wil...

    Authors: Chen-Ming Hsu, Chien-Yu Chen and Baw-Jhiune Liu

    Citation: Algorithms for Molecular Biology 2011 6:6

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  27. Content type: Research

    The discovery of surprisingly frequent patterns is of paramount interest in bioinformatics and computational biology. Among the patterns considered, those consisting of pairs of solid words that co-occur withi...

    Authors: Alberto Apostolico, Cinzia Pizzi and Esko Ukkonen

    Citation: Algorithms for Molecular Biology 2011 6:5

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  28. Content type: Software article

    Fast seed-based alignment heuristics such as BLAST and BLAT have become indispensable tools in comparative genomics for all studies aiming at the evolutionary relations of proteins, genes, and non-coding RNAs. Th...

    Authors: Christian Otto, Steve Hoffmann, Jan Gorodkin and Peter F Stadler

    Citation: Algorithms for Molecular Biology 2011 6:4

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  29. Content type: Research

    The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility ...

    Authors: Stephan H Bernhart, Ullrike Mückstein and Ivo L Hofacker

    Citation: Algorithms for Molecular Biology 2011 6:3

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  30. Content type: Software article

    Many k- mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding...

    Authors: Michael Hackenberg, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Ángel M Alganza and José L Oliver

    Citation: Algorithms for Molecular Biology 2011 6:2

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  31. Content type: Research

    Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space consumption implied by the dynamic programmin...

    Authors: Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen and S Cenk Sahinalp

    Citation: Algorithms for Molecular Biology 2010 5:39

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  32. Content type: Research

    Hidden Markov models are widely employed by numerous bioinformatics programs used today. Applications range widely from comparative gene prediction to time-series analyses of micro-array data. The parameters o...

    Authors: Tin Y Lam and Irmtraud M Meyer

    Citation: Algorithms for Molecular Biology 2010 5:38

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  33. Content type: Research

    The detection of modules or community structure is widely used to reveal the underlying properties of complex networks in biology, as well as physical and social sciences. Since the adoption of modularity as a me...

    Authors: Gang Xu, Laura Bennett, Lazaros G Papageorgiou and Sophia Tsoka

    Citation: Algorithms for Molecular Biology 2010 5:36

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  34. Content type: Research

    Unigenic evolution is a large-scale mutagenesis experiment used to identify residues that are potentially important for protein function. Both currently-used methods for the analysis of unigenic evolution data...

    Authors: Andrew D Fernandes, Benjamin P Kleinstiver, David R Edgell, Lindi M Wahl and Gregory B Gloor

    Citation: Algorithms for Molecular Biology 2010 5:35

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  35. Content type: Research

    Affinity purification followed by mass spectrometry identification (AP-MS) is an increasingly popular approach to observe protein-protein interactions (PPI) in vivo. One drawback of AP-MS, however, is that it is ...

    Authors: Ethan DH Kim, Ashish Sabharwal, Adrian R Vetta and Mathieu Blanchette

    Citation: Algorithms for Molecular Biology 2010 5:34

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  36. Content type: Research

    Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists ofte...

    Authors: Ye Tian, Christopher Deutsch and Bala Krishnamoorthy

    Citation: Algorithms for Molecular Biology 2010 5:33

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