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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. Content type: Research

    Searching optima is one of the most challenging tasks in clustering genes from available experimental data or given functions. SA, GA, PSO and other similar efficient global optimization methods are used by bi...

    Authors: Ming Zheng, Gui-xia Liu, Chun-guang Zhou, Yan-chun Liang and Yan Wang

    Citation: Algorithms for Molecular Biology 2010 5:32

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  29. Content type: Software article

    The specific position of functionally related genes along the DNA has been shown to reflect the interplay between chromosome structure and genetic regulation. By investigating the statistical properties of the...

    Authors: Ivan Junier, Joan Hérisson and François Képès

    Citation: Algorithms for Molecular Biology 2010 5:31

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  30. Content type: Research

    Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand ...

    Authors: Pavel V Mazin, Mikhail S Gelfand, Andrey A Mironov, Aleksandra B Rakhmaninova, Anatoly R Rubinov, Robert B Russell and Olga V Kalinina

    Citation: Algorithms for Molecular Biology 2010 5:29

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  31. Content type: Research

    Mass spectrometry (MS) based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an ef...

    Authors: Hannes Planatscher, Jochen Supper, Oliver Poetz, Dieter Stoll, Thomas Joos, Markus F Templin and Andreas Zell

    Citation: Algorithms for Molecular Biology 2010 5:28

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  32. Content type: Research

    RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure) and additional cross-serial base pair...

    Authors: James ZM Gao, Linda YM Li and Christian M Reidys

    Citation: Algorithms for Molecular Biology 2010 5:27

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  33. Content type: Software article

    Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus ...

    Authors: Darío Guerrero, Rocío Bautista, David P Villalobos, Francisco R Cantón and M Gonzalo Claros

    Citation: Algorithms for Molecular Biology 2010 5:24

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  34. Content type: Research

    Biclustering is an important analysis procedure to understand the biological mechanisms from microarray gene expression data. Several algorithms have been proposed to identify biclusters, but very little effor...

    Authors: Burton Kuan Hui Chia and R Krishna Murthy Karuturi

    Citation: Algorithms for Molecular Biology 2010 5:23

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  35. Content type: Research

    Many regulatory non-coding RNAs (ncRNAs) function through complementary binding with mRNAs or other ncRNAs, e.g., microRNAs, snoRNAs and bacterial sRNAs. Predicting these RNA interactions is essential for functio...

    Authors: Stefan E Seemann, Andreas S Richter, Jan Gorodkin and Rolf Backofen

    Citation: Algorithms for Molecular Biology 2010 5:22

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  36. Content type: Research

    The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs o...

    Authors: Gordon Blackshields, Fabian Sievers, Weifeng Shi, Andreas Wilm and Desmond G Higgins

    Citation: Algorithms for Molecular Biology 2010 5:21

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  37. Content type: Meeting report

    A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincaré, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in System...

    Authors: Pierre-Yves Bourguignon, Areejit Samal, François Képès, Jürgen Jost and Olivier C Martin

    Citation: Algorithms for Molecular Biology 2010 5:20

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