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  1. 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

    Content type: Research

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  3. 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

    Content type: Research

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  4. 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

    Content type: Research

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  5. 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

    Content type: Research

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  6. 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

    Content type: Research

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  8. 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

    Content type: Research

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  9. 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

    Content type: Research

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  10. 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

    Content type: Research

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  11. 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

    Content type: Software article

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  12. 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

    Content type: Research

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  13. 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

    Content type: Software article

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  15. 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

    Content type: Research

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  16. 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

    Content type: Research

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  18. 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

    Content type: Research

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  19. 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

    Content type: Research

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  20. 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

    Content type: Research

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  21. 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

    Content type: Research

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  22. 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

    Content type: Research

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  23. 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

    Content type: Software article

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  25. 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

    Content type: Research

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  26. 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

    Content type: Research

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  27. 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

    Content type: Research

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  30. 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

    Content type: Software article

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  31. 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

    Content type: Research

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  32. 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

    Content type: Research

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  33. 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

    Content type: Research

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  34. 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

    Content type: Meeting report

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  35. We introduce a method to help identify how the genetic diversity of a species within a geographic region might have arisen. This problem appears, for example, in the context of identifying refugia in phylogeog...

    Authors: Binh Nguyen, Andreas Spillner, Brent C Emerson and Vincent Moulton

    Citation: Algorithms for Molecular Biology 2010 5:19

    Content type: Research

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  36. Supertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. Supertree methods bas...

    Authors: Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein and David Fernández-Baca

    Citation: Algorithms for Molecular Biology 2010 5:18

    Content type: Research

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  37. The causes of complex diseases are difficult to grasp since many different factors play a role in their onset. To find a common genetic background, many of the existing studies divide their population into con...

    Authors: Sandra Waaijenborg and Aeilko H Zwinderman

    Citation: Algorithms for Molecular Biology 2010 5:17

    Content type: Research

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  38. This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecul...

    Authors: Chris Conow, Daniel Fielder, Yaniv Ovadia and Ran Libeskind-Hadas

    Citation: Algorithms for Molecular Biology 2010 5:16

    Content type: Software article

    Published on:

  39. In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.). Although many methodological approaches a...

    Authors: Gregory Nuel, Leslie Regad, Juliette Martin and Anne-Claude Camproux

    Citation: Algorithms for Molecular Biology 2010 5:15

    Content type: Research

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  42. Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that have gone through conformational changes can be captured effectively if ...

    Authors: Saeed Salem, Mohammed J Zaki and Chris Bystroff

    Citation: Algorithms for Molecular Biology 2010 5:12

    Content type: Research

    Published on:

  43. Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organ...

    Authors: Crystal L Kahn, Shay Mozes and Benjamin J Raphael

    Citation: Algorithms for Molecular Biology 2010 5:11

    Content type: Research

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  44. This paper considers the problem of identifying pathways through metabolic networks that relate to a specific biological response. Our proposed model, HME3M, first identifies frequently traversed network paths...

    Authors: Timothy Hancock and Hiroshi Mamitsuka

    Citation: Algorithms for Molecular Biology 2010 5:10

    Content type: Research

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  45. The fingerprint of a molecule is a bitstring based on its structure, constructed such that structurally similar molecules will have similar fingerprints. Molecular fingerprints can be used in an initial phase ...

    Authors: Thomas G Kristensen, Jesper Nielsen and Christian NS Pedersen

    Citation: Algorithms for Molecular Biology 2010 5:9

    Content type: Research

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  46. Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the enti...

    Authors: M Shel Swenson, François Barbançon, Tandy Warnow and C Randal Linder

    Citation: Algorithms for Molecular Biology 2010 5:8

    Content type: Research

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  48. Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of gene...

    Authors: Matthew Hansen, Logan Everett, Larry Singh and Sridhar Hannenhalli

    Citation: Algorithms for Molecular Biology 2010 5:4

    Content type: Research

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  49. Supertree methods combine the phylogenetic information from multiple partially-overlapping trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to...

    Authors: Jianrong Dong, David Fernández-Baca and FR McMorris

    Citation: Algorithms for Molecular Biology 2010 5:2

    Content type: Research

    Published on:

  • ISSN: 1748-7188 (electronic)

Algorithms for Molecular Biology

ISSN: 1748-7188