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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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

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  19. 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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  20. 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

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  21. 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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  22. 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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  23. 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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  24. 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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  25. Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for eff...

    Authors: Raheleh Salari, Rolf Backofen and S Cenk Sahinalp

    Citation: Algorithms for Molecular Biology 2010 5:5

    Content type: Research

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  26. 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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  27. Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping ...

    Authors: Peter Husemann and Jens Stoye

    Citation: Algorithms for Molecular Biology 2010 5:3

    Content type: Research

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  28. 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

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  29. With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete...

    Authors: Eric S Ho, Christopher D Jakubowski and Samuel I Gunderson

    Citation: Algorithms for Molecular Biology 2009 4:14

    Content type: Research

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  30. Discriminative models are designed to naturally address classification tasks. However, some applications require the inclusion of grammar rules, and in these cases generative models, such as Hidden Markov Mode...

    Authors: Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli and Rita Casadio

    Citation: Algorithms for Molecular Biology 2009 4:13

    Content type: Research

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  31. Hierarchical clustering methods like Ward's method have been used since decades to understand biological and chemical data sets. In order to get a partition of the data set, it is necessary to choose an optima...

    Authors: László A Zahoránszky, Gyula Y Katona, Péter Hári, András Málnási-Csizmadia, Katharina A Zweig and Gergely Zahoránszky-Köhalmi

    Citation: Algorithms for Molecular Biology 2009 4:12

    Content type: Research

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  32. Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic arch...

    Authors: Sheron Wen, Chenguang Wang, Arthur Berg, Yao Li, Myron M Chang, Roger B Fillingim, Margaret R Wallace, Roland Staud, Lee Kaplan and Rongling Wu

    Citation: Algorithms for Molecular Biology 2009 4:11

    Content type: Research

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  33. With the increasing availability of live cell imaging technology, tracking cells and other moving objects in live cell videos has become a major challenge for bioimage informatics. An inherent problem for most...

    Authors: Axel Mosig, Stefan Jäger, Chaofeng Wang, Sumit Nath, Ilker Ersoy, Kannap-pan Palaniappan and Su-Shing Chen

    Citation: Algorithms for Molecular Biology 2009 4:10

    Content type: Research

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  34. The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is criti...

    Authors: Sara C Madeira and Arlindo L Oliveira

    Citation: Algorithms for Molecular Biology 2009 4:8

    Content type: Research

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  35. To identify differentially expressed genes (DEGs) from microarray data, users of the Affymetrix GeneChip system need to select both a preprocessing algorithm to obtain expression-level measurements and a way o...

    Authors: Koji Kadota, Yuji Nakai and Kentaro Shimizu

    Citation: Algorithms for Molecular Biology 2009 4:7

    Content type: Research

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  36. Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 hu...

    Authors: WB Langdon and AP Harrison

    Citation: Algorithms for Molecular Biology 2009 4:6

    Content type: Research

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  37. A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networ...

    Authors: Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma R Chandra and I Saira Mian

    Citation: Algorithms for Molecular Biology 2009 4:5

    Content type: Research

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  38. Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA stru...

    Authors: Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro and Danny Barash

    Citation: Algorithms for Molecular Biology 2009 4:4

    Content type: Research

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  39. Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic...

    Authors: Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira do Lago, Nadia Pisanti and Marie-France Sagot

    Citation: Algorithms for Molecular Biology 2009 4:3

    Content type: Research

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