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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degene...

    Authors: Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu and Yixue Li

    Citation: Algorithms for Molecular Biology 2009 4:2

    Content type: Software article

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  15. MicroRNAs (miRs) are small noncoding RNAs that bind to complementary/partially complementary sites in the 3' untranslated regions of target genes to regulate protein production of the target transcript and to ...

    Authors: Jishou Ruan, Hanzhe Chen, Lukasz Kurgan, Ke Chen, Chunsheng Kang and Peiyu Pu

    Citation: Algorithms for Molecular Biology 2008 3:16

    Content type: Research

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  16. Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. The quality and stability of the underlyi...

    Authors: Holger Wagner, Burkhard Morgenstern and Andreas Dress

    Citation: Algorithms for Molecular Biology 2008 3:15

    Content type: Short report

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  17. The improvement of microarray calibration methods is an essential prerequisite for quantitative expression analysis. This issue requires the formulation of an appropriate model describing the basic relationshi...

    Authors: Hans Binder and Stephan Preibisch

    Citation: Algorithms for Molecular Biology 2008 3:12

    Content type: Research

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  18. One of the goals of global metabolomic analysis is to identify metabolic markers that are hidden within a large background of data originating from high-throughput analytical measurements. Metabolite-based clu...

    Authors: Peter Meinicke, Thomas Lingner, Alexander Kaever, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, Petr Karlovsky and Burkhard Morgenstern

    Citation: Algorithms for Molecular Biology 2008 3:9

    Content type: Research

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  19. Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large num...

    Authors: Andreas WM Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J Prohaska and Peter F Stadler

    Citation: Algorithms for Molecular Biology 2008 3:7

    Content type: Software article

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  20. DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets tha...

    Authors: Amarendran R Subramanian, Michael Kaufmann and Burkhard Morgenstern

    Citation: Algorithms for Molecular Biology 2008 3:6

    Content type: Research

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  21. The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is "...

    Authors: Kord Eickmeyer, Peter Huggins, Lior Pachter and Ruriko Yoshida

    Citation: Algorithms for Molecular Biology 2008 3:5

    Content type: Research

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  22. Protein structure alignments are usually based on very different techniques to sequence alignments. We propose a method which treats sequence, structure and even combined sequence + structure in a single frame...

    Authors: Gundolf Schenk, Thomas Margraf and Andrew E Torda

    Citation: Algorithms for Molecular Biology 2008 3:4

    Content type: Research

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  23. Experimental identification of microRNA (miRNA) targets is a difficult and time consuming process. As a consequence several computational prediction methods have been devised in order to predict targets for fo...

    Authors: Simon Moxon, Vincent Moulton and Jan T Kim

    Citation: Algorithms for Molecular Biology 2008 3:3

    Content type: Research

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  24. The application of machine learning to classification problems that depend only on positive examples is gaining attention in the computational biology community. We and others have described the use of two-cla...

    Authors: Malik Yousef, Segun Jung, Louise C Showe and Michael K Showe

    Citation: Algorithms for Molecular Biology 2008 3:2

    Content type: Research

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  25. In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is...

    Authors: Gang Wu, Ming-Yang Kao, Guohui Lin and Jia-Huai You

    Citation: Algorithms for Molecular Biology 2008 3:1

    Content type: Research

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  26. cis-Regulatory modules (CRMs) of eukaryotic genes often contain multiple binding sites for transcription factors. The phenomenon that binding sites form clusters in CRMs is exploited in many algorithms to locate ...

    Authors: Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A Roytberg and Vsevolod J Makeev

    Citation: Algorithms for Molecular Biology 2007 2:13

    Content type: Research

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  27. Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues – coevolution. Our goal is to find these coevolving residues.

    Authors: Rodrigo Gouveia-Oliveira and Anders G Pedersen

    Citation: Algorithms for Molecular Biology 2007 2:12

    Content type: Research

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  28. We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, t...

    Authors: Gilles Didier and Carito Guziolowski

    Citation: Algorithms for Molecular Biology 2007 2:11

    Content type: Research

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  29. This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence ...

    Authors: Raffaele Giancarlo, Alessandro Siragusa, Enrico Siragusa and Filippo Utro

    Citation: Algorithms for Molecular Biology 2007 2:10

    Content type: Software article

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  30. The optimal score for ungapped local alignments of infinitely long random sequences is known to follow a Gumbel extreme value distribution. Less is known about the important case, where gaps are allowed. For t...

    Authors: Stefan Wolfsheimer, Bernd Burghardt and Alexander K Hartmann

    Citation: Algorithms for Molecular Biology 2007 2:9

    Content type: Research

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  31. Neighbor-Net is a novel method for phylogenetic analysis that is currently being widely used in areas such as virology, bacteriology, and plant evolution. Given an input distance matrix, Neighbor-Net produces ...

    Authors: David Bryant, Vincent Moulton and Andreas Spillner

    Citation: Algorithms for Molecular Biology 2007 2:8

    Content type: Research

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  32. Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in th...

    Authors: Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Michael Trelinski and Peter Ortoleva

    Citation: Algorithms for Molecular Biology 2007 2:2

    Content type: Research

    Published on: