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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for additional sites. However, few statisti...

    Authors: C Steven Carmack, Lee Ann McCue, Lee A Newberg and Charles E Lawrence
    Citation: Algorithms for Molecular Biology 2007 2:1
  32. The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clu...

    Authors: Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan
    Citation: Algorithms for Molecular Biology 2006 1:24