Skip to main content

Advertisement

Articles

Page 7 of 8

  1. 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

    Published on:

  2. 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

    Published on:

  3. 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

    Published on:

  4. 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

    Published on:

  5. 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

    Published on:

  6. 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

    Published on:

  7. 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

    Published on:

  8. 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

    Published on:

  9. 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

    Published on:

  10. 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

    Published on:

  11. 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

    Published on:

  12. 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

    Published on:

  13. 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

    Published on:

  14. 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

    Published on:

  15. 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

    Published on:

  16. 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

    Published on:

  17. 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

    Published on:

  18. 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:

  19. 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

    Content type: Research

    Published on:

  20. 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

    Content type: Research

    Published on:

  21. A structured motif allows variable length gaps between several components, where each component is a simple motif, which allows either no gaps or only fixed length gaps. The motif can either be represented as a p...

    Authors: Yongqiang Zhang and Mohammed J Zaki

    Citation: Algorithms for Molecular Biology 2006 1:22

    Content type: Research

    Published on:

  22. Extracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient a...

    Authors: Yongqiang Zhang and Mohammed J Zaki

    Citation: Algorithms for Molecular Biology 2006 1:21

    Content type: Research

    Published on:

  23. The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for t...

    Authors: Andreas Wilm, Indra Mainz and Gerhard Steger

    Citation: Algorithms for Molecular Biology 2006 1:19

    Content type: Research

    Published on:

  24. A number of algorithms have been developed for calculating the quartet distance between two evolutionary trees on the same set of species. The quartet distance is the number of quartets – sub-trees induced by ...

    Authors: Chris Christiansen, Thomas Mailund, Christian NS Pedersen, Martin Randers and Martin Stig Stissing

    Citation: Algorithms for Molecular Biology 2006 1:16

    Content type: Research

    Published on:

  25. Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these...

    Authors: Gregory A Grothaus, Adeel Mufti and TM Murali

    Citation: Algorithms for Molecular Biology 2006 1:15

    Content type: Research

    Published on:

  26. The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings...

    Authors: Giuseppe Lancia and Romeo Rizzi

    Citation: Algorithms for Molecular Biology 2006 1:12

    Content type: Research

    Published on:

  27. Bifurcation analysis has proven to be a powerful method for understanding the qualitative behavior of gene regulatory networks. In addition to the more traditional forward problem of determining the mapping from ...

    Authors: James Lu, Heinz W Engl and Peter Schuster

    Citation: Algorithms for Molecular Biology 2006 1:11

    Content type: Research

    Published on:

  28. Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by m...

    Authors: Peter Meinicke, Thomas Brodag, Wolfgang Florian Fricke and Stephan Waack

    Citation: Algorithms for Molecular Biology 2006 1:10

    Content type: Research

    Published on:

  29. Given a set S of n locally aligned sequences, it is a needed prerequisite to partition it into groups of very similar sequences to facilitate subsequent computations, such as the generation of a phylogenetic tree...

    Authors: Katharina A Lehmann, Michael Kaufmann, Stephan Steigele and Kay Nieselt

    Citation: Algorithms for Molecular Biology 2006 1:9

    Content type: Research

    Published on: