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  1. Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, c...

    Authors: Andrew V Uzilov, Joshua M Keegan and David H Mathews
    Citation: BMC Bioinformatics 2006 7:173
  2. The design of oligonucleotides and PCR primers for studying large genomes is complicated by the redundancy of sequences. The eukaryotic genomes are particularly difficult to study due to abundant repeats. The ...

    Authors: Reidar Andreson, Eric Reppo, Lauris Kaplinski and Maido Remm
    Citation: BMC Bioinformatics 2006 7:172
  3. Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks. Formalization of this knowledge is necessary for computational analysis and is achieved ...

    Authors: Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia and Ilya Mazo
    Citation: BMC Bioinformatics 2006 7:171
  4. The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect da...

    Authors: Vincent Le Texier, Jean-Jack Riethoven, Vasudev Kumanduri, Chellappa Gopalakrishnan, Fabrice Lopez, Daniel Gautheret and Thangavel Alphonse Thanaraj
    Citation: BMC Bioinformatics 2006 7:169
  5. Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell simulation are labor-intensive, manual...

    Authors: Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama and Masaru Tomita
    Citation: BMC Bioinformatics 2006 7:168
  6. Both direct and indirect interactions determine molecular recognition of ligands by proteins. Indirect interactions can be defined as effects on recognition controlled from distant sites in the proteins, e.g. ...

    Authors: Peteris Prusis, Staffan Uhlén, Ramona Petrovska, Maris Lapinsh and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2006 7:167
  7. Manually finding subtle yet statistically significant links to distantly related homologues becomes practically impossible for very populated protein families due to the sheer number of similarity searches to ...

    Authors: Georg Schneider, Georg Neuberger, Michael Wildpaner, Sun Tian, Igor Berezovsky and Frank Eisenhaber
    Citation: BMC Bioinformatics 2006 7:164
  8. Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the poten...

    Authors: Beltran Rodriguez-Brito, Forest Rohwer and Robert A Edwards
    Citation: BMC Bioinformatics 2006 7:162
  9. Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subse...

    Authors: Arunachalam Vinayagam, Coral del Val, Falk Schubert, Roland Eils, Karl-Heinz Glatting, Sándor Suhai and Rainer König
    Citation: BMC Bioinformatics 2006 7:161
  10. Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing the motif versus the number...

    Authors: Pieter Monsieurs, Gert Thijs, Abeer A Fadda, Sigrid CJ De Keersmaecker, Jozef Vanderleyden, Bart De Moor and Kathleen Marchal
    Citation: BMC Bioinformatics 2006 7:160
  11. The annotations of Affymetrix DNA microarray probe sets with Gene Ontology terms are carefully selected for correctness. This results in very accurate but incomplete annotations which is not always desirable f...

    Authors: Enrique M Muro, Carolina Perez-Iratxeta and Miguel A Andrade-Navarro
    Citation: BMC Bioinformatics 2006 7:159
  12. We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field...

    Authors: Lars Malmström, György Marko-Varga, Gunilla Westergren-Thorsson, Thomas Laurell and Johan Malmström
    Citation: BMC Bioinformatics 2006 7:158
  13. Serial Analysis of Gene Expressions (SAGE) produces gene expression measurements on a discrete scale, due to the finite number of molecules in the sample. This means that part of the variance in SAGE data shou...

    Authors: Helene H Thygesen and Aeilko H Zwinderman
    Citation: BMC Bioinformatics 2006 7:157
  14. Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the ...

    Authors: Erik Arner, Martti T Tammi, Anh-Nhi Tran, Ellen Kindlund and Bjorn Andersson
    Citation: BMC Bioinformatics 2006 7:155
  15. As a variety of functional genomic and proteomic techniques become available, there is an increasing need for functional analysis methodologies that integrate heterogeneous data sources.

    Authors: Zizhen Yao and Walter L Ruzzo
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S11

    This article is part of a Supplement: Volume 7 Supplement 1

  16. Biologists regularly search DNA or protein databases for sequences that share an evolutionary or functional relationship with a given query sequence. Traditional search methods, such as BLAST and PSI-BLAST, fo...

    Authors: Jason Weston, Rui Kuang, Christina Leslie and William Stafford Noble
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S10

    This article is part of a Supplement: Volume 7 Supplement 1

  17. Support Vector Machines (SVMs) – using a variety of string kernels – have been successfully applied to biological sequence classification problems. While SVMs achieve high classification accuracy they lack int...

    Authors: Gunnar Rätsch, Sören Sonnenburg and Christin Schäfer
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S9

    This article is part of a Supplement: Volume 7 Supplement 1

  18. Sequence homologs are an important source of information about proteins. Amino acid profiles, representing the position-specific mutation probabilities found in profiles, are a richer encoding of biological se...

    Authors: Sean O'Rourke, Gal Chechik, Robin Friedman and Eleazar Eskin
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S8

    This article is part of a Supplement: Volume 7 Supplement 1

  19. Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide "reverse engineering" of such netw...

    Authors: Adam A Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera and Andrea Califano
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S7

    This article is part of a Supplement: Volume 7 Supplement 1

  20. Neuronal communication is tightly regulated in time and in space. The neuronal transmission takes place in the nerve terminal, at a specialized structure called the synapse. Following neuronal activation, an e...

    Authors: Michal Linial
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S6

    This article is part of a Supplement: Volume 7 Supplement 1

  21. We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called GeneClass. GeneClass is motivated by the ...

    Authors: Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris H Wiggins, Yoav Freund and Christina Leslie
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S5

    This article is part of a Supplement: Volume 7 Supplement 1

  22. Prediction of human cell response to anti-cancer drugs (compounds) from microarray data is a challenging problem, due to the noise properties of microarrays as well as the high variance of living cell response...

    Authors: Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul B Horton, Koji Tsuda and Wataru Fujibuchi
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S4

    This article is part of a Supplement: Volume 7 Supplement 1

  23. Many different aspects of cellular signalling, trafficking and targeting mechanisms are mediated by interactions between proteins and peptides. Representative examples are MHC-peptide complexes in the immune s...

    Authors: Tomer Hertz and Chen Yanover
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S3

    This article is part of a Supplement: Volume 7 Supplement 1

  24. The protein-protein interaction networks of even well-studied model organisms are sketchy at best, highlighting the continued need for computational methods to help direct experimentalists in the search for no...

    Authors: Asa Ben-Hur and William Stafford Noble
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S2

    This article is part of a Supplement: Volume 7 Supplement 1

  25. Computing exact multipoint LOD scores for extended pedigrees rapidly becomes infeasible as the number of markers and untyped individuals increase. When markers are excluded from the computation, significant po...

    Authors: Cornelis A Albers, Martijn AR Leisink and Hilbert J Kappen
    Citation: BMC Bioinformatics 2006 7(Suppl 1):S1

    This article is part of a Supplement: Volume 7 Supplement 1

  26. T cells recognize a complex between a specific major histocompatibility complex (MHC) molecule and a particular pathogen-derived epitope. A given epitope will elicit a response only in individuals that express...

    Authors: Huynh-Hoa Bui, John Sidney, Kenny Dinh, Scott Southwood, Mark J Newman and Alessandro Sette
    Citation: BMC Bioinformatics 2006 7:153
  27. Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is spa...

    Authors: Kevin A Snyder, Howard J Feldman, Michel Dumontier, John J Salama and Christopher WV Hogue
    Citation: BMC Bioinformatics 2006 7:152
  28. The ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under a variety of experimental conditions is an important but difficult resource for investigators to utilize e...

    Authors: Jason M Doherty, Lynn K Carmichael and Jason C Mills
    Citation: BMC Bioinformatics 2006 7:151
  29. Unigenic evolution is a powerful genetic strategy involving random mutagenesis of a single gene product to delineate functionally important domains of a protein. This method involves selection of variants of t...

    Authors: Colleen D Behrsin, Chris J Brandl, David W Litchfield, Brian H Shilton and Lindi M Wahl
    Citation: BMC Bioinformatics 2006 7:150
  30. Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and util...

    Authors: JR Semeiks, A Rizki, MJ Bissell and IS Mian
    Citation: BMC Bioinformatics 2006 7:147
  31. The rapid growth of protein interactome data has elevated the necessity and importance of network analysis tools. However, unlike pure text data, network search spaces are of exponential complexity. This poses...

    Authors: Aaron N Chang, Jason McDermott, Zachary Frazier, Michal Guerquin and Ram Samudrala
    Citation: BMC Bioinformatics 2006 7:146
  32. RNA editing is one of several post-transcriptional modifications that may contribute to organismal complexity in the face of limited gene complement in a genome. One form, known as CU editing, appears to exist...

    Authors: James Thompson and Shuba Gopal
    Citation: BMC Bioinformatics 2006 7:145

    The Erratum to this article has been published in BMC Bioinformatics 2006 7:406

  33. The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable, especially in protein sequences. They a...

    Authors: Markus Seiler, Alexander Mehrle, Annemarie Poustka and Stefan Wiemann
    Citation: BMC Bioinformatics 2006 7:144
  34. Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changin...

    Authors: Stephan Waack, Oliver Keller, Roman Asper, Thomas Brodag, Carsten Damm, Wolfgang Florian Fricke, Katharina Surovcik, Peter Meinicke and Rainer Merkl
    Citation: BMC Bioinformatics 2006 7:142
  35. Short oligonucleotide arrays for transcript profiling have been available for several years. Generally, raw data from these arrays are analysed with the aid of the Microarray Analysis Suite or GeneChip Operati...

    Authors: Frank F Millenaar, John Okyere, Sean T May, Martijn van Zanten, Laurentius ACJ Voesenek and Anton JM Peeters
    Citation: BMC Bioinformatics 2006 7:137
  36. Alternative splicing (AS) is important for evolution and major biological functions in complex organisms. However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult...

    Authors: Feng-Chi Chen, Chuang-Jong Chen, Jar-Yi Ho and Trees-Juen Chuang
    Citation: BMC Bioinformatics 2006 7:136

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