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  2. The heterokonts are a particularly interesting group of eukaryotic organisms; they include many key species of planktonic and coastal algae and several important pathogens. To understand the biology of these o...

    Authors: Bernhard Gschloessl, Yann Guermeur and J Mark Cock
    Citation: BMC Bioinformatics 2008 9:393
    Content type: Methodology article Published on:

  3. Several eukaryotic proteins associated to the extracellular leaflet of the plasma membrane carry a Glycosylphosphatidylinositol (GPI) anchor, which is linked to the C-terminal residue after a proteolytic cleav...

    Authors: Andrea Pierleoni, Pier Luigi Martelli and Rita Casadio
    Citation: BMC Bioinformatics 2008 9:392
    Content type: Research article Published on:

  4. Sequences and structures provide valuable complementary information on protein features and functions. However, it is not always straightforward for users to gather information concurrently from the sequence a...

    Authors: Fabrice PA David and Yum L Yip
    Citation: BMC Bioinformatics 2008 9:391
    Content type: Research article Published on:

  5. R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each pa...

    Authors: Gonzalo Vera, Ritsert C Jansen and Remo L Suppi
    Citation: BMC Bioinformatics 2008 9:390
    Content type: Software Published on:

  6. Predicting a protein's structural or functional class from its amino acid sequence or structure is a fundamental problem in computational biology. Recently, there has been considerable interest in using discri...

    Authors: Iain Melvin, Jason Weston, Christina S Leslie and William S Noble
    Citation: BMC Bioinformatics 2008 9:389
    Content type: Research article Published on:

  7. Residue depth allows determining how deeply a given residue is buried, in contrast to the solvent accessibility that differentiates between buried and solvent-exposed residues. When compared with the solvent a...

    Authors: Hua Zhang, Tuo Zhang, Ke Chen, Shiyi Shen, Jishou Ruan and Lukasz Kurgan
    Citation: BMC Bioinformatics 2008 9:388
    Content type: Methodology article Published on:

  8. Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to aut...

    Authors: Pornpat Nikamanon, Elroy Pun, Wayne Chou, Marek D Koter and Paul D Gershon
    Citation: BMC Bioinformatics 2008 9:387
    Content type: Research article Published on:

  9. Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to an...

    Authors: F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening and RA Edwards
    Citation: BMC Bioinformatics 2008 9:386
    Content type: Software Published on:

  11. Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structu...

    Authors: René Ranzinger, Stephan Herget, Thomas Wetter and Claus-Wilhelm von der Lieth
    Citation: BMC Bioinformatics 2008 9:384
    Content type: Database Published on:

  12. The main limitations of most existing clustering methods used in genomic data analysis include heuristic or random algorithm initialization, the potential of finding poor local optima, the lack of cluster numb...

    Authors: Yitan Zhu, Huai Li, David J Miller, Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric P Hoffman and Yue Wang
    Citation: BMC Bioinformatics 2008 9:383
    Content type: Methodology article Published on:

  13. The functional characterization of newly discovered proteins has been a challenge in the post-genomic era. Protein-protein interactions provide insights into the functional analysis because the function of unk...

    Authors: Young-Rae Cho, Lei Shi, Murali Ramanathan and Aidong Zhang
    Citation: BMC Bioinformatics 2008 9:382
    Content type: Methodology article Published on:

  14. Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the M...

    Authors: Michael E Sparks and Volker Brendel
    Citation: BMC Bioinformatics 2008 9:381
    Content type: Software Published on:

  16. Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-usin...

    Authors: Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Tim Aitman and Laurence Game
    Citation: BMC Bioinformatics 2008 9:379
    Content type: Database Published on:

  17. There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some propert...

    Authors: Johan Leyritz, Stéphane Schicklin, Sylvain Blachon, Céline Keime, Céline Robardet, Jean-François Boulicaut, Jérémy Besson, Ruggero G Pensa and Olivier Gandrillon
    Citation: BMC Bioinformatics 2008 9:378
    Content type: Database Published on:

  18. The exponential growth of available biological data has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the computational power needed by bioinformatics...

    Authors: Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu and Bertil Schmidt
    Citation: BMC Bioinformatics 2008 9:377
    Content type: Software Published on:

  20. Liquid chromatography coupled to mass spectrometry (LC-MS) has become a prominent tool for the analysis of complex proteomics and metabolomics samples. In many applications multiple LC-MS measurements need to ...

    Authors: Eva Lange, Ralf Tautenhahn, Steffen Neumann and Clemens Gröpl
    Citation: BMC Bioinformatics 2008 9:375
    Content type: Research article Published on:

  21. Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become ...

    Authors: Jifeng Tang, Samantha J Baldwin, Jeanne ME Jacobs, C Gerard van der Linden, Roeland E Voorrips, Jack AM Leunissen, Herman van Eck and Ben Vosman
    Citation: BMC Bioinformatics 2008 9:374
    Content type: Methodology article Published on:

  22. Simulating the major molecular events inside an Escherichia coli cell can lead to a very large number of reactions that compose its overall behaviour. Not only should the model be accurate, but it is imperative f...

    Authors: Marco AJ Iafolla, Guang Qiang Dong and David R McMillen
    Citation: BMC Bioinformatics 2008 9:373
    Content type: Research article Published on:

  23. In analyzing the stability of DNA replication origins in Saccharomyces cerevisiae we faced the question whether one set of sequences is significantly enriched in the number and/or the quality of the matches of a ...

    Authors: Uri Keich, Hong Gao, Jeffrey S Garretson, Anand Bhaskar, Ivan Liachko, Justin Donato and Bik K Tye
    Citation: BMC Bioinformatics 2008 9:372
    Content type: Research article Published on:

  24. There is great interest in probing the temporal and spatial patterns of cytosine methylation states in genomes of a variety of organisms. It is hoped that this will shed light on the biological roles of DNA me...

    Authors: Eyal Gruntman, Yijun Qi, R Keith Slotkin, Ted Roeder, Robert A Martienssen and Ravi Sachidanandam
    Citation: BMC Bioinformatics 2008 9:371
    Content type: Software Published on:

  25. In addition to their use in detecting undesired real-time PCR products, melting temperatures are useful for detecting variations in the desired target sequences. Methodological improvements in recent years all...

    Authors: Christoffer Nellåker, Fredrik Uhrzander, Joanna Tyrcha and Håkan Karlsson
    Citation: BMC Bioinformatics 2008 9:370
    Content type: Methodology article Published on:

  26. Exonic splicing enhancers (ESEs) activate nearby splice sites and promote the inclusion (vs. exclusion) of exons in which they reside, while being a binding site for SR proteins. To study the impact of ESEs on...

    Authors: Britta Mersch, Alexander Gepperth, Sándor Suhai and Agnes Hotz-Wagenblatt
    Citation: BMC Bioinformatics 2008 9:369
    Content type: Research article Published on:

  27. Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than specific pri...

    Authors: Wah Heng Lee, Christopher W Wong, Wan Yee Leong, Lance D Miller and Wing Kin Sung
    Citation: BMC Bioinformatics 2008 9:368
    Content type: Software Published on:

  29. Genome survey sequences (GSS) offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation...

    Authors: Thomas D Otto, Leonardo HF Gomes, Marcelo Alves-Ferreira, Antonio B de Miranda and Wim M Degrave
    Citation: BMC Bioinformatics 2008 9:366
    Content type: Methodology article Published on:

  30. Epigenetics is the study of heritable changes in gene function that cannot be explained by changes in DNA sequence. One of the most commonly studied epigenetic alterations is cytosine methylation, which is a w...

    Authors: E Andres Houseman, Brock C Christensen, Ru-Fang Yeh, Carmen J Marsit, Margaret R Karagas, Margaret Wrensch, Heather H Nelson, Joseph Wiemels, Shichun Zheng, John K Wiencke and Karl T Kelsey
    Citation: BMC Bioinformatics 2008 9:365
    Content type: Methodology article Published on:

  31. FREGENE simulates sequence-level data over large genomic regions in large populations. Because, unlike coalescent simulators, it works forwards through time, it allows complex scenarios of selection, demography, ...

    Authors: Marc Chadeau-Hyam, Clive J Hoggart, Paul F O'Reilly, John C Whittaker, Maria De Iorio and David J Balding
    Citation: BMC Bioinformatics 2008 9:364
    Content type: Software Published on:

  32. The G-protein coupled receptor (GPCR) superfamily is currently the largest class of therapeutic targets. In silico prediction of interactions between GPCRs and small molecules in the transmembrane ligand-binding ...

    Authors: Laurent Jacob, Brice Hoffmann, Véronique Stoven and Jean-Philippe Vert
    Citation: BMC Bioinformatics 2008 9:363
    Content type: Research article Published on:

  33. Many methods have been developed to test the enrichment of genes related to certain phenotypes or cell states in gene sets. These approaches usually combine gene expression data with functionally related gene ...

    Authors: Xiting Yan and Fengzhu Sun
    Citation: BMC Bioinformatics 2008 9:362
    Content type: Methodology article Published on:

  34. In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-valu...

    Authors: Stefano Moretti, Danitsja van Leeuwen, Hans Gmuender, Stefano Bonassi, Joost van Delft, Jos Kleinjans, Fioravante Patrone and Domenico Franco Merlo
    Citation: BMC Bioinformatics 2008 9:361
    Content type: Methodology article Published on:

  36. The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This make...

    Authors: James M Eales, John W Pinney, Robert D Stevens and David L Robertson
    Citation: BMC Bioinformatics 2008 9:359
    Content type: Research article Published on:

  38. The problem of accurate prediction of protein secondary structure continues to be one of the challenging problems in Bioinformatics. It has been previously suggested that amino acid relative solvent accessibil...

    Authors: Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk and Sayed-Amir Marashi
    Citation: BMC Bioinformatics 2008 9:357
    Content type: Research article Published on:

  40. The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments.

    Authors: Bernhard Y Renard, Marc Kirchner, Hanno Steen, Judith AJ Steen and Fred A Hamprecht
    Citation: BMC Bioinformatics 2008 9:355
    Content type: Methodology article Published on:

  42. Despite significant improvements in computational annotation of genomes, sequences of abnormal, incomplete or incorrectly predicted genes and proteins remain abundant in public databases. Since the majority of...

    Authors: Alinda Nagy, Hédi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, László Bányai and László Patthy
    Citation: BMC Bioinformatics 2008 9:353
    Content type: Research article Published on:

  43. Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies...

    Authors: Roberto Mosca, Barbara Brannetti and Thomas R Schneider
    Citation: BMC Bioinformatics 2008 9:352
    Content type: Methodology article Published on:

  44. In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently ...

    Authors: Jörg Lehmann, Peter F Stadler and Sonja J Prohaska
    Citation: BMC Bioinformatics 2008 9:351
    Content type: Methodology article Published on:

  45. In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Mos...

    Authors: Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif and Eric D Kolaczyk
    Citation: BMC Bioinformatics 2008 9:350
    Content type: Methodology article Published on:

  46. Structural similarities among proteins can provide valuable insight into their functional mechanisms and relationships. As the number of available three-dimensional (3D) protein structures increases, a greater...

    Authors: Shih-Yen Ku and Yuh-Jyh Hu
    Citation: BMC Bioinformatics 2008 9:349
    Content type: Methodology article Published on:

  47. Microarray experiments measure changes in the expression of thousands of genes. The resulting lists of genes with changes in expression are then searched for biologically related sets using several divergent m...

    Authors: Stephen W Tanner and Pankaj Agarwal
    Citation: BMC Bioinformatics 2008 9:348
    Content type: Methodology article Published on:

  48. Rejection of false positive peptide matches in database searches of shotgun proteomic experimental data is highly desirable. Several methods have been developed to use the peptide retention time as to refine a...

    Authors: Hua Xu, Lanhao Yang and Michael A Freitas
    Citation: BMC Bioinformatics 2008 9:347
    Content type: Research article Published on:

  49. The acceptor photobleaching fluorescence resonance energy transfer (FRET) method is widely used for monitoring molecular interactions in cells. This method of FRET, while among those with the simplest mathemat...

    Authors: János Roszik, János Szöllősi and György Vereb
    Citation: BMC Bioinformatics 2008 9:346
    Content type: Software Published on:

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