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  1. Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline th...

    Authors: Chenggang Yu, Nela Zavaljevski, Valmik Desai, Seth Johnson, Fred J Stevens and Jaques Reifman
    Citation: BMC Bioinformatics 2008 9:52
  2. Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are tolerated. The rise in available protein s...

    Authors: Jonathan R Manning, Emily R Jefferson and Geoffrey J Barton
    Citation: BMC Bioinformatics 2008 9:51
  3. Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also provide the means for identifying and discr...

    Authors: Mark Bauer, Sheldon M Schuster and Khalid Sayood
    Citation: BMC Bioinformatics 2008 9:48
  4. Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods are emerging to engineer cells...

    Authors: Erwin P Gianchandani, Matthew A Oberhardt, Anthony P Burgard, Costas D Maranas and Jason A Papin
    Citation: BMC Bioinformatics 2008 9:43
  5. Hierarchical clustering is a widely applied tool in the analysis of microarray gene expression data. The assessment of cluster stability is a major challenge in clustering procedures. Statistical methods are r...

    Authors: Irina M Gana Dresen, Tanja Boes, Johannes Huesing, Markus Neuhaeuser and Karl-Heinz Joeckel
    Citation: BMC Bioinformatics 2008 9:42
  6. Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. ...

    Authors: Jeong-Gu Kim, Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Yeong Tae Kim, Young-Jin Park, Hee Jung Cho, Hyunseok Park, Ki-Bong Kim, Kyong-Oh Yoon, Soo-Jun Park, Byoung-Moo Lee and Jong Bhak
    Citation: BMC Bioinformatics 2008 9:41
  7. Prediction of 3-dimensional protein structures from amino acid sequences represents one of the most important problems in computational structural biology. The community-wide Critical Assessment of Structure P...

    Authors: Yang Zhang
    Citation: BMC Bioinformatics 2008 9:40
  8. MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experime...

    Authors: Shay Artzi, Adam Kiezun and Noam Shomron
    Citation: BMC Bioinformatics 2008 9:39
  9. The discovery of biomarkers is an important step towards the development of criteria for early diagnosis of disease status. Recently electrospray ionization (ESI) and matrix assisted laser desorption (MALDI) t...

    Authors: Samiran Ghosh, David F Grant, Dipak K Dey and Dennis W Hill
    Citation: BMC Bioinformatics 2008 9:38
  10. The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints) has become a common strategy to predict cis-acting regulatory elements. Several software tools are routinely used t...

    Authors: Rekin's Janky and Jacques van Helden
    Citation: BMC Bioinformatics 2008 9:37
  11. To meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurately align gene sequences to the genome of ...

    Authors: Leming Zhou, Jonathan Stanton and Liliana Florea
    Citation: BMC Bioinformatics 2008 9:36
  12. It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i....

    Authors: Jose MG Izarzugaza, David Juan, Carles Pons, Florencio Pazos and Alfonso Valencia
    Citation: BMC Bioinformatics 2008 9:35
  13. Aligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for strict structural alignments, have been propos...

    Authors: Yasuo Tabei, Hisanori Kiryu, Taishin Kin and Kiyoshi Asai
    Citation: BMC Bioinformatics 2008 9:33
  14. This paper discusses the problem of automated annotation. It is a continuation of the previous work on the A4-algorithm (Adaptive algorithm of automated annotation) developed by Leontovich and others.

    Authors: Andrey M Leontovich, Konstantin Y Tokmachev and Hans C van Houwelingen
    Citation: BMC Bioinformatics 2008 9:31
  15. Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods,...

    Authors: Ramon Diaz-Uriarte
    Citation: BMC Bioinformatics 2008 9:30
  16. Analysis of complex samples with tandem mass spectrometry (MS/MS) has become routine in proteomic research. However, validation of database search results creates a bottleneck in MS/MS data processing. Recentl...

    Authors: Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu and Fuchu He
    Citation: BMC Bioinformatics 2008 9:29
  17. MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a universal standard: First, MAGE...

    Authors: Don Maier, Farrell Wymore, Gavin Sherlock and Catherine A Ball
    Citation: BMC Bioinformatics 2008 9:28
  18. The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models) have also been applied on the level of sequence repeats inside a gene/protein. Ph...

    Authors: Botond Sipos, Kálmán Somogyi, István Andó and Zsolt Pénzes
    Citation: BMC Bioinformatics 2008 9:27
  19. The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have th...

    Authors: Alexandre Kuhn, Ruth Luthi-Carter and Mauro Delorenzi
    Citation: BMC Bioinformatics 2008 9:26
  20. Normalization is essential in dual-labelled microarray data analysis to remove non-biological variations and systematic biases. Many normalization methods have been used to remove such biases within slides (Gl...

    Authors: Huiling Xiong, Dapeng Zhang, Christopher J Martyniuk, Vance L Trudeau and Xuhua Xia
    Citation: BMC Bioinformatics 2008 9:25
  21. A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data ...

    Authors: Jonathan G Lees and Robert W Janes
    Citation: BMC Bioinformatics 2008 9:24
  22. The inference of a genetic network is a problem in which mutual interactions among genes are deduced using time-series of gene expression patterns. While a number of models have been proposed to describe genet...

    Authors: Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura and Mariko Hatakeyama
    Citation: BMC Bioinformatics 2008 9:23
  23. Prediction of disulfide bridges from protein sequences is useful for characterizing structural and functional properties of proteins. Several methods based on different machine learning algorithms have been ap...

    Authors: Marc Vincent, Andrea Passerini, Matthieu Labbé and Paolo Frasconi
    Citation: BMC Bioinformatics 2008 9:20
  24. Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally develope...

    Authors: Mutlu DoÄŸruel, Thomas A Down and Tim JP Hubbard
    Citation: BMC Bioinformatics 2008 9:19
  25. Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D temp...

    Authors: David M Kristensen, R Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y Chen, Viacheslav Y Fofanov, Marek Kimmel, Lydia E Kavraki and Olivier Lichtarge
    Citation: BMC Bioinformatics 2008 9:17
  26. The huge amount of data generated by DNA chips is a powerful basis to classify various pathologies. However, constant evolution of microarray technology makes it difficult to mix data from different chip types...

    Authors: Thierry Rème, Dirk Hose, John De Vos, Aurélien Vassal, Pierre-Olivier Poulain, Véronique Pantesco, Hartmut Goldschmidt and Bernard Klein
    Citation: BMC Bioinformatics 2008 9:16
  27. Ultraconserved elements are nucleotide or protein sequences with 100% identity (no mismatches, insertions, or deletions) in the same organism or between two or more organisms. Studies indicate that these conse...

    Authors: Scott Christley, Neil F Lobo and Greg Madey
    Citation: BMC Bioinformatics 2008 9:15
  28. Gene expression data frequently contain missing values, however, most down-stream analyses for microarray experiments require complete data. In the literature many methods have been proposed to estimate missin...

    Authors: Guy N Brock, John R Shaffer, Richard E Blakesley, Meredith J Lotz and George C Tseng
    Citation: BMC Bioinformatics 2008 9:12
  29. The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome [1] would not have been possible without advanced assembly algorithms....

    Authors: Andreas Döring, David Weese, Tobias Rausch and Knut Reinert
    Citation: BMC Bioinformatics 2008 9:11
  30. Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attem...

    Authors: Jin-Dong Kim, Tomoko Ohta and Jun'ichi Tsujii
    Citation: BMC Bioinformatics 2008 9:10
  31. Protein sumoylation is an essential dynamic, reversible post translational modification that plays a role in dozens of cellular activities, especially the regulation of gene expression and the maintenance of g...

    Authors: Jialin Xu, Yun He, Boqin Qiang, Jiangang Yuan, Xiaozhong Peng and Xian-Ming Pan
    Citation: BMC Bioinformatics 2008 9:8
  32. The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer tr...

    Authors: Michelle N Knowlton, Tongbin Li, Yongliang Ren, Brent R Bill, Lynda BM Ellis and Stephen C Ekker
    Citation: BMC Bioinformatics 2008 9:7
  33. Recent approaches for predicting the three-dimensional (3D) structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potential functions and a reduced representation of t...

    Authors: Jean-François Taly, Antoine Marin and Jean-François Gibrat
    Citation: BMC Bioinformatics 2008 9:6
  34. Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector region...

    Authors: Javier Forment, Francisco Gilabert, Antonio Robles, Vicente Conejero, Fernando Nuez and Jose M Blanca
    Citation: BMC Bioinformatics 2008 9:5
  35. In spite of two-dimensional gel electrophoresis (2-DE) being an effective and widely used method to screen the proteome, its data standardization has still not matured to the level of microarray genomics data ...

    Authors: Romesh Stanislaus, John M Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen and Jonas S Almeida
    Citation: BMC Bioinformatics 2008 9:4
  36. High-throughput technologies like functional screens and gene expression analysis produce extended lists of candidate genes. Gene-Set Enrichment Analysis is a commonly used and well established technique to te...

    Authors: Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann and Tim Beissbarth
    Citation: BMC Bioinformatics 2008 9:3
  37. Inference of protein interaction networks from various sources of data has become an important topic of both systems and computational biology. Here we present a supervised approach to identification of gene e...

    Authors: Cuong C To and Jiri Vohradsky
    Citation: BMC Bioinformatics 2008 9:2

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