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  1. Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families (<0.5%) have had the residues responsible for catalysis determined. To increase the active site...

    Authors: Jaina Mistry, Alex Bateman and Robert D Finn
    Citation: BMC Bioinformatics 2007 8:298
  2. The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, ...

    Authors: Nigam H Shah, Daniel L Rubin, Inigo Espinosa, Kelli Montgomery and Mark A Musen
    Citation: BMC Bioinformatics 2007 8:296
  3. The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational rei...

    Authors: Marija Cvijović, Daniel Dalevi, Elizabeth Bilsland, Graham JL Kemp and Per Sunnerhagen
    Citation: BMC Bioinformatics 2007 8:295
  4. The relationship between divergence of amino-acid sequence and divergence of function among homologous proteins is complex. The assumption that homologs share function – the basis of transfer of annotations in...

    Authors: Vineet Sangar, Daniel J Blankenberg, Naomi Altman and Arthur M Lesk
    Citation: BMC Bioinformatics 2007 8:294
  5. Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implementation of a state-of-the-art Natural Langua...

    Authors: Carlos Rodríguez-Penagos, Heladia Salgado, Irma Martínez-Flores and Julio Collado-Vides
    Citation: BMC Bioinformatics 2007 8:293
  6. Clustering analysis of microarray data is often criticized for giving ambiguous results because of sensitivity to data perturbation or clustering techniques used. In this paper, we describe a new method based ...

    Authors: Gul S Dalgin, Gabriela Alexe, Daniel Scanfeld, Pablo Tamayo, Jill P Mesirov, Shridar Ganesan, Charles DeLisi and Gyan Bhanot
    Citation: BMC Bioinformatics 2007 8:291
  7. Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated me...

    Authors: Brian J Holden, John W Pinney, Simon C Lovell, Grigoris D Amoutzias and David L Robertson
    Citation: BMC Bioinformatics 2007 8:289
  8. Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomog...

    Authors: Cédric MessaoudiI, Thomas Boudier, Carlos Oscar Sanchez Sorzano and Sergio Marco
    Citation: BMC Bioinformatics 2007 8:288
  9. Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced...

    Authors: Yasunori Yamamoto and Toshihisa Takagi
    Citation: BMC Bioinformatics 2007 8:287
  10. The study of microRNAs (miRNAs) is attracting great considerations. Recent studies revealed that miRNAs play as important regulators of gene expression and some even as cancer players or inhibitors. Many studi...

    Authors: Feng Tian, Huayue Zhang, Xinyu Zhang, Chi Song, Yongjing Xia, Yiqing Wu and Xiangjun Liu
    Citation: BMC Bioinformatics 2007 8:285
  11. Transcriptional modules (TM) consist of groups of co-regulated genes and transcription factors (TF) regulating their expression. Two high-throughput (HT) experimental technologies, gene expression microarrays ...

    Authors: Xiangdong Liu, Walter J Jessen, Siva Sivaganesan, Bruce J Aronow and Mario Medvedovic
    Citation: BMC Bioinformatics 2007 8:283
  12. There are a number of different methods for generation of trees and algorithms for phylogenetic analysis in the study of bacterial taxonomy. Genotypic information, such as SSU rRNA gene sequences, now plays a ...

    Authors: Naoto Tanaka, Masataka Uchino, Satoru Miyazaki and Hideaki Sugawara
    Citation: BMC Bioinformatics 2007 8:281
  13. Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated biological data. Rather, p...

    Authors: Timur Shtatland, Daniel Guettler, Misha Kossodo, Misha Pivovarov and Ralph Weissleder
    Citation: BMC Bioinformatics 2007 8:280
  14. Docking algorithms are developed to predict in which orientation two proteins are likely to bind under natural conditions. The currently used methods usually consist of a sampling step followed by a scoring st...

    Authors: Philipp Heuser and Dietmar Schomburg
    Citation: BMC Bioinformatics 2007 8:279
  15. Single nucleotide polymorphisms (SNPs) and genes that exhibit presence/absence variation have provided informative marker sets for bacterial and viral genotyping. Identification of marker sets optimised for th...

    Authors: Erin P Price, John Inman-Bamber, Venugopal Thiruvenkataswamy, Flavia Huygens and Philip M Giffard
    Citation: BMC Bioinformatics 2007 8:278
  16. To look for genetic linkage between angiotensin-I converting enzyme(ACE) gene and hypertension in a Korean adolescent cohort, we developed a powerful test using the covariances between marginal differences and...

    Authors: Chung Mo Nam, Dae Ryong Kang and Jinheum Kim
    Citation: BMC Bioinformatics 2007 8:277
  17. Affymetrix gene expression arrays incorporate paired perfect match (PM) and mismatch (MM) probes to distinguish true signals from those arising from cross-hybridization events. A MM signal often shows greater ...

    Authors: Sunita Kumari, Lalit K Verma and Jennifer W Weller
    Citation: BMC Bioinformatics 2007 8:276
  18. Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a gi...

    Authors: Benjamin B Andken, In Lim, Gary Benson, John J Vincent, Matthew T Ferenc, Bianca Heinrich, Larissa A Jarzylo, Heng-Ye Man and James O Deshler
    Citation: BMC Bioinformatics 2007 8:274
  19. A major goal of computational studies of gene regulation is to accurately predict the expression of genes based on the cis-regulatory content of their promoters. The development of computational methods to dec...

    Authors: Robert D Zeigler, Jason Gertz and Barak A Cohen
    Citation: BMC Bioinformatics 2007 8:272
  20. In structural genomics, an important goal is the detection and classification of protein–protein interactions, given the structures of the interacting partners. We have developed empirical energy functions to ...

    Authors: Guillaume Launay, Raul Mendez, Shoshana Wodak and Thomas Simonson
    Citation: BMC Bioinformatics 2007 8:270
  21. The Immune Epitope Database contains information on immune epitopes curated manually from the scientific literature. Like similar projects in other knowledge domains, significant effort is spent on identifying...

    Authors: Peng Wang, Alexander A Morgan, Qing Zhang, Alessandro Sette and Bjoern Peters
    Citation: BMC Bioinformatics 2007 8:269
  22. Although testing for simultaneous divergence (vicariance) across different population-pairs that span the same barrier to gene flow is of central importance to evolutionary biology, researchers often equate th...

    Authors: Michael J Hickerson, Eli Stahl and Naoki Takebayashi
    Citation: BMC Bioinformatics 2007 8:268
  23. The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction ne...

    Authors: Young-Rae Cho, Woochang Hwang, Murali Ramanathan and Aidong Zhang
    Citation: BMC Bioinformatics 2007 8:265
  24. Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs ...

    Authors: Sneh Lata, BK Sharma and GPS Raghava
    Citation: BMC Bioinformatics 2007 8:263
  25. Unsupervised annotation of proteins by software pipelines suffers from very high error rates. Spurious functional assignments are usually caused by unwarranted homology-based transfer of information from exist...

    Authors: Irena I Artamonova, Goar Frishman and Dmitrij Frishman
    Citation: BMC Bioinformatics 2007 8:261
  26. The study of the functional role of alternative splice isoforms of a gene is a very active area of research in biology. The difficulty of the experimental approach (in particular, in its high-throughput versio...

    Authors: David Talavera, Adam Hospital, Modesto Orozco and Xavier de la Cruz
    Citation: BMC Bioinformatics 2007 8:260
  27. Matching functional sites is a key problem for the understanding of protein function and evolution. The commonly used graph theoretic approach, and other related approaches, require adjustment of a matching di...

    Authors: Kanti V Mardia, Vysaul B Nyirongo, Peter J Green, Nicola D Gold and David R Westhead
    Citation: BMC Bioinformatics 2007 8:257
  28. Isotope-coded affinity tags (ICAT) is a method for quantitative proteomics based on differential isotopic labeling, sample digestion and mass spectrometry (MS). The method allows the identification and relativ...

    Authors: Mario Cannataro, Giovanni Cuda, Marco Gaspari, Sergio Greco, Giuseppe Tradigo and Pierangelo Veltri
    Citation: BMC Bioinformatics 2007 8:255
  29. The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation step...

    Authors: Matthias Kruspe and Peter F Stadler
    Citation: BMC Bioinformatics 2007 8:254
  30. Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate f...

    Authors: Paolo Ferragina, Raffaele Giancarlo, Valentina Greco, Giovanni Manzini and Gabriel Valiente
    Citation: BMC Bioinformatics 2007 8:252
  31. The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both individual biological pathways and the integrat...

    Authors: Curtis Huttenhower, Avi I Flamholz, Jessica N Landis, Sauhard Sahi, Chad L Myers, Kellen L Olszewski, Matthew A Hibbs, Nathan O Siemers, Olga G Troyanskaya and Hilary A Coller
    Citation: BMC Bioinformatics 2007 8:250

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