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  1. 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
    Content type: Database Published on:

  2. 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
    Content type: Methodology article Published on:

  3. 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
    Content type: Methodology article Published on:

  6. 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
    Content type: Database Published on:

  8. 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
    Content type: Methodology article Published on:

  10. 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
    Content type: Research article Published on:

  11. 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
    Content type: Research article Published on:

  12. 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
    Content type: Software Published on:

  15. 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
    Content type: Methodology article Published on:

  17. 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
    Content type: Methodology article Published on:

  19. 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
    Content type: Methodology article Published on:

  20. 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
    Content type: Methodology article Published on:

  23. 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
    Content type: Research article Published on:

  25. 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
    Content type: Software Published on:

  26. 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
    Content type: Methodology article Published on:

  28. 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
    Content type: Research article Published on:

  30. 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
    Content type: Software Published on:

  31. Despite the diversity of motif representations and search algorithms, the de novo computational identification of transcription factor binding sites remains constrained by the limited accuracy of existing algorit...

    Authors: Arijit Chakravarty, Jonathan M Carlson, Radhika S Khetani and Robert H Gross
    Citation: BMC Bioinformatics 2007 8:249
    Content type: Methodology article Published on:

  34. Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or vot...

    Authors: Ricardo ZN Vêncio, Leonardo Varuzza, Carlos A de B Pereira, Helena Brentani and Ilya Shmulevich
    Citation: BMC Bioinformatics 2007 8:246
    Content type: Software Published on:

  35. Oral delivery is a highly desirable property for candidate drugs under development. Computational modeling could provide a quick and inexpensive way to assess the intestinal permeability of a molecule. Althoug...

    Authors: Eunkyoung Jung, Junhyoung Kim, Minkyoung Kim, Dong Hyun Jung, Hokyoung Rhee, Jae-Min Shin, Kihang Choi, Sang-Kee Kang, Min-Kook Kim, Cheol-Heui Yun, Yun-Jaie Choi and Seung-Hoon Choi
    Citation: BMC Bioinformatics 2007 8:245
    Content type: Research article Published on:

  36. Using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an Enzyme Commission number. Here we p...

    Authors: Yannick Pouliot and Peter D Karp
    Citation: BMC Bioinformatics 2007 8:244
    Content type: Research article Published on:

  37. Uncovering cellular roles of a protein is a task of tremendous importance and complexity that requires dedicated experimental work as well as often sophisticated data mining and processing tools. Protein funct...

    Authors: Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Ilya Mazo and Iaroslav Ispolatov
    Citation: BMC Bioinformatics 2007 8:243
    Content type: Research article Published on:

  38. Gene-set analysis evaluates the expression of biological pathways, or a priori defined gene sets, rather than that of individual genes, in association with a binary phenotype, and is of great biologic interest in...

    Authors: Irina Dinu, John D Potter, Thomas Mueller, Qi Liu, Adeniyi J Adewale, Gian S Jhangri, Gunilla Einecke, Konrad S Famulski, Philip Halloran and Yutaka Yasui
    Citation: BMC Bioinformatics 2007 8:242
    Content type: Methodology article Published on:

  40. Researchers using RNA expression microarrays in experimental designs with more than two treatment groups often identify statistically significant genes with ANOVA approaches. However, the ANOVA test does not d...

    Authors: Randall Hulshizer and Eric M Blalock
    Citation: BMC Bioinformatics 2007 8:240
    Content type: Methodology article Published on:

  46. Classifying nuclear magnetic resonance (NMR) spectra is a crucial step in many metabolomics experiments. Since several multivariate classification techniques depend upon the variance of the data, it is importa...

    Authors: Helen M Parsons, Christian Ludwig, Ulrich L Günther and Mark R Viant
    Citation: BMC Bioinformatics 2007 8:234
    Content type: Research article Published on:

  47. In practice many biological time series measurements, including gene microarrays, are conducted at time points that seem to be interesting in the biologist's opinion and not necessarily at fixed time intervals...

    Authors: Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, llya Shmulevich and Olli Yli-Harja
    Citation: BMC Bioinformatics 2007 8:233
    Content type: Methodology article Published on:

  50. Proteins are the primary regulatory agents of transcription even though mRNA expression data alone, from systems like DNA microarrays, are widely used. In addition, the regulation process in genetic systems is...

    Authors: Reuben Thomas, Carlos J Paredes, Sanjay Mehrotra, Vassily Hatzimanikatis and Eleftherios T Papoutsakis
    Citation: BMC Bioinformatics 2007 8:228
    Content type: Methodology article Published on:

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