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  1. Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN...

    Authors: Chun-Chi Liu, Chin-Chung Lin, Ker-Chau Li, Wen-Shyen E Chen, Jiun-Ching Chen, Ming-Te Yang, Pan-Chyr Yang, Pei-Chun Chang and Jeremy JW Chen
    Citation: BMC Bioinformatics 2007 8:164
  2. Structural genomics initiatives are producing increasing numbers of three-dimensional (3D) structures for which there is little functional information. Structure-based annotation of molecular function is there...

    Authors: Sungroh Yoon, Jessica C Ebert, Eui-Young Chung, Giovanni De Micheli and Russ B Altman
    Citation: BMC Bioinformatics 2007 8(Suppl 4):S10

    This article is part of a Supplement: Volume 8 Supplement 4

  3. Many protein sequences are still poorly annotated. Functional characterization of a protein is often improved by the identification of its interaction partners. Here, we aim to predict protein-protein interact...

    Authors: Andreas Henschel, Christof Winter, Wan Kyu Kim and Michael Schroeder
    Citation: BMC Bioinformatics 2007 8(Suppl 4):S5

    This article is part of a Supplement: Volume 8 Supplement 4

  4. The size and magnitude of the metabolome, the ratio between individual metabolites and the response of metabolic networks is controlled by multiple cellular factors. A tight control over metabolite ratios will...

    Authors: Frank Kose, Jan Budczies, Matthias Holschneider and Oliver Fiehn
    Citation: BMC Bioinformatics 2007 8:162
  5. Recent analyses have suggested that many genes possess multiple transcription start sites (TSSs) that are differentially utilized in different tissues and cell lines. We have identified a huge number of TSSs m...

    Authors: Kazuro Shimokawa, Yuko Okamura-Oho, Takio Kurita, Martin C Frith, Jun Kawai, Piero Carninci and Yoshihide Hayashizaki
    Citation: BMC Bioinformatics 2007 8:161
  6. Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been ...

    Authors: Mihaela Pertea, Stephen M Mount and Steven L Salzberg
    Citation: BMC Bioinformatics 2007 8:159
  7. When conducting multiple hypothesis tests, it is important to control the number of false positives, or the False Discovery Rate (FDR). However, there is a tradeoff between controlling FDR and maximizing power...

    Authors: Xin Lu and David L Perkins
    Citation: BMC Bioinformatics 2007 8:157
  8. The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-l...

    Authors: BD Pascal, MJ Chalmers, SA Busby, CC Mader, MR Southern, NF Tsinoremas and PR Griffin
    Citation: BMC Bioinformatics 2007 8:156
  9. SAGE has been used widely to study the expression of known transcripts, but much less to annotate new transcribed regions. LongSAGE produces tags that are sufficiently long to be reliably mapped to a whole-gen...

    Authors: Céline Keime, Marie Sémon, Dominique Mouchiroud, Laurent Duret and Olivier Gandrillon
    Citation: BMC Bioinformatics 2007 8:154
  10. Gene expression is governed by complex networks, and differences in expression patterns between distinct biological conditions may therefore be complex and multivariate in nature. Yet, current statistical meth...

    Authors: Roland Nilsson, José M Peña, Johan Björkegren and Jesper Tegnér
    Citation: BMC Bioinformatics 2007 8:150
  11. Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biom...

    Authors: James L Chen, Yang Liu, Lee T Sam, Jianrong Li and Yves A Lussier
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S7

    This article is part of a Supplement: Volume 8 Supplement 3

  12. Recent advances in Web and information technologies with the increasing decentralization of organizational structures have resulted in massive amounts of information resources and domain-specific services in T...

    Authors: Huajun Chen, Yuxin Mao, Xiaoqing Zheng, Meng Cui, Yi Feng, Shuiguang Deng, Aining Yin, Chunying Zhou, Jinming Tang, Xiaohong Jiang and Zhaohui Wu
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S6

    This article is part of a Supplement: Volume 8 Supplement 3

  13. A key abstraction in representing proteomics knowledge is the notion of unique identifiers for individual entities (e.g. proteins) and the massive graph of relationships among them. These relationships are som...

    Authors: Andrew K Smith, Kei-Hoi Cheung, Kevin Y Yip, Martin Schultz and Mark B Gerstein
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S5

    This article is part of a Supplement: Volume 8 Supplement 3

  14. Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering c...

    Authors: Hugo YK Lam, Luis Marenco, Tim Clark, Yong Gao, June Kinoshita, Gordon Shepherd, Perry Miller, Elizabeth Wu, Gwendolyn T Wong, Nian Liu, Chiquito Crasto, Thomas Morse, Susie Stephens and Kei-Hoi Cheung
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S4

    This article is part of a Supplement: Volume 8 Supplement 3

  15. The development of e-Science presents a major set of opportunities and challenges for the future progress of biological and life scientific research. Major new tools are required and corresponding demands are ...

    Authors: Joanne S Luciano and Robert D Stevens
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S3

    This article is part of a Supplement: Volume 8 Supplement 3

  16. A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. ...

    Authors: Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens…
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S2

    This article is part of a Supplement: Volume 8 Supplement 3

  17. The Semantic Web technologies provide enhanced capabilities that allow data and the meaning of the data to be shared and reused across application, enterprise, and community boundaries, better enabling integra...

    Authors: Huajun Chen, Yimin Wang and Zhaohui Wu
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S1

    This article is part of a Supplement: Volume 8 Supplement 3

  18. Biochemical investigations over the last decades have elucidated an increasingly complete image of the cellular metabolism. To derive a systems view for the regulation of the metabolism when cells adapt to env...

    Authors: Gunnar Schramm, Marc Zapatka, Roland Eils and Rainer König
    Citation: BMC Bioinformatics 2007 8:149
  19. Evolutionary processes, such as gene family evolution or parasite-host co-speciation, can often be viewed as a tree evolving inside another tree. Relating two given trees under such a constraint is known as re...

    Authors: Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren and Lars Arvestad
    Citation: BMC Bioinformatics 2007 8:148
  20. Recognition of binding sites in proteins is a direct computational approach to the characterization of proteins in terms of biological and biochemical function. Residue preferences have been widely used in man...

    Authors: Qiwen Dong, Xiaolong Wang, Lei Lin and Yi Guan
    Citation: BMC Bioinformatics 2007 8:147
  21. Microarrays have been used extensively to analyze the expression profiles for thousands of genes in parallel. Most of the widely used methods for analyzing Affymetrix Genechip microarray data, including RMA, G...

    Authors: Alexander C Cambon, Abdelnaby Khalyfa, Nigel GF Cooper and Caryn M Thompson
    Citation: BMC Bioinformatics 2007 8:146
  22. DNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping arrays ...

    Authors: Tianwei Yu, Hui Ye, Wei Sun, Ker-Chau Li, Zugen Chen, Sharoni Jacobs, Dione K Bailey, David T Wong and Xiaofeng Zhou
    Citation: BMC Bioinformatics 2007 8:145
  23. We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of...

    Authors: Volker Roth and Bernd Fischer
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S12

    This article is part of a Supplement: Volume 8 Supplement 2

  24. Human endogenous retroviruses (HERVs) are surviving traces of ancient retrovirus infections and now reside within the human DNA. Recently HERV expression has been detected in both normal tissues and diseased p...

    Authors: Merja Oja, Jaakko Peltonen, Jonas Blomberg and Samuel Kaski
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S11

    This article is part of a Supplement: Volume 8 Supplement 2

  25. Features of a DNA sequence can be found by compressing the sequence under a suitable model; good compression implies low information content. Good DNA compression models consider repetition, differences betwee...

    Authors: Trevor I Dix, David R Powell, Lloyd Allison, Julie Bernal, Samira Jaeger and Linda Stern
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S10

    This article is part of a Supplement: Volume 8 Supplement 2

  26. Haplotype Reconstruction is the problem of resolving the hidden phase information in genotype data obtained from laboratory measurements. Solving this problem is an important intermediate step in gene association...

    Authors: Niels Landwehr, Taneli Mielikäinen, Lauri Eronen, Hannu Toivonen and Heikki Mannila
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S9

    This article is part of a Supplement: Volume 8 Supplement 2

  27. A key challenge in metabonomics is to uncover quantitative associations between multidimensional spectroscopic data and biochemical measures used for disease risk assessment and diagnostics. Here we focus on c...

    Authors: Aki Vehtari, Ville-Petteri Mäkinen, Pasi Soininen, Petri Ingman, Sanna M Mäkelä, Markku J Savolainen, Minna L Hannuksela, Kimmo Kaski and Mika Ala-Korpela
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S8

    This article is part of a Supplement: Volume 8 Supplement 2

  28. When analyzing microarray gene expression data, missing values are often encountered. Most multivariate statistical methods proposed for microarray data analysis cannot be applied when the data have missing va...

    Authors: Dankyu Yoon, Eun-Kyung Lee and Taesung Park
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S6

    This article is part of a Supplement: Volume 8 Supplement 2

  29. In recent years, several authors have used probabilistic graphical models to learn expression modules and their regulatory programs from gene expression data. Despite the demonstrated success of such algorithm...

    Authors: Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper, Kathleen Marchal and Yves Van de Peer
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S5

    This article is part of a Supplement: Volume 8 Supplement 2

  30. Elucidating biological networks between proteins appears nowadays as one of the most important challenges in systems biology. Computational approaches to this problem are important to complement high-throughpu...

    Authors: Pierre Geurts, Nizar Touleimat, Marie Dutreix and Florence d'Alché-Buc
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S4

    This article is part of a Supplement: Volume 8 Supplement 2

  31. Causal networks based on the vector autoregressive (VAR) process are a promising statistical tool for modeling regulatory interactions in a cell. However, learning these networks is challenging due to the low ...

    Authors: Rainer Opgen-Rhein and Korbinian Strimmer
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S3

    This article is part of a Supplement: Volume 8 Supplement 2

  32. In many approaches to the inference and modeling of regulatory interactions using microarray data, the expression of the gene coding for the transcription factor is considered to be an accurate surrogate for t...

    Authors: Simon Rogers, Raya Khanin and Mark Girolami
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S2

    This article is part of a Supplement: Volume 8 Supplement 2

  33. This supplement contains extended versions of a selected subset of papers presented at the workshop PMSB 2007, Probabilistic Modeling and Machine Learning in Structural and Systems Biology, Tuusula, Finland, f...

    Authors: Samuel Kaski, Juho Rousu and Esko Ukkonen
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S1

    This article is part of a Supplement: Volume 8 Supplement 2

  34. Classification studies using gene expression datasets are usually based on small numbers of samples and tens of thousands of genes. The selection of those genes that are important for distinguishing the differ...

    Authors: Malik Yousef, Segun Jung, Louise C Showe and Michael K Showe
    Citation: BMC Bioinformatics 2007 8:144
  35. Trypanosomes are coated with a variant surface glycoprotein (VSG) that is so densely packed that it physically protects underlying proteins from effectors of the host immune system. Periodically cells expressi...

    Authors: Lucio Marcello, Suraj Menon, Pauline Ward, Jonathan M Wilkes, Nicola G Jones, Mark Carrington and J David Barry
    Citation: BMC Bioinformatics 2007 8:143
  36. Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error tha...

    Authors: Marianna Zahurak, Giovanni Parmigiani, Wayne Yu, Robert B Scharpf, David Berman, Edward Schaeffer, Shabana Shabbeer and Leslie Cope
    Citation: BMC Bioinformatics 2007 8:142
  37. Most methods for predicting functional sites in protein 3D structures, rely on information on related proteins and cannot be applied to proteins with no known relatives. Another limitation of these methods is ...

    Authors: Benoît H Dessailly, Marc F Lensink and Shoshana J Wodak
    Citation: BMC Bioinformatics 2007 8:141
  38. Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of id...

    Authors: Matthew DeJongh, Kevin Formsma, Paul Boillot, John Gould, Matthew Rycenga and Aaron Best
    Citation: BMC Bioinformatics 2007 8:139
  39. The analysis of the promoter sequence of genes with similar expression patterns is a basic tool to annotate common regulatory elements. Multiple sequence alignments are on the basis of most comparative approac...

    Authors: Enrique Blanco, Roderic Guigó and Xavier Messeguer
    Citation: BMC Bioinformatics 2007 8:138

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