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  4. 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
    Content type: Methodology article Published on:

  5. 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
    Content type: Research Published on:

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

  6. 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
    Content type: Research Published on:

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

  7. 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
    Content type: Research Published on:

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

  8. 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
    Content type: Research Published on:

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

  9. 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
    Content type: Research Published on:

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

  10. 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
    Content type: Methodology Published on:

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

  11. 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
    Content type: Introduction Published on:

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

  12. 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
    Content type: Methodology article Published on:

  13. 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
    Content type: Software Published on:

  14. 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
    Content type: Research article Published on:

  15. 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
    Content type: Research article Published on:

  16. 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
    Content type: Methodology article Published on:

  17. 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
    Content type: Research Published on:

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

  18. 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
    Content type: Research Published on:

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

  19. 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
    Content type: Research Published on:

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

  20. 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
    Content type: Research Published on:

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

  21. 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
    Content type: Research Published on:

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

  23. 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
    Content type: Research Published on:

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

  24. 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
    Content type: Research Published on:

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

  25. 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
    Content type: Research Published on:

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

  26. 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
    Content type: Research Published on:

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

  27. 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
    Content type: Research Published on:

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

  28. 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
    Content type: Introduction Published on:

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

  29. 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
    Content type: Research article Published on:

  30. 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
    Content type: Database Published on:

  31. 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
    Content type: Research article Published on:

  32. 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
    Content type: Research article Published on:

  34. 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
    Content type: Research article Published on:

  35. 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
    Content type: Research article Published on:

  36. Periodogram analysis of time-series is widespread in biology. A new challenge for analyzing the microarray time series data is to identify genes that are periodically expressed. Such challenge occurs due to th...

    Authors: Alan Wee-Chung Liew, Jun Xian, Shuanhu Wu, David Smith and Hong Yan
    Citation: BMC Bioinformatics 2007 8:137
    Content type: Methodology article Published on:

  41. The Affymetrix GeneChip technology uses multiple probes per gene to measure its expression level. Individual probe signals can vary widely, which hampers proper interpretation. This variation can be caused by ...

    Authors: Rudi Alberts, Peter Terpstra, Menno Hardonk, Leonid V Bystrykh, Gerald de Haan, Rainer Breitling, Jan-Peter Nap and Ritsert C Jansen
    Citation: BMC Bioinformatics 2007 8:132
    Content type: Research article Published on:

  42. PCR has the potential to detect and precisely quantify specific DNA sequences, but it is not yet often used as a fully quantitative method. A number of data collection and processing strategies have been descr...

    Authors: Yann Karlen, Alan McNair, Sébastien Perseguers, Christian Mazza and Nicolas Mermod
    Citation: BMC Bioinformatics 2007 8:131
    Content type: Methodology article Published on:

  43. Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ cons...

    Authors: Arif Ozgun Harmanci, Gaurav Sharma and David H Mathews
    Citation: BMC Bioinformatics 2007 8:130
    Content type: Methodology article Published on:

  44. Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. It is cultivated mostly by po...

    Authors: Xianfeng Chen, Thomas W Laudeman, Paul J Rushton, Thomas A Spraggins and Michael P Timko
    Citation: BMC Bioinformatics 2007 8:129
    Content type: Database Published on:

  45. A nearly complete collection of gene-deletion mutants (96% of annotated open reading frames) of the yeast Saccharomyces cerevisiae has been systematically constructed. Tag microarrays are widely used to measure t...

    Authors: Chulyun Kim, Sangkyum Kim, Russell Dorer, Dan Xie, Jiawei Han and Sheng Zhong
    Citation: BMC Bioinformatics 2007 8:128
    Content type: Software Published on:

  47. Post-translational protein modification with ubiquitin, or ubiquitylation, is one of the hottest topics in a modern biology due to a dramatic impact on diverse metabolic pathways and involvement in pathogenesi...

    Authors: Alexander L Chernorudskiy, Alejandro Garcia, Eugene V Eremin, Anastasia S Shorina, Ekaterina V Kondratieva and Murat R Gainullin
    Citation: BMC Bioinformatics 2007 8:126
    Content type: Database Published on:

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