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  1. DNA methylation by the Dnmt family occurs in vertebrates and invertebrates, including ascidians, and is thought to play important roles in gene regulation and genome stability, especially in vertebrates. Howev...

    Authors: Kohji Okamura, Kazuaki A Matsumoto and Kenta Nakai
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  2. Computational prediction of noncoding RNAs (ncRNAs) is an important task in the post-genomic era. One common approach is to utilize the profile information contained in alignment data rather than single sequen...

    Authors: Yutaka Saito, Kengo Sato and Yasubumi Sakakibara
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  3. Orthologs are genes derived from the same ancestor gene loci after speciation events. Orthologous proteins usually have similar sequences and perform comparable biological functions. Therefore, ortholog identi...

    Authors: Ting-wen Chen, Timothy H Wu, Wailap V Ng and Wen-chang Lin
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  4. In order to characterize mammalian intrinsically disordered domains (IDDs) we examined the patterns in their amino acid abundance as well as overrepresented local sequence motifs. We considered IDDs from mouse...

    Authors: Shunsuke Teraguchi, Ashwini Patil and Daron M Standley
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  5. Protein-protein interactions (PPIs) play important roles in various cellular processes. However, the low quality of current PPI data detected from high-throughput screening techniques has diminished the potent...

    Authors: Min Wu, Xiaoli Li, Hon Nian Chua, Chee-Keong Kwoh and See-Kiong Ng
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  6. Understanding cellular systems requires the knowledge of a protein's subcellular localization (SCL). Although experimental and predicted data for protein SCL are archived in various databases, SCL prediction r...

    Authors: Gaurav Kumar and Shoba Ranganathan
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  7. Recent studies have found that overexpression of the High-mobility group box-1 (HMGB1) protein, in conjunction with its receptors for advanced glycation end products (RAGEs) and toll-like receptors (TLRs), is ...

    Authors: Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R Faeder and Edmund M Clarke
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  8. Mathematical modeling has been applied to the study and analysis of complex biological systems for a long time. Some processes in biological systems, such as the gene expression and feedback control in signal ...

    Authors: Wu Hsiung Wu, Feng Sheng Wang and Maw Shang Chang
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  9. The Triplex cell vaccine is a cancer cellular vaccine that can prevent almost completely the mammary tumor onset in HER-2/neu transgenic mice. In a translational perspective, the activity of the Triplex vaccin...

    Authors: Marzio Pennisi, Francesco Pappalardo, Ariannna Palladini, Giordano Nicoletti, Patrizia Nanni, Pier-Luigi Lollini and Santo Motta
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  10. Nuclear factor kappa B (NF-κB) is a chief nuclear transcription factor that controls the transcription of various genes; and its activation is tightly controlled by Inhibitor kappa B kinase (IKK). The irregula...

    Authors: Shanthi Nagarajan, Hyunah Choo, Yong Seo Cho, Kye Jung Shin, Kwang-Seok Oh, Byung Ho Lee and Ae Nim Pae
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  11. Human papillomaviruses (HPVs) are the most common on sexually transmitted viruses in the world. HPVs are responsible for a large spectrum of deseases, both benign and malignant. The certain types of HPV are in...

    Authors: Usman Sumo Friend Tambunan and Evi Kristin Wulandari
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  12. Novel strategies are required in order to handle the huge amount of data produced by microarray technologies. To infer gene regulatory networks, the first step is to find direct regulatory relationships betwee...

    Authors: Isabel A Nepomuceno-Chamorro, Jesus S Aguilar-Ruiz and Jose C Riquelme
    Citation: BMC Bioinformatics 2010 11:517
    Content type: Methodology article Published on:

  15. Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selectio...

    Authors: Yong Li, Lili Liu, Xi Bai, Hua Cai, Wei Ji, Dianjing Guo and Yanming Zhu
    Citation: BMC Bioinformatics 2010 11:520
    Content type: Research article Published on:

  17. Extensive and automated data integration in bioinformatics facilitates the construction of large, complex biological networks. However, the challenge lies in the interpretation of these networks. While most re...

    Authors: Mara L Hartsperger, Florian Blöchl, Volker Stümpflen and Fabian J Theis
    Citation: BMC Bioinformatics 2010 11:522
    Content type: Methodology article Published on:

  18. The goal of class prediction studies is to develop rules to accurately predict the class membership of new samples. The rules are derived using the values of the variables available for each subject: the main ...

    Authors: Rok Blagus and Lara Lusa
    Citation: BMC Bioinformatics 2010 11:523
    Content type: Research article Published on:

  19. It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been pu...

    Authors: Pengyi Yang, Joshua WK Ho, Albert Y Zomaya and Bing B Zhou
    Citation: BMC Bioinformatics 2010 11:524
    Content type: Methodology article Published on:

  20. A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires several generations of backcrosses and a...

    Authors: Isaak Y Tecle, Naama Menda, Robert M Buels, Esther van der Knaap and Lukas A Mueller
    Citation: BMC Bioinformatics 2010 11:525
    Content type: Database Published on:

  21. Complexity and noise in expression quantitative trait loci (eQTL) studies make it difficult to distinguish potential regulatory relationships among the many interactions. The predominant method of identifying ...

    Authors: Andrew K Rider, Geoffrey Siwo, Nitesh V Chawla, Michael Ferdig and Scott J Emrich
    Citation: BMC Bioinformatics 2010 11:526
    Content type: Methodology article Published on:

  22. Genome-wide association studies have been successful in finding common variants influencing common traits. However, these associations only account for a fraction of trait heritability. There has been a shift ...

    Authors: Robert Lawrence, Aaron G Day-Williams, Katherine S Elliott, Andrew P Morris and Eleftheria Zeggini
    Citation: BMC Bioinformatics 2010 11:527
    Content type: Software Published on:

  23. Microarray experiments have become very popular in life science research. However, if such experiments are only considered independently, the possibilities for analysis and interpretation of many life science ...

    Authors: Eric Bareke, Michael Pierre, Anthoula Gaigneaux, Bertrand De Meulder, Sophie Depiereux, Naji Habra and Eric Depiereux
    Citation: BMC Bioinformatics 2010 11:528
    Content type: Database Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2010 11:541

  24. The information provided by dense genome-wide markers using high throughput technology is of considerable potential in human disease studies and livestock breeding programs. Genome-wide association studies rel...

    Authors: Ross K Shepherd, Theo HE Meuwissen and John A Woolliams
    Citation: BMC Bioinformatics 2010 11:529
    Content type: Research article Published on:

  25. The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ...

    Authors: Jennifer I Deegan (née Clark), Emily C Dimmer and Christopher J Mungall
    Citation: BMC Bioinformatics 2010 11:530
    Content type: Methodology article Published on:

  26. The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms ...

    Authors: Andreas Hildebrandt, Anna Katharina Dehof, Alexander Rurainski, Andreas Bertsch, Marcel Schumann, Nora C Toussaint, Andreas Moll, Daniel Stöckel, Stefan Nickels, Sabine C Mueller, Hans-Peter Lenhof and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2010 11:531
    Content type: Software Published on:

  27. The occurrence of a genetic bottleneck in HIV sexual or mother-to-infant transmission has been well documented. This results in a majority of new infections being homogeneous, i.e., initiated by a single genetic ...

    Authors: Elena E Giorgi, Bob Funkhouser, Gayathri Athreya, Alan S Perelson, Bette T Korber and Tanmoy Bhattacharya
    Citation: BMC Bioinformatics 2010 11:532
    Content type: Software Published on:

  28. We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are ...

    Authors: Pavel P Kuksa and Vladimir Pavlovic
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  29. The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational tools for analysis and inference. This arti...

    Authors: Jonathan E Bronson, Jake M Hofman, Jingyi Fei, Ruben L Gonzalez Jr. and Chris H Wiggins
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  30. Quantitative phenotypes emerge everywhere in systems biology and biomedicine due to a direct interest for quantitative traits, or to high individual variability that makes hard or impossible to classify sample...

    Authors: Giorgio Guzzetta, Giuseppe Jurman and Cesare Furlanello
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  31. This paper demonstrates how a Neural Grammar Network learns to classify and score molecules for a variety of tasks in chemistry and toxicology. In addition to a more detailed analysis on datasets previously st...

    Authors: Eddie YT Ma, Christopher JF Cameron and Stefan C Kremer
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  32. The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Le...

    Authors: Christian Widmer, Nora C Toussaint, Yasemin Altun and Gunnar Rätsch
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  33. Determination of protein subcellular localization plays an important role in understanding protein function. Knowledge of the subcellular localization is also essential for genome annotation and drug discovery...

    Authors: Cornelia Caragea, Doina Caragea, Adrian Silvescu and Vasant Honavar
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  34. String kernels are commonly used for the classification of biological sequences, nucleotide as well as amino acid sequences. Although string kernels are already very powerful, when it comes to amino acids they...

    Authors: Nora C Toussaint, Christian Widmer, Oliver Kohlbacher and Gunnar Rätsch
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  35. We present an infinite mixture-of-experts model to find an unknown number of sub-groups within a given patient cohort based on survival analysis. The effect of patient features on survival is modeled using the...

    Authors: Sudhir Raman, Thomas J Fuchs, Peter J Wild, Edgar Dahl, Joachim M Buhmann and Volker Roth
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  36. Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent studies exist on the analysis and sequence-...

    Authors: Shandar Ahmad, Yumlembam Hemajit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita and Kenji Mizuguchi
    Citation: BMC Bioinformatics 2010 11:533
    Content type: Research article Published on:

  37. The Medium-chain Dehydrogenases/Reductases (MDR) form a protein superfamily whose size and complexity defeats traditional means of subclassification; it currently has over 15000 members in the databases, the p...

    Authors: Joel Hedlund, Hans Jörnvall and Bengt Persson
    Citation: BMC Bioinformatics 2010 11:534
    Content type: Research article Published on:

  39. Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene exp...

    Authors: Hsun-Hsien Chang, Michael McGeachie, Gil Alterovitz and Marco F Ramoni
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  40. Given the rapid growth of translational research and personalized healthcare paradigms, the ability to relate and reason upon networks of bio-molecular and phenotypic variables at various levels of granularity...

    Authors: Philip RO Payne, Kun Huang, Kristin Keen-Circle, Abhisek Kundu, Jie Zhang and Tara B Borlawsky
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  41. Diagnosis and treatment of patients in the clinical setting is often driven by known symptomatic factors that distinguish one particular condition from another. Treatment based on noticeable symptoms, however,...

    Authors: David P Chen, Joel T Dudley and Atul J Butte
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  42. Chronic lymphocytic leukemia (CLL) is the most common adult leukemia. It is a highly heterogeneous disease, and can be divided roughly into indolent and progressive stages based on classic clinical markers. Im...

    Authors: Jie Zhang, Yang Xiang, Liya Ding, Kristin Keen-Circle, Tara B Borlawsky, Hatice Gulcin Ozer, Ruoming Jin, Philip Payne and Kun Huang
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  43. Combining the results of studies using highly parallelized measurements of gene expression such as microarrays and RNAseq offer unique challenges in meta analysis. Motivated by a need for a deeper understandin...

    Authors: Alexander A Morgan, Purvesh Khatri, Richard Hayden Jones, Minnie M Sarwal and Atul J Butte
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  44. Multi-item adverse drug event (ADE) associations are associations relating multiple drugs to possibly multiple adverse events. The current standard in pharmacovigilance is bivariate association analysis, where...

    Authors: Rave Harpaz, Herbert S Chase and Carol Friedman
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  45. The amount of data deposited in the Gene Expression Omnibus (GEO) has expanded significantly. It is important to ensure that these data are properly annotated with clinical data and descriptions of experimenta...

    Authors: Ronilda Lacson, Michael Mbagwu, Hisham Yousif and Lucila Ohno-Machado
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  46. A key challenge in pharmacogenomics is the identification of genes whose variants contribute to drug response phenotypes, which can include severe adverse effects. Pharmacogenomics GWAS attempt to elucidate ge...

    Authors: Nicholas P Tatonetti, Joel T Dudley, Hersh Sagreiya, Atul J Butte and Russ B Altman
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  47. In pursuing personalized medicine, pharmacogenomic (PGx) knowledge may help guide prescribing drugs based on a person’s genotype. Here we evaluate the feasibility of incorporating PGx knowledge, combined with ...

    Authors: Casey Lynnette Overby, Peter Tarczy-Hornoch, James I Hoath, Ira J Kalet and David L Veenstra
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  48. Mouse xenograft models, in which human cancer cells are implanted in immune-suppressed mice, have been popular for studying the mechanisms of novel therapeutic targets, tumor progression and metastasis. We hyp...

    Authors: Xinan Yang, Younghee Lee, Yong Huang, James L Chen, Rosie H Xing and Yves A Lussier
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  49. In humans, copies of the Long Interspersed Nuclear Element 1 (LINE-1) retrotransposon comprise 21% of the reference genome, and have been shown to modulate expression and produce novel splice isoforms of trans...

    Authors: Eric Rouchka, Diego E Montoya-Durango, Vilius Stribinskis, Kenneth Ramos and Ted Kalbfleisch
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

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