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  1. 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

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

  2. 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

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

  3. 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

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

  4. 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

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

  5. 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

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

  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

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

  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. Quantitative trait locus (QTL) mapping identifies genomic regions that likely contain genes regulating a quantitative trait. However, QTL regions may encompass tens to hundreds of genes. To find the most promi...

    Authors: Rudi Alberts and Klaus Schughart
    Citation: BMC Bioinformatics 2010 11:516
  20. 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

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

  21. 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

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

  22. In metagenomic sequence data, majority of sequences/reads originate from new or partially characterized genomes, the corresponding sequences of which are absent in existing reference databases. Since taxonomic...

    Authors: Tarini Shankar Ghosh, Monzoorul Haque M and Sharmila S Mande
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S14

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

  23. 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

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

  24. 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

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

  25. sRNAs, which belong to the non-coding RNA family and range from approximately 50 to 400 nucleotides, serve various important gene regulatory roles. Most are believed to be trans-regulating and function by being c...

    Authors: Timothy H Wu, Ian Yi-Feng Chang, Li-chieh Julie Chu, Hsuan-Cheng Huang and Wailap Victor Ng
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S11

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

  26. 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

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

  27. 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

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

  28. 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

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

  29. 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

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

  30. 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

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

  31. Homozygosity mapping is a powerful procedure that is capable of detecting recessive disease-causing genes in a few patients from families with a history of inbreeding. We report here a homozygosity mapping alg...

    Authors: Huqun*, Shun-ichiro Fukuyama, Hiroyuki Morino, Hiroshi Miyazawa, Tomoaki Tanaka, Tomoko Suzuki, Masakazu Kohda, Hideshi Kawakami, Yasushi Okazaki, Kuniaki Seyama and Koichi Hagiwara
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S5

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

  32. Effectors of Type III Secretion System (T3SS) play a pivotal role in establishing and maintaining pathogenicity in the host and therefore the identification of these effectors is important in understanding vir...

    Authors: Daniel Ming Ming Tay, Kunde Ramamoorthy Govindarajan, Asif M Khan, Terenze Yao Rui Ong, Hanif M Samad, Wei Wei Soh, Minyan Tong, Fan Zhang and Tin Wee Tan
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S4

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

  33. 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

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

  34. 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

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

  35. The International Conference on Bioinformatics (InCoB), the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted in one of countries of the Asia-Pacific region. The 2010 conferenc...

    Authors: Christian Schönbach, Kenta Nakai, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Bioinformatics 2010 11(Suppl 7):S1

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

  36. Comprehensively understanding corticosteroid pharmacogenomic effects is an essential step towards an insight into the underlying molecular mechanisms for both beneficial and detrimental clinical effects. Never...

    Authors: Tung T Nguyen, Richard R Almon, Debra C DuBois, William J Jusko and Ioannis P Androulakis
    Citation: BMC Bioinformatics 2010 11:515
  37. High-throughput sequencing (HTS) technologies play important roles in the life sciences by allowing the rapid parallel sequencing of very large numbers of relatively short nucleotide sequences, in applications...

    Authors: Kenny Daily, Paul Rigor, Scott Christley, Xiaohui Xie and Pierre Baldi
    Citation: BMC Bioinformatics 2010 11:514
  38. Data integration is an escalating problem in bioinformatics. We have developed a web tool and warehousing system, Booly, that features a simple yet flexible data model coupled with the ability to perform power...

    Authors: Long H Do, Francisco F Esteves, Harvey J Karten and Ethan Bier
    Citation: BMC Bioinformatics 2010 11:513
  39. Microarray data is frequently used to characterize the expression profile of a whole genome and to compare the characteristics of that genome under several conditions. Geneset analysis methods have been descri...

    Authors: Fabrice Berger, Bertrand De Meulder, Anthoula Gaigneaux, Sophie Depiereux, Eric Bareke, Michael Pierre, Benoît De Hertogh, Mauro Delorenzi and Eric Depiereux
    Citation: BMC Bioinformatics 2010 11:510
  40. Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) method produces allele-specific DNA bands of different lengths by adding four designed primers and it achieves the single nucleotide polym...

    Authors: Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang and Hsueh-Wei Chang
    Citation: BMC Bioinformatics 2010 11:509
  41. Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) hosted by the NCBI, or the DNA Data Ban...

    Authors: James Gurtowski, Anthony Cancio, Hardik Shah, Chaya Levovitz, Ajish George, Robert Homann and Ravi Sachidanandam
    Citation: BMC Bioinformatics 2010 11:506
  42. In many protein-protein interaction (PPI) networks, densely connected hub proteins are more likely to be essential proteins. This is referred to as the "centrality-lethality rule", which indicates that the top...

    Authors: Kang Ning, Hoong Kee Ng, Sriganesh Srihari, Hon Wai Leong and Alexey I Nesvizhskii
    Citation: BMC Bioinformatics 2010 11:505
  43. The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several i...

    Authors: Sriganesh Srihari, Kang Ning and Hon Wai Leong
    Citation: BMC Bioinformatics 2010 11:504

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