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  1. Researchers are using the intraductal approach to advance breast cancer risk assessment, prevention, diagnosis, and treatment. Procedures and technologies that can access and interrogate the ductal-alveolar sy...

    Authors: Susan Rochman, Dixie Mills, Julian Kim, Henry Kuerer and Susan Love
    Citation: BMC Proceedings 2009 3(Suppl 5):I1
    Content type: Meeting report Published on:

    This article is part of a Supplement: Volume 3 Supplement 5

  2. Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a ...

    Authors: Vincent Jouffe, Suzanne Rowe, Laurence Liaubet, Bart Buitenhuis, Henrik HornshĆøj, Magali SanCristobal, Pierre MormĆØde and DJ de Koning
    Citation: BMC Proceedings 2009 3(Suppl 4):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  3. The aim of this work was to study the performances of 2 predictive statistical tools on a data set that was given to all participants of the Eadgene-SABRE Post Analyses Working Group, namely the Pig data set o...

    Authors: ChristĆØle Robert-GraniĆ©, Kim-Anh LĆŖ Cao and Magali SanCristobal
    Citation: BMC Proceedings 2009 3(Suppl 4):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  4. Often, software available for biological pathways reconstruction rely on literature search to find links between genes. The aim of this study is to reconstruct gene networks from microarray data, using Graphic...

    Authors: Florence Jaffrezic and Gwenola Tosser-Klopp
    Citation: BMC Proceedings 2009 3(Suppl 4):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  5. As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these...

    Authors: AgnĆØs Bonnet, Sandrine Lagarrigue, Laurence Liaubet, ChristĆØle Robert-GraniĆ©, Magali SanCristobal and Gwenola Tosser-Klopp
    Citation: BMC Proceedings 2009 3(Suppl 4):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  6. Gene set analysis is a commonly used method for analysing microarray data by considering groups of functionally related genes instead of individual genes. Here we present the use of two gene set analysis appro...

    Authors: Ina Hulsegge, Arun Kommadath and Mari A Smits
    Citation: BMC Proceedings 2009 3(Suppl 4):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  7. This paper describes the results of a Gene Ontology (GO) term enrichment analysis of chicken microarray data using the Bioconductor packages. By checking the enriched GO terms in three contrasts, MM8-PM8, MM8-...

    Authors: Haisheng Nie, Pieter BT Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack AM Leunissen and Martien AM Groenen
    Citation: BMC Proceedings 2009 3(Suppl 4):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  8. Gene set analysis is considered to be a way of improving our biological interpretation of the observed expression patterns. This paper describes different methods applied to analyse expression data from a chic...

    Authors: Axel Skarman, Li Jiang, Henrik HornshĆøj, Bart Buitenhuis, Jakob Hedegaard, Lene N Conley and Peter SĆørensen
    Citation: BMC Proceedings 2009 3(Suppl 4):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  9. Microarrays allow genome-wide assays of gene expression. There is a need for user-friendly software to visualise and analyse these data. Analysing microarray data in the context of biological pathways is now c...

    Authors: Dennis Prickett and Michael Watson
    Citation: BMC Proceedings 2009 3(Suppl 4):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  10. Once a list of differentially expressed genes has been identified from a microarray experiment, a subsequent post-analysis task is required in order to find the main biological processes associated to the expe...

    Authors: Ɓngeles JimƩnez-Marƭn, Melania Collado-Romero, Marƭa Ramirez-Boo, Cristina Arce and Juan J Garrido
    Citation: BMC Proceedings 2009 3(Suppl 4):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  11. The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edg...

    Authors: Jakob Hedegaard, Cristina Arce, Silvio Bicciato, AgnĆØs Bonnet, Bart Buitenhuis, Melania Collado-Romero, Lene N Conley, Magali SanCristobal, Francesco Ferrari, Juan J Garrido, Martien AM Groenen, Henrik HornshĆøj, Ina Hulsegge, Li Jiang, Ɓngeles JimĆ©nez-MarĆ­n, Arun Kommadath…
    Citation: BMC Proceedings 2009 3(Suppl 4):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  12. High throughput gene expression studies using oligonucleotide microarrays depend on the specificity of each oligonucleotide (oligo or probe) for its target gene. However, target specific probes can only be des...

    Authors: Pieter BT Neerincx, Han Rauwerda, Haisheng Nie, Martien AM Groenen, Timo M Breit and Jack AM Leunissen
    Citation: BMC Proceedings 2009 3(Suppl 4):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  13. Microarray is a powerful technology enabling to monitor tens of thousands of genes in a single experiment. Most microarrays are now using oligo-sets. The design of the oligo-nucleotides is time consuming and e...

    Authors: Pierrot Casel, FranƧois Moreews, Sandrine Lagarrigue and Christophe Klopp
    Citation: BMC Proceedings 2009 3(Suppl 4):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  15. Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the a...

    Authors: Pieter BT Neerincx, Pierrot Casel, Dennis Prickett, Haisheng Nie, Michael Watson, Jack AM Leunissen, Martien AM Groenen and Christophe Klopp
    Citation: BMC Proceedings 2009 3(Suppl 4):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 3 Supplement 4

  26. Biotechnology research and development in Egypt was addressed in the 2009 annual American University in Cairo (AUC) research conference held at the AUC new campus in Cairo, Egypt, that took place on April 5th ...

    Authors: Rania Siam
    Citation: BMC Proceedings 2009 3(Suppl 3):I1
    Content type: Meeting report Published on:

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

  28. The importance of toxicogenomics was recognized early in Korea and a group of researchers was trying to build up a research infrastructure and educational system. However, since the scale of the Korean pharmac...

    Authors: Tae-Hoon Chung, Jin-Ho Yoo, Jae-Chun Ryu and Yang-Seok Kim
    Citation: BMC Proceedings 2009 3(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 2

  29. ebTrack is being developed as an integrated bioinformatics system for environmental research and analysis by addressing the issues of integration, curation, management, first level analysis and interpretation ...

    Authors: Minjun Chen, Jackson Martin, Hong Fang, Sastry Isukapalli, Panos G Georgopoulos, William J Welsh and Weida Tong
    Citation: BMC Proceedings 2009 3(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 2

  30. Recent publications have raised concerns about the reliability of microarray technology because of the lack of reproducibility of differentially expressed genes (DEGs) from highly similar studies across labora...

    Authors: Xiaohui Fan, Leming Shi, Hong Fang, Stephen Harris, Roger Perkins and Weida Tong
    Citation: BMC Proceedings 2009 3(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 2

  33. The First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007) was held at the North Carolina State University McKimmon Center in Raleigh, North Carolina on October 25t...

    Authors: Pierre R Bushel, Dahlia Nielsen and Weida Tong
    Citation: BMC Proceedings 2009 3(Suppl 2):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 3 Supplement 2

  34. The availability of a large amount of SNP markers throughout the genome of different livestock species offers the opportunity to estimate genomic breeding values (GEBVs). However, the estimation of many effect...

    Authors: NicolĆ² PP Macciotta, Giustino Gaspa, Roberto Steri, Camillo Pieramati, Paolo Carnier and Corrado Dimauro
    Citation: BMC Proceedings 2009 3(Suppl 1):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  35. The study focuses on the impact of different sets of single nucleotide polymorphisms (SNPs) selected from the available data set on prediction of genomewide breeding values (GBVs) of animals. Correlations betw...

    Authors: Kacper Żukowski, Tomasz Suchocki, Anna Gontarek and Joanna Szyda
    Citation: BMC Proceedings 2009 3(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  36. In this study we compared different statistical procedures for estimating SNP effects using the simulated data set from the XII QTL-MAS workshop. Five procedures were considered and tested in a reference popul...

    Authors: Eduardo CG Pimentel, Sven Kƶnig, Flavio S Schenkel and Henner Simianer
    Citation: BMC Proceedings 2009 3(Suppl 1):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  37. Breeding values for animals with marker data are estimated using a genomic selection approach where data is analyzed using Bayesian multi-marker association models. Fourteen model scenarios with varying haplot...

    Authors: Trine Michelle Villumsen and Luc Janss
    Citation: BMC Proceedings 2009 3(Suppl 1):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  38. Genomic breeding values were estimated using a Gibbs sampler that avoided the use of the Metropolis-Hastings step as implemented in the BayesB model of Meuwissen et al., Genetics 2001, 157:1819ā€“1829.

    Authors: Mario PL Calus, Sander PW de Roos and Roel F Veerkamp
    Citation: BMC Proceedings 2009 3(Suppl 1):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  39. Genome-wide association studies have successfully identified several loci underlying complex diseases in humans. The development of high density SNP maps in domestic animal species should allow the detection o...

    Authors: MĆ“nica CorrĆŖa Ledur, Nicolas Navarro and Miguel PĆ©rez-Enciso
    Citation: BMC Proceedings 2009 3(Suppl 1):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  40. The ultimate goal of QTL studies is to find causative mutations, which requires additional expression studies. Given the limited amount of time and funds, the smart option is to identify the most important QTL...

    Authors: Henri CM Heuven, John WM Bastiaansen and StƩphanie M van den Berg
    Citation: BMC Proceedings 2009 3(Suppl 1):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  42. We applied a range of genome-wide association (GWA) methods to map quantitative trait loci (QTL) in the simulated dataset provided by the 12th QTLMAS workshop in order to derive an effective strategy.

    Authors: Alex C Lam, Joseph Powell, Wen-Hua Wei, Dirk-Jan de Koning and Chris S Haley
    Citation: BMC Proceedings 2009 3(Suppl 1):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  43. Genome-wide approaches to analyze single nucleotide polymorphism (SNP) data have proliferated due to the increased availability and affordability of markers, but in practice a small number of markers may be se...

    Authors: Matthew A Cleveland and Nader Deeb
    Citation: BMC Proceedings 2009 3(Suppl 1):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  44. To compare the power of various QTL mapping methodologies, a dataset was simulated within the framework of 12th QTLMAS workshop. A total of 5865 diploid individuals was simulated, spanning seven generations, with...

    Authors: Marco CAM Bink and Fred A van Eeuwijk
    Citation: BMC Proceedings 2009 3(Suppl 1):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  45. Dense marker maps require efficient statistical methods for QTL fine mapping that work fast and efficiently with a large number of markers. In this study, the simulated dataset for the XIIth QTLMAS workshop wa...

    Authors: Joaquim Tarres, FranƧois Guillaume and SƩbastien Fritz
    Citation: BMC Proceedings 2009 3(Suppl 1):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  46. As part of the QTLMAS XII workshop, a simulated dataset was distributed and participants were invited to submit analyses of the data based on genome-wide association, fine mapping and genomic selection. We hav...

    Authors: Lucy Crooks, Goutam Sahana, Dirk-Jan de Koning, Mogens SandĆø Lund and Ɩrjan Carlborg
    Citation: BMC Proceedings 2009 3(Suppl 1):S2
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  47. A dataset was simulated and distributed to participants of the QTLMAS XII workshop who were invited to develop genomic selection models. Each contributing group was asked to describe the model development and ...

    Authors: Mogens SandĆø Lund, Goutam Sahana, Dirk-Jan de Koning, Guosheng Su and Ɩrjan Carlborg
    Citation: BMC Proceedings 2009 3(Suppl 1):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  48. Nitrogen is an essential nutrient for all life forms. Like most unicellular organisms, the yeast Saccharomyces cerevisiae transports and catabolizes good nitrogen sources in preference to poor ones. Nitrogen cata...

    Authors: Kevin Kontos, Patrice Godard, Bruno AndrƩ, Jacques van Helden and Gianluca Bontempi
    Citation: BMC Proceedings 2008 2(Suppl 4):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 2 Supplement 4

  49. Identifying gene functional modules is an important step towards elucidating gene functions at a global scale. Clustering algorithms mostly rely on co-expression of genes, that is group together genes having s...

    Authors: Etienne BirmelƩ, Mohamed Elati, CƩline Rouveirol and Christophe Ambroise
    Citation: BMC Proceedings 2008 2(Suppl 4):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 2 Supplement 4

  50. This supplement contains extended versions of a selected subset of papers presented at the workshop MLSB 2007, Machine Learning in Systems Biology, Evry, France, from September 24 to 25, 2007.

    Authors: Florence d'AlchƩ-Buc and Louis Wehenkel
    Citation: BMC Proceedings 2008 2(Suppl 4):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 2 Supplement 4

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