Volume 11 Supplement 1

International Workshop on Computational Systems Biology: Approaches to Analysis of Genome Complexity and Regulatory Gene Networks

Research

Edited by Vladimir A Kuznetsov and Jun Liu

Publication of this supplement was made possible with help from the Bioinformatics Agency for Science, Technology and Research of Singapore and the Institute for Mathematical Sciences at the National University of Singapore.

International Workshop on Computational Systems Biology Approaches to Analysis of Genome Complexity and Regulatory Gene Networks. Go to conference site.

Singapore

20-25 November 2008

  1. Research

    Mechanisms of chromosomal rearrangement in the human genome

    Many human cancers are associated with characteristic chromosomal rearrangements, especially hematopoietic cancers such as leukemias and lymphomas. The first and most critical step in the rearrangement process...

    Albert G Tsai and Michael R Lieber

    BMC Genomics 2010 11(Suppl 1):S1

    Published on: 10 February 2010

  2. Research

    Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha

    Recent literature has revealed that genetic exchange of microRNA between cells can be essential for cell-cell communication, tissue-specificity and developmental processes. In stem cells, as in other cells, th...

    Winston Koh, Chen Tian Sheng, Betty Tan, Qian Yi Lee, Vladimir Kuznetsov, Lim Sai Kiang and Vivek Tanavde

    BMC Genomics 2010 11(Suppl 1):S6

    Published on: 10 February 2010

  3. Research

    Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction

    Cancer progression is a complex process involving host-tumor interactions by multiple molecular and cellular factors of the tumor microenvironment. Tumor cells that challenge immune activity may be vulnerable ...

    Bernhard Mlecnik, Fatima Sanchez-Cabo, Pornpimol Charoentong, Gabriela Bindea, Franck Pagès, Anne Berger, Jerome Galon and Zlatko Trajanoski

    BMC Genomics 2010 11(Suppl 1):S7

    Published on: 10 February 2010

  4. Research

    Bimodal gene expression patterns in breast cancer

    We identified a set of genes with an unexpected bimodal distribution among breast cancer patients in multiple studies. The property of bimodality seems to be common, as these genes were found on multiple micro...

    Marina Bessarabova, Eugene Kirillov, Weiwei Shi, Andrej Bugrim, Yuri Nikolsky and Tatiana Nikolskaya

    BMC Genomics 2010 11(Suppl 1):S8

    Published on: 10 February 2010

  5. Research

    Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression

    A sense-antisense gene pair (SAGP) is a gene pair where two oppositely transcribed genes share a common nucleotide sequence region. In eukaryotic genomes, SAGPs can be organized in complex sense-antisense arch...

    Oleg V Grinchuk, Efthimios Motakis and Vladimir A Kuznetsov

    BMC Genomics 2010 11(Suppl 1):S9

    Published on: 10 February 2010

  6. Research

    Transposon identification using profile HMMs

    Transposons are "jumping genes" that account for large quantities of repetitive content in genomes. They are known to affect transcriptional regulation in several different ways, and are implicated in many hum...

    Paul T Edlefsen and Jun S Liu

    BMC Genomics 2010 11(Suppl 1):S10

    Published on: 10 February 2010

  7. Research

    Modeling neutral evolution of Alu elements using a branching process

    Alu elements occupy about eleven percent of the human genome and are still growing in copy numbers. Since Alu elements substantially impact the shape of our genome, there is a need for modeling the amplificati...

    Marek Kimmel and Matthias Mathaes

    BMC Genomics 2010 11(Suppl 1):S11

    Published on: 10 February 2010

  8. Research

    Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction

    Tandem mass spectrometry (MS/MS) has become a standard method for identification of proteins extracted from biological samples but the huge number and the noise contamination of MS/MS spectra obstruct swift an...

    Nedim Mujezinovic, Georg Schneider, Michael Wildpaner, Karl Mechtler and Frank Eisenhaber

    BMC Genomics 2010 11(Suppl 1):S13

    Published on: 10 February 2010

  9. Research

    Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases

    A bioinformatic search was carried for plant homologues of human serine-threonine protein kinases involved in regulation of cell division and microtubule protein phosphorylation (SLK, PAK6, PAK7, MARK1, MAST2,...

    Pavel A Karpov, Elena S Nadezhdina, Alla I Yemets, Vadym G Matusov, Alexey Yu Nyporko, Nadezhda Yu Shashina and Yaroslav B Blume

    BMC Genomics 2010 11(Suppl 1):S14

    Published on: 10 February 2010

  10. Research

    Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset

    Algorithms designed to predict protein disorder play an important role in structural and functional genomics, as disordered regions have been reported to participate in important cellular processes. Consequent...

    Fernanda L Sirota, Hong-Sain Ooi, Tobias Gattermayer, Georg Schneider, Frank Eisenhaber and Sebastian Maurer-Stroh

    BMC Genomics 2010 11(Suppl 1):S15

    Published on: 10 February 2010

Portable peer review

The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Axios Review or Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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