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Volume 11 Supplement 1

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


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.

Singapore20-25 November 2008

  1. Content type: Research

    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...

    Authors: Albert G Tsai and Michael R Lieber

    Citation: BMC Genomics 2010 11(Suppl 1):S1

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  2. Content type: Research

    We consider the problem of biological complexity via a projection of protein-coding genes of complex organisms onto the functional space of the proteome. The latter can be defined as a set of all functions com...

    Authors: Alexander A Kanapin, Nicola Mulder and Vladimir A Kuznetsov

    Citation: BMC Genomics 2010 11(Suppl 1):S4

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  3. Content type: Research

    The N terminal transactivation domain of p53 is regulated by ligases and coactivator proteins. The functional conformation of this region appears to be an alpha helix which is necessary for its appropriate int...

    Authors: Jagadeesh N Mavinahalli, Arumugam Madhumalar, Roger W Beuerman, David P Lane and Chandra Verma

    Citation: BMC Genomics 2010 11(Suppl 1):S5

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  4. Content type: Research

    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...

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

    Citation: BMC Genomics 2010 11(Suppl 1):S6

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  5. Content type: Research

    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 ...

    Authors: Bernhard Mlecnik, Fatima Sanchez-Cabo, Pornpimol Charoentong, Gabriela Bindea, Franck Pag├Ęs, Anne Berger, Jerome Galon and Zlatko Trajanoski

    Citation: BMC Genomics 2010 11(Suppl 1):S7

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  6. Content type: Research

    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...

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

    Citation: BMC Genomics 2010 11(Suppl 1):S8

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  7. Content type: Research

    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...

    Authors: Oleg V Grinchuk, Efthimios Motakis and Vladimir A Kuznetsov

    Citation: BMC Genomics 2010 11(Suppl 1):S9

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  8. Content type: Research

    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...

    Authors: Paul T Edlefsen and Jun S Liu

    Citation: BMC Genomics 2010 11(Suppl 1):S10

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  9. Content type: Research

    Transcription factor (TF)-DNA binding loci are explored by analyzing massive datasets generated with application of Chromatin Immuno-Precipitation (ChIP)-based high-throughput sequencing technologies. These da...

    Authors: Vladimir A Kuznetsov, Onkar Singh and Piroon Jenjaroenpun

    Citation: BMC Genomics 2010 11(Suppl 1):S12

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  10. Content type: Research

    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...

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

    Citation: BMC Genomics 2010 11(Suppl 1):S13

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  11. Content type: Research

    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,...

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

    Citation: BMC Genomics 2010 11(Suppl 1):S14

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  12. Content type: Research

    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...

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

    Citation: BMC Genomics 2010 11(Suppl 1):S15

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