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Volume 12 Supplement 10

Proceedings of the Eighth Annual MCBIOS Conference. Computational Biology and Bioinformatics for a New Decade


Edited by Jonathan D Wren (senior editor), Doris M Kupfer, Edward J Perkins, Susan Bridges, Stephen Winters-Hilt, Mikhail G Dozmorov and Ulisses Braga-Neto

Eighth Annual MCBIOS Conference. Computational Biology and Bioinformatics for a New Decade. Go to conference site.

College Station, TX, USA1-2 April 2011

  1. Genomic biomarkers play an increasing role in both preclinical and clinical application. Development of genomic biomarkers with microarrays is an area of intensive investigation. However, despite sustained and...

    Authors: Minjun Chen, Leming Shi, Reagan Kelly, Roger Perkins, Hong Fang and Weida Tong
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S3
  2. Each organ has a specific function in the body. “Organ-specificity” refers to differential expressions of the same gene across different organs. An organ-specific gene/protein is defined as a gene/protein whos...

    Authors: Fan Zhang and Jake Y Chen
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S4
  3. RNA-Seq is the recently developed high-throughput sequencing technology for profiling the entire transcriptome in any organism. It has several major advantages over current hybridization-based approach such as...

    Authors: Ying Wang, Noushin Ghaffari, Charles D Johnson, Ulisses M Braga-Neto, Hui Wang, Rui Chen and Huaijun Zhou
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S5
  4. Comparative network analysis aims to identify common subnetworks in biological networks. It can facilitate the prediction of conserved functional modules across different species and provide deep insights into...

    Authors: Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S6
  5. Protein-protein interactions (PPIs) are a critical component for many underlying biological processes. A PPI network can provide insight into the mechanisms of these processes, as well as the relationships amo...

    Authors: Venkata-Swamy Martha, Zhichao Liu, Li Guo, Zhenqiang Su, Yanbin Ye, Hong Fang, Don Ding, Weida Tong and Xiaowei Xu
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S7
  6. Recent advances in genomics and proteomics have allowed us to study the nuances of the Warburg effect – a long-standing puzzle in cancer energy metabolism – at an unprecedented level of detail. While modern ne...

    Authors: Aleksandra A Markovets and Damir Herman
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S8
  7. Accumulation of gene mutations in cells is known to be responsible for tumor progression, driving it from benign states to malignant states. However, previous studies have shown that the detailed sequence of g...

    Authors: Mohammad Shahrokh Esfahani, Byung-Jun Yoon and Edward R Dougherty
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S9
  8. One of the most important goals of the mathematical modeling of gene regulatory networks is to alter their behavior toward desirable phenotypes. Therapeutic techniques are derived for intervention in terms of ...

    Authors: Noushin Ghaffari, Ivan Ivanov, Xiaoning Qian and Edward R Dougherty
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S10
  9. In all amyloid diseases, protein aggregates have been implicated fully or partly, in the etiology of the disease. Due to their significance in human pathologies, there have been unprecedented efforts towards p...

    Authors: Srisairam Achuthan, Bong Jae Chung, Preetam Ghosh, Vijayaraghavan Rangachari and Ashwin Vaidya
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S13
  10. Hypertension may increase tortuosity or twistedness of arteries. We applied a centerline extraction algorithm and tortuosity metric to magnetic resonance angiography (MRA) brain images to quantitatively measur...

    Authors: Karl T Diedrich, John A Roberts, Richard H Schmidt, Chang-Ki Kang, Zang-Hee Cho and Dennis L Parker
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S15
  11. Biology is rapidly becoming a data intensive, data-driven science. It is essential that data is represented and connected in ways that best represent its full conceptual content and allows both automated integ...

    Authors: Shelton D Griffith, Daniel J Quest, Thomas S Brettin and Robert W Cottingham
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S17
  12. Proteins search along the DNA for targets, such as transcription initiation sequences, according to one-dimensional diffusion, which is interrupted by micro- and macro-hopping events and intersegmental transfe...

    Authors: Michael L Mayo, Edward J Perkins and Preetam Ghosh
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S18
  13. Identification of transcription factors (TFs) responsible for modulation of differentially expressed genes is a key step in deducing gene regulatory pathways. Most current methods identify TFs by searching for...

    Authors: Sujoy Roy, Kevin Heinrich, Vinhthuy Phan, Michael W Berry and Ramin Homayouni
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S19
  14. Gene Regulatory Networks (GRNs) provide integrated views of gene interactions that control biological processes. Many public databases contain biological interactions extracted from experimentally validated li...

    Authors: Ying Li, Ping Gong, Edward J Perkins, Chaoyang Zhang and Nan Wang
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S20
  15. Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequ...

    Authors: Stephen Winters-Hilt, Evenie Horton-Chao and Eric Morales
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S21
  16. It is commonly believed that including domain knowledge in a prediction model is desirable. However, representing and incorporating domain information in the learning process is, in general, a challenging prob...

    Authors: Xiaofei Nan, Gang Fu, Zhengdong Zhao, Sheng Liu, Ronak Y Patel, Haining Liu, Pankaj R Daga, Robert J Doerksen, Xin Dang, Yixin Chen and Dawn Wilkins
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S22

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