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  1. Cluster analysis, and in particular hierarchical clustering, is widely used to extract information from gene expression data. The aim is to discover new classes, or sub-classes, of either individuals or genes....

    Authors: Eva Freyhult, Mattias Landfors, Jenny Önskog, Torgeir R Hvidsten and Patrik Rydén
    Citation: BMC Bioinformatics 2010 11:503
    Content type: Research article Published on:

  3. Drugs can influence the whole metabolic system by targeting enzymes which catalyze metabolic reactions. The existence of interactions between drugs and metabolic reactions suggests a potential way to discover ...

    Authors: Limin Li, Xiaobo Zhou, Wai-Ki Ching and Ping Wang
    Citation: BMC Bioinformatics 2010 11:501
    Content type: Research article Published on:

  4. Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cle...

    Authors: Ilenia Giangreco, Orazio Nicolotti, Angelo Carotti, Francesco De Carlo, Gianfranco Gargano and Roberto Bellotti
    Citation: BMC Bioinformatics 2010 11:500
    Content type: Research article Published on:

  5. Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer opti...

    Authors: Melissa J Morine, Jolene McMonagle, Sinead Toomey, Clare M Reynolds, Aidan P Moloney, Isobel C Gormley, Peadar Ó Gaora and Helen M Roche
    Citation: BMC Bioinformatics 2010 11:499
    Content type: Research article Published on:

  6. The use of ontologies to control vocabulary and structure annotation has added value to genome-scale data, and contributed to the capture and re-use of knowledge across research domains. Gene Ontology (GO) is ...

    Authors: Melissa J Davis, Muhammad Shoaib B Sehgal and Mark A Ragan
    Citation: BMC Bioinformatics 2010 11:498
    Content type: Methodology article Published on:

  7. Functional genomics technologies that measure genome expression at a global scale are accelerating biological knowledge discovery. Generating these high throughput datasets is relatively easy compared to the d...

    Authors: Prashanti Manda, McKinley G Freeman, Susan M Bridges, TJ Jankun-Kelly, Bindu Nanduri, Fiona M McCarthy and Shane C Burgess
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S29
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  8. An introgression library is a family of near-isogenic lines in a common genetic background, each of which carries one or more genomic regions contributed by a donor genome. Near-isogenic lines are powerful gen...

    Authors: Christopher A Bottoms, Sherry Flint-Garcia and Michael D McMullen
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S28
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  9. Dynamic Bayesian Networks (DBNs) are widely used in regulatory network structure inference with gene expression data. Current methods assumed that the underlying stochastic processes that generate the gene exp...

    Authors: Yi Jia and Jun Huan
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S27
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  10. Computer-aided segmentation and border detection in dermoscopic images is one of the core components of diagnostic procedures and therapeutic interventions for skin cancer. Automated assessment tools for dermo...

    Authors: Sinan Kockara, Mutlu Mete, Bernard Chen and Kemal Aydin
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S26
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  11. Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain....

    Authors: Rowena Y Kelley, Cathy Gresham, Jonathan Harper, Susan M Bridges, Marilyn L Warburton, Leigh K Hawkins, Olga Pechanova, Bela Peethambaran, Tibor Pechan, Dawn S Luthe, J E Mylroie, Arunkanth Ankala, Seval Ozkan, W B Henry and W P Williams
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S25
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  12. The aggregates of a protein called, ‘Aβ’ found in brains of Alzheimer’s patients are strongly believed to be the cause for neuronal death and cognitive decline. Among the different forms of Aβ aggregates, smal...

    Authors: Preetam Ghosh, Amit Kumar, Bhaswati Datta and Vijayaraghavan Rangachari
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  13. Dermoscopy is one of the major imaging modalities used in the diagnosis of melanoma and other pigmented skin lesions. Automated assessment tools for dermoscopy images have become an important field of research...

    Authors: Mutlu Mete and Nikolay Metodiev Sirakov
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  14. PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PH...

    Authors: Chao Di, Wenying Xu, Zhen Su and Joshua S Yuan
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  15. Determining the secondary structure of RNA from the primary structure is a challenging computational problem. A number of algorithms have been developed to predict the secondary structure from the primary stru...

    Authors: Denise R Koessler, Debra J Knisley, Jeff Knisley and Teresa Haynes
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  16. RNA transcripts from genomic sequences showing dyad symmetry typically adopt hairpin-like, cloverleaf, or similar structures that act as recognition sites for proteins. Such structures often are the precursors...

    Authors: Cyriac Kandoth, Fikret Ercal and Ronald L Frank
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  17. A number of models and algorithms have been proposed in the past for gene regulatory network (GRN) inference; however, none of them address the effects of the size of time-series microarray expression data in ...

    Authors: Vijender Chaitankar, Preetam Ghosh, Edward J Perkins, Ping Gong and Chaoyang Zhang
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  18. Comparative sequence analysis of the 16S rRNA gene is frequently used to characterize the microbial diversity of environmental samples. However, sequence similarities do not always imply functional or evolutio...

    Authors: Samuel A Smits and Cleber C Ouverney
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  19. One of the major challenges in biology is the correct identification of promoter regions. Computational methods based on motif searching have been the traditional approach taken. Recent studies have shown that...

    Authors: Charles Bland, Abigail S Newsome and Aleksandra A Markovets
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  20. Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system. Identification of these PPIs is important for understanding the underlying biological mechanism of inf...

    Authors: Ranjit Kumar and Bindu Nanduri
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  21. Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused ...

    Authors: Daniel J Quest, Miriam L Land, Thomas S Brettin and Robert W Cottingham
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  22. Searching the enormous amount of information available in biomedical literature to extract novel functional relationships among genes remains a challenge in the field of bioinformatics. While numerous (softwar...

    Authors: Elina Tjioe, Michael W Berry and Ramin Homayouni
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  24. Enzyme dynamics has recently been shown to be crucial for structure-function relationship. Among various structure dynamics analysis platforms, HDX (hydrogen deuterium exchange) mass spectrometry stands out as...

    Authors: Ugur Uzuner, Weibing Shi, Lantao Liu, Sanmin Liu, Susie Y Dai and Joshua S Yuan
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  25. Until quite recently spinal disorder problems in the U.S. have been operated by fusing cervical vertebrae instead of replacement of the cervical disc with an artificial disc. Cervical disc replacement is a rec...

    Authors: Tansel Halic, Sinan Kockara, Coskun Bayrak and Richard Rowe
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  26. The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailab...

    Authors: Zhining Wen, Charles Wang, Quan Shi, Ying Huang, Zhenqiang Su, Huixiao Hong, Weida Tong and Leming Shi
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  27. Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: n...

    Authors: Mais Ammari, Fiona M McCarthy, Bindu Nanduri and Lesya M Pinchuk
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  28. Finding reliable gene markers for accurate disease classification is very challenging due to a number of reasons, including the small sample size of typical clinical data, high noise in gene expression measure...

    Authors: Junjie Su, Byung-Jun Yoon and Edward R Dougherty
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  29. Protein isoform generation, which may derive from alternative splicing, genetic polymorphism, and posttranslational modification, is an essential source of achieving molecular diversity by eukaryotic cells. Pr...

    Authors: Ao Zhou, Fan Zhang and Jake Y Chen
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  30. Recent advances in high-throughput genotyping technology are paving the way for research in personalized medicine and nutrition. However, most of the genetic markers identified from association studies account...

    Authors: Joshua Xu, Carolyn Wise, Vijayalakshmi Varma, Hong Fang, Baitang Ning, Huixiao Hong, Weida Tong and Jim Kaput
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  31. Endocrine disruptors (EDs) and their broad range of potential adverse effects in humans and other animals have been a concern for nearly two decades. Many putative EDs are widely used in commercial products re...

    Authors: Don Ding, Lei Xu, Hong Fang, Huixiao Hong, Roger Perkins, Steve Harris, Edward D Bearden, Leming Shi and Weida Tong
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  32. Advances in microbial genomics and bioinformatics are offering greater insights into the emergence and spread of foodborne pathogens in outbreak scenarios. The Food and Drug Administration (FDA) has developed ...

    Authors: Hong Fang, Joshua Xu, Don Ding, Scott A Jackson, Isha R Patel, Jonathan G Frye, Wen Zou, Rajesh Nayak, Steven Foley, James Chen, Zhenqiang Su, Yanbin Ye, Steve Turner, Steve Harris, Guangxu Zhou, Carl Cerniglia…
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  33. Phylogenetic analyses reveal probable patterns of divergence of present day organisms from common ancestors. The points of divergence of lineages can be dated if a corresponding historical or fossil record exi...

    Authors: Ulrich Melcher
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  34. Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active potent signalling compounds. Developing inhibitors for LOX is of high interest to researchers. Modelling...

    Authors: Shuju Bai, Tianchuan Du and Ebrahim Khosravi
    Citation: BMC Bioinformatics 2010 11(Suppl 6):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

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