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  1. Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium that is the causative agent of furunculosis, a bacterial septicaemia of salmonid fish. While other species of Aeromonas are opportunistic path...

    Authors: Michael E Reith, Rama K Singh, Bruce Curtis, Jessica M Boyd, Anne Bouevitch, Jennifer Kimball, Janet Munholland, Colleen Murphy, Darren Sarty, Jason Williams, John HE Nash, Stewart C Johnson and Laura L Brown
    Citation: BMC Genomics 2008 9:427
    Content type: Research article Published on:

  2. The IN hibitor of G rowth (ING) family of type II tumor suppressors (ING1–ING5) is involved in many cellular processes such as cell aging, apoptosis, DNA repair and tumorigenesis. To expand our understanding of t...

    Authors: Paul MK Gordon, Mohamed A Soliman, Pinaki Bose, Quang Trinh, Christoph W Sensen and Karl Riabowol
    Citation: BMC Genomics 2008 9:426
    Content type: Research article Published on:

  4. Bursicon is a heterodimer neuropeptide responsible for regulating cuticle sclerotization and wing expansion in several insect species. Recent studies indicate that the action of bursicon is mediated by a speci...

    Authors: Shiheng An, Songjie Wang, Lawrence I Gilbert, Brenda Beerntsen, Mark Ellersieck and Qisheng Song
    Citation: BMC Genomics 2008 9:424
    Content type: Research article Published on:

  5. Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-t...

    Authors: Javier Terol, M Angel Naranjo, Patrick Ollitrault and Manuel Talon
    Citation: BMC Genomics 2008 9:423
    Content type: Research article Published on:

  6. Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide t...

    Authors: Florian Odronitz, Holger Pillmann, Oliver Keller, Stephan Waack and Martin Kollmar
    Citation: BMC Genomics 2008 9:422
    Content type: Software Published on:

  7. Zinc (Zn) is an essential trace element. However, Zn bioavailability from commonly consumed plants may be reduced due to phytic acid. Zn supplementation has been used to treat diarrheal disease in children, an...

    Authors: Michelle M Martínez-Montemayor, Gretchen M Hill, Nancy E Raney, Valencia D Rilington, Robert J Tempelman, Jane E Link, Christopher P Wilkinson, Antonio M Ramos and Catherine W Ernst
    Citation: BMC Genomics 2008 9:421
    Content type: Research article Published on:

  9. Mouse and rat models are mainstays in pharmacology, toxicology and drug development – but differences between strains and between species complicate data interpretation and application to human health. Dioxin-...

    Authors: Paul C Boutros, Rui Yan, Ivy D Moffat, Raimo Pohjanvirta and Allan B Okey
    Citation: BMC Genomics 2008 9:419
    Content type: Research article Published on:

  10. "Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression), LongSAGE and MPSS (Massively Para...

    Authors: Lucie Hanriot, Céline Keime, Nadine Gay, Claudine Faure, Carole Dossat, Patrick Wincker, Céline Scoté-Blachon, Christelle Peyron and Olivier Gandrillon
    Citation: BMC Genomics 2008 9:418
    Content type: Methodology article Published on:

  11. Establishment of aspergillosis is depending upon the exit from dormancy and germination of the conidia of Aspergillus fumigatus in the lung. To gain an understanding of the molecular mechanisms underlying the ear...

    Authors: Claude Lamarre, Sergueï Sokol, Jean-Paul Debeaupuis, Christine Henry, Céline Lacroix, Philippe Glaser, Jean-Yves Coppée, Jean-Marie François and Jean-Paul Latgé
    Citation: BMC Genomics 2008 9:417
    Content type: Research article Published on:

  12. Small non-coding RNAs (sRNAs) have emerged as ubiquitous regulatory elements in bacteria and other life domains. However, few sRNAs have been identified outside several well-studied species of gamma-proteobact...

    Authors: Claudio Valverde, Jonathan Livny, Jan-Philip Schlüter, Jan Reinkensmeier, Anke Becker and Gustavo Parisi
    Citation: BMC Genomics 2008 9:416
    Content type: Research article Published on:

  14. Protein interactions are essential for most cellular functions. Interactions mediated by domains that appear in a large number of proteins are of particular interest since they are expected to have an impact o...

    Authors: Siyuan Ren, Vladimir N Uversky, Zhengjun Chen, A Keith Dunker and Zoran Obradovic
    Citation: BMC Genomics 2008 9(Suppl 2):S26
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  15. We have previously shown that using multiple prediction methods improves the accuracy of disorder predictions. It is, however, a time-consuming procedure, since individual outputs of multiple predictions have ...

    Authors: Philippe Lieutaud, Bruno Canard and Sonia Longhi
    Citation: BMC Genomics 2008 9(Suppl 2):S25
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  16. Dimension reduction is a critical issue in the analysis of microarray data, because the high dimensionality of gene expression microarray data set hurts generalization performance of classifiers. It consists o...

    Authors: Guo-Zheng Li, Hua-Long Bu, Mary Qu Yang, Xue-Qiang Zeng and Jack Y Yang
    Citation: BMC Genomics 2008 9(Suppl 2):S24
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  17. We present a mixture model-based analysis for identifying differences in the distribution of RNA polymerase II (Pol II) in transcribed regions, measured using ChIP-seq (chromatin immunoprecipitation following ...

    Authors: Weixing Feng, Yunlong Liu, Jiejun Wu, Kenneth P Nephew, Tim HM Huang and Lang Li
    Citation: BMC Genomics 2008 9(Suppl 2):S23
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  18. Prostate cancer is one of the leading causes of cancer death in men. Androgen ablation, the most commonly-used therapy for progressive prostate cancer, is ineffective once the cancer cells become androgen-inde...

    Authors: Guohua Wang, Yadong Wang, Weixing Feng, Xin Wang, Jack Y Yang, Yuming Zhao, Yue Wang and Yunlong Liu
    Citation: BMC Genomics 2008 9(Suppl 2):S22
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  19. Gene expression profiles based on microarray data are recognized as potential diagnostic indices of cancer. Molecular tumor classifications resulted from these data and learning algorithms have advanced our un...

    Authors: Rattikorn Hewett and Phongphun Kijsanayothin
    Citation: BMC Genomics 2008 9(Suppl 2):S21
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  20. Microarrays have the capacity to measure the expressions of thousands of genes in parallel over many experimental samples. The unsupervised classification technique of bicluster analysis has been employed prev...

    Authors: Kenneth Bryan and Pádraig Cunningham
    Citation: BMC Genomics 2008 9(Suppl 2):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  22. Microarray technology is often used to identify the genes that are differentially expressed between two biological conditions. On the other hand, since microarray datasets contain a small number of samples and...

    Authors: Min Xu, Mengxia Zhu and Louxin Zhang
    Citation: BMC Genomics 2008 9(Suppl 2):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  23. Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci and the reliable det...

    Authors: Heng Huang, Nha Nguyen, Soontorn Oraintara and An Vo
    Citation: BMC Genomics 2008 9(Suppl 2):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  24. Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the aus...

    Authors: Jingshan Huang, Jiangbo Dang, Michael N Huhns and W Jim Zheng
    Citation: BMC Genomics 2008 9(Suppl 2):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  25. Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become ...

    Authors: Feng Yue, Meng Zhang and Jijun Tang
    Citation: BMC Genomics 2008 9(Suppl 2):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  26. Gene expression data extracted from microarray experiments have been used to study the difference between mRNA abundance of genes under different conditions. In one of such experiments, thousands of genes are ...

    Authors: Xin Yan and Tian Zheng
    Citation: BMC Genomics 2008 9(Suppl 2):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  28. As studies of molecular biology system attempt to achieve a comprehensive understanding of a particular system, Type 1 errors may be a significant problem. However, few investigators are inclined to accept the...

    Authors: Jian Wu, Nataliya I Lenchik and Ivan C Gerling
    Citation: BMC Genomics 2008 9(Suppl 2):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  29. Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistic...

    Authors: Mehdi Pirooznia, Ping Gong, Jack Y Yang, Mary Qu Yang, Edward J Perkins and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 2):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  30. BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time co...

    Authors: Mehdi Pirooznia, Edward J Perkins and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 2):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  31. Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors up...

    Authors: Jack Y Yang, Andrzej Niemierko, Mary Qu Yang and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 2):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  33. The growing body of DNA microarray data has the potential to advance our understanding of the molecular basis of disease. However annotating microarray datasets with clinically useful information is not always...

    Authors: Cole Harris and Noushin Ghaffari
    Citation: BMC Genomics 2008 9(Suppl 2):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  34. Sudden death syndrome (SDS) of soybean (Glycine max L. Merr.) is an economically important disease, caused by the semi-biotrophic fungus Fusarium solani f. sp. glycines, recently renamed Fusarium virguliforme (Fv...

    Authors: Jiazheng Yuan, Mengxia Zhu, David A Lightfoot, M Javed Iqbal, Jack Y Yang and Khalid Meksem
    Citation: BMC Genomics 2008 9(Suppl 2):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  35. Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results u...

    Authors: Yunfeng Yang, Mengxia Zhu, Liyou Wu and Jizhong Zhou
    Citation: BMC Genomics 2008 9(Suppl 2):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  36. To examine the usefulness of protein disorder predictions as a tool for the comparative analysis of viral proteins, a relational database has been constructed. The database includes proteins from influenza A a...

    Authors: Gerard Kian-Meng Goh, A Keith Dunker and Vladimir N Uversky
    Citation: BMC Genomics 2008 9(Suppl 2):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  37. Bidirectional promoters lie between adjacent genes, which are transcribed from opposite strands of DNA. The functional mechanisms underlying the activation of bidirectional promoters are currently uncharacteri...

    Authors: Mary Qu Yang and Laura L Elnitski
    Citation: BMC Genomics 2008 9(Suppl 2):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  38. Structural genomics efforts contribute new protein structures that often lack significant sequence and fold similarity to known proteins. Traditional sequence and structure-based methods may not be sufficient ...

    Authors: Inbal Halperin, Dariya S Glazer, Shirley Wu and Russ B Altman
    Citation: BMC Genomics 2008 9(Suppl 2):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  39. Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker ...

    Authors: A Keith Dunker, Christopher J Oldfield, Jingwei Meng, Pedro Romero, Jack Y Yang, Jessica Walton Chen, Vladimir Vacic, Zoran Obradovic and Vladimir N Uversky
    Citation: BMC Genomics 2008 9(Suppl 2):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  40. Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International Journal of Fun...

    Authors: Jack Y Yang, Mary Qu Yang, Hamid R Arabnia and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 2):I1
    Content type: Introductory Review Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  41. A fundamental requirement for genomic studies is the availability of genetic material of good quality and quantity. The desired quantity and quality are often hard to obtain when target DNA is composed of comp...

    Authors: Muhammad Shoaib, Sonia Baconnais, Undine Mechold, Eric Le Cam, Marc Lipinski and Vasily Ogryzko
    Citation: BMC Genomics 2008 9:415
    Content type: Methodology article Published on:

  42. The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data ...

    Authors: Rajesh Gollapudi, Kashi Vishwanath Revanna, Chris Hemmerich, Sarah Schaack and Qunfeng Dong
    Citation: BMC Genomics 2008 9:414
    Content type: Software Published on:

  43. Bacille Calmette-Guérin (BCG) is an attenuated strain of Mycobacterium bovis currently used as a vaccine against tuberculosis. Global distribution and propagation of BCG has contributed to the in vitro evolution ...

    Authors: Andrea S Leung, Vanessa Tran, Zuowei Wu, Xuping Yu, David C Alexander, George Fu Gao, Baoli Zhu and Jun Liu
    Citation: BMC Genomics 2008 9:413
    Content type: Research article Published on:

  45. Staphylococcus aureus (S. aureus), is responsible for many infectious diseases, ranging from benign skin infections to life-threatening endocarditis and toxic shock syndrome. Ortho-phenylphenol (OPP) is an antimi...

    Authors: Hyeung-Jin Jang, Chantal Nde, Freshteh Toghrol and William E Bentley
    Citation: BMC Genomics 2008 9:411
    Content type: Research article Published on:

  48. Sox10, a member of the Sry-related HMG-Box gene family, is a critical transcription factor for several important cell lineages, most notably the neural crest stem cells and the derivative peripheral glial cell...

    Authors: Kyung Eun Lee, Seungyoon Nam, Eun-ah Cho, Ikjoo Seong, Jin-Kyung Limb, Sanghyuk Lee and Jaesang Kim
    Citation: BMC Genomics 2008 9:408
    Content type: Research article Published on:

  49. Multiplex ligation-dependent probe amplification (MLPA) is an efficient and reliable technique for gene dosage analysis. Currently MLPA can be conducted on two platforms: traditional electrophoresis-based, and...

    Authors: Jizu Zhi and Eli Hatchwell
    Citation: BMC Genomics 2008 9:407
    Content type: Software Published on:

  50. ASAP is a newly characterized microtubule-associated protein (MAP) essential for proper cell-cycling. We have previously shown that expression deregulation of human ASAP results in profound defects in mitotic ...

    Authors: Magali Venoux, Karine Delmouly, Ollivier Milhavet, Sophie Vidal-Eychenié, Dominique Giorgi and Sylvie Rouquier
    Citation: BMC Genomics 2008 9:406
    Content type: Research article Published on:

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BMC Genomics

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