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  1. A large number of probabilistic models used in sequence analysis assign non-zero probability values to most input sequences. To decide when a given probability is sufficient the most common way is bayesian bin...

    Authors: Ariane Machado-Lima, André Yoshiaki Kashiwabara and Alan Mitchell Durham
    Citation: BMC Genomics 2010 11(Suppl 5):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  2. Molecular docking simulation is the Rational Drug Design (RDD) step that investigates the affinity between protein receptors and ligands. Typically, molecular docking algorithms consider receptors as rigid bod...

    Authors: Karina S Machado, Ana T Winck, Duncan DA Ruiz and Osmar Norberto de Souza
    Citation: BMC Genomics 2010 11(Suppl 5):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  3. Acute enteritis caused by Salmonella is a public health concern. Salmonella infection is also known to increase the risk of inflammatory bowel diseases and cancer. Therefore, it is important to understand how Sal...

    Authors: Xingyin Liu, Rong Lu, Yinglin Xia and Jun Sun
    Citation: BMC Genomics 2010 11:722
    Content type: Research article Published on:

  4. Members of the makorin (mkrn) gene family encode RING/C3H zinc finger proteins with U3 ubiquitin ligase activity. Although these proteins have been described in a variety of eukaryotes such as plants, fungi, inve...

    Authors: Astrid Böhne, Amandine Darras, Helena D'Cotta, Jean-Francois Baroiller, Delphine Galiana-Arnoux and Jean-Nicolas Volff
    Citation: BMC Genomics 2010 11:721
    Content type: Research article Published on:

  6. The AP2/ERF protein family contains transcription factors that play a crucial role in plant growth and development and in response to biotic and abiotic stress conditions in plants. Grapevine (Vitis vinifera) is ...

    Authors: Francesco Licausi, Federico M Giorgi, Sara Zenoni, Fabio Osti, Mario Pezzotti and Pierdomenico Perata
    Citation: BMC Genomics 2010 11:719
    Content type: Research article Published on:

  7. Although the importance and widespread occurrence of iron limitation in the contemporary ocean is well documented, we still know relatively little about genetic adaptation of phytoplankton to these environment...

    Authors: Markus Lommer, Alexandra-Sophie Roy, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel and Julie LaRoche
    Citation: BMC Genomics 2010 11:718
    Content type: Research article Published on:

  8. While the number of newly sequenced genomes and genes is constantly increasing, elucidation of their function still is a laborious and time-consuming task. This has led to the development of a wide range of me...

    Authors: Samira Jaeger, Christine T Sers and Ulf Leser
    Citation: BMC Genomics 2010 11:717
    Content type: Research article Published on:

  9. MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique ...

    Authors: Henk PJ Buermans, Yavuz Ariyurek, Gertjan van Ommen, Johan T den Dunnen and Peter AC 't Hoen
    Citation: BMC Genomics 2010 11:716
    Content type: Methodology article Published on:

  10. MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution.

    Authors: Marianthi Karali, Ivana Peluso, Vincenzo A Gennarino, Marchesa Bilio, Roberta Verde, Giampiero Lago, Pascal Dollé and Sandro Banfi
    Citation: BMC Genomics 2010 11:715
    Content type: Research article Published on:

  11. Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a...

    Authors: Camille Rustenholz, Pete E Hedley, Jenny Morris, Frédéric Choulet, Catherine Feuillet, Robbie Waugh and Etienne Paux
    Citation: BMC Genomics 2010 11:714
    Content type: Research article Published on:

  12. Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution t...

    Authors: Taryn P Stewart, Hyoung Yon Kim, Arnold M Saxton and Jung Han Kim
    Citation: BMC Genomics 2010 11:713
    Content type: Research article Published on:

  15. The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two oth...

    Authors: Alexandra Sirota-Madi, Tsviya Olender, Yael Helman, Colin Ingham, Ina Brainis, Dalit Roth, Efrat Hagi, Leonid Brodsky, Dena Leshkowitz, Vladimir Galatenko, Vladimir Nikolaev, Raja C Mugasimangalam, Sharron Bransburg-Zabary, David L Gutnick, Doron Lancet and Eshel Ben-Jacob
    Citation: BMC Genomics 2010 11:710
    Content type: Research article Published on:

  16. Arsenic is present in numerous ecosystems and microorganisms have developed various mechanisms to live in such hostile environments. Herminiimonas arsenicoxydans, a bacterium isolated from arsenic contaminated sl...

    Authors: Jessica Cleiss-Arnold, Sandrine Koechler, Caroline Proux, Marie-Laure Fardeau, Marie-Agnès Dillies, Jean-Yves Coppee, Florence Arsène-Ploetze and Philippe N Bertin
    Citation: BMC Genomics 2010 11:709
    Content type: Research article Published on:

  17. In recent years numerous studies have undertaken to measure the impact of patents, material transfer agreements, data-withholding and commercialization pressures on biomedical researchers. Of particular concer...

    Authors: Matthew R Voell, Lily Farris, Edwin Levy and Emily Marden
    Citation: BMC Genomics 2010 11:708
    Content type: Correspondence Published on:

  18. Considerations in applying association mapping (AM) to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. T...

    Authors: Alfonso Cuesta-Marcos, Péter Szűcs, Timothy J Close, Tanya Filichkin, Gary J Muehlbauer, Kevin P Smith and Patrick M Hayes
    Citation: BMC Genomics 2010 11:707
    Content type: Research article Published on:

  19. Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA variation in vertebrates and may be used as genetic markers for a range of applications. This has led to an increased interest i...

    Authors: Rune Andreassen, Sigbjørn Lunner and Bjørn Høyheim
    Citation: BMC Genomics 2010 11:706
    Content type: Research article Published on:

  20. Oryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.). It contains various valuable traits with respect to tolerance to biotic a...

    Authors: Haiyuan Yang, Liwei Hu, Thomas Hurek and Barbara Reinhold-Hurek
    Citation: BMC Genomics 2010 11:705
    Content type: Research article Published on:

  22. Horned beetles, in particular in the genus Onthophagus, are important models for studies on sexual selection, biological radiations, the origin of novel traits, developmental plasticity, biocontrol, conservation,...

    Authors: Jeong-Hyeon Choi, Teiya Kijimoto, Emilie Snell-Rood, Hongseok Tae, Youngik Yang, Armin P Moczek and Justen Andrews
    Citation: BMC Genomics 2010 11:703
    Content type: Research article Published on:

  23. A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their res...

    Authors: Eduard D Akhunov, Alina R Akhunova, Olin D Anderson, James A Anderson, Nancy Blake, Michael T Clegg, Devin Coleman-Derr, Emily J Conley, Curt C Crossman, Karin R Deal, Jorge Dubcovsky, Bikram S Gill, Yong Q Gu, Jakub Hadam, Hwayoung Heo, Naxin Huo…
    Citation: BMC Genomics 2010 11:702
    Content type: Research article Published on:

  24. Changes in promoter DNA methylation pattern of genes involved in key biological pathways have been reported in glioblastoma. Genome-wide assessments of DNA methylation levels are now required to decipher the e...

    Authors: Amandine Etcheverry, Marc Aubry, Marie de Tayrac, Elodie Vauleon, Rachel Boniface, Frederique Guenot, Stephan Saikali, Abderrahmane Hamlat, Laurent Riffaud, Philippe Menei, Veronique Quillien and Jean Mosser
    Citation: BMC Genomics 2010 11:701
    Content type: Research article Published on:

  26. Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific e...

    Authors: Anu Sironen, Pekka Uimari, Szabolcs Nagy, Sándor Paku, Magnus Andersson and Johanna Vilkki
    Citation: BMC Genomics 2010 11:699
    Content type: Research article Published on:

  27. Comparative analysis of gene expression among serotypes within a species can provide valuable information on important differences between related genomes. For the pig lung pathogen Actinobacillus pleuropneumonia...

    Authors: Kirstine Klitgaard, Carsten Friis, Øystein Angen and Mette Boye
    Citation: BMC Genomics 2010 11:698
    Content type: Research article Published on:

  28. Several novel immunoglobulin-like transcripts (NILTs) which have previously been identified in the salmonid species rainbow trout (Oncorhynchus mykiss) contain either one or two extracellular Ig domains of the V-...

    Authors: Anders E Østergaard, Krzysztof P Lubieniecki, Samuel AM Martin, René JM Stet, William S Davidson and Christopher J Secombes
    Citation: BMC Genomics 2010 11:697
    Content type: Research article Published on:

  29. Pax3 is a key upstream regulator of the onset of myogenesis, controlling progenitor cell survival and behaviour as well as entry into the myogenic programme. It functions in the dermomyotome of the somite from...

    Authors: Mounia Lagha, Takahiko Sato, Béatrice Regnault, Ana Cumano, Aimée Zuniga, Jonathan Licht, Frédéric Relaix and Margaret Buckingham
    Citation: BMC Genomics 2010 11:696
    Content type: Research article Published on:

  30. The New World screw-worm (NWS), Cochliomyia hominivorax, is one of the most important myiasis-causing flies, causing severe losses to the livestock industry. In its current geographical distribution, this species...

    Authors: Renato A Carvalho, Ana Maria L Azeredo-Espin and Tatiana T Torres
    Citation: BMC Genomics 2010 11:695
    Content type: Research article Published on:

  31. The reptiles, characterized by both diversity and unique evolutionary adaptations, provide a comprehensive system for comparative studies of metabolism, physiology, and development. However, molecular resource...

    Authors: Tonia S Schwartz, Hongseok Tae, Youngik Yang, Keithanne Mockaitis, John L Van Hemert, Stephen R Proulx, Jeong-Hyeon Choi and Anne M Bronikowski
    Citation: BMC Genomics 2010 11:694
    Content type: Research article Published on:

  32. Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protei...

    Authors: Bruno Vincent, Martha Kaeslin, Thomas Roth, Manfred Heller, Julie Poulain, François Cousserans, Johann Schaller, Marylène Poirié, Beatrice Lanzrein, Jean-Michel Drezen and Sébastien JM Moreau
    Citation: BMC Genomics 2010 11:693
    Content type: Research article Published on:

  33. A five-dimensional (5-D) clone pooling strategy for screening of bacterial artificial chromosome (BAC) clones with molecular markers utilizing highly-parallel Illumina GoldenGate assays and PCR facilitates hig...

    Authors: Frank M You, Ming-Cheng Luo, Kenong Xu, Karin R Deal, Olin D Anderson and Jan Dvorak
    Citation: BMC Genomics 2010 11:692
    Content type: Methodology article Published on:

  34. Simple sequence repeats (SSRs) are highly variable features of all genomes. Their rapid evolution makes them useful for tracing the evolutionary history of populations and investigating patterns of selection a...

    Authors: Way Sung, Abraham Tucker, R Daniel Bergeron, Michael Lynch and W Kelley Thomas
    Citation: BMC Genomics 2010 11:691
    Content type: Research article Published on:

  35. The addition of an acetyl group to protein N-termini is a widespread co-translational modification. NatB is one of the main N-acetyltransferases that targets a subset of proteins possessing an N-terminal methi...

    Authors: Andreas O Helbig, Sara Rosati, Pim WWM Pijnappel, Bas van Breukelen, Marc HTH Timmers, Shabaz Mohammed, Monique Slijper and Albert JR Heck
    Citation: BMC Genomics 2010 11:685
    Content type: Research article Published on:

  36. Microarray technology is limited to monitoring the expression of previously annotated genes that have corresponding probes on the array. Computationally annotated genes have not fully been validated, because E...

    Authors: Hiroshi Mizuno, Yoshihiro Kawahara, Hiroaki Sakai, Hiroyuki Kanamori, Hironobu Wakimoto, Harumi Yamagata, Youko Oono, Jianzhong Wu, Hiroshi Ikawa, Takeshi Itoh and Takashi Matsumoto
    Citation: BMC Genomics 2010 11:683
    Content type: Research article Published on:

  37. The 2010 International Conference on Bioinformatics, InCoB2010, which is the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet) has agreed to publish conference papers in compliance with t...

    Authors: Tin Wee Tan, Joo Chuan Tong, Asif M Khan, Mark de Silva, Kuan Siong Lim and Shoba Ranganathan
    Citation: BMC Genomics 2010 11(Suppl 4):S27
    Content type: Perspective Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  38. Aging is a complex and challenging phenomenon that requires interdisciplinary efforts to unravel its mystery. Insight into genes relevant to the aging process would offer the chance to delay and avoid some of ...

    Authors: Jekeun Kwon, Byungwook Lee and Haeyoung Chung
    Citation: BMC Genomics 2010 11(Suppl 4):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  39. Variety of information relating between genome and the pathological findings in disease will yield a wealth of clues to discover new function, the role of genes and pathways, and future medicine. In addition t...

    Authors: Kazuro Shimokawa, Kaoru Mogushi, Satoshi Shoji, Atsuko Hiraishi, Keisuke Ido, Hiroshi Mizushima and Hiroshi Tanaka
    Citation: BMC Genomics 2010 11(Suppl 4):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  40. Appropriate regulation of respective gene expressions is a bottleneck for the realization of artificial biological systems inside living cells. The modification of several promoter sequences is required to ach...

    Authors: Shotaro Ayukawa, Akio Kobayashi, Yusaku Nakashima, Hidemasa Takagi, Shogo Hamada, Masahiko Uchiyama, Katsuyuki Yugi, Satoshi Murata, Yasubumi Sakakibara, Masami Hagiya, Masayuki Yamamura and Daisuke Kiga
    Citation: BMC Genomics 2010 11(Suppl 4):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  41. The UPP (ubiquitin proteasome pathway) is the major proteolytic system in the cytosol and nucleus of all eukaryotic cells which regulates cellular events, including mitotis, differentiation, signal transductio...

    Authors: Abhinav Grover, Ashutosh Shandilya, Virendra S Bisaria and Durai Sundar
    Citation: BMC Genomics 2010 11(Suppl 4):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  42. In eukaryotes, the cell is divided into several compartments enclosed by unitary membranes. Such compartmentalization is critical for cells to restrict different pathways to be carried out in different subcell...

    Authors: Min Zhao and Hong Qu
    Citation: BMC Genomics 2010 11(Suppl 4):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  43. RNA editing is a transcript-based layer of gene regulation. To date, no systemic study on RNA editing of plant nuclear genes has been reported. Here, a transcriptome-wide search for editing sites in nuclear tr...

    Authors: Yijun Meng, Dijun Chen, YongFeng Jin, Chuanzao Mao, Ping Wu and Ming Chen
    Citation: BMC Genomics 2010 11(Suppl 4):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  44. Orthologues are genes in different species that are related through divergent evolution from a common ancestor and are expected to have similar functions. Many databases have been created to describe orthologo...

    Authors: Yizhen Jia, Thomas KF Wong, You-Qiang Song, Siu-Ming Yiu and David K Smith
    Citation: BMC Genomics 2010 11(Suppl 4):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  45. With the increase in genomic and transcriptomic data produced by the recent advancements in next generation sequencers and microarrays, it is now easier than ever to conduct large-scale comparative genomic stu...

    Authors: Atsushi Ogura, Masa-aki Yoshida, Mutsumi Fukuzaki and Jun Sese
    Citation: BMC Genomics 2010 11(Suppl 4):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  46. MicroRNAs (miRNAs) are endogenous non-protein-coding RNA genes which exist in a wide variety of organisms, including animals, plants, virus and even unicellular organisms. Medaka (Oryzias latipes) is a useful mod...

    Authors: Sung-Chou Li, Wen-Ching Chan, Meng-Ru Ho, Kuo-Wang Tsai, Ling-Yueh Hu, Chun-Hung Lai, Chun-Nan Hsu, Pung-Pung Hwang and Wen-chang Lin
    Citation: BMC Genomics 2010 11(Suppl 4):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  47. Nucleic acid hybridization is an extensively adopted principle in biomedical research, in which the performance of any hybridization-based method depends on the specificity of probes to their targets. To deter...

    Authors: Shu-Hwa Chen, Chen-Zen Lo, Sheng-Yao Su, Bao-Han Kuo, Chao A Hsiung and Chung-Yen Lin
    Citation: BMC Genomics 2010 11(Suppl 4):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  48. MicroRNAs (miRNAs) are small noncoding RNAs about 22 nt long that negatively regulate gene expression at the post-transcriptional level. Their key effects on various biological processes, e.g., embryonic devel...

    Authors: Zhen Yang, Fei Ren, Changning Liu, Shunmin He, Gang Sun, Qian Gao, Lei Yao, Yangde Zhang, Ruoyu Miao, Ying Cao, Yi Zhao, Yang Zhong and Haitao Zhao
    Citation: BMC Genomics 2010 11(Suppl 4):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  49. RNA-binding proteins (RBPs) play crucial roles in post-transcriptional control of RNA. RBPs are designed to efficiently recognize specific RNA sequences after it is derived from the DNA sequence. To satisfy di...

    Authors: Yu-Feng Huang, Li-Yuan Chiu, Chun-Chin Huang and Chien-Kang Huang
    Citation: BMC Genomics 2010 11(Suppl 4):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  50. The 2010 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia’s oldest bioinformatics organisation formed in 1998, was organized as the 9th International Conference on Bioinformatics (InC...

    Authors: Shoba Ranganathan, Christian Schönbach, Kenta Nakai and Tin Wee Tan
    Citation: BMC Genomics 2010 11(Suppl 4):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

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