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  2. In many taxa, males and females are very distinct phenotypically, and these differences often reflect divergent selective pressures acting on the sexes. Phenotypic sexual dimorphism almost certainly reflects d...

    Authors: Clayton M Small, Ginger E Carney, Qianxing Mo, Marina Vannucci and Adam G Jones
    Citation: BMC Genomics 2009 10:579
    Content type: Research article Published on:

  3. Implementation of molecular breeding in rye (Secale cereale L.) improvement programs depends on the availability of high-density molecular linkage maps. However, the number of sequence-specific PCR-based markers ...

    Authors: Hanna Bolibok-Brągoszewska, Katarzyna Heller-Uszyńska, Peter Wenzl, Grzegorz Uszyński, Andrzej Kilian and Monika Rakoczy-Trojanowska
    Citation: BMC Genomics 2009 10:578
    Content type: Research article Published on:

  4. Pituitary tumor transforming gene (PTTG), also known as securin, is highly expressed in various tumors including pituitary, thyroid, colon, ovary, testis, lung, and breast. An overexpression of PTTG enhances c...

    Authors: Siva K Panguluri and Sham S Kakar
    Citation: BMC Genomics 2009 10:577
    Content type: Research article Published on:

  5. YY1 is an epigenetic regulator for a large number of mammalian genes. While performing genome-wide YY1 binding motif searches, we discovered that the olfactory receptor (OLFR) genes have an unusual cluster of ...

    Authors: Christopher D Faulk and Joomyeong Kim
    Citation: BMC Genomics 2009 10:576
    Content type: Research article Published on:

  6. The development of high throughput experimental technologies have given rise to the "-omics" era where terabyte-scale datasets for systems-level measurements of various cellular and molecular phenomena pose co...

    Authors: Tin Wee Tan, Shen Jean Lim, Asif M Khan and Shoba Ranganathan
    Citation: BMC Genomics 2009 10(Suppl 3):S36
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  7. A disease-causing mutation refers to a heritable genetic change that is associated with a specific phenotype (disease). The detection of a mutation from a patient's sample is critical for the diagnosis, treatm...

    Authors: Sungwoong Jho, Byoung-Chul Kim, Ho Ghang, Ji-Han Kim, Daeui Park, Hak-Min Kim, Soo-young Jung, Ki-young Yoo, Hee-Jin Kim, Sunghoon Lee and Jong Bhak
    Citation: BMC Genomics 2009 10(Suppl 3):S35
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  8. Medical and biological data are commonly with small sample size, missing values, and most importantly, imbalanced class distribution. In this study we propose a particle swarm based hybrid system for remedying...

    Authors: Pengyi Yang, Liang Xu, Bing B Zhou, Zili Zhang and Albert Y Zomaya
    Citation: BMC Genomics 2009 10(Suppl 3):S34
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  9. Lysosomal α-mannosidase is an enzyme that acts to degrade N-linked oligosaccharides and hence plays an important role in mannose metabolism in humans and other mammalian species, especially livestock. Mutation...

    Authors: Javed Mohammed Khan and Shoba Ranganathan
    Citation: BMC Genomics 2009 10(Suppl 3):S33
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  10. Parkinson's disease (PD) is one of the most common neurodegenerative disorders, clinically characterized by impaired motor function. Since the etiology of PD is diverse and complex, many researchers have creat...

    Authors: Jin Ok Yang, Woo-Yeon Kim, So-Young Jeong, Jung-Hwa Oh, Sungwoong Jho, Jong Bhak and Nam-Soon Kim
    Citation: BMC Genomics 2009 10(Suppl 3):S32
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  11. Rate-limiting enzymes, because of their relatively low velocity, are believed to influence metabolic flux in pathways. To investigate their regulatory role in metabolic networks, we look at the global organiza...

    Authors: Min Zhao and Hong Qu
    Citation: BMC Genomics 2009 10(Suppl 3):S31
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  12. Human immunodeficiency virus-1 (HIV-1) has a minimal genome of only 9 genes, which encode 15 proteins. HIV-1 thus depends on the human host for virtually every aspect of its life cycle. The universal language ...

    Authors: Sivaraman Balakrishnan, Oznur Tastan, Jaime Carbonell and Judith Klein-Seetharaman
    Citation: BMC Genomics 2009 10(Suppl 3):S30
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  13. Gene regulation is a key mechanism in higher eukaryotic cellular processes. One of the major challenges in gene regulation studies is to identify regulators affecting the expression of their target genes in sp...

    Authors: Je-Keun Rhee, Je-Gun Joung, Jeong-Ho Chang, Zhangjun Fei and Byoung-Tak Zhang
    Citation: BMC Genomics 2009 10(Suppl 3):S29
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  14. Time delays are often found in gene regulation though most techniques of building gene regulatory networks are not capable of capturing such phenomena. Here we look at the delays in the DNA repair system of Mycob...

    Authors: Iti Chaturvedi and Jagath C Rajapakse
    Citation: BMC Genomics 2009 10(Suppl 3):S28
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  15. Eukaryotic genomes are packaged into chromatin, a compact structure containing fundamental repeating units, the nucleosomes. The mobility of nucleosomes plays important roles in many DNA-related processes by r...

    Authors: Ngoc Tu Le, Tu Bao Ho and Dang Hung Tran
    Citation: BMC Genomics 2009 10(Suppl 3):S27
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  16. The steady-state behaviour of gene regulatory networks (GRNs) can provide crucial evidence for detecting disease-causing genes. However, monitoring the dynamics of GRNs is particularly difficult because biolog...

    Authors: Haseong Kim and Erol Gelenbe
    Citation: BMC Genomics 2009 10(Suppl 3):S26
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  17. Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics t...

    Authors: Pramod Kumar Prasad, Veena Tandon, Devendra Kumar Biswal, Lalit Mohan Goswami and Anupam Chatterjee
    Citation: BMC Genomics 2009 10(Suppl 3):S25
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  18. It is known that the highly pathogenic avian influenza A virus H5N1 binds strongly and with high specificity to the avian-type receptor by its hemagglutinin surface protein. This specificity is normally a barr...

    Authors: Nipa Jongkon, Wanwimon Mokmak, Daungmanee Chuakheaw, Philip J Shaw, Sissades Tongsima and Chak Sangma
    Citation: BMC Genomics 2009 10(Suppl 3):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  19. Protein-DNA interactions are essential for fundamental biological activities including DNA transcription, replication, packaging, repair and rearrangement. Proteins interacting with DNA can be classified into ...

    Authors: Yu-Feng Huang, Chun-Chin Huang, Yu-Cheng Liu, Yen-Jen Oyang and Chien-Kang Huang
    Citation: BMC Genomics 2009 10(Suppl 3):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  20. Proteins are dynamic macromolecules which may undergo conformational transitions upon changes in environment. As it has been observed in laboratories that protein flexibility is correlated to essential biologi...

    Authors: Yu-Cheng Liu, Meng-Han Yang, Win-Li Lin, Chien-Kang Huang and Yen-Jen Oyang
    Citation: BMC Genomics 2009 10(Suppl 3):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  21. In this paper, we introduce a novel inter-range interaction integrated approach for protein domain boundary prediction. It involves (1) the design of modular kernel algorithm, which is able to effectively expl...

    Authors: Paul D Yoo, Bing Bing Zhou and Albert Y Zomaya
    Citation: BMC Genomics 2009 10(Suppl 3):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  22. Mitochondria play a vital role in the energy production and apoptotic process of eukaryotic cells. Proteins in the mitochondria are encoded by nuclear and mitochondrial genes. Owing to a large increase in the ...

    Authors: Rohit Reja, AJ Venkatakrishnan, Jungwoo Lee, Byoung-Chul Kim, Jea-Woon Ryu, Sungsam Gong, Jong Bhak and Daeui Park
    Citation: BMC Genomics 2009 10(Suppl 3):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  23. The PolyGalacturonase-Inhibiting Proteins (PGIP) of plant cell wall limit the invasion of phytopathogenic organisms by interacting with the enzyme PolyGalacturonase (PG) they secrete to degrade pectin present ...

    Authors: Aditi Maulik, Hiren Ghosh and Soumalee Basu
    Citation: BMC Genomics 2009 10(Suppl 3):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  24. Pseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organis...

    Authors: Seong-Jin Park, Jong-Soon Choi, Byoung-Chul Kim, Seong-Woong Jho, Jea-Woon Ryu, Daeui Park, Kyung-A Lee, Jong Bhak and Seung Il Kim
    Citation: BMC Genomics 2009 10(Suppl 3):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  25. The reconstruction of gene regulatory networks from high-throughput "omics" data has become a major goal in the modelling of living systems. Numerous approaches have been proposed, most of which attempt only "...

    Authors: Sidath Randeni Kadupitige, Kin Chun Leung, Julia Sellmeier, Jane Sivieng, Daniel R Catchpoole, Michael E Bain and Bruno A Gaëta
    Citation: BMC Genomics 2009 10(Suppl 3):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  26. It has been a long-standing biological challenge to understand the molecular regulatory mechanisms behind mammalian ageing. Harnessing the availability of many ageing microarray datasets, a number of studies h...

    Authors: Joshua WK Ho, Maurizio Stefani, Cristobal G dos Remedios and Michael A Charleston
    Citation: BMC Genomics 2009 10(Suppl 3):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  27. Gene expression similarity measuring methods were developed and applied to search rapidly growing public microarray databases. However, current expression similarity measuring methods need to be improved to ac...

    Authors: Changwon Keum, Jung Hoon Woo, Won Seok Oh, Sue-Nie Park and Kyoung Tai No
    Citation: BMC Genomics 2009 10(Suppl 3):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  28. Grouping genes into clusters on the basis of similarity between their expression profiles has been the main approach to predict functional modules, from which important inference or further investigation decis...

    Authors: Viet-Anh Nguyen and Pietro Lió
    Citation: BMC Genomics 2009 10(Suppl 3):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  29. Alternative splicing (AS) is a primary mechanism of functional regulation in the human genome, with 60% to 80% of human genes being alternatively spliced. As part of the bovine genome annotation team, we have ...

    Authors: Elsa Chacko and Shoba Ranganathan
    Citation: BMC Genomics 2009 10(Suppl 3):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  30. The characterisation, or binning, of metagenome fragments is an important first step to further downstream analysis of microbial consortia. Here, we propose a one-dimensional signature, OFDEG, derived from the...

    Authors: Isaam Saeed and Saman K Halgamuge
    Citation: BMC Genomics 2009 10(Suppl 3):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  31. DNA triplexes can naturally occur, co-localize and interact with many other regulatory DNA elements (e.g. G-quadruplex (G4) DNA motifs), specific DNA-binding proteins (e.g. transcription factors (TFs)), and mi...

    Authors: Piroon Jenjaroenpun and Vladimir A Kuznetsov
    Citation: BMC Genomics 2009 10(Suppl 3):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  32. DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on ...

    Authors: Jeongheui Lim, Sang-Yoon Kim, Sungmin Kim, Hae-Seok Eo, Chang-Bae Kim, Woon Kee Paek, Won Kim and Jong Bhak
    Citation: BMC Genomics 2009 10(Suppl 3):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  33. Insertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB)...

    Authors: Wenwei Yang, Ke Jin, Xing Xie, Dongsheng Li, Jigang Yang, Li Wang, Ning Gu, Yang Zhong and Ling V Sun
    Citation: BMC Genomics 2009 10(Suppl 3):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  34. Caspases belong to a class of cysteine proteases which function as critical effectors in cellular processes such as apoptosis and inflammation by cleaving substrates immediately after unique tetrapeptide sites...

    Authors: Lawrence JK Wee, Joo Chuan Tong, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Genomics 2009 10(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  35. Activation of PPARs has been reported to inhibit the proliferation of malignant cells from different lineages. They are involved in transcription regulation of genes upon activation by a ligand. The binding of...

    Authors: Gireedhar Venkatachalam, Alan Prem Kumar, Loo Ser Yue, Shazib Pervaiz, Marie Veronique Clement and Meena Kishore Sakharkar
    Citation: BMC Genomics 2009 10(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  36. Polymerase chain reaction (PCR) is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools...

    Authors: Jittima Piriyapongsa, Chumpol Ngamphiw, Anunchai Assawamakin, Pongsakorn Wangkumhang, Payiarat Suwannasri, Uttapong Ruangrit, Gallissara Agavatpanitch and Sissades Tongsima
    Citation: BMC Genomics 2009 10(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  37. Oligonucleotide design is known as a time-consuming work in bioinformatics. In order to accelerate and be efficient the oligonucleotide design process, one of widely used approach is the prescreening unreliabl...

    Authors: Won-Hyoung Chung and Seong-Bae Park
    Citation: BMC Genomics 2009 10(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  38. Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymor...

    Authors: Shu-Qi Zhao, Jun Wang, Li Zhang, Jiong-Tang Li, Xiaocheng Gu, Ge Gao and Liping Wei
    Citation: BMC Genomics 2009 10(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  39. The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics...

    Authors: Shoba Ranganathan, Frank Eisenhaber, Joo Chuan Tong and Tin Wee Tan
    Citation: BMC Genomics 2009 10(Suppl 3):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  40. Although many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test t...

    Authors: Guillaume Le Mignon, Colette Désert, Frédérique Pitel, Sophie Leroux, Olivier Demeure, Gregory Guernec, Behnam Abasht, Madeleine Douaire, Pascale Le Roy and Sandrine Lagarrigue
    Citation: BMC Genomics 2009 10:575
    Content type: Research article Published on:

  41. An essential driving component in the co-evolution of plants and insects is the ability to produce and handle bioactive compounds. Plants produce bioactive natural products for defense, but some insects detoxi...

    Authors: Mika Zagrobelny, Karsten Scheibye-Alsing, Niels Bjerg Jensen, Birger Lindberg Møller, Jan Gorodkin and Søren Bak
    Citation: BMC Genomics 2009 10:574
    Content type: Research article Published on:

  44. Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the mo...

    Authors: George E Liu, Mario Ventura, Angelo Cellamare, Lin Chen, Ze Cheng, Bin Zhu, Congjun Li, Jiuzhou Song and Evan E Eichler
    Citation: BMC Genomics 2009 10:571
    Content type: Research article Published on:

  45. Saturated brines are extreme environments of low diversity. Salinibacter ruber is the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in...

    Authors: Lejla Pašić, Beltran Rodriguez-Mueller, Ana-Belen Martin-Cuadrado, Alex Mira, Forest Rohwer and Francisco Rodriguez-Valera
    Citation: BMC Genomics 2009 10:570
    Content type: Research article Published on:

  47. It is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/o...

    Authors: Keiichi Mochida, Taku Furuta, Kaworu Ebana, Kazuo Shinozaki and Jun Kikuchi
    Citation: BMC Genomics 2009 10:568
    Content type: Research article Published on:

  48. While attempting to reanalyze published data from Agilent 4 × 44 human expression chips, we found that some of the 60-mer olignucleotide features could not be interpreted as representing single human genes. Fo...

    Authors: E Michael Gertz, Kundan Sengupta, Michael J Difilippantonio, Thomas Ried and Alejandro A Schäffer
    Citation: BMC Genomics 2009 10:566
    Content type: Research article Published on:

  49. Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expressio...

    Authors: Kai N Stölting, Gerrit Gort, Christian Wüst and Anthony B Wilson
    Citation: BMC Genomics 2009 10:565
    Content type: Research article Published on:

  50. Despite many studies on the biogenesis, molecular structure and biological functions of microRNAs, little is known about the transcriptional regulatory mechanisms controlling the spatiotemporal expression patt...

    Authors: Tong J Gu, Xiang Yi, Xi W Zhao, Yi Zhao and James Q Yin
    Citation: BMC Genomics 2009 10:563
    Content type: Research article Published on:

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