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  1. Rye is an important European crop used for food, feed, and bioenergy. Several quality and yield-related traits are of agronomic relevance for rye breeding programs. Profound knowledge of the genetic architectu...

    Authors: Thomas Miedaner, Marlen Hübner, Viktor Korzun, Brigitta Schmiedchen, Eva Bauer, Grit Haseneyer, Peer Wilde and Jochen C Reif
    Citation: BMC Genomics 2012 13:706
    Content type: Research article Published on:

  2. Gene expression data are noisy due to technical and biological variability. Consequently, analysis of gene expression data is complex. Different statistical methods produce distinct sets of genes. In addition,...

    Authors: Lijing Xu, Cheng Cheng, E Olusegun George and Ramin Homayouni
    Citation: BMC Genomics 2012 13(Suppl 8):S23
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  3. The discovery of molecular pathways is a challenging problem and its solution relies on the identification of causal molecular interactions in genomics data. Causal molecular interactions can be discovered usi...

    Authors: Alexander Statnikov, Mikael Henaff, Nikita I Lytkin and Constantin F Aliferis
    Citation: BMC Genomics 2012 13(Suppl 8):S22
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  4. Many cancer clinical trials now specify the particular status of a genetic lesion in a patient's tumor in the inclusion or exclusion criteria for trial enrollment. To facilitate search and identification of ge...

    Authors: Yonghui Wu, Mia A Levy, Christine M Micheel, Paul Yeh, Buzhou Tang, Michael J Cantrell, Stacy M Cooreman and Hua Xu
    Citation: BMC Genomics 2012 13(Suppl 8):S21
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  5. Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. ...

    Authors: Jérôme Jourquin, Dexter Duncan, Zhiao Shi and Bing Zhang
    Citation: BMC Genomics 2012 13(Suppl 8):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  6. The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacteria...

    Authors: Jennifer M Fettweis, Myrna G Serrano, Nihar U Sheth, Carly M Mayer, Abigail L Glascock, J Paul Brooks, Kimberly K Jefferson and Gregory A Buck
    Citation: BMC Genomics 2012 13(Suppl 8):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  7. A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to prod...

    Authors: Zhongming Zhao, An-Yuan Guo, Edwin JCG van den Oord, Fazil Aliev, Peilin Jia, Howard J Edenberg, Brien P Riley, Danielle M Dick, Jill C Bettinger, Andrew G Davies, Michael S Grotewiel, Marc A Schuckit, Arpana Agrawal, John Kramer, John I Nurnberger Jr, Kenneth S Kendler…
    Citation: BMC Genomics 2012 13(Suppl 8):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  8. Since the initial annotation of microRNAs (miRNAs) in 2001, many studies have sought to identify additional miRNAs experimentally or computationally in various species. MiRNAs act with the Argonaut family of p...

    Authors: Linxia Wan, Jiandong Ding, Ting Jin, Jihong Guan and Shuigeng Zhou
    Citation: BMC Genomics 2012 13(Suppl 8):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  9. Hepatocellular carcinoma (HCC) is one of the most fatal cancers in the world, and metastasis is a significant cause to the high mortality in patients with HCC. However, the molecular mechanism behind HCC metas...

    Authors: Lingyao Zeng, Jian Yu, Tao Huang, Huliang Jia, Qiongzhu Dong, Fei He, Weilan Yuan, Lunxiu Qin, Yixue Li and Lu Xie
    Citation: BMC Genomics 2012 13(Suppl 8):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  10. MicroRNAs (miRNAs) are 19-25 nucleotides non-coding RNAs known to have important post-transcriptional regulatory functions. The computational target prediction algorithm is vital to effective experimental test...

    Authors: Dong Yue, Maozu Guo, Yidong Chen and Yufei Huang
    Citation: BMC Genomics 2012 13(Suppl 8):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  11. Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount o...

    Authors: Christina Schweikert, Stuart Brown, Zuojian Tang, Phillip R Smith and D Frank Hsu
    Citation: BMC Genomics 2012 13(Suppl 8):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  12. High-throughput RNA interference (RNAi) screens have been used to find genes that, when silenced, result in sensitivity to certain chemotherapy drugs. Researchers therefore can further identify drug-sensitive ...

    Authors: Fei Ye, Joshua A Bauer, Jennifer A Pietenpol and Yu Shyr
    Citation: BMC Genomics 2012 13(Suppl 8):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  13. Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype ...

    Authors: Hui Zhang, Shou-Zhi Wang, Zhi-Peng Wang, Yang Da, Ning Wang, Xiao-Xiang Hu, Yuan-Dan Zhang, Yu-Xiang Wang, Li Leng, Zhi-Quan Tang and Hui Li
    Citation: BMC Genomics 2012 13:704
    Content type: Research article Published on:

  15. The use of dispersants can be an effective way to deal with acute oil spills to limit environmental damage, however very little is known about whether chemically dispersed oil have the same toxic effect on mar...

    Authors: Pål A Olsvik, Kai K Lie, Trond Nordtug and Bjørn Henrik Hansen
    Citation: BMC Genomics 2012 13:702
    Content type: Research article Published on:

  16. Filamentous fungi such as Aspergillus niger are well known for their exceptionally high capacity for secretion of proteins, organic acids, and secondary metabolites and they are therefore used in biotechnology as...

    Authors: Min Jin Kwon, Thomas R Jørgensen, Benjamin M Nitsche, Mark Arentshorst, Joohae Park, Arthur FJ Ram and Vera Meyer
    Citation: BMC Genomics 2012 13:701
    Content type: Research article Published on:

  17. Tha Wang and Tham Phang coasts, though situated at similar oceanographic positions on Sichang island, Chonburi province, Thailand, are different in bay geography and amount of municipal disturbances. These aff...

    Authors: Naraporn Somboonna, Anunchai Assawamakin, Alisa Wilantho, Sithichoke Tangphatsornruang and Sissades Tongsima
    Citation: BMC Genomics 2012 13(Suppl 7):S29
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  18. State-of-the-art high-throughput sequencers, e.g., the Illumina HiSeq series, generate sequencing reads that are longer than 150 bp up to a total of 600 Gbp of data per run. The high-throughput sequencers gene...

    Authors: Yu-Jung Chang, Chien-Chih Chen, Chuen-Liang Chen and Jan-Ming Ho
    Citation: BMC Genomics 2012 13(Suppl 7):S28
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  19. High throughput experiments resulted in many genomic datasets and hundreds of candidate disease genes. To discover the real disease genes from a set of candidate genes, computational methods have been proposed...

    Authors: Yongjin Li and Jinyan Li
    Citation: BMC Genomics 2012 13(Suppl 7):S27
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  20. Microarray experiments produce expression measurements in genomic scale. A way to derive functional understanding of the data is to focus on functional sets of genes, such as pathways, instead of individual ge...

    Authors: Seungwoo Hwang
    Citation: BMC Genomics 2012 13(Suppl 7):S26
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  21. In biological systems, pathways coordinate or interact with one another to achieve a complex biological process. Studying how they influence each other is essential for understanding the intricacies of a biolo...

    Authors: Chia-Lang Hsu and Ueng-Cheng Yang
    Citation: BMC Genomics 2012 13(Suppl 7):S25
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  22. The overwhelming amount of network data in functional genomics is making its visualization cluttered with jumbling nodes and edges. Such cluttered network visualization, which is known as "hair-balls", is sign...

    Authors: Thanet Praneenararat, Toshihisa Takagi and Wataru Iwasaki
    Citation: BMC Genomics 2012 13(Suppl 7):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  23. Drug resistance in bacterial pathogens is an increasing problem, which stimulates research. However, our understanding of drug resistance mechanisms remains incomplete. Fortunately, the fast-growing number of ...

    Authors: Michal Wozniak, Jerzy Tiuryn and Limsoon Wong
    Citation: BMC Genomics 2012 13(Suppl 7):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  24. Molecular chaperones appear to have been evolved to facilitate protein folding in the cell through entrapment of folding intermediates on the interior of a large cavity formed between GroEL and its co-chaperon...

    Authors: Vipul Kumar, Ankita Punetha, Durai Sundar and Tapan K Chaudhuri
    Citation: BMC Genomics 2012 13(Suppl 7):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  25. To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often...

    Authors: Yi-Yuan Chiu, Chun-Yu Lin, Chih-Ta Lin, Kai-Cheng Hsu, Li-Zen Chang and Jinn-Moon Yang
    Citation: BMC Genomics 2012 13(Suppl 7):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  26. Leishmaniasis is caused by several species of leishmania protozoan and is one of the major vector-born diseases after malaria and sleeping sickness. Toxicity of available drugs and drug resistance development ...

    Authors: Abhinav Grover, Shashank Prakash Katiyar, Jeyaraman Jeyakanthan, Vikash Kumar Dubey and Durai Sundar
    Citation: BMC Genomics 2012 13(Suppl 7):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  27. A number of apicomplexan genomes have been sequenced successfully in recent years and this would help in understanding the biology of apicomplexan parasites. The members of the phylum Apicomplexa are important...

    Authors: Jamshaid Ali, Shashi Rekha Thummala and Akash Ranjan
    Citation: BMC Genomics 2012 13(Suppl 7):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  28. MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in breast cancer progression by downregulating gene expression. The detailed mechanisms and biolog...

    Authors: Hong-Tai Chang, Sung-Chou Li, Meng-Ru Ho, Hung-Wei Pan, Luo-Ping Ger, Ling-Yueh Hu, Shou-Yu Yu, Wen-Hsiung Li and Kuo-Wang Tsai
    Citation: BMC Genomics 2012 13(Suppl 7):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  29. Functional annotations are available only for a very small fraction of microRNAs (miRNAs) and very few miRNA target genes are experimentally validated. Therefore, functional analysis of miRNA clusters has typi...

    Authors: Su Yeon Lee, Kyung-Ah Sohn and Ju Han Kim
    Citation: BMC Genomics 2012 13(Suppl 7):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  30. MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of ...

    Authors: Somrak Numnark, Wuttichai Mhuantong, Supawadee Ingsriswang and Duangdao Wichadakul
    Citation: BMC Genomics 2012 13(Suppl 7):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  31. The microRNA-based gene-silencing machinery has been recognized as a promising approach to control viral replication and used for improving safety for the live attenuated virus vaccines. The effective host mic...

    Authors: Duangdao Wichadakul, Wuttichai Mhuantong, Anan Jongkaewwattana and Supawadee Ingsriswang
    Citation: BMC Genomics 2012 13(Suppl 7):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  32. MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate the target gene expression at post-transcriptional level. They are widely involved in biological processes, such as embryonic development, c...

    Authors: Zhen Yang, Dong Dong, Zhaolei Zhang, M James C Crabbe, Li Wang and Yang Zhong
    Citation: BMC Genomics 2012 13(Suppl 7):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  33. The sRNAs of bacterial pathogens are known to be involved in various cellular roles including environmental adaptation as well as regulation of virulence and pathogenicity. It is expected that sRNAs may also h...

    Authors: Jia-Shiun Khoo, Shiao-Fei Chai, Rahmah Mohamed, Sheila Nathan and Mohd Firdaus-Raih
    Citation: BMC Genomics 2012 13(Suppl 7):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  34. Researches have been conducted for the identification of differentially expressed genes (DEGs) by generating and mining of cDNA expressed sequence tags (ESTs) for more than a decade. Although the availability ...

    Authors: Timothy H Wu, Lichieh J Chu, Jian-Chiao Wang, Ting-Wen Chen, Yin-Jing Tien, Wen-Chang Lin and Wailap V Ng
    Citation: BMC Genomics 2012 13(Suppl 7):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  35. Multiple transcription factors (TFs) are involved in the generation of gene expression patterns, such as tissue-specific gene expression and pleiotropic immune responses. However, how combinations of TFs orche...

    Authors: Alexis Vandenbon, Yutaro Kumagai, Shizuo Akira and Daron M Standley
    Citation: BMC Genomics 2012 13(Suppl 7):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  36. Teladorsagia circumcincta (order Strongylida) is an economically important parasitic nematode of small ruminants (including sheep and goats) in temperate climatic regions of the world. Improved insights into the ...

    Authors: Ranjeeta Menon, Robin B Gasser, Makedonka Mitreva and Shoba Ranganathan
    Citation: BMC Genomics 2012 13(Suppl 7):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  37. Recent developments in high-throughput sequencing (HTS) technologies have made it feasible to sequence the complete transcriptomes of non-model organisms or metatranscriptomes from environmental samples. The c...

    Authors: Ting-Wen Chen, Ruei-Chi Richie Gan, Timothy H Wu, Po-Jung Huang, Cheng-Yang Lee, Yi-Ywan M Chen, Che-Chun Chen and Petrus Tang
    Citation: BMC Genomics 2012 13(Suppl 7):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  38. Helminths are important socio-economic organisms, responsible for causing major parasitic infections in humans, other animals and plants. These infections impose a significant public health and economic burden...

    Authors: Gagan Garg and Shoba Ranganathan
    Citation: BMC Genomics 2012 13(Suppl 7):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  39. Dengue is the world's most common mosquito-borne viral disease. Poor proofreading by RNA polymerase during its replication results in the accumulation of mutations in its genome. This leads to a diversity of g...

    Authors: Kwanrutai Chin-inmanu, Aroonroong Suttitheptumrong, Duangjai Sangsrakru, Sithichoke Tangphatsornruang, Somvong Tragoonrung, Prida Malasit, Sumalee Tungpradabkul and Prapat Suriyaphol
    Citation: BMC Genomics 2012 13(Suppl 7):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  40. The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates...

    Authors: Pimlapas Leekitcharoenphon, Rolf S Kaas, Martin Christen Frølund Thomsen, Carsten Friis, Simon Rasmussen and Frank M Aarestrup
    Citation: BMC Genomics 2012 13(Suppl 7):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  41. Mitochondrial dysfunction is associated with various aging diseases. The copy number of mtDNA in human cells may therefore be a potential biomarker for diagnostics of aging. Here we propose a new computational...

    Authors: Hsueh-Ting Chu, William WL Hsiao, Theresa TH Tsao, Ching-Mao Chang, Yen-Wenn Liu, Chen-Chieh Fan, Han Lin, Hen-Hong Chang, Tze-Jung Yeh, Jen-Chih Chen, Dun-Ming Huang, Chaur-Chin Chen and Cheng-Yan Kao
    Citation: BMC Genomics 2012 13(Suppl 7):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  42. The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua Christian Hospital, Taiwan. The KT strain of M...

    Authors: Yu-Tin Chen, Hwei-Ling Peng, Wei-Chung Shia, Fang-Rong Hsu, Chuian-Fu Ken, Yu-Ming Tsao, Chang-Hua Chen, Chun-Eng Liu, Ming-Feng Hsieh, Huang-Chi Chen, Chuan-Yi Tang and Tien-Hsiung Ku
    Citation: BMC Genomics 2012 13(Suppl 7):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  43. The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or...

    Authors: Dan B Jensen, Tammi C Vesth, Peter F Hallin, Anders G Pedersen and David W Ussery
    Citation: BMC Genomics 2012 13(Suppl 7):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  44. Genome-wide association studies (GWAS) do not provide a full account of the heritability of genetic diseases since gene-gene interactions, also known as epistasis are not considered in single locus GWAS. To ad...

    Authors: Jittima Piriyapongsa, Chumpol Ngamphiw, Apichart Intarapanich, Supasak Kulawonganunchai, Anunchai Assawamakin, Chaiwat Bootchai, Philip J Shaw and Sissades Tongsima
    Citation: BMC Genomics 2012 13(Suppl 7):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  45. The theme of the 2012 International Conference on Bioinformatics (InCoB) in Bangkok, Thailand was "From Biological Data to Knowledge to Technological Breakthroughs." Besides providing a forum for life scientis...

    Authors: Shoba Ranganathan, Sissades Tongsima, Jonathan Chan, Tin Wee Tan and Christian Schönbach
    Citation: BMC Genomics 2012 13(Suppl 7):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  46. Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mech...

    Authors: Guoqin Liu, Wanshun Li, Penghua Zheng, Tong Xu, Lijuan Chen, Dongfeng Liu, Sayed Hussain and Yuanwen Teng
    Citation: BMC Genomics 2012 13:700
    Content type: Research article Published on:

  47. One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method f...

    Authors: Hideto Takami, Takeaki Taniguchi, Yuki Moriya, Tomomi Kuwahara, Minoru Kanehisa and Susumu Goto
    Citation: BMC Genomics 2012 13:699
    Content type: Methodology article Published on:

  48. The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fum...

    Authors: Vinita Joardar, Natalie F Abrams, Jessica Hostetler, Paul J Paukstelis, Suchitra Pakala, Suman B Pakala, Nikhat Zafar, Olukemi O Abolude, Gary Payne, Alex Andrianopoulos, David W Denning and William C Nierman
    Citation: BMC Genomics 2012 13:698
    Content type: Research article Published on:

  49. Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway, leading to expressio...

    Authors: Ian Carter-O’Connell, Michael T Peel, Dennis D Wykoff and Erin K O’Shea
    Citation: BMC Genomics 2012 13:697
    Content type: Research article Published on:

  50. Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracel...

    Authors: Musa A Hassan, Mariane B Melo, Brian Haas, Kirk D C Jensen and Jeroen P J Saeij
    Citation: BMC Genomics 2012 13:696
    Content type: Research article Published on:

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