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  1. Caenorhabditis elegans provides a genetically tractable model organism to investigate the network of genes involved in fat metabolism and how regulation is perturbed to produce the complex phenotype of obesity. C...

    Authors: Cecilia Castro, Funda Sar, W Robert Shaw, Masanori Mishima, Eric A Miska and Julian L Griffin
    Citation: BMC Genomics 2012 13:36
    Content type: Research article Published on:

  2. With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data.

    Authors: Michael Baitaluk, Sergey Kozhenkov, Yulia Dubinina and Julia Ponomarenko
    Citation: BMC Genomics 2012 13:35
    Content type: Database Published on:

  3. High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs) in genetic studie...

    Authors: John P Didion, Hyuna Yang, Keith Sheppard, Chen-Ping Fu, Leonard McMillan, Fernando Pardo-Manuel de Villena and Gary A Churchill
    Citation: BMC Genomics 2012 13:34
    Content type: Methodology article Published on:

  4. During embryogenesis the liver is derived from endodermal cells lining the digestive tract. These endodermal progenitor cells contribute to forming the parenchyma of a number of organs including the liver and ...

    Authors: Janice S Lee, William O Ward, Geremy Knapp, Hongzu Ren, Beena Vallanat, Barbara Abbott, Karen Ho, Seth J Karp and J Christopher Corton
    Citation: BMC Genomics 2012 13:33
    Content type: Research article Published on:

  5. Next-Generation Sequencing (NGS) is increasingly being used as a molecular epidemiologic tool for discerning ancestry and traceback of the most complicated, difficult to resolve bacterial pathogens. Making a l...

    Authors: Marc W Allard, Yan Luo, Errol Strain, Cong Li, Christine E Keys, Insook Son, Robert Stones, Steven M Musser and Eric W Brown
    Citation: BMC Genomics 2012 13:32
    Content type: Research article Published on:

  6. The feline genome is valuable to the veterinary and model organism genomics communities because the cat is an obligate carnivore and a model for endangered felids. The initial public release of the Felis catus...

    Authors: Kristopher J Irizarry, Sukhaswami B Malladi, Xiangming Gao, Katherine Mitsouras, Lynda Melendez, Patricia A Burris, Jeffrey A Brockman and Samer W Al-Murrani
    Citation: BMC Genomics 2012 13:31
    Content type: Research article Published on:

  7. The traditional Japanese medicine juzentaihoto (JTX) is a pharmaceutical grade multi-herbal medicine widely used for the prevention of cancer metastasis and infection in immuno-compromized patients in Japan. T...

    Authors: Kaori Munakata, Kiyoe Takashima, Mitsue Nishiyama, Naoko Asano, Akihito Mase, Kyoji Hioki, Yasuyuki Ohnishi, Masahiro Yamamoto and Kenji Watanabe
    Citation: BMC Genomics 2012 13:30
    Content type: Research article Published on:

  8. African trypanosomes belong to a eukaryotic lineage which displays many unusual genetic features. The mechanisms of chromosome segregation in these diploid protozoan parasites are poorly understood. Centromere...

    Authors: Maria C Echeverry, Christopher Bot, Samson O Obado, Martin C Taylor and John M Kelly
    Citation: BMC Genomics 2012 13:29
    Content type: Research article Published on:

  9. Transcriptome analysis is of great interest in clinical research, where significant differences between individuals can be translated into biomarkers of disease. Although next generation sequencing provides ro...

    Authors: Anastasios Mastrokolias, Johan T den Dunnen, GertJan B van Ommen, Peter AC 't Hoen and Willeke MC van Roon-Mom
    Citation: BMC Genomics 2012 13:28
    Content type: Research article Published on:

  10. DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variabilit...

    Authors: Kelly J Vining, Kyle R Pomraning, Larry J Wilhelm, Henry D Priest, Matteo Pellegrini, Todd C Mockler, Michael Freitag and Steven H Strauss
    Citation: BMC Genomics 2012 13:27
    Content type: Research article Published on:

  12. Invasion of intestinal epithelial cells by Salmonella enterica serovar Typhimurium (S. Typhimurium) requires expression of the extracellular virulence gene expression programme (STEX), activation of which is depe...

    Authors: Vinoy K Ramachandran, Neil Shearer, Jobin J Jacob, Cynthia M Sharma and Arthur Thompson
    Citation: BMC Genomics 2012 13:25
    Content type: Research article Published on:

  13. The success of marker assisted selection depends on the amount of linkage disequilibrium (LD) across the genome. To implement marker assisted selection in the swine breeding industry, information about extent ...

    Authors: Yvonne M Badke, Ronald O Bates, Catherine W Ernst, Clint Schwab and Juan P Steibel
    Citation: BMC Genomics 2012 13:24
    Content type: Research article Published on:

  14. Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics,...

    Authors: Trupti Joshi, Kapil Patil, Michael R Fitzpatrick, Levi D Franklin, Qiuming Yao, Jeffrey R Cook, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry T Nguyen and Dong Xu
    Citation: BMC Genomics 2012 13(Suppl 1):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  15. Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization f...

    Authors: Guoqing Lei, Yong Dou, Wen Wan, Fei Xia, Rongchun Li, Meng Ma and Dan Zou
    Citation: BMC Genomics 2012 13(Suppl 1):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  16. MicroRNAs (miRNAs) are small non-protein-coding RNAs. miRNA genes need several biogenesis steps to form function miRNAs. However, the precise mechanism and biology involved in the mature miRNA molecules are no...

    Authors: Sung-Chou Li, Yu-Lun Liao, Meng-Ru Ho, Kuo-Wang Tsai, Chun-Hung Lai and Wen-chang Lin
    Citation: BMC Genomics 2012 13(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  17. Bayesian networks (BNs) have been widely used to estimate gene regulatory networks. Many BN methods have been developed to estimate networks from microarray data. However, two serious problems reduce the effec...

    Authors: Yukito Watanabe, Shigeto Seno, Yoichi Takenaka and Hideo Matsuda
    Citation: BMC Genomics 2012 13(Suppl 1):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  18. Head-to-head (h2h) genes are prone to have association in expression and in functionality and have been shown conserved in evolution. Currently there are many studies on such h2h gene pairs. We found that the ...

    Authors: Darby Tien-Hao Chang, Chi-Yeh Wu and Chen-Yu Fan
    Citation: BMC Genomics 2012 13(Suppl 1):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  19. Gene orthology has been well studied in the evolutionary area and is thought to be an important implication to functional genome annotations. As the accumulation of transcriptomic data, alternative splicing is...

    Authors: Gloria C-L Fu and Wen-chang Lin
    Citation: BMC Genomics 2012 13(Suppl 1):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  20. Plant n on-s pecific l ipid t ransfer p roteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, partici...

    Authors: Nai-Jyuan Wang, Chi-Ching Lee, Chao-Sheng Cheng, Wei-Cheng Lo, Ya-Fen Yang, Ming-Nan Chen and Ping-Chiang Lyu
    Citation: BMC Genomics 2012 13(Suppl 1):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  21. Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion of multi-gene DNA segments is controversi...

    Authors: David Sankoff, Chunfang Zheng and Baoyong Wang
    Citation: BMC Genomics 2012 13(Suppl 1):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  23. In the analysis of effects by cell treatment such as drug dosing, identifying changes on gene network structures between normal and treated cells is a key task. A possible way for identifying the changes is to...

    Authors: Kaname Kojima, Seiya Imoto, Rui Yamaguchi, André Fujita, Mai Yamauchi, Noriko Gotoh and Satoru Miyano
    Citation: BMC Genomics 2012 13(Suppl 1):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  24. We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-...

    Authors: Narges Sharif Razavian, Hetunandan Kamisetty and Christopher J Langmead
    Citation: BMC Genomics 2012 13(Suppl 1):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  25. Neglected tropical diseases, especially those caused by helminths, constitute some of the most common infections of the world's poorest people. Development of techniques for automated, high-throughput drug scr...

    Authors: Hyokyeong Lee, Asher Moody-Davis, Utsab Saha, Brian M Suzuki, Daniel Asarnow, Steven Chen, Michelle Arkin, Conor R Caffrey and Rahul Singh
    Citation: BMC Genomics 2012 13(Suppl 1):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  26. Sequence features in promoter regions are involved in regulating gene transcription initiation. Although numerous computational methods have been developed for predicting transcriptional start sites (TSSs) or ...

    Authors: Tzong-Yi Lee, Wen-Chi Chang, Justin Bo-Kai Hsu, Tzu-Hao Chang and Dray-Ming Shien
    Citation: BMC Genomics 2012 13(Suppl 1):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  27. Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that...

    Authors: Alena Myšičková and Martin Vingron
    Citation: BMC Genomics 2012 13(Suppl 1):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  28. Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is increasingly being applied to study genome-wide binding sites of transcription factors. There is an increasing interest in...

    Authors: Hatice Ulku Osmanbeyoglu, Ryan J Hartmaier, Steffi Oesterreich and Xinghua Lu
    Citation: BMC Genomics 2012 13(Suppl 1):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  30. Small interfering and non-coding RNAs regulate gene expression across all kingdoms of life. MicroRNAs constitute an important group of metazoan small RNAs regulating development but also disease. Accordingly, ...

    Authors: Soroush Sharbati, Jutta Sharbati, Lena Hoeke, Marc Bohmer and Ralf Einspanier
    Citation: BMC Genomics 2012 13:23
    Content type: Research article Published on:

  31. Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole). The steroid andros...

    Authors: Vivi R Gregersen, Lene N Conley, Kirsten K Sørensen, Bernt Guldbrandtsen, Ingela H Velander and Christian Bendixen
    Citation: BMC Genomics 2012 13:22
    Content type: Research article Published on:

  32. Eimeria tenella is an apicomplexan parasite that causes coccidiosis in the domestic fowl. Infection with this parasite is diagnosed frequently in intensively reared poultry and its control is usually accorded a h...

    Authors: Nadzirah Amiruddin, Xin-Wei Lee, Damer P Blake, Yutaka Suzuki, Yea-Ling Tay, Lik-Sin Lim, Fiona M Tomley, Junichi Watanabe, Chihiro Sugimoto and Kiew-Lian Wan
    Citation: BMC Genomics 2012 13:21
    Content type: Research article Published on:

  33. Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have ma...

    Authors: Binod B Sahu, Rishi Sumit, Subodh K Srivastava and Madan K Bhattacharyya
    Citation: BMC Genomics 2012 13:20
    Content type: Methodology article Published on:

  34. Chinese bayberry (Myrica rubra Sieb. and Zucc.) is an important subtropical fruit crop and an ideal species for fruit quality research due to the rapid and substantial changes that occur during development and ri...

    Authors: Chao Feng, Ming Chen, Chang-jie Xu, Lin Bai, Xue-ren Yin, Xian Li, Andrew C Allan, Ian B Ferguson and Kun-song Chen
    Citation: BMC Genomics 2012 13:19
    Content type: Research article Published on:

  35. Sweet cherry (Prunus avium L.), a non-model crop with narrow genetic diversity, is an important member of sub-family Amygdoloideae within Rosaceae. Compared to other important members like peach and apple, sweet ...

    Authors: Tyson Koepke, Scott Schaeffer, Vandhana Krishnan, Derick Jiwan, Artemus Harper, Matthew Whiting, Nnadozie Oraguzie and Amit Dhingra
    Citation: BMC Genomics 2012 13:18
    Content type: Methodology article Published on:

  36. Udder infections with environmental pathogens like Escherichia coli are a serious problem for the dairy industry. Reduction of incidence and severity of mastitis is desirable and mild priming of the immune system...

    Authors: Juliane Günther, Wolfram Petzl, Holm Zerbe, Hans-Joachim Schuberth, Dirk Koczan, Leopold Goetze and Hans-Martin Seyfert
    Citation: BMC Genomics 2012 13:17
    Content type: Research article Published on:

  37. The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within thi...

    Authors: Michael P Mullen, Christopher J Creevey, Donagh P Berry, Matt S McCabe, David A Magee, Dawn J Howard, Aideen P Killeen, Stephen D Park, Paul A McGettigan, Matt C Lucy, David E MacHugh and Sinead M Waters
    Citation: BMC Genomics 2012 13:16
    Content type: Research article Published on:

  38. Digitalis purpurea is an important ornamental and medicinal plant. There is considerable interest in exploring its transcriptome.

    Authors: Bin Wu, Ying Li, Haixia Yan, Yimian Ma, Hongmei Luo, Lichai Yuan, Shilin Chen and Shanfa Lu
    Citation: BMC Genomics 2012 13:15
    Content type: Research article Published on:

  40. With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment bi...

    Authors: Patrick Ollitrault, Javier Terol, Andres Garcia-Lor, Aurélie Bérard, Aurélie Chauveau, Yann Froelicher, Caroline Belzile, Raphaël Morillon, Luis Navarro, Dominique Brunel and Manuel Talon
    Citation: BMC Genomics 2012 13:13
    Content type: Research article Published on:

  42. MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Deve...

    Authors: Teshome T Bizuayehu, Carlos FC Lanes, Tomasz Furmanek, Bård O Karlsen, Jorge MO Fernandes, Steinar D Johansen and Igor Babiak
    Citation: BMC Genomics 2012 13:11
    Content type: Research article Published on:

  43. The transcriptome of the fruit pulp of the sweet orange variety Anliu (WT) and that of its red fleshed mutant Hong Anliu (MT) were compared to understand the dynamics and differential expression of genes expre...

    Authors: Keqin Yu, Qiang Xu, Xinlei Da, Fei Guo, Yuduan Ding and Xiuxin Deng
    Citation: BMC Genomics 2012 13:10
    Content type: Research article Published on:

  44. Desirable apple varieties are clonally propagated by grafting vegetative scions onto rootstocks. Rootstocks influence many phenotypic traits of the scion, including resistance to pathogens such as Erwinia amylovo...

    Authors: Philip J Jensen, Noemi Halbrendt, Gennaro Fazio, Izabela Makalowska, Naomi Altman, Craig Praul, Siela N Maximova, Henry K Ngugi, Robert M Crassweller, James W Travis and Timothy W McNellis
    Citation: BMC Genomics 2012 13:9
    Content type: Research article Published on:

  45. Identification of protein-protein interactions is a fundamental aspect of understanding protein function. A commonly used method for identifying protein interactions is the yeast two-hybrid system.

    Authors: Jennifer D Lewis, Janet Wan, Rachel Ford, Yunchen Gong, Pauline Fung, Hardeep Nahal, Pauline W Wang, Darrell Desveaux and David S Guttman
    Citation: BMC Genomics 2012 13:8
    Content type: Research article Published on:

  46. MicroRNAs (miRNAs), a ubiquitous class of short RNAs, play vital roles in physiological and biochemical processes in plants by mediating gene silencing at post-transcriptional (PTGS) level. Tomato is a model s...

    Authors: Jinhua Zuo, Benzhong Zhu, Daqi Fu, Yi Zhu, Yuanzheng Ma, Lihong Chi, Zheng Ju, Yunxiang Wang, Baiqiang Zhai and Yunbo Luo
    Citation: BMC Genomics 2012 13:7
    Content type: Research article Published on:

  47. Bed bugs (Cimex lectularius) are hematophagous nocturnal parasites of humans that have attained high impact status due to their worldwide resurgence. The sudden and rampant resurgence of C. lectularius has been a...

    Authors: Praveen Mamidala, Asela J Wijeratne, Saranga Wijeratne, Karl Kornacker, Babu Sudhamalla, Loren J Rivera-Vega, Andrew Hoelmer, Tea Meulia, Susan C Jones and Omprakash Mittapalli
    Citation: BMC Genomics 2012 13:6
    Content type: Research article Published on:

  48. The data from high throughput genomics technologies provide unique opportunities for studies of complex biological systems, but also pose many new challenges. The shift to the genome scale in evolutionary biol...

    Authors: Francisco Prosdocimi, Benjamin Linard, Pierre Pontarotti, Olivier Poch and Julie D Thompson
    Citation: BMC Genomics 2012 13:5
    Content type: Research article Published on:

  49. MicroRNAs (miRNAs) play key roles in regulating post-transcriptional gene expression and are essential for development in the free-living nematode Caenorhabditis elegans and in higher organisms. Whether microRNAs...

    Authors: Alan D Winter, William Weir, Martin Hunt, Matthew Berriman, John S Gilleard, Eileen Devaney and Collette Britton
    Citation: BMC Genomics 2012 13:4
    Content type: Research article Published on:

  50. Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In s...

    Authors: Samuel O Oyola, Thomas D Otto, Yong Gu, Gareth Maslen, Magnus Manske, Susana Campino, Daniel J Turner, Bronwyn MacInnis, Dominic P Kwiatkowski, Harold P Swerdlow and Michael A Quail
    Citation: BMC Genomics 2012 13:1
    Content type: Methodology article Published on:

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BMC Genomics

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