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  1. Understanding hepatic zonation is important both for liver physiology and pathology. There is currently no effective systemic chemotherapy for human hepatocellular carcinoma (HCC) and its pathogenesis is of sp...

    Authors: Shu Cheng, Jean-Matthieu Prot, Eric Leclerc and Frédéric Y Bois
    Citation: BMC Genomics 2012 13:54
  2. Chromosomal inversions have been pervasive during the evolution of the genus Drosophila, but there is significant variation between lineages in the rate of rearrangement fixation. D. mojavensis, an ecological spe...

    Authors: Yolanda Guillén and Alfredo Ruiz
    Citation: BMC Genomics 2012 13:53
  3. Many biological systems respond to the presence or absence of gravity. Since experiments performed in space are expensive and can only be undertaken infrequently, Earth-based simulation techniques are used to ...

    Authors: Raul Herranz, Oliver J Larkin, Camelia E Dijkstra, Richard JA Hill, Paul Anthony, Michael R Davey, Laurence Eaves, Jack JWA van Loon, F Javier Medina and Roberto Marco
    Citation: BMC Genomics 2012 13:52
  4. The liver X receptors (LXRs) are oxysterol sensing nuclear receptors with multiple effects on metabolism and immune cells. However, the complete genome-wide cistrome of LXR in cells of human origin has not yet...

    Authors: Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynänen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R Steffensen and Carsten Carlberg
    Citation: BMC Genomics 2012 13:50
  5. Hitchhiking mapping and association studies are two popular approaches to map genotypes to phenotypes. In this study we combine both approaches to complement their specific strengths and weaknesses, resulting ...

    Authors: Hermann Schwarzenbacher, Marlies Dolezal, Krzysztof Flisikowski, Franz Seefried, Christine Wurmser, Christian Schlötterer and Ruedi Fries
    Citation: BMC Genomics 2012 13:48
  6. Sequencing projects using a clone-by-clone approach require the availability of a robust physical map. The SNaPshot technology, based on pair-wise comparisons of restriction fragments sizes, has been used rece...

    Authors: Romain Philippe, Frédéric Choulet, Etienne Paux, Jan van Oeveren, Jifeng Tang, Alexander HJ Wittenberg, Antoine Janssen, Michiel JT van Eijk, Keith Stormo, Adriana Alberti, Patrick Wincker, Eduard Akhunov, Edwin van der Vossen and Catherine Feuillet
    Citation: BMC Genomics 2012 13:47
  7. Okadaic acid (OA), a toxin produced by several dinoflagellate species is responsible for frequent food poisonings associated to shellfish consumption. Although several studies have documented the OA effects on...

    Authors: Vanessa Valdiglesias, Juan Fernández-Tajes, Eduardo Pásaro, Josefina Méndez and Blanca Laffon
    Citation: BMC Genomics 2012 13:46
  8. Cow milk is a complex bioactive fluid consumed by humans beyond infancy. Even though the chemical and physical properties of cow milk are well characterized, very limited research has been done on characterizi...

    Authors: Saumya Wickramasinghe, Gonzalo Rincon, Alma Islas-Trejo and Juan F Medrano
    Citation: BMC Genomics 2012 13:45
  9. Single nucleotide polymorphisms (SNPs) can lead to the susceptibility and onset of diseases through their effects on gene expression at the posttranscriptional level. Recent findings indicate that SNPs could c...

    Authors: Andrew E Bruno, Li Li, James L Kalabus, Yuzhuo Pan, Aiming Yu and Zihua Hu
    Citation: BMC Genomics 2012 13:44
  10. The multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcod...

    Authors: Jing Tu, Qinyu Ge, Shengqin Wang, Lei Wang, Beili Sun, Qi Yang, Yunfei Bai and Zuhong Lu
    Citation: BMC Genomics 2012 13:43
  11. The combination of chromatin immunoprecipitation with two-channel microarray technology enables genome-wide mapping of binding sites of DNA-interacting proteins (ChIP-on-chip) or sites with methylated CpG di-n...

    Authors: Michiel E Adriaens, Magali Jaillard, Lars MT Eijssen, Claus-Dieter Mayer and Chris TA Evelo
    Citation: BMC Genomics 2012 13:42
  12. Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the...

    Authors: Domenico De Paola, Federica Cattonaro, Domenico Pignone and Gabriella Sonnante
    Citation: BMC Genomics 2012 13:41
  13. Ribonuclease 8 is a member of the RNase A family of secretory ribonucleases; orthologs of this gene have been found only in primate genomes. RNase 8 is a divergent paralog of RNase 7, which is lysine-enriched,...

    Authors: Calvin C Chan, Jennifer M Moser, Kimberly D Dyer, Caroline M Percopo and Helene F Rosenberg
    Citation: BMC Genomics 2012 13:40
  14. Since the first genome of a halophilic archaeon was sequenced in 2000, biologists have been advancing the understanding of genomic characteristics that allow for survival in the harsh natural environments of t...

    Authors: Melinda D Capes, Priya DasSarma and Shiladitya DasSarma
    Citation: BMC Genomics 2012 13:39
  15. Staphylococcus belongs to the Gram-positive low G + C content group of the Firmicutes division of bacteria. Staphylococcus aureus is an important human and veterinary pathogen that causes a broad spectrum of dise...

    Authors: Haruo Suzuki, Tristan Lefébure, Paulina Pavinski Bitar and Michael J Stanhope
    Citation: BMC Genomics 2012 13:38
  16. Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in t...

    Authors: Geir Å Hansen, Rafi Ahmad, Erik Hjerde, Christopher G Fenton, Nils-Peder Willassen and Peik Haugen
    Citation: BMC Genomics 2012 13:37
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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

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

  30. 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

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

  31. 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

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

  32. 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

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

  33. 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

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

  34. 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

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

  35. 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

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

  36. 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

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

  37. 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

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

  38. 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

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

  39. 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

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

  40. 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

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

  41. 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

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

  42. 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

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

  43. 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
  44. 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
  45. 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
  46. 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

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