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  1. The most important disease of dairy cattle is mastitis, caused by the infection of the mammary gland by various micro-organisms. Although the transcriptional response of bovine mammary gland cells to in vitro inf...

    Authors: Kirsty Jensen, Juliane Günther, Richard Talbot, Wolfram Petzl, Holm Zerbe, Hans-Joachim Schuberth, Hans-Martin Seyfert and Elizabeth J Glass
    Citation: BMC Genomics 2013 14:36
    Content type: Research article Published on:

  2. MicroRNAs (miRNAs) regulate gene expression via mRNA cleavage or translation inhibition. In spite of barley being a cereal of great economic importance, very little data is available concerning its miRNA bioge...

    Authors: Katarzyna Kruszka, Andrzej Pacak, Aleksandra Swida-Barteczka, Agnieszka K Stefaniak, Elzbieta Kaja, Izabela Sierocka, Wojciech Karlowski, Artur Jarmolowski and Zofia Szweykowska-Kulinska
    Citation: BMC Genomics 2013 14:34
    Content type: Research article Published on:

  3. Actinobacteria form a major bacterial phylum that includes numerous human pathogens. Actinobacteria are primary contributors to carbon cycling and also represent a primary source of industrial high value produ...

    Authors: Esteban Marcellin, Tim R Mercer, Cuauhtemoc Licona-Cassani, Robin W Palfreyman, Marcel E Dinger, Jennifer A Steen, John S Mattick and Lars K Nielsen
    Citation: BMC Genomics 2013 14:15
    Content type: Research article Published on:

  4. The annotation of many genomes is limited, with a large proportion of identified genes lacking functional assignments. The construction of gene co-expression networks is a powerful approach that presents a way...

    Authors: Dragana Stanley, Nathan S Watson-Haigh, Christopher JE Cowled and Robert J Moore
    Citation: BMC Genomics 2013 14:13
    Content type: Research article Published on:

  5. Reduced representation bisulfite sequencing (RRBS) was developed to measure DNA methylation of high-CG regions at single base-pair resolution, and has been widely used because of its minimal DNA requirements a...

    Authors: Junwen Wang, Yudong Xia, Lili Li, Desheng Gong, Yu Yao, Huijuan Luo, Hanlin Lu, Na Yi, Honglong Wu, Xiuqing Zhang, Qian Tao and Fei Gao
    Citation: BMC Genomics 2013 14:11
    Content type: Methodology article Published on:

  6. Subtelomeric multigene families of malaria parasites encode virulent determinants. The published genome sequence of Plasmodium vivax revealed the largest subtelomeric multigene family of human malaria parasites, ...

    Authors: Francisco Javier Lopez, Maria Bernabeu, Carmen Fernandez-Becerra and Hernando A del Portillo
    Citation: BMC Genomics 2013 14:8
    Content type: Research article Published on:

  7. The ATP-binding cassette (ABC) transporters belong to a large superfamily of proteins that have important physiological functions in all living organisms. Most are integral membrane proteins that transport a b...

    Authors: Gunnar Broehan, Tobias Kroeger, Marcé Lorenzen and Hans Merzendorfer
    Citation: BMC Genomics 2013 14:6
    Content type: Research article Published on:

  8. The methylotrophic yeast Pichia pastoris is widely used as a bioengineering platform for producing industrial and biopharmaceutical proteins, studying protein expression and secretion mechanisms, and analyzing me...

    Authors: Shuli Liang, Bin Wang, Li Pan, Yanrui Ye, Minghui He, Shuangyan Han, Suiping Zheng, Xiaoning Wang and Ying Lin
    Citation: BMC Genomics 2012 13:738
    Content type: Research article Published on:

  9. DNA microarrays are used both for research and for diagnostics. In research, Affymetrix arrays are commonly used for genome wide association studies, resequencing, and for gene expression analysis. These array...

    Authors: Yasminka A Jakubek and David J Cutler
    Citation: BMC Genomics 2012 13:737
    Content type: Methodology article Published on:

  10. Trypanosoma cruzi, the causal agent of Chagas Disease, affects more than 16 million people in Latin America. The clinical outcome of the disease results from a complex interplay between environmental factors and ...

    Authors: Alejandro A Ackermann, Leonardo G Panunzi, Raul O Cosentino, Daniel O Sánchez and Fernán Agüero
    Citation: BMC Genomics 2012 13:736
    Content type: Research article Published on:

  11. Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are α-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for applicat...

    Authors: Ernesto Ormeño-Orrillo, Pâmela Menna, Luiz Gonzaga P Almeida, Francisco Javier Ollero, Marisa Fabiana Nicolás, Elisete Pains Rodrigues, Andre Shigueyoshi Nakatani, Jesiane Stefânia Silva Batista, Ligia Maria Oliveira Chueire, Rangel Celso Souza, Ana Tereza Ribeiro Vasconcelos, Manuel Megías, Mariangela Hungria and Esperanza Martínez-Romero
    Citation: BMC Genomics 2012 13:735
    Content type: Research article Published on:

  13. Copy number variation (CNV) is a major source of structural variants and has been commonly identified in mammalian genome. It is associated with gene expression and may present a major genetic component of phe...

    Authors: Congying Chen, Ruimin Qiao, Rongxing Wei, Yuanmei Guo, Huashui Ai, Junwu Ma, Jun Ren and Lusheng Huang
    Citation: BMC Genomics 2012 13:733
    Content type: Research article Published on:

  14. A major goal of the field of systems biology is to translate genome-wide profiling data (e.g., mRNAs, miRNAs) into interpretable functional networks. However, employing a systems biology approach to better und...

    Authors: Seungyoon Nam, Xinghua Long, ChangHyuk Kwon, Sun Kim and Kenneth P Nephew
    Citation: BMC Genomics 2012 13:732
    Content type: Research article Published on:

  15. MicroRNAs (miRNAs) have been implicated in the regulation of milk protein synthesis and development of the mammary gland (MG). However, the specific functions of miRNAs in these regulations are not clear. Ther...

    Authors: Zhen Li, Hongyun Liu, Xiaolu Jin, Lijan Lo and Jianxin Liu
    Citation: BMC Genomics 2012 13:731
    Content type: Research article Published on:

  16. Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to stu...

    Authors: Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun and Xuegong Zhang
    Citation: BMC Genomics 2012 13:730
    Content type: Research article Published on:

  17. MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by targeting mRNAs for translation repression or mRNA degradation. Although many miRNAs have been discovered and studied in...

    Authors: Zhen Wang, Kan He, Qishan Wang, Yumei Yang and Yuchun Pan
    Citation: BMC Genomics 2012 13:729
    Content type: Research article Published on:

  19. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes. The zebra finch (Taeniopygia guttata), an oscine songbird with characteris...

    Authors: Guan-Zheng Luo, Markus Hafner, Zhimin Shi, Miguel Brown, Gui-Hai Feng, Thomas Tuschl, Xiu-Jie Wang and XiaoChing Li
    Citation: BMC Genomics 2012 13:727
    Content type: Research article Published on:

  20. Next Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP) discovery in Acacia auriculiformis and Acacia mangium. Like other non-m...

    Authors: Melissa ML Wong, Charles H Cannon and Ratnam Wickneswari
    Citation: BMC Genomics 2012 13:726
    Content type: Research article Published on:

  21. Recent studies have shown that copy number variation (CNV) in mammalian genomes contributes to phenotypic diversity, including health and disease status. In domestic pigs, CNV has been catalogued by several re...

    Authors: Yan Li, Shuqi Mei, Xuying Zhang, Xianwen Peng, Gang Liu, Hu Tao, Huayu Wu, Siwen Jiang, Yuanzhu Xiong and Fenge Li
    Citation: BMC Genomics 2012 13:725
    Content type: Research article Published on:

  22. Salmonids are popular sport fishes, and as such have been subjected to widespread stocking throughout western North America. Historically, stocking was done with little regard for genetic variation among popul...

    Authors: Derek D Houston, David B Elzinga, Peter J Maughan, Scott M Smith, John SK Kauwe, R Paul Evans, Ryan B Stinger and Dennis K Shiozawa
    Citation: BMC Genomics 2012 13:724
    Content type: Methodology article Published on:

  23. Thermacetogenium phaeum is a thermophilic strictly anaerobic bacterium oxidizing acetate to CO2 in syntrophic association with a methanogenic partner. It can also grow in pure culture, e.g., by fermentation of me...

    Authors: Dirk Oehler, Anja Poehlein, Andreas Leimbach, Nicolai Müller, Rolf Daniel, Gerhard Gottschalk and Bernhard Schink
    Citation: BMC Genomics 2012 13:723
    Content type: Research article Published on:

  24. Tandemly arranged nuclear ribosomal DNA (rDNA), encoding 18S, 5.8S and 26S ribosomal RNA (rRNA), exhibit concerted evolution, a pattern thought to result from the homogenisation of rDNA arrays. However rDNA ho...

    Authors: Roman Matyášek, Simon Renny-Byfield, Jaroslav Fulneček, Jiří Macas, Marie-Angele Grandbastien, Richard Nichols, Andrew Leitch and Aleš Kovařík
    Citation: BMC Genomics 2012 13:722
    Content type: Research article Published on:

  25. Cis- natural antisense transcripts (cis- NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including micro...

    Authors: Tingting Lu, Chuanrang Zhu, Guojun Lu, Yunli Guo, Yan Zhou, Zhiyong Zhang, Yan Zhao, Wenjun Li, Ying Lu, Weihua Tang, Qi Feng and Bin Han
    Citation: BMC Genomics 2012 13:721
    Content type: Research article Published on:

  26. Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic a...

    Authors: Mateus F Santana, José CF Silva, Aline D Batista, Lílian E Ribeiro, Gilvan F da Silva, Elza F de Araújo and Marisa V de Queiroz
    Citation: BMC Genomics 2012 13:720
    Content type: Research article Published on:

  27. It has recently emerged that common epithelial cancers such as breast cancers have fusion genes like those in leukaemias. In a representative breast cancer cell line, ZR-75-30, we searched for fusion genes, by...

    Authors: Ina Schulte, Elizabeth M Batty, Jessica CM Pole, Katherine A Blood, Steven Mo, Susanna L Cooke, Charlotte Ng, Kevin L Howe, Suet-Feung Chin, James D Brenton, Carlos Caldas, Karen D Howarth and Paul AW Edwards
    Citation: BMC Genomics 2012 13:719
    Content type: Research article Published on:

  28. The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary q...

    Authors: Yan Zhu, Geir Skogerbø, Qianqian Ning, Zhen Wang, Biqing Li, Shuang Yang, Hong Sun and Yixue Li
    Citation: BMC Genomics 2012 13:718
    Content type: Research article Published on:

  29. New genes that originate from non-coding DNA rather than being duplicated from parent genes are called de novo genes. Their short evolution time and lack of parent genes provide a chance to study the evolution...

    Authors: Zing Tsung-Yeh Tsai, Huai-Kuang Tsai, Jen-Hao Cheng, Chih-Hsu Lin, Yuan-Fan Tsai and Daryi Wang
    Citation: BMC Genomics 2012 13:717
    Content type: Research article Published on:

  31. The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequ...

    Authors: Chang Liu, Linchun Shi, Yingjie Zhu, Haimei Chen, Jianhui Zhang, Xiaohan Lin and Xiaojun Guan
    Citation: BMC Genomics 2012 13:715
    Content type: Software Published on:

  32. MicroRNAs play a vital role in the regulation of gene expression and have been identified in every animal with a sequenced genome examined thus far, except for the placozoan Trichoplax. The genomic repertoires of...

    Authors: Evan K Maxwell, Joseph F Ryan, Christine E Schnitzler, William E Browne and Andreas D Baxevanis
    Citation: BMC Genomics 2012 13:714
    Content type: Research article Published on:

  33. Phenotypic evolution in animals is thought to be driven in large part by differences in gene expression patterns, which can result from sequence changes in cis- regulatory elements (cis- changes) or from changes ...

    Authors: Ana Ariza-Cosano, Axel Visel, Len A Pennacchio, Hunter B Fraser, José Luis Gómez-Skarmeta, Manuel Irimia and José Bessa
    Citation: BMC Genomics 2012 13:713
    Content type: Research article Published on:

  34. Secretoglobin 1A1 (SCGB 1A1), also called Clara cell secretory protein, is the most abundantly secreted protein of the airway. The SCGB1A1 gene has been characterized in mammals as a single copy in the genome. Ho...

    Authors: Olivier Côté, Brandon N Lillie, Michael Anthony Hayes, Mary Ellen Clark, Laura van den Bosch, Paula Katavolos, Laurent Viel and Dorothee Bienzle
    Citation: BMC Genomics 2012 13:712
    Content type: Research article Published on:

  35. Traditional candidate gene approach has been widely used for the study of complex diseases including obesity. However, this approach is largely limited by its dependence on existing knowledge of presumed biolo...

    Authors: Jaemin Kim, Taeheon Lee, Tae-Hun Kim, Kyung-Tai Lee and Heebal Kim
    Citation: BMC Genomics 2012 13:711
    Content type: Research article Published on:

  36. Cia5a is a locus on rat chromosome 10 that regulates disease severity and joint damage in two models of rheumatoid arthritis, collagen- and pristane-induced arthritis (PIA). In this study, we aimed to identify ce...

    Authors: Max Brenner and Pércio S Gulko
    Citation: BMC Genomics 2012 13:710
    Content type: Research article Published on:

  37. We have shown previously that pan-HDAC inhibitors (HDACIs) m-carboxycinnamic acid bis-hydroxamide (CBHA) and trichostatin A (TSA) attenuated cardiac hypertrophy in BALB/c mice by inducing hyper-acetylation of ...

    Authors: Gipsy Majumdar, Piyatilake Adris, Neha Bhargava, Hao Chen and Rajendra Raghow
    Citation: BMC Genomics 2012 13:709
    Content type: Research article Published on:

  38. In higher eukaryotes, gene expression is regulated at different levels. In particular, 3′UTRs play a central role in translation, stability and subcellular localization of transcripts. In recent years, the develo...

    Authors: Marcos Morgan, Alessandra Iaconcig and Andrés Fernando Muro
    Citation: BMC Genomics 2012 13:708
    Content type: Methodology article Published on:

  40. Detecting the borders between coding and non-coding regions is an essential step in the genome annotation. And information entropy measures are useful for describing the signals in genome sequence. However, th...

    Authors: Suping Deng, Yixiang Shi, Liyun Yuan, Yixue Li and Guohui Ding
    Citation: BMC Genomics 2012 13(Suppl 8):S19
    Content type: Research Published on:

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

  41. Identifying the location of transcription factor bindings is crucial to understand transcriptional regulation. Currently, Chromatin Immunoprecipitation followed with high-throughput Sequencing (ChIP-seq) is ab...

    Authors: Yupeng He, Yizhe Zhang, Guangyong Zheng and Chaochun Wei
    Citation: BMC Genomics 2012 13(Suppl 8):S18
    Content type: Research Published on:

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

  42. Differential expression detection for RNA-seq experiments is often biased by normalization algorithms due to their sensitivity to parametric assumptions on the gene count distributions, extreme values of gene ...

    Authors: Hatice Gulcin Ozer, Jeffrey D Parvin and Kun Huang
    Citation: BMC Genomics 2012 13(Suppl 8):S11
    Content type: Research Published on:

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

  43. Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understan...

    Authors: Ao Zhou, Marcus R Breese, Yangyang Hao, Howard J Edenberg, Lang Li, Todd C Skaar and Yunlong Liu
    Citation: BMC Genomics 2012 13(Suppl 8):S10
    Content type: Research Published on:

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

  44. RNA sequencing (RNA-seq) has become a major tool for biomedical research. A key step in analyzing RNA-seq data is to infer the origin of short reads in the source genome, and for this purpose, many read alignm...

    Authors: Yuan Yuan, Clift Norris, Yanxun Xu, Kam-Wah Tsui, Yuan Ji and Han Liang
    Citation: BMC Genomics 2012 13(Suppl 8):S9
    Content type: Research Published on:

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

  45. Accurate calling of SNPs and genotypes from next-generation sequencing data is an essential prerequisite for most human genetics studies. A number of computational steps are required or recommended when transl...

    Authors: Qi Liu, Yan Guo, Jiang Li, Jirong Long, Bing Zhang and Yu Shyr
    Citation: BMC Genomics 2012 13(Suppl 8):S8
    Content type: Research Published on:

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

  46. DNA methylation, which mainly occurs at CpG dinucleotides, is a dynamic epigenetic regulation mechanism in most eukaryotic genomes. It is already known that methylated CpG dinucleotides can lead to a high rate...

    Authors: Junfeng Xia, Leng Han and Zhongming Zhao
    Citation: BMC Genomics 2012 13(Suppl 8):S7
    Content type: Research Published on:

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

  47. DNA methylation is an important epigenetic mark and dysregulation of DNA methylation is associated with many diseases including cancer. Advances in next-generation sequencing now allow unbiased methylome profi...

    Authors: Michael P Trimarchi, Mark Murphy, David Frankhouser, Benjamin AT Rodriguez, John Curfman, Guido Marcucci, Pearlly Yan and Ralf Bundschuh
    Citation: BMC Genomics 2012 13(Suppl 8):S6
    Content type: Research Published on:

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

  48. Histone modification plays an important role in cell differentiation and tissue development. A recent study has shown that the dimethylation of lysine 4 residue on histone 3 (H3K4me2) marks the gene body area ...

    Authors: Jie Zhang, Jeffrey Parvin and Kun Huang
    Citation: BMC Genomics 2012 13(Suppl 8):S5
    Content type: Research Published on:

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

  49. While genome-wide association studies identified some promising candidates for schizophrenia, the majority of risk genes remained unknown. We were interested in testing whether integration gene expression and ...

    Authors: Junzhe Xu, Jingchun Sun, Jingchun Chen, Lily Wang, Anna Li, Matthew Helm, Steven L Dubovsky, Silviu-Alin Bacanu, Zhongming Zhao and Xiangning Chen
    Citation: BMC Genomics 2012 13(Suppl 8):S2
    Content type: Research Published on:

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

  50. We present a report of the 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) and the editorial report of the supplement to BMC Genomics that includes 22 research papers selected from ...

    Authors: Zhongming Zhao, Yufei Huang, Bing Zhang, Yu Shyr and Hua Xu
    Citation: BMC Genomics 2012 13(Suppl 8):S1
    Content type: Introduction Published on:

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

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