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  1. Radish (Raphanus sativus L., 2n = 2× = 18) is an economically important vegetable crop worldwide. A large collection of radish expressed sequence tags (ESTs) has been generated but remains largely uncharacterized...

    Authors: Di Shen, Honghe Sun, Mingyun Huang, Yi Zheng, Yang Qiu, Xixiang Li and Zhangjun Fei
    Citation: BMC Genomics 2013 14:721
    Content type: Research article Published on:

  3. Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this vari...

    Authors: Fayeza F Khan, Danielle Carpenter, Laura Mitchell, Omniah Mansouri, Holly A Black, Jess Tyson and John AL Armour
    Citation: BMC Genomics 2013 14:719
    Content type: Methodology article Published on:

  4. Salmonella enterica serovar Typhimurium (or simply Typhimurium) is the most common serovar in both human infections and farm animals in Australia and many other countries. Typhimurium is a broad host range serova...

    Authors: Stanley Pang, Sophie Octavia, Lu Feng, Bin Liu, Peter R Reeves, Ruiting Lan and Lei Wang
    Citation: BMC Genomics 2013 14:718
    Content type: Research article Published on:

  5. Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation. Identification of large numbers of SNPs is helpful for genetic diversity analysis, map-based cloning, genome-wide associati...

    Authors: Shunmou Huang, Linbin Deng, Mei Guan, Jiana Li, Kun Lu, Hanzhong Wang, Donghui Fu, Annaliese S Mason, Shengyi Liu and Wei Hua
    Citation: BMC Genomics 2013 14:717
    Content type: Research article Published on:

  6. Predicting molecular responses in human by extrapolating results from model organisms requires a precise understanding of the architecture and regulation of biological mechanisms across species.

    Authors: Ajay Prasad, Suchitra Suresh Kumar, Christophe Dessimoz, Stefan Bleuler, Oliver Laule, Tomas Hruz, Wilhelm Gruissem and Philip Zimmermann
    Citation: BMC Genomics 2013 14:716
    Content type: Research article Published on:

  7. Neutral lipid storage is enhanced by nitrogen deprivation (ND) in numbers of green microalgal species. However, little is known about the metabolic pathways whose transcription levels are most significantly al...

    Authors: Deying Sun, Jiaqi Zhu, Lei Fang, Xin Zhang, Yvonne Chow and Jianhua Liu
    Citation: BMC Genomics 2013 14:715
    Content type: Research article Published on:

  8. Recent discoveries on bacterial transcriptomes gave evidence that small RNAs (sRNAs) have important regulatory roles in prokaryotic cells. Modern high-throughput sequencing approaches (RNA-Seq) enable the most...

    Authors: Almut Mentz, Armin Neshat, Katharina Pfeifer-Sancar, Alfred Pühler, Christian Rückert and Jörn Kalinowski
    Citation: BMC Genomics 2013 14:714
    Content type: Research article Published on:

  9. Arginine biosynthesis in Corynebacterium glutamicum consists of eight enzymatic steps, starting with acetylation of glutamate, catalysed by N-acetylglutamate synthase (NAGS). There are different kinds of known NA...

    Authors: Kathrin Petri, Frederik Walter, Marcus Persicke, Christian Rückert and Jörn Kalinowski
    Citation: BMC Genomics 2013 14:713
    Content type: Research article Published on:

  11. Usually, next generation sequencing (NGS) technology has the property of ultra-high throughput but the read length is remarkably short compared to conventional Sanger sequencing. Paired-end NGS could computati...

    Authors: Jue Ruan, Lan Jiang, Zechen Chong, Qiang Gong, Heng Li, Chunyan Li, Yong Tao, Caihong Zheng, Weiwei Zhai, David Turissini, Charles H Cannon, Xuemei Lu and Chung-I Wu
    Citation: BMC Genomics 2013 14:711
    Content type: Methodology article Published on:

  12. Bovine tuberculosis (bTB) is a disease with major implications for animal welfare and productivity, as well as having the potential for zoonotic transmission. In Great Britain (GB) alone, controlling bTB costs...

    Authors: Paul Golby, Javier Nunez, Adam Witney, Jason Hinds, Michael A Quail, Stephen Bentley, Simon Harris, Noel Smith, R Glyn Hewinson and Stephen V Gordon
    Citation: BMC Genomics 2013 14:710
    Content type: Research article Published on:

  13. Chronic infections have been demonstrated to maintain low-grade systemic inflammation and associate with atherosclerosis. We studied the inflammation- and lipid homeostasis-related effects of Aggregatibacter acti...

    Authors: Kati Hyvärinen, Anita M Tuomainen, Saara Laitinen, Georg Alfthan, Irma Salminen, Maija Leinonen, Pekka Saikku, Petri T Kovanen, Matti Jauhiainen and Pirkko J Pussinen
    Citation: BMC Genomics 2013 14:709
    Content type: Research article Published on:

  14. Conopeptides, often generically referred to as conotoxins, are small neurotoxins found in the venom of predatory marine cone snails. These molecules are highly stable and are able to efficiently and selectivel...

    Authors: Vincent Lavergne, Sébastien Dutertre, Ai-hua Jin, Richard J Lewis, Ryan J Taft and Paul F Alewood
    Citation: BMC Genomics 2013 14:708
    Content type: Methodology article Published on:

  15. Competition between bacteria for habitat and resources is very common in the natural environment and is considered to be a selective force for survival. Many strains of the genus Pseudoalteromonas were confirmed ...

    Authors: Min Yu, Kaihao Tang, Jiwen Liu, Xiaochong Shi, Tobias AM Gulder and Xiao-Hua Zhang
    Citation: BMC Genomics 2013 14:707
    Content type: Research article Published on:

  16. MicroRNAs (miRNAs) are small, endogenously expressed, non-coding RNA molecules involved in gene transcription and expression that combine with specific mRNA site of target genes to inhibit protein synthesis or...

    Authors: Xuemei Chen, Wenhui Gao, Jinfa Zhang, Xianlong Zhang and Zhongxu Lin
    Citation: BMC Genomics 2013 14:706
    Content type: Research article Published on:

  17. MicroRNAs (miRNAs) are key components in post-transcriptional gene regulation in multicellular organisms. As they control cooperatively a large number of their target genes, they affect the complexity of gene ...

    Authors: Young-Ji Na and Ju Han Kim
    Citation: BMC Genomics 2013 14(Suppl 5):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  18. Metagenomics seeks to understand microbial communities and assemblages by DNA sequencing. Technological advances in next generation sequencing technologies are fuelling a rapid growth in the number and scope o...

    Authors: Suparna Mitra, Karin Förster-Fromme, Antje Damms-Machado, Tim Scheurenbrand, Saskia Biskup, Daniel H Huson and Stephan C Bischoff
    Citation: BMC Genomics 2013 14(Suppl 5):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  19. Many biological processes are carried out by proteins interacting with each other in the form of protein complexes. However, large-scale detection of protein complexes has remained constrained by experimental ...

    Authors: Daniel Lin-Kit Wong, Xiao-Li Li, Min Wu, Jie Zheng and See-Kiong Ng
    Citation: BMC Genomics 2013 14(Suppl 5):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  20. As the output of biological assays increase in resolution and volume, the body of specialized biological data, such as functional annotations of gene and protein sequences, enables extraction of higher-level k...

    Authors: Lars Rønn Olsen, Ulrich Johan Kudahl, Ole Winther and Vladimir Brusic
    Citation: BMC Genomics 2013 14(Suppl 5):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  21. Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scienti...

    Authors: Tin Wee Tan, Chao Xie, Mark De Silva, Kuan Siong Lim, C Pawan K Patro, Shen Jean Lim, Kunde Ramamoorthy Govindarajan, Joo Chuan Tong, Khar Heng Choo, Shoba Ranganathan and Asif M Khan
    Citation: BMC Genomics 2013 14(Suppl 5):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  22. MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in colorectal cancer (CRC) progression through silencing gene expression. Numerous dysregulated miRNA...

    Authors: Wei-Shone Chen, Ting-Wen Chen, Tzu-Hsien Yang, Ling-Yueh Hu, Hung-Wei Pan, Chung-Man Leung, Sung-Chou Li, Meng-Ru Ho, Chih-Wen Shu, Pei-Feng Liu, Shou-Yu Yu, Ya-Ting Tu, Wen-Chang Lin, Tony T Wu and Kuo-Wang Tsai
    Citation: BMC Genomics 2013 14(Suppl 5):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  23. Computational methods for the prediction of Major Histocompatibility Complex (MHC) class II binding peptides play an important role in facilitating the understanding of immune recognition and the process of ep...

    Authors: Linyuan Guo, Cheng Luo and Shanfeng Zhu
    Citation: BMC Genomics 2013 14(Suppl 5):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  24. Schizophrenic patients show lower incidences of cancer, implicating schizophrenia may be a protective factor against cancer. To study the genetic correlation between the two diseases, a specific PPI network wa...

    Authors: Kuo-Chuan Huang, Ko-Chun Yang, Han Lin, Theresa Tsao Tsun-Hui, Wen-Kuei Lee, Sheng-An Lee and Cheng-Yan Kao
    Citation: BMC Genomics 2013 14(Suppl 5):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  25. The large-scale sequencing of 5' cap enriched cDNA promises to reveal the diversity of transcription initiation across entire genomes. The process of transcription is noisy, and there is often no single, exact...

    Authors: Dario Strbenac, Nicola J Armstrong and Jean YH Yang
    Citation: BMC Genomics 2013 14(Suppl 5):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

    The Erratum to this article has been published in BMC Genomics 2013 14:767

  26. Human aneuploidy is the leading cause of early pregnancy loss, mental retardation, and multiple congenital anomalies. Due to the high mortality associated with aneuploidy, the pathophysiological mechanisms of ...

    Authors: Ruosi Zhang, Lili Hao, Lingping Wang, Meili Chen, Wen Li, Rujiao Li, Jun Yu, Jingfa Xiao and Jiayan Wu
    Citation: BMC Genomics 2013 14(Suppl 5):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  27. Plant cell wall-degrading enzymes (PCWDEs) play significant roles throughout the fungal life including acquisition of nutrients and decomposition of plant cell walls. In addition, many of PCWDEs are also utili...

    Authors: Jaeyoung Choi, Ki-Tae Kim, Jongbum Jeon and Yong-Hwan Lee
    Citation: BMC Genomics 2013 14(Suppl 5):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  28. Coffee contains several compounds that have the potential to influence breast cancer risk and survival. However, epidemiologic data on the relation between coffee compounds and breast cancer survival are spars...

    Authors: Babita Shashni, Karun Sharma, Rumani Singh, Kishore R Sakharkar, Sarinder K Dhillon, Yukio Nagasaki and Meena K Sakharkar
    Citation: BMC Genomics 2013 14(Suppl 5):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  29. The adaptive immune response is antigen-specific and triggered by pathogen recognition through T cells. Although the interactions and mechanisms of TCR-peptide-MHC (TCR-pMHC) have been studied over three decad...

    Authors: I-Hsin Liu, Yu-Shu Lo and Jinn-Moon Yang
    Citation: BMC Genomics 2013 14(Suppl 5):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  30. Recent discovery in tumor development indicates that the tumor microenvironment (mostly stroma cells) plays an important role in cancer development. To understand how the tumor microenvironment (TME) interacts...

    Authors: Yang Xiang, Jie Zhang and Kun Huang
    Citation: BMC Genomics 2013 14(Suppl 5):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  31. While more and more long intergenic non-coding RNAs (lincRNAs) were identified to take important roles in both maintaining pluripotency and regulating differentiation, how these lincRNAs may define and drive c...

    Authors: Xing Tang, Mei Hou, Yang Ding, Zhaohui Li, Lichen Ren and Ge Gao
    Citation: BMC Genomics 2013 14(Suppl 5):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  32. Cell type and TF specific interactions between Transcription Factors (TFs) and cofactors are essential for transcriptional regulation through recruitment of general transcription machinery to gene promoter reg...

    Authors: Chin Lui Goi, Peter Little and Chao Xie
    Citation: BMC Genomics 2013 14(Suppl 5):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  33. Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources ...

    Authors: Susana L Torales, Máximo Rivarola, María F Pomponio, Sergio Gonzalez, Cintia V Acuña, Paula Fernández, Diego L Lauenstein, Aníbal R Verga, H Esteban Hopp, Norma B Paniego and Susana N Marcucci Poltri
    Citation: BMC Genomics 2013 14:705
    Content type: Research article Published on:

  34. Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the re...

    Authors: Sebastian Baumgarten, Till Bayer, Manuel Aranda, Yi Jin Liew, Adrian Carr, Gos Micklem and Christian R Voolstra
    Citation: BMC Genomics 2013 14:704
    Content type: Research article Published on:

  35. G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disea...

    Authors: Dharmendra B Goswami, Lisa M Ogawa, Joshua M Ward, Gregory M Miller and Eric J Vallender
    Citation: BMC Genomics 2013 14:703
    Content type: Research article Published on:

  36. EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breedi...

    Authors: Ishminder K Mann, Jill L Wegrzyn and Om P Rajora
    Citation: BMC Genomics 2013 14:702
    Content type: Research article Published on:

  37. Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are pa...

    Authors: Elena A Vidal, Tomás C Moyano, Gabriel Krouk, Manpreet S Katari, Milos Tanurdzic, W Richard McCombie, Gloria M Coruzzi and Rodrigo A Gutiérrez
    Citation: BMC Genomics 2013 14:701
    Content type: Research article Published on:

  38. Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and ...

    Authors: Choumouss Kamoun, Thibaut Payen, Aurélie Hua-Van and Jonathan Filée
    Citation: BMC Genomics 2013 14:700
    Content type: Methodology article Published on:

  39. Accurate bacterial genome annotations provide a framework to understanding cellular functions, behavior and pathogenicity and are essential for metabolic engineering. Annotations based only on in silico predictio...

    Authors: Esteban Marcellin, Cuauhtemoc Licona-Cassani, Tim R Mercer, Robin W Palfreyman and Lars K Nielsen
    Citation: BMC Genomics 2013 14:699
    Content type: Research article Published on:

  40. Mercury is a ubiquitous environmental toxicant that exists in multiple chemical forms. A paucity of information exists regarding the differences or similarities by which different mercurials act at the molecul...

    Authors: Matthew K McElwee, Lindsey A Ho, Jeff W Chou, Marjolein V Smith and Jonathan H Freedman
    Citation: BMC Genomics 2013 14:698
    Content type: Research article Published on:

  41. The white shark (Carcharodon carcharias) is a globally distributed, apex predator possessing physical, physiological, and behavioral traits that have garnered it significant public attention. In addition to inter...

    Authors: Vincent P Richards, Haruo Suzuki, Michael J Stanhope and Mahmood S Shivji
    Citation: BMC Genomics 2013 14:697
    Content type: Research article Published on:

  42. MicroRNAs (miRNAs) have recently been shown to play important roles in development of the immune system and in fine-tuning of immune responses. Human miR-146 family members are known as inflammation-inducible ...

    Authors: Anita Ordas, Zakia Kanwal, Valesca Lindenberg, Julien Rougeot, Matyas Mink, Herman P Spaink and Annemarie H Meijer
    Citation: BMC Genomics 2013 14:696
    Content type: Research article Published on:

  43. The dimorphic fungus Histoplasma capsulatum causes respiratory and systemic disease in mammalian hosts by expression of factors that enable survival within phagocytic cells of the immune system. Histoplasma’s dim...

    Authors: Jessica A Edwards, Chenxi Chen, Megan M Kemski, Jinnan Hu, Thomas K Mitchell and Chad A Rappleye
    Citation: BMC Genomics 2013 14:695
    Content type: Research article Published on:

  44. The initial interaction between host cell and pathogen sets the stage for the ensuing infection and ultimately determine the course of disease. However, there is limited knowledge of the transcripts utilized b...

    Authors: Elise A Lamont, Wayne W Xu and Srinand Sreevatsan
    Citation: BMC Genomics 2013 14:694
    Content type: Research article Published on:

  45. Lyme disease is caused by spirochete bacteria from the Borrelia burgdorferi sensu lato (B. burgdorferi s.l.) species complex. To reconstruct the evolution of B. burgdorferi s.l. and identify the genomic basis of ...

    Authors: Emmanuel F Mongodin, Sherwood R Casjens, John F Bruno, Yun Xu, Elliott Franco Drabek, David R Riley, Brandi L Cantarel, Pedro E Pagan, Yozen A Hernandez, Levy C Vargas, John J Dunn, Steven E Schutzer, Claire M Fraser, Wei-Gang Qiu and Benjamin J Luft
    Citation: BMC Genomics 2013 14:693
    Content type: Research article Published on:

  46. CpG dinucleotide-rich genomic DNA regions, known as CpG islands (CGIs), can be methylated at their cytosine residues as an epigenetic mark that is stably inherited during cell mitosis. Differentially methylate...

    Authors: Sergio Cocozza, Giovanni Scala, Gennaro Miele, Imma Castaldo and Antonella Monticelli
    Citation: BMC Genomics 2013 14:692
    Content type: Research article Published on:

  47. Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary mod...

    Authors: You-Jun Huang, Li-Li Liu, Jian-Qin Huang, Zheng-Jia Wang, Fang-Fang Chen, Qi-Xiang Zhang, Bing-Song Zheng and Ming Chen
    Citation: BMC Genomics 2013 14:691
    Content type: Research article Published on:

  48. The Oncotype DX® Prostate Cancer Assay is a multi-gene RT-PCR expression assay that was developed for use with fixed paraffin-embedded (FPE) diagnostic prostate needle biopsies containing as little as 1 mm of pro...

    Authors: Dejan Knezevic, Audrey D Goddard, Nisha Natraj, Diana B Cherbavaz, Kim M Clark-Langone, Jay Snable, Drew Watson, Sara M Falzarano, Cristina Magi-Galluzzi, Eric A Klein and Christopher Quale
    Citation: BMC Genomics 2013 14:690
    Content type: Methodology article Published on:

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BMC Genomics

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