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  1. Pistachio (Pistacia vera L.) is a dioecious species that has a long juvenility period. Therefore, development of marker-assisted selection (MAS) techniques would greatly facilitate pistachio cultivar-breeding pro...

    Authors: Salih Kafkas, Mortaza Khodaeiaminjan, Murat Güney and Ebru Kafkas
    Citation: BMC Genomics 2015 16:98
    Content type: Research article Published on:

  2. RNA-Seq has become increasingly popular in transcriptome profiling. One aspect of transcriptome research is to quantify the expression levels of genomic elements, such as genes, their transcripts and exons. Ac...

    Authors: Shanrong Zhao and Baohong Zhang
    Citation: BMC Genomics 2015 16:97
    Content type: Research article Published on:

  3. MicroRNAs (miRNAs) represent new and potentially informative diagnostic targets for disease detection and prognosis. However, little work exists documenting the effect of TRIzol, a common viral inactivation an...

    Authors: Janice Duy, Jeffrey W Koehler, Anna N Honko and Timothy D Minogue
    Citation: BMC Genomics 2015 16:95
    Content type: Methodology article Published on:

  4. The protozoan Eimeria tenella is a common parasite of chickens, causing avian coccidiosis, a disease of on-going concern to agricultural industries. The high prevalence of E. tenella can be attributed to the resi...

    Authors: Robert A Walker, Philippa A Sharman, Catherine M Miller, Christoph Lippuner, Michal Okoniewski, Ramon M Eichenberger, Chandra Ramakrishnan, Fabien Brossier, Peter Deplazes, Adrian B Hehl and Nicholas C Smith
    Citation: BMC Genomics 2015 16:94
    Content type: Research article Published on:

  5. Brucellosis is an important zoonotic disease that affects both humans and animals. We sequenced the full genome and characterised the genetic diversity of two Brucella melitensis isolates from Malaysia and the Ph...

    Authors: Kim-Kee Tan, Yung-Chie Tan, Li-Yen Chang, Kok Wei Lee, Siti Sarah Nore, Wai-Yan Yee, Mohd Noor Mat Isa, Faizatul Lela Jafar, Chee-Choong Hoh and Sazaly AbuBakar
    Citation: BMC Genomics 2015 16:93
    Content type: Research article Published on:

  6. The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversi...

    Authors: Gaurav Thareja, Sumi Elsa John, Prashantha Hebbar, Kazem Behbehani, Thangavel Alphonse Thanaraj and Osama Alsmadi
    Citation: BMC Genomics 2015 16:92
    Content type: Research article Published on:

  7. 20(S)-hydroxycholesterol (20(S)) potentially reduces adipogenesis in mammalian cells. The role of this oxysterol and molecular mechanisms underlying the adipogenesis of preadipocytes from laying hens have not ...

    Authors: Alemu Regassa and Woo Kyun Kim
    Citation: BMC Genomics 2015 16:91
    Content type: Research article Published on:

  8. The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools ...

    Authors: Weinan Zhu, Jin Wang, Yongzhang Zhu, Biao Tang, Yunyi Zhang, Ping He, Yan Zhang, Boyu Liu, Xiaokui Guo, Guoping Zhao and Jinhong Qin
    Citation: BMC Genomics 2015 16:90
    Content type: Research article Published on:

  9. Crossing over assures the correct segregation of the homologous chromosomes to both poles of the dividing meiocyte. This exchange of DNA creates new allelic combinations thus increasing the genetic variation p...

    Authors: Antoine Ederveen, Yuching Lai, Marc A van Driel, Tom Gerats and Janny L Peters
    Citation: BMC Genomics 2015 16:89
    Content type: Research article Published on:

  10. The pig, which shares greater similarities with human than with mouse, is important for agriculture and for studying human diseases. However, similarities in the genetic architecture and molecular regulations ...

    Authors: Jun Zhu, Congying Chen, Bin Yang, Yuanmei Guo, Huashui Ai, Jun Ren, Zhiyu Peng, Zhidong Tu, Xia Yang, Qingying Meng, Stephen Friend and Lusheng Huang
    Citation: BMC Genomics 2015 16:88
    Content type: Research article Published on:

  11. Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidat...

    Authors: Olgert Denas, Richard Sandstrom, Yong Cheng, Kathryn Beal, Javier Herrero, Ross C Hardison and James Taylor
    Citation: BMC Genomics 2015 16:87
    Content type: Research Published on:

  12. Annona squamosa L., a popular fruit tree, is the most widely cultivated species of the genus Annona. The lack of transcriptomic and genomic information limits the scope of genome investigations...

    Authors: Yogesh Gupta, Ashish K Pathak, Kashmir Singh, Shrikant S Mantri, Sudhir P Singh and Rakesh Tuli
    Citation: BMC Genomics 2015 16:86
    Content type: Research article Published on:

  13. Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Sever...

    Authors: Jianping Jiang, Jianlei Gu, Liang Zhang, Chenyi Zhang, Xiao Deng, Tonghai Dou, Guoping Zhao and Yan Zhou
    Citation: BMC Genomics 2015 16:85
    Content type: Methodology article Published on:

  14. Alzheimer’s disease (AD) is a complex, irreversible neurodegenerative disorder. At present there are neither reliable markers to diagnose AD at an early stage nor therapy. To investigate underlying disease mec...

    Authors: Amir M Hossini, Matthias Megges, Alessandro Prigione, Bjoern Lichtner, Mohammad R Toliat, Wasco Wruck, Friederike Schröter, Peter Nuernberg, Hartmut Kroll, Eugenia Makrantonaki, Christos C Zoubouliss and James Adjaye
    Citation: BMC Genomics 2015 16:84
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2015 16:433

  15. Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized populat...

    Authors: Luyuan Pan, Arish N Shah, Ian G Phelps, Dan Doherty, Eric A Johnson and Cecilia B Moens
    Citation: BMC Genomics 2015 16:83
    Content type: Methodology article Published on:

  16. Reverse transcription quantitative PCR (RT-qPCR) is considered the gold standard for quantifying relative gene expression. Normalization of RT-qPCR data is commonly achieved by subtracting the Ct values of the in...

    Authors: Xiangqin Cui, Shaohua Yu, Ashutosh Tamhane, Zenoria L Causey, Adam Steg, Maria I Danila, Richard J Reynolds, Jinyi Wang, Keith C Wanzeck, Qi Tang, Stephanie S Ledbetter, David T Redden, Martin R Johnson and S Louis Bridges Jr.
    Citation: BMC Genomics 2015 16:82
    Content type: Methodology article Published on:

  17. Nuclear receptors have crucial roles in all metazoan animals as regulators of gene transcription. A wide range of studies have elucidated molecular and biological significance of nuclear receptors but there ar...

    Authors: Christiane Eichner, Sussie Dalvin, Rasmus Skern-Mauritzen, Ketil Malde, Heidi Kongshaug and Frank Nilsen
    Citation: BMC Genomics 2015 16:81
    Content type: Research article Published on:

  18. Social amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species...

    Authors: Hideko Urushihara, Hidekazu Kuwayama, Kensuke Fukuhara, Takehiko Itoh, Hiroshi Kagoshima, Tadasu Shin-I, Atsushi Toyoda, Kazuyo Ohishi, Tateaki Taniguchi, Hideki Noguchi, Yoko Kuroki, Takashi Hata, Kyoko Uchi, Kurato Mohri, Jason S King, Robert H Insall…
    Citation: BMC Genomics 2015 16:80
    Content type: Research article Published on:

  19. Influenza viruses exist as a large group of closely related viral genomes, also called quasispecies. The composition of this influenza viral quasispecies can be determined by an accurate and sensitive sequenci...

    Authors: Silvie Van den Hoecke, Judith Verhelst, Marnik Vuylsteke and Xavier Saelens
    Citation: BMC Genomics 2015 16:79
    Content type: Research article Published on:

  20. The ribosome translates mRNA to protein with the aid of a number of accessory protein factors. Translational GTPases (trGTPases) are an integral part of the ‘core set’ of essential translational factors, and a...

    Authors: Gemma Catherine Atkinson
    Citation: BMC Genomics 2015 16:78
    Content type: Research article Published on:

  21. Disease resistance (R) genes from different Rosaceae species have been identified by map-based cloning for resistance breeding. However, there are few reports describing the pattern of R-gene evolution in Rosacea...

    Authors: Yan Zhong, Huan Yin, Daniel James Sargent, Mickael Malnoy and Zong-Ming (Max) Cheng
    Citation: BMC Genomics 2015 16:77
    Content type: Research article Published on:

  22. Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, roles in B cell development. PU.1 and Spi-B are both exp...

    Authors: Lauren A Solomon, Stephen KH Li, Jan Piskorz, Li S Xu and Rodney P DeKoter
    Citation: BMC Genomics 2015 16:76
    Content type: Research article Published on:

  23. Larvae of the tenebrionids Tenebrio molitor and Tribolium castaneum have highly compartmentalized guts, with primarily cysteine peptidases in the acidic anterior midgut that contribute to the early stages of prot...

    Authors: Alexander G Martynov, Elena N Elpidina, Lindsey Perkin and Brenda Oppert
    Citation: BMC Genomics 2015 16:75
    Content type: Research article Published on:

  24. The moon jellyfish Aurelia aurita is a widespread scyphozoan species that forms large seasonal blooms. Here we provide the first comprehensive view of the entire complex life of the Aurelia Red Sea strain by empl...

    Authors: Vera Brekhman, Assaf Malik, Brian Haas, Noa Sher and Tamar Lotan
    Citation: BMC Genomics 2015 16:74
    Content type: Research article Published on:

  25. Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Together with its ability to produce high yields of amino acids, the relevance of thi...

    Authors: Marta Irla, Armin Neshat, Trygve Brautaset, Christian Rückert, Jörn Kalinowski and Volker F Wendisch
    Citation: BMC Genomics 2015 16:73
    Content type: Research article Published on:

  26. The RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene ex...

    Authors: Vânia Pobre and Cecília M Arraiano
    Citation: BMC Genomics 2015 16:72
    Content type: Research article Published on:

  28. Distinct, partly competing, “waves” have been proposed to explain human migration in(to) today’s Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high ...

    Authors: Sibylle M Gomes, Martin Bodner, Luis Souto, Bettina Zimmermann, Gabriela Huber, Christina Strobl, Alexander W Röck, Alessandro Achilli, Anna Olivieri, Antonio Torroni, Francisco Côrte-Real and Walther Parson
    Citation: BMC Genomics 2015 16:70
    Content type: Research article Published on:

  29. Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major...

    Authors: Javier Terol, Victoria Ibañez, José Carbonell, Roberto Alonso, Leandro H Estornell, Concetta Licciardello, Ivo G Gut, Joaquín Dopazo and Manuel Talon
    Citation: BMC Genomics 2015 16:69
    Content type: Research article Published on:

  32. The apicomplexan parasite Toxoplasma gondii is cosmopolitan in nature, largely as a result of its highly flexible life cycle. Felids are its only definitive hosts and a wide range of mammals and birds serve as in...

    Authors: Adrian B Hehl, Walter U Basso, Christoph Lippuner, Chandra Ramakrishnan, Michal Okoniewski, Robert A Walker, Michael E Grigg, Nicholas C Smith and Peter Deplazes
    Citation: BMC Genomics 2015 16:66
    Content type: Research article Published on:

  33. Several de novo transcriptome assemblers have been developed recently to assemble the short reads generated from the next-generation sequencing platforms and different strategies were employed for assembling tran...

    Authors: Bin He, Shirong Zhao, Yuehong Chen, Qinghua Cao, Changhe Wei, Xiaojie Cheng and Yizheng Zhang
    Citation: BMC Genomics 2015 16:65
    Content type: Research article Published on:

  34. The northern elephant seal, Mirounga angustirostris, is a valuable animal model of fasting adaptation and hypoxic stress tolerance. However, no reference sequence is currently available for this and many other ma...

    Authors: Jane I Khudyakov, Likit Preeyanon, Cory D Champagne, Rudy M Ortiz and Daniel E Crocker
    Citation: BMC Genomics 2015 16:64
    Content type: Research article Published on:

  35. The Western honey bee (Apis mellifera L.) is a critical component of human agriculture through its pollination activities. For years, beekeepers have controlled deadly pathogens such as Paenibacillus larvae, Nose...

    Authors: Maria Marta Guarna, Andony P Melathopoulos, Elizabeth Huxter, Immacolata Iovinella, Robert Parker, Nikolay Stoynov, Amy Tam, Kyung-Mee Moon, Queenie WT Chan, Paolo Pelosi, Rick White, Stephen F Pernal and Leonard J Foster
    Citation: BMC Genomics 2015 16:63
    Content type: Research article Published on:

  36. Adhesion G protein-coupled receptors (aGPCRs) are the second largest of the five GPCR families and are essential for a wide variety of physiological processes. Zebrafish have proven to be a very effective mode...

    Authors: Breanne L Harty, Arunkumar Krishnan, Nicholas E Sanchez, Helgi B Schiöth and Kelly R Monk
    Citation: BMC Genomics 2015 16:62
    Content type: Research article Published on:

  37. The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating populatio...

    Authors: Jie Huang, Yu-Zhi Li, Lian-Ming Du, Bo Yang, Fu-Jun Shen, He-Min Zhang, Zhi-He Zhang, Xiu-Yue Zhang and Bi-Song Yue
    Citation: BMC Genomics 2015 16:61
    Content type: Research article Published on:

  39. Recent studies have indicated that low serum testosterone levels are associated with increased risk of developing hepatic steatosis; however, the mechanisms mediating this phenomenon have not been fully elucid...

    Authors: Zhaowei Cai, Xiaoling Jiang, Yongming Pan, Liang Chen, Lifan Zhang, Keyan Zhu, Yueqin Cai, Yun Ling, Fangming Chen, Xiaoping Xu and Minli Chen
    Citation: BMC Genomics 2015 16:59
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2020 21:51

  40. Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as we...

    Authors: Tapan Kumar Mohanta, Pankaj Kumar Arora, Nibedita Mohanta, Pratap Parida and Hanhong Bae
    Citation: BMC Genomics 2015 16:58
    Content type: Research article Published on:

  41. High light tolerance of microalgae is a desired phenotype for efficient cultivation in large scale production systems under fluctuating outdoor conditions. Outdoor cultivation requires the use of either wild-t...

    Authors: Lisa Schierenbeck, David Ries, Kristin Rogge, Sabrina Grewe, Bernd Weisshaar and Olaf Kruse
    Citation: BMC Genomics 2015 16:57
    Content type: Research article Published on:

  43. Tetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing ...

    Authors: Cairui Lu, Changsong Zou, Youping Zhang, Daoqian Yu, Hailiang Cheng, Pengfei Jiang, Wencui Yang, Qiaolian Wang, Xiaoxu Feng, Mtawa Andrew Prosper, Xiaoping Guo and Guoli Song
    Citation: BMC Genomics 2015 16:55
    Content type: Research article Published on:

  44. Alternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive.

    Authors: Bin-Bin Xie, Dan Li, Wei-Ling Shi, Qi-Long Qin, Xiao-Wei Wang, Jin-Cheng Rong, Cai-Yun Sun, Feng Huang, Xi-Ying Zhang, Xiao-Wei Dong, Xiu-Lan Chen, Bai-Cheng Zhou, Yu-Zhong Zhang and Xiao-Yan Song
    Citation: BMC Genomics 2015 16:54
    Content type: Research article Published on:

  45. In recent years, the perception of transposable genetic elements has changed from “junk DNA” to a focus of interest when appearing near or inside genes. Bov-A2 is a short interspersed nuclear element (SINE) th...

    Authors: Yaron Dekel, Yossy Machluf, Shifra Ben-Dor, Oren Yifa, Aviad Stoler, Izhar Ben-Shlomo and Dani Bercovich
    Citation: BMC Genomics 2015 16:53
    Content type: Research article Published on:

  46. RNA-binding proteins (RBPs) play essential roles in gene expression regulation through their interactions with RNA transcripts, including coding, canonical non-coding and long non-coding RNAs. Large amounts of...

    Authors: Yu-Cheng T Yang, Chao Di, Boqin Hu, Meifeng Zhou, Yifang Liu, Nanxi Song, Yang Li, Jumpei Umetsu and Zhi John Lu
    Citation: BMC Genomics 2015 16:51
    Content type: Database Published on:

  48. The pathways regulating the transition of mammalian cells from quiescence to proliferation are mediated by multiple miRNAs. Despite significant improvements in our understanding of miRNA targeting, the majorit...

    Authors: Damon Polioudakis, Nathan S Abell and Vishwanath R Iyer
    Citation: BMC Genomics 2015 16:40
    Content type: Research article Published on:

  49. In bacterial genomes, the compactly encoded genes and operons are well organized, with genes in the same biological pathway or operons in the same regulon close to each other on the genome sequence. In additio...

    Authors: Ting Xie, Liang-Yu Fu, Qing-Yong Yang, Heng Xiong, Hongrui Xu, Bin-Guang Ma and Hong-Yu Zhang
    Citation: BMC Genomics 2015 16:37
    Content type: Research article Published on:

  50. The human pathogen Mycobacterium tuberculosis has the capacity to escape eradication by professional phagocytes. During infection, M. tuberculosis resists the harsh environment of phagosomes and actively manipula...

    Authors: Rienk A Rienksma, Maria Suarez-Diez, Hans-Joachim Mollenkopf, Gregory M Dolganov, Anca Dorhoi, Gary K Schoolnik, Vitor AP Martins dos Santos, Stefan HE Kaufmann, Peter J Schaap and Martin Gengenbacher
    Citation: BMC Genomics 2015 16:34
    Content type: Research article Published on:

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BMC Genomics

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