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  1. The majority of non-coding RNAs (ncRNAs) involved in mRNA metabolism in mammals have been believed to downregulate the corresponding mRNA expression level in a pre- or post-transcriptional manner by forming sh...

    Authors: Masahiro Uesaka, Osamu Nishimura, Yasuhiro Go, Kinichi Nakashima, Kiyokazu Agata and Takuya Imamura
    Citation: BMC Genomics 2014 15:35
    Content type: Research article Published on:

  2. Lichen is a classic mutualistic organism and the lichenization is one of the fungal symbioses. The lichen-forming fungus Endocarpon pusillum is living in symbiosis with the green alga Diplosphaera chodatii Bialsu...

    Authors: Yan-Yan Wang, Bin Liu, Xin-Yu Zhang, Qi-Ming Zhou, Tao Zhang, Hui Li, Yu-Fei Yu, Xiao-Ling Zhang, Xi-Yan Hao, Meng Wang, Lei Wang and Jiang-Chun Wei
    Citation: BMC Genomics 2014 15:34
    Content type: Research article Published on:

  3. Subterranean mammals have been of great interest for evolutionary biologists because of their highly specialized traits for the life underground. Owing to the convergence of morphological traits and the incong...

    Authors: Gong-Hua Lin, Kun Wang, Xiao-Gong Deng, Eviatar Nevo, Fang Zhao, Jian-Ping Su, Song-Chang Guo, Tong-Zuo Zhang and Huabin Zhao
    Citation: BMC Genomics 2014 15:32
    Content type: Research article Published on:

  4. Environmental factors during perinatal development may influence developmental plasticity and disease susceptibility via alterations to the epigenome. Developmental exposure to the endocrine active compound, b...

    Authors: Jung H Kim, Maureen A Sartor, Laura S Rozek, Christopher Faulk, Olivia S Anderson, Tamara R Jones, Muna S Nahar and Dana C Dolinoy
    Citation: BMC Genomics 2014 15:30
    Content type: Research article Published on:

  5. The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The p...

    Authors: Anuradha Singh, Shrikant Mantri, Monica Sharma, Ashok Chaudhury, Rakesh Tuli and Joy Roy
    Citation: BMC Genomics 2014 15:29
    Content type: Research article Published on:

  6. Negative energy balance (NEB), an altered metabolic state, occurs in early postpartum dairy cattle when energy demands to support lactation exceed energy intake. During NEB the liver undergoes oxidative stress...

    Authors: Attia Fatima, Sinead Waters, Padraig O’Boyle, Cathal Seoighe and Dermot G Morris
    Citation: BMC Genomics 2014 15:28
    Content type: Research article Published on:

  7. A protein may bind to its target DNA sites constitutively, i.e., regardless of cell type. Intuitively, constitutive binding sites should be biologically functional. A prerequisite for understanding their funct...

    Authors: Yuanyuan Li, David M Umbach and Leping Li
    Citation: BMC Genomics 2014 15:27
    Content type: Methodology article Published on:

  8. Sporeformers in the order Bacillales are important contributors to spoilage of pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6°C, the majority of Paenibacillus isolate...

    Authors: Andrea I Moreno Switt, Alexis D Andrus, Matthew L Ranieri, Renato H Orsi, Reid Ivy, Henk C den Bakker, Nicole H Martin, Martin Wiedmann and Kathryn J Boor
    Citation: BMC Genomics 2014 15:26
    Content type: Research article Published on:

  9. In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elemen...

    Authors: Hongjun Liu, Cheng Qin, Zhe Chen, Tao Zuo, Xuerong Yang, Huangkai Zhou, Meng Xu, Shiliang Cao, Yaou Shen, Haijian Lin, Xiujing He, Yinchao Zhang, Lujiang Li, Haiping Ding, Thomas Lübberstedt, Zhiming Zhang…
    Citation: BMC Genomics 2014 15:25
    Content type: Research article Published on:

  10. At later stages of folliculogenesis, the mammalian ovarian follicle contains layers of epithelial granulosa cells surrounding an antral cavity. During follicle development granulosa cells replicate, secrete ho...

    Authors: Nicholas Hatzirodos, Helen F Irving-Rodgers, Katja Hummitzsch, Margaret L Harland, Stephanie E Morris and Raymond J Rodgers
    Citation: BMC Genomics 2014 15:24
    Content type: Research article Published on:

  11. Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. In this study, the genome sequences of three C. pecor...

    Authors: Michelle Sait, Morag Livingstone, Ewan M Clark, Nick Wheelhouse, Lucy Spalding, Bryan Markey, Simone Magnino, Frederick A Lainson, Garry SA Myers and David Longbottom
    Citation: BMC Genomics 2014 15:23
    Content type: Research article Published on:

  12. The field of genomics is often cited as the branch of biology that has led the way in data sharing. In most cases, sequencing data are made publicly available immediately after generation and often before the ...

    Authors: Shreeya Nanda and Maria K Kowalczuk
    Citation: BMC Genomics 2014 15:5
    Content type: Editorial Published on:

  13. The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate le...

    Authors: Silvia Picossi, Enrique Flores and Antonia Herrero
    Citation: BMC Genomics 2014 15:22
    Content type: Research article Published on:

  14. Chromosome ends are composed of telomeric repeats and subtelomeric regions, which are patchworks of genes interspersed with repeated elements. Although chromosome ends display similar arrangements in different...

    Authors: María C Dalmasso, Santiago J Carmona, Sergio O Angel and Fernán Agüero
    Citation: BMC Genomics 2014 15:21
    Content type: Research article Published on:

  15. Regulatory function of small non-coding RNAs (sRNA) in response to environmental and developmental cues has been established. Additionally, sRNA, also plays an important role in maintaining the heterochromatin...

    Authors: Rishi Aryal, Guru Jagadeeswaran, Yun Zheng, Qingyi Yu, Ramanjulu Sunkar and Ray Ming
    Citation: BMC Genomics 2014 15:20
    Content type: Research article Published on:

  16. Eukaryotic cells express a complex layer of noncoding RNAs. An intriguing family of regulatory RNAs includes transcripts from the opposite strand of protein coding genes, so called natural antisense transcript...

    Authors: Andreas Werner, Simon Cockell, Jane Falconer, Mark Carlile, Sammer Alnumeir and John Robinson
    Citation: BMC Genomics 2014 15:19
    Content type: Research article Published on:

  17. Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled by Rps genes. However, little is known regarding the Rps-induced molecular responses to P. sojae and how they actually ...

    Authors: Feng Lin, Meixia Zhao, Douglas D Baumann, Jieqing Ping, Lianjun Sun, Yunfeng Liu, Biao Zhang, Zongxiang Tang, Elisa Hughes, Rebecca W Doerge, Teresa J Hughes and Jianxin Ma
    Citation: BMC Genomics 2014 15:18
    Content type: Research article Published on:

  18. Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide...

    Authors: Kerry K Cooper, Robert E Mandrell, Jacqueline W Louie, Jonas Korlach, Tyson A Clark, Craig T Parker, Steven Huynh, Patrick S Chain, Sanaa Ahmed and Michelle Qiu Carter
    Citation: BMC Genomics 2014 15:17
    Content type: Research article Published on:

  19. High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome comp...

    Authors: Maja P Greminger, Kai N Stölting, Alexander Nater, Benoit Goossens, Natasha Arora, Rémy Bruggmann, Andrea Patrignani, Beatrice Nussberger, Reeta Sharma, Robert H S Kraus, Laurentius N Ambu, Ian Singleton, Lounes Chikhi, Carel P van Schaik and Michael Krützen
    Citation: BMC Genomics 2014 15:16
    Content type: Research article Published on:

  20. Degradation is essential for RNA maturation, turnover, and quality control. RNA degradome sequencing that integrates a modified 5′-rapid amplification of cDNA ends protocol with next-generation sequencing tech...

    Authors: Cheng-Yu Hou, Ming-Tsung Wu, Shin-Hua Lu, Yue-Ie Hsing and Ho-Ming Chen
    Citation: BMC Genomics 2014 15:15
    Content type: Research article Published on:

  21. The completion of whole-genome sequencing for Corynebacterium pseudotuberculosis strain 1002 has contributed to major advances in research aimed at understanding the biology of this microorganism. This bacterium ...

    Authors: Anne Cybelle Pinto, Pablo Henrique Caracciolo Gomes de Sá, Rommel T J Ramos, Silvanira Barbosa, Hivana P Melo Barbosa, Adriana Carneiro Ribeiro, Wanderson Marques Silva, Flávia Souza Rocha, Mariana Passos Santana, Thiago Luiz de Paula Castro, Anderson Miyoshi, Maria P C Schneider, Artur Silva and Vasco Azevedo
    Citation: BMC Genomics 2014 15:14
    Content type: Research article Published on:

  22. While the possible sources underlying the so-called ‘missing heritability’ evident in current genome-wide association studies (GWAS) of complex traits have been actively pursued in recent years, resolving this...

    Authors: Shengjie Yang, Yiyuan Liu, Ning Jiang, Jing Chen, Lindsey Leach, Zewei Luo and Minghui Wang
    Citation: BMC Genomics 2014 15:13
    Content type: Research article Published on:

  23. DNA methylation is an important epigenetic modification that is essential for epigenetic gene regulation in development and disease. To date, the genome-wide DNA methylation maps of many organisms have been re...

    Authors: Jianmin Su, Yongsheng Wang, Xupeng Xing, Jun Liu and Yong Zhang
    Citation: BMC Genomics 2014 15:12
    Content type: Research article Published on:

  24. Polyploid species contribute to Oryza diversity. However, the mechanisms underlying gene and genome evolution in Oryza polyploids remain largely unknown. The allotetraploid Oryza minuta, which is estimated to hav...

    Authors: Yi Sui, Bo Li, Jinfeng Shi and Mingsheng Chen
    Citation: BMC Genomics 2014 15:11
    Content type: Research article Published on:

  26. A major production constraint on the important ornamental species chrysanthemum is black spot which is caused by the necrotrophic fungus Alternaria tenuissima. The molecular basis of host resistance to A. tenuiss...

    Authors: Huiyun Li, Sumei Chen, Aiping Song, Haibin Wang, Weimin Fang, Zhiyong Guan, Jiafu Jiang and Fadi Chen
    Citation: BMC Genomics 2014 15:9
    Content type: Research article Published on:

  27. Comparative genomics is a powerful approach for studying variation in physiological traits as well as the evolution and ecology of microorganisms. Recent technological advances have enabled sequencing large nu...

    Authors: Matthew N Benedict, James R Henriksen, William W Metcalf, Rachel J Whitaker and Nathan D Price
    Citation: BMC Genomics 2014 15:8
    Content type: Software Published on:

  28. Phages infecting spoilage microorganisms have been considered as alternative biocontrol agents, and the study of their genomes is essential to their safe use in foods. UFV-P2 is a new Pseudomonas fluorescens-spec...

    Authors: Monique R Eller, Pedro M P Vidigal, Rafael L Salgado, Maura P Alves, Roberto S Dias, Cynthia C da Silva, Antônio F de Carvalho, Andrew Kropinski and Sérgio O De Paula
    Citation: BMC Genomics 2014 15:7
    Content type: Research article Published on:

  29. The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrospor...

    Authors: Zhongtao Zhao, Huiquan Liu, Chenfang Wang and Jin-Rong Xu
    Citation: BMC Genomics 2014 15:6
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2013 14:274

  30. Because few studies exist to describe the unique molecular network regulation behind pig pre-implantation embryonic development (PED), genetic engineering in the pig embryo is limited. Also, this lack of resea...

    Authors: Suying Cao, Jianyong Han, Jun Wu, Qiuyan Li, Shichao Liu, Wei Zhang, Yangli Pei, Xiaoan Ruan, Zhonghua Liu, Xumin Wang, Bing Lim and Ning Li
    Citation: BMC Genomics 2014 15:4
    Content type: Research article Published on:

  31. Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassic...

    Authors: Jingyin Yu, Sadia Tehrim, Fengqi Zhang, Chaobo Tong, Junyan Huang, Xiaohui Cheng, Caihua Dong, Yanqiu Zhou, Rui Qin, Wei Hua and Shengyi Liu
    Citation: BMC Genomics 2014 15:3
    Content type: Research article Published on:

  32. GSL1 and GSL2, Gibberellin Stimulated-Like proteins (also known as Snakin-1 and Snakin-2), are cysteine-rich peptides from potato (Solanum tuberosum L.) with antimicrobial properties. Similar peptides in other sp...

    Authors: Sathiyamoorthy Meiyalaghan, Susan J Thomson, Mark WEJ Fiers, Philippa J Barrell, Julie M Latimer, Sara Mohan, E Eirian Jones, Anthony J Conner and Jeanne ME Jacobs
    Citation: BMC Genomics 2014 15:2
    Content type: Research article Published on:

  33. Association analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (QTL) and provides relatively high resolution in terms of defining the g...

    Authors: Eun-Young Hwang, Qijian Song, Gaofeng Jia, James E Specht, David L Hyten, Jose Costa and Perry B Cregan
    Citation: BMC Genomics 2014 15:1
    Content type: Research article Published on:

  34. Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observ...

    Authors: Linhuan Wu, Qinglan Sun, Hideaki Sugawara, Song Yang, Yuguang Zhou, Kevin McCluskey, Alexander Vasilenko, Ken-Ichiro Suzuki, Moriya Ohkuma, Yeonhee Lee, Vincent Robert, Supawadee Ingsriswang, François Guissart, Desmeth Philippe and Juncai Ma
    Citation: BMC Genomics 2013 14:933
    Content type: Database Published on:

  35. Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions th...

    Authors: Zlatko Satovic, Carmen M Avila, Serafin Cruz-Izquierdo, Ramón Díaz-Ruíz, Gloria M García-Ruíz, Carmen Palomino, Natalia Gutiérrez, Stefania Vitale, Sara Ocaña-Moral, María Victoria Gutiérrez, José I Cubero and Ana M Torres
    Citation: BMC Genomics 2013 14:932
    Content type: Research article Published on:

  36. Accumulating evidence demonstrates that non-coding RNAs (ncRNAs) are indispensable components of many organisms and play important roles in cellular events, regulation, and development.

    Authors: Tao Liu, Xianwen Ren, Tengfei Xiao, Jian Yang, Xingye Xu, Jie Dong, Lilian Sun, Runsheng Chen and Qi Jin
    Citation: BMC Genomics 2013 14:931
    Content type: Research article Published on:

  37. 3,4-methylenedioxymethamphetamine (MDMA, "ecstasy") is a widely used recreational drug known to impair cognitive functions on the long-run. Both hippocampal and frontal cort...

    Authors: Peter Petschner, Viola Tamasi, Csaba Adori, Eszter Kirilly, Romeo D Ando, Laszlo Tothfalusi and Gyorgy Bagdy
    Citation: BMC Genomics 2013 14:930
    Content type: Research article Published on:

    The Retraction Note to this article has been published in BMC Genomics 2016 17:721

  38. The application of RNA-seq has accelerated gene expression profiling and identification of gene-associated SNPs in many species. However, the integrated studies of gene expression along with SNP mapping have b...

    Authors: Ruijia Wang, Luyang Sun, Lisui Bao, Jiaren Zhang, Yanliang Jiang, Jun Yao, Lin Song, Jianbin Feng, Shikai Liu and Zhanjiang Liu
    Citation: BMC Genomics 2013 14:929
    Content type: Methodology article Published on:

  39. The fungus gardens of leaf-cutting ants are natural biomass conversion systems that turn fresh plant forage into fungal biomass to feed the farming ants. However, the decomposition potential of the symbiont Leuco...

    Authors: Morten N Grell, Tore Linde, Sanne Nygaard, Kåre L Nielsen, Jacobus J Boomsma and Lene Lange
    Citation: BMC Genomics 2013 14:928
    Content type: Research article Published on:

  40. Mixed Lineage Leukemia 1 (MLL1) is a mammalian ortholog of the Drosophila Trithorax. In Drosophila, Trithorax complexes transmit the memory of active genes to daughter cells through interactions with Trithorax Re...

    Authors: Minou Bina, Phillip Wyss, Elise Novorolsky, Noorfatin Zulkelfi, Jing Xue, Randi Price, Matthew Fay, Zach Gutmann, Brian Fogler and Daidong Wang
    Citation: BMC Genomics 2013 14:927
    Content type: Research article Published on:

  41. Microalgae are gaining importance as sustainable production hosts in the fields of biotechnology and bioenergy. A robust biomass accumulating strain of the genus Monoraphidium (SAG 48.87) was investigated in this...

    Authors: Christian Bogen, Arwa Al-Dilaimi, Andreas Albersmeier, Julian Wichmann, Michael Grundmann, Oliver Rupp, Kyle J Lauersen, Olga Blifernez-Klassen, Jörn Kalinowski, Alexander Goesmann, Jan H Mussgnug and Olaf Kruse
    Citation: BMC Genomics 2013 14:926
    Content type: Research article Published on:

  42. Haemophilus influenzae is a significant cause of childhood otitis media, and also has an absolute growth requirement for heme. Recent microarray studies using three H. influenzae isolates were used to propose a p...

    Authors: Paul W Whitby, Timothy M VanWagoner, Thomas W Seale, Daniel J Morton and Terrence L Stull
    Citation: BMC Genomics 2013 14:925
    Content type: Research article Published on:

  43. With genomic sequences of many closely related bacterial strains made available by deep sequencing, it is now possible to investigate trends in prokaryotic microevolution. Positive selection is a sub-process o...

    Authors: Fei Su, Hong-Yu Ou, Fei Tao, Hongzhi Tang and Ping Xu
    Citation: BMC Genomics 2013 14:924
    Content type: Software Published on:

  44. The genetics of development in the nematode Caenorhabditis elegans has been described in exquisite detail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and the Enoplea. While the d...

    Authors: Philipp H Schiffer, Michael Kroiher, Christopher Kraus, Georgios D Koutsovoulos, Sujai Kumar, Julia I R Camps, Ndifon A Nsah, Dominik Stappert, Krystalynne Morris, Peter Heger, Janine Altmüller, Peter Frommolt, Peter Nürnberg, W Kelley Thomas, Mark L Blaxter and Einhard Schierenberg
    Citation: BMC Genomics 2013 14:923
    Content type: Research article Published on:

  45. Standard 3′ Affymetrix gene expression arrays have contributed a significantly higher volume of existing gene expression data than other microarray platforms. These arrays were designed to identify differentia...

    Authors: Neelima Chitturi, Govindkumar Balagannavar, Darshan S Chandrashekar, Sadashivam Abinaya, Vasan S Srini and Kshitish K Acharya
    Citation: BMC Genomics 2013 14:922
    Content type: Software Published on:

  46. Infertility affects ~10-15% of couples trying to have children, in which the rate of male fertility problems is approximately at 30-50%. Copy number variations (CNVs) are DNA sequences greater than or equal to...

    Authors: Daniele Cassatella, Nicola Antonio Martino, Luisa Valentini, Antonio Ciro Guaricci, Maria Francesca Cardone, Flavia Pizzi, Maria Elena Dell’Aquila and Mario Ventura
    Citation: BMC Genomics 2013 14:921
    Content type: Research article Published on:

  47. Streptococcus agalactiae is a major cause of bovine mastitis, which is the dominant health disorder affecting milk production within the dairy industry and is responsible for substantial financial losses to the i...

    Authors: Vincent P Richards, Sang Chul Choi, Paulina D Pavinski Bitar, Abhijit A Gurjar and Michael J Stanhope
    Citation: BMC Genomics 2013 14:920
    Content type: Research article Published on:

  48. A lack of competence to form adventitious roots by cuttings of Chrysanthemum (Chrysanthemum morifolium) is an obstacle for the rapid fixation of elite genotypes. We performed a proteomic analysis of cutting bases...

    Authors: Ruixia Liu, Sumei Chen, Jiafu Jiang, Lu Zhu, Chen Zheng, Shuang Han, Jing Gu, Jing Sun, Huiyun Li, Haibin Wang, Aiping Song and Fadi Chen
    Citation: BMC Genomics 2013 14:919
    Content type: Research article Published on:

  49. Systems biology experiments studying different topics and organisms produce thousands of data values across different types of genomic data. Further, data mining analyses are yielding ranked and heterogeneous ...

    Authors: Jake Lin, Richard Kreisberg, Aleksi Kallio, Aimée M Dudley, Matti Nykter, Ilya Shmulevich, Patrick May and Reija Autio
    Citation: BMC Genomics 2013 14:918
    Content type: Software Published on:

  50. Myzus persicae, the green peach aphid, is a polyphagous herbivore that feeds from hundreds of species of mostly dicot crop plants. Like other phloem-feeding aphids, M. persicae rely on the endosymbiotic bacterium...

    Authors: Zhijie Jiang, Derek H Jones, Sawsan Khuri, Nicholas F Tsinoremas, Tania Wyss, Georg Jander and Alex C C Wilson
    Citation: BMC Genomics 2013 14:917
    Content type: Research article Published on:

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BMC Genomics

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