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  1. Primula species are important early spring garden plants with a centre of diversity and speciation in the East Himalaya-Hengduan Mountains in Western China. Studies on population genetics, speciation and phylogen...

    Authors: Lu Zhang, Hai-Fei Yan, Wei Wu, Hui Yu and Xue-Jun Ge
    Citation: BMC Genomics 2013 14:329
    Content type: Research article Published on:

  2. The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (si...

    Authors: Vidhyavathi Raman, Stacey A Simon, Amanda Romag, Feray Demirci, Sandra M Mathioni, Jixian Zhai, Blake C Meyers and Nicole M Donofrio
    Citation: BMC Genomics 2013 14:326
    Content type: Research article Published on:

  4. In recent years, various types of cellular networks have penetrated biology and are nowadays used omnipresently for studying eukaryote and prokaryote organisms. Still, the relation and the biological overlap a...

    Authors: Ricardo de Matos Simoes, Matthias Dehmer and Frank Emmert-Streib
    Citation: BMC Genomics 2013 14:324
    Content type: Research article Published on:

  6. Root-knot nematodes (RKN– Meloidogyne genus) present extensive challenges to soybean crop. The soybean line (PI 595099) is known to be resistant against specific strains and races of nematode species, thus its di...

    Authors: Magda Aparecida Beneventi, Orzenil Bonfim da Silva Jr, Maria Eugênia Lisei de Sá, Alexandre Augusto Pereira Firmino, Regina Maria Santos de Amorim, Érika Valéria Saliba Albuquerque, Maria Cristina Mattar da Silva, Joseane Padilha da Silva, Magnólia de Araújo Campos, Marcus José Conceição Lopes, Roberto Coiti Togawa, Georgios Joanis Pappas Jr and Maria Fatima Grossi–de–Sa
    Citation: BMC Genomics 2013 14:322
    Content type: Research article Published on:

  7. We hypothesized that genes that are up-regulated in the uterine endometrium at the initiation of conceptus elongation in cattle, and that encode for secreted proteins, contribute to the composition of the uter...

    Authors: Niamh Forde, Jai P Mehta, Paul A McGettigan, Solomon Mamo, Fuller W Bazer, Thomas E Spencer and Pat Lonergan
    Citation: BMC Genomics 2013 14:321
    Content type: Research article Published on:

  8. Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms durin...

    Authors: Sergei A Solonenko, J César Ignacio-Espinoza, Adriana Alberti, Corinne Cruaud, Steven Hallam, Kostas Konstantinidis, Gene Tyson, Patrick Wincker and Matthew B Sullivan
    Citation: BMC Genomics 2013 14:320
    Content type: Research article Published on:

  9. Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers....

    Authors: Xiaoyi Huang, Tiezheng Yuan, Michael Tschannen, Zhifu Sun, Howard Jacob, Meijun Du, Meihua Liang, Rachel L Dittmar, Yong Liu, Mingyu Liang, Manish Kohli, Stephen N Thibodeau, Lisa Boardman and Liang Wang
    Citation: BMC Genomics 2013 14:319
    Content type: Research article Published on:

  10. Leucine-rich repeat receptor-like kinases (LRR-RLKs) comprise the largest group within the receptor-like kinase (RLK) superfamily in plants. This gene family plays critical and diverse roles in plant growth, d...

    Authors: Yanjun Zan, Yan Ji, Yu Zhang, Shaohui Yang, Yingjin Song and Jiehua Wang
    Citation: BMC Genomics 2013 14:318
    Content type: Research article Published on:

  11. The ABC (ATP-binding cassette) gene superfamily is widespread across all living species. The majority of ABC genes encode ABC transporters, which are membrane-spanning proteins capable of transferring substrat...

    Authors: Wannes Dermauw, Edward John Osborne, Richard M Clark, Miodrag Grbić, Luc Tirry and Thomas Van Leeuwen
    Citation: BMC Genomics 2013 14:317
    Content type: Research article Published on:

  12. Prion proteins conform a special class among amyloids due to their ability to transmit aggregative folds. Prions are known to act as infectious agents in neurodegenerative diseases in animals, or as key elemen...

    Authors: Vladimir Espinosa Angarica, Salvador Ventura and Javier Sancho
    Citation: BMC Genomics 2013 14:316
    Content type: Methodology article Published on:

  13. The common sole (Solea solea) is a promising candidate for European aquaculture; however, the limited knowledge of the physiological mechanisms underlying larval development in this species has hampered the estab...

    Authors: Serena Ferraresso, Alessio Bonaldo, Luca Parma, Stefano Cinotti, Paola Massi, Luca Bargelloni and Pier Paolo Gatta
    Citation: BMC Genomics 2013 14:315
    Content type: Research article Published on:

  15. Identification of QTL with large phenotypic effects conserved across genetic backgrounds and environments is one of the prerequisites for crop improvement using marker assisted selection (MAS). The objectives ...

    Authors: Kassa Semagn, Yoseph Beyene, Marilyn L Warburton, Amsal Tarekegne, Stephen Mugo, Barbara Meisel, Pierre Sehabiague and Boddupalli M Prasanna
    Citation: BMC Genomics 2013 14:313
    Content type: Research article Published on:

  16. Probiotic bifidobacteria in combination with prebiotic carbohydrates have documented positive effects on human health regarding gastrointestinal disorders and improved immunity, however the selective routes of...

    Authors: Joakim M Andersen, Rodolphe Barrangou, Maher Abou Hachem, Sampo J Lahtinen, Yong Jun Goh, Birte Svensson and Todd R Klaenhammer
    Citation: BMC Genomics 2013 14:312
    Content type: Research article Published on:

  17. When faced with climate change, species must either shift their home range or adapt in situ in order to maintain optimal physiological balance with their environment. The American pika (Ochotona princeps) is a sm...

    Authors: Matthew A Lemay, Philippe Henry, Clayton T Lamb, Kelsey M Robson and Michael A Russello
    Citation: BMC Genomics 2013 14:311
    Content type: Research article Published on:

  18. Specific chromatin structures are associated with active or inactive gene transcription. The gene regulatory elements are intrinsically dynamic and alternate between inactive and active states through the recr...

    Authors: Chia-Chun Yang, Michael J Buck, Min-Hsuan Chen, Yun-Fan Chen, Hsin-Chi Lan, Jeremy JW Chen, Chao Cheng and Chun-Chi Liu
    Citation: BMC Genomics 2013 14:310
    Content type: Methodology article Published on:

  19. Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong i...

    Authors: Matteo Brilli, Pietro Liò, Vincent Lacroix and Marie-France Sagot
    Citation: BMC Genomics 2013 14:309
    Content type: Research article Published on:

  21. Genetic information based on molecular markers has increasingly being used in cattle breeding improvement programmes, as a mean to improve conventionally phenotypic selection. Advances in molecular genetics ha...

    Authors: Anis Djari, Diane Esquerré, Bernard Weiss, Frédéric Martins, Cédric Meersseman, Mekki Boussaha, Christophe Klopp and Dominique Rocha
    Citation: BMC Genomics 2013 14:307
    Content type: Research article Published on:

  23. Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate...

    Authors: Rafael Espigolan, Fernando Baldi, Arione A Boligon, Fabio RP Souza, Daniel GM Gordo, Rafael L Tonussi, Diércles F Cardoso, Henrique N Oliveira, Humberto Tonhati, Mehdi Sargolzaei, Flavio S Schenkel, Roberto Carvalheiro, Jesus A Ferro and Lucia G Albuquerque
    Citation: BMC Genomics 2013 14:305
    Content type: Research article Published on:

  24. Directed cell migration is a fundamental process in normal development and in tumor metastasis. In C. elegans the MAB-5/Hox transcription factor is a determinant of posterior migration of the Q neuroblast descend...

    Authors: Joel V Tamayo, Mahekta Gujar, Stuart J Macdonald and Erik A Lundquist
    Citation: BMC Genomics 2013 14:304
    Content type: Research article Published on:

  25. Traumatic brain injury (TBI) induces arachidonic acid (ArA) release from cell membranes. ArA metabolites form a class of over 50 bioactive eicosanoids that can induce both adaptive and/or maladaptive brain res...

    Authors: Matthew Birnie, Ryan Morrison, Ramatoulie Camara and Kenneth I Strauss
    Citation: BMC Genomics 2013 14:303
    Content type: Research article Published on:

  26. The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often tryin...

    Authors: Alexis Christoforides, John D Carpten, Glen J Weiss, Michael J Demeure, Daniel D Von Hoff and David W Craig
    Citation: BMC Genomics 2013 14:302
    Content type: Methodology article Published on:

  27. Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves th...

    Authors: Victoria A Jenkins, Geraint R Barton, Brian D Robertson and Kerstin J Williams
    Citation: BMC Genomics 2013 14:301
    Content type: Research article Published on:

  28. The Bacillus subtilis genome (BGM) vector is a novel cloning system for large DNA fragments, in which the entire 4.2 Mb genome of B. subtilis functions as a vector. The BGM vector system has several attractive pr...

    Authors: Tetsuo Iwata, Shinya Kaneko, Yuh Shiwa, Takayuki Enomoto, Hirofumi Yoshikawa and Junji Hirota
    Citation: BMC Genomics 2013 14:300
    Content type: Methodology article Published on:

  29. Enterococcus faecium is a Gram-positive commensal bacterium of the mammalian intestinal tract. In the last two decades it has also emerged as a multi-resistant nosocomial pathogen. In order to survive in and colo...

    Authors: Xinglin Zhang, Damien Bierschenk, Janetta Top, Iacovos Anastasiou, Marc JM Bonten, Rob JL Willems and Willem van Schaik
    Citation: BMC Genomics 2013 14:299
    Content type: Research article Published on:

  30. Small RNAs complex with proteins to mediate a variety of functions in animals and plants. Some small RNAs, particularly miRNAs, circulate in mammalian blood and may carry out a signaling function by entering t...

    Authors: Joseph M Dhahbi, Stephen R Spindler, Hani Atamna, Amy Yamakawa, Dario Boffelli, Patricia Mote and David IK Martin
    Citation: BMC Genomics 2013 14:298
    Content type: Research article Published on:

  31. Auxin plays important roles in hormone crosstalk and the plant’s stress response. The auxin-responsive Gretchen Hagen3 (GH3) gene family maintains hormonal homeostasis by conjugating excess indole-3-acetic acid (...

    Authors: Huazhao Yuan, Kai Zhao, Hengjiu Lei, Xinjie Shen, Yun Liu, Xiong Liao and Tianhong Li
    Citation: BMC Genomics 2013 14:297
    Content type: Research article Published on:

  32. The lactating mammary gland responds to changes in milking frequency by modulating milk production. This response is locally regulated and, in dairy cows, the udder is particularly sensitive during early lacta...

    Authors: Emma H Wall, Jeffrey P Bond and Thomas B McFadden
    Citation: BMC Genomics 2013 14:296
    Content type: Research article Published on:

  33. The editors of BMC Genomics would like to thank all our reviewers who have contributed to the journal in volume 13 (2012).

    Authors: Catherine M Rice
    Citation: BMC Genomics 2013 14:231
    Content type: Reviewer acknowledgement Published on:

  34. Aquaculture is the quickest growing sector in agriculture. However, QTL for important traits have been only identified in a few aquaculture species. We conducted QTL mapping for growth traits in an Asian seaba...

    Authors: Jun Hong Xia, Grace Lin, Xiaoping He, Peng Liu, Feng Liu, Fei Sun, Rongjian Tu and Gen Hua Yue
    Citation: BMC Genomics 2013 14:295
    Content type: Research article Published on:

  35. The fucoid brown algae (Heterokontophyta, Phaeophyceae) are increasingly the focus of ecological genetics, biodiversity, biogeography and speciation research. The molecular genetics underlying mating system va...

    Authors: Maria João F Martins, Catarina F Mota and Gareth A Pearson
    Citation: BMC Genomics 2013 14:294
    Content type: Research article Published on:

  36. As the most stable and experimentally accessible epigenetic mark, DNA methylation is of great interest to the research community. The landscape of DNA methylation across tissues, through development and in dis...

    Authors: Ruth Pidsley, Chloe C Y Wong, Manuela Volta, Katie Lunnon, Jonathan Mill and Leonard C Schalkwyk
    Citation: BMC Genomics 2013 14:293
    Content type: Methodology article Published on:

  37. Mesorhizobium metallidurans STM 2683T and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils. They tolerate unusually high Zin...

    Authors: Géraldine Maynaud, Brigitte Brunel, Damien Mornico, Maxime Durot, Dany Severac, Emeric Dubois, Elisabeth Navarro, Jean-Claude Cleyet-Marel and Antoine Le Quéré
    Citation: BMC Genomics 2013 14:292
    Content type: Research article Published on:

  38. The principal toxicity of acute organophosphate (OP) pesticide poisoning is the disruption of neurotransmission through inhibition of acetylcholinesterase (AChE). However, other mechanisms leading to persisten...

    Authors: John A Lewis, Elizabeth A Gehman, Christine E Baer and David A Jackson
    Citation: BMC Genomics 2013 14:291
    Content type: Research article Published on:

  39. Amyloid-β plaques are a defining characteristic of Alzheimer Disease. However, Amyloid-β deposition is also found in other forms of dementia and in non-pathological contexts. Amyloid-β deposition is variable a...

    Authors: William G Tharp and Indra Neil Sarkar
    Citation: BMC Genomics 2013 14:290
    Content type: Research article Published on:

  40. With the emergence of next-generation sequencing, the availability of prokaryotic genome sequences is expanding rapidly. A total of 5,276 genomes have been released since 2008, yet only 1,692 genomes were comp...

    Authors: Biao Tang, Qi Wang, Minjun Yang, Feng Xie, Yongqiang Zhu, Ying Zhuo, Shengyue Wang, Hong Gao, Xiaoming Ding, Lixin Zhang, Guoping Zhao and Huajun Zheng
    Citation: BMC Genomics 2013 14:289
    Content type: Software Published on:

  41. The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference ...

    Authors: Konstantin Tretyakov, Tatyana Goldberg, Victor X Jin and Paul Horton
    Citation: BMC Genomics 2013 14(Suppl 2):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  42. DNA methylation analysis is useful for investigation of male fertility in mammals, whereas the reliance on tissues limits the research on human. We have previously found the presence of high concentration of c...

    Authors: Chunlin Wu, Xiaofang Ding, Honggang Li, Changhong Zhu and Chengliang Xiong
    Citation: BMC Genomics 2013 14:288
    Content type: Research article Published on:

  43. Pigmentation patterns are one of the most recognizable phenotypes across the animal kingdom. They play an important role in camouflage, communication, mate recognition and mate choice. Most progress on underst...

    Authors: Claire T O’Quin, Alexi C Drilea, Matthew A Conte and Thomas D Kocher
    Citation: BMC Genomics 2013 14:287
    Content type: Research article Published on:

  44. Nocardia cyriacigeorgica is recognized as one of the most prevalent etiological agents of human nocardiosis. Human exposure to these Actinobacteria stems from direct contact with contaminated environmental matric...

    Authors: Anthony Zoropogui, Petar Pujic, Philippe Normand, Valérie Barbe, Patrick Belli, Arnault Graindorge, David Roche, David Vallenet, Sophie Mangenot, Patrick Boiron, Véronica Rodriguez-Nava, Sebastien Ribun, Yves Richard, Benoit Cournoyer and Didier Blaha
    Citation: BMC Genomics 2013 14:286
    Content type: Research article Published on:

  45. The saprophytic pathogen Listeria monocytogenes has to cope with a variety of acidic habitats during its life cycle. The impact of low-temperature coupled with pH decrease for global gene expression and subsequen...

    Authors: Klaus Neuhaus, Peter Satorhelyi, Kristina Schauer, Siegfried Scherer and Thilo M Fuchs
    Citation: BMC Genomics 2013 14:285
    Content type: Research article Published on:

  46. Eukaryotic chromatin architecture is affected by intrinsic histone-DNA sequence preferences, steric exclusion between nucleosome particles, formation of higher-order structures, and in vivo activity of chromatin ...

    Authors: George Locke, Devorah Haberman, Steven M Johnson and Alexandre V Morozov
    Citation: BMC Genomics 2013 14:284
    Content type: Research article Published on:

  47. Butterflies are popular model organisms to study physiological mechanisms underlying variability in oogenesis and egg provisioning in response to environmental conditions. Nothing is known, however, about; the...

    Authors: Jean-Michel Carter, Simon C Baker, Ryan Pink, David RF Carter, Aiden Collins, Jeremie Tomlin, Melanie Gibbs and Casper J Breuker
    Citation: BMC Genomics 2013 14:283
    Content type: Research article Published on:

  48. Traumatic brain injury (TBI) results in irreversible damage at the site of impact and initiates cellular and molecular processes that lead to secondary neural injury in the surrounding tissue. We used microarr...

    Authors: Todd E White, Gregory D Ford, Monique C Surles-Zeigler, Alicia S Gates, Michelle C LaPlaca and Byron D Ford
    Citation: BMC Genomics 2013 14:282
    Content type: Research article Published on:

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BMC Genomics

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