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  1. Transcriptional gene regulation is a fundamental process in nature, and the experimental and computational investigation of DNA binding motifs and their binding sites is a prerequisite for elucidating this pro...

    Authors: Martin Nettling, Hendrik Treutler, Jesus Cerquides and Ivo Grosse
    Citation: BMC Genomics 2016 17:347
    Content type: Methodology Article Published on:

  2. Ciliate metallothioneins (MTs) are included in family 7 of the MT superfamily. This family has been divided into two main subfamilies: 7a or CdMTs and 7b or CuMTs. All ciliate MTs reported have been isolated f...

    Authors: Patricia de Francisco, Laura María Melgar, Silvia Díaz, Ana Martín-González and Juan Carlos Gutiérrez
    Citation: BMC Genomics 2016 17:346
    Content type: Research article Published on:

  3. Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, ...

    Authors: Nuria Rius, Yolanda Guillén, Alejandra Delprat, Aurélie Kapusta, Cédric Feschotte and Alfredo Ruiz
    Citation: BMC Genomics 2016 17:344
    Content type: Research Article Published on:

  4. WRKY genes, as the most pivotal transcription factors in plants, play the indispensable roles in regulating various physiological processes, including plant growth and development as well as in response to str...

    Authors: Hong Yue, Meng Wang, Siyan Liu, Xianghong Du, Weining Song and Xiaojun Nie
    Citation: BMC Genomics 2016 17:343
    Content type: Research article Published on:

  5. While active LINE-1 (L1) elements possess the ability to mobilize flanking sequences to different genomic loci through a process termed transduction influencing genomic content and structure, an approach for d...

    Authors: Jelena Tica, Eunjung Lee, Andreas Untergasser, Sascha Meiers, David A. Garfield, Omer Gokcumen, Eileen E.M. Furlong, Peter J. Park, Adrian M. Stütz and Jan O. Korbel
    Citation: BMC Genomics 2016 17:342
    Content type: Methodology article Published on:

  6. Despite substantial progress in mosquito genomic and genetic research, few cis-regulatory elements (CREs), DNA sequences that control gene expression, have been identified in mosquitoes or other non-model inse...

    Authors: Susanta K. Behura, Joseph Sarro, Ping Li, Keshava Mysore, David W. Severson, Scott J. Emrich and Molly Duman-Scheel
    Citation: BMC Genomics 2016 17:341
    Content type: Research article Published on:

  8. Lizards are evolutionarily the most closely related vertebrates to humans that can lose and regrow an entire appendage. Regeneration in lizards involves differential expression of hundreds of genes that regula...

    Authors: Elizabeth D. Hutchins, Walter L. Eckalbar, Justin M. Wolter, Marco Mangone and Kenro Kusumi
    Citation: BMC Genomics 2016 17:339
    Content type: Research article Published on:

  9.  High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. This methodology is frequently used to valid...

    Authors: Austin E. Gillen, Tomomi M. Yamamoto, Enos Kline, Jay R. Hesselberth and Peter Kabos
    Citation: BMC Genomics 2016 17:338
    Content type: Methodology article Published on:

  10. A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays...

    Authors: E. V. Evtushenko, V. G. Levitsky, E. A. Elisafenko, K. V. Gunbin, A. I. Belousov, J. Šafář, J. Doležel and A. V. Vershinin
    Citation: BMC Genomics 2016 17:337
    Content type: Research article Published on:

  11. Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a hi...

    Authors: Xiaomei Fang, Kongjun Dong, Xiaoqin Wang, Tianpeng Liu, Jihong He, Ruiyu Ren, Lei Zhang, Rui Liu, Xueying Liu, Man Li, Mengzhu Huang, Zhengsheng Zhang and Tianyu Yang
    Citation: BMC Genomics 2016 17:336
    Content type: Research article Published on:

  12. Dysregulation of the common stress responsive transcription factor ATF3 has been causally linked to many important human diseases such as cancer, atherosclerosis, infections, and hypospadias. Although it is be...

    Authors: Jonathan Zhao, Xingyao Li, Mingxiong Guo, Jindan Yu and Chunhong Yan
    Citation: BMC Genomics 2016 17:335
    Content type: Research article Published on:

  13. Despite the fundamental biological importance and clinical relevance of characterizing the effects of chronic hypoxia exposure on central nervous system (CNS) development, the changes in gene expression from h...

    Authors: Brett Milash, Jingxia Gao, Tamara J. Stevenson, Jong-Hyun Son, Tiffanie Dahl and Joshua L. Bonkowsky
    Citation: BMC Genomics 2016 17:334
    Content type: Research article Published on:

  14. Reproductive success is dependent on development of hypothalamic circuits involving many hormonal systems working in concert to regulate gonadal function and sexual behavior. The timing of pubertal initiation ...

    Authors: Monika M. Kaczmarek, Tamra Mendoza and Leslie P. Kozak
    Citation: BMC Genomics 2016 17:333
    Content type: Research article Published on:

  15. Studies on vertebrate DNA methylomes have revealed a regulatory role of tissue specific DNA methylation in relation to gene expression. However, it is not well known how tissue-specific methylation varies betw...

    Authors: Martijn F. L. Derks, Kyle M. Schachtschneider, Ole Madsen, Elio Schijlen, Koen J. F. Verhoeven and Kees van Oers
    Citation: BMC Genomics 2016 17:332
    Content type: Research article Published on:

  16. Burkholderia pseudomallei is the causative agent of melioidosis, a severe invasive disease of humans and animals. Initial screening of a B. pseudomallei signature-tagged mutagenesis li...

    Authors: Natalie R. Lazar Adler, Elizabeth M. Allwood, Deanna Deveson Lucas, Paul Harrison, Stephen Watts, Alexandra Dimitropoulos, Puthayalai Treerat, Priyangi Alwis, Rodney J. Devenish, Mark Prescott, Brenda Govan, Ben Adler, Marina Harper and John D. Boyce
    Citation: BMC Genomics 2016 17:331
    Content type: Research article Published on:

  17. Penicillium expansum is a destructive phytopathogen that causes decay in deciduous fruits during postharvest handling and storage. During colonization the fungus secretes D-gluconic ac...

    Authors: Shiri Barad, Noa Sela, Dilip Kumar, Amit Kumar-Dubey, Nofar Glam-Matana, Amir Sherman and Dov Prusky
    Citation: BMC Genomics 2016 17:330
    Content type: Research article Published on:

  18. Meat type chickens have limited capacities to cope with high environmental temperatures, this sometimes leading to mortality on farms and subsequent economic losses. A strategy to alleviate this problem is to ...

    Authors: Thomas Loyau, Christelle Hennequet-Antier, Vincent Coustham, Cécile Berri, Marie Leduc, Sabine Crochet, Mélanie Sannier, Michel Jacques Duclos, Sandrine Mignon-Grasteau, Sophie Tesseraud, Aurélien Brionne, Sonia Métayer-Coustard, Marco Moroldo, Jérôme Lecardonnel, Patrice Martin, Sandrine Lagarrigue…
    Citation: BMC Genomics 2016 17:329
    Content type: Research article Published on:

  19. MicroRNAs (miRNAs) represent a second regulatory network that has important effects on gene expression and protein translation during biological process. However, the possible role of miRNAs in the early stage...

    Authors: Wenjing Tao, Lina Sun, Hongjuan Shi, Yunying Cheng, Dongneng Jiang, Beide Fu, Matthew A. Conte, William J. Gammerdinger, Thomas D. Kocher and Deshou Wang
    Citation: BMC Genomics 2016 17:328
    Content type: Research article Published on:

  20. Most living organisms use sunlight as a source of energy and/or information about their environment. Consequently, they have developed mechanisms to sense light quality and quantity. In the fungus Trichoderma atr...

    Authors: José E. Cetz-Chel, Edgar Balcázar-López, Edgardo U. Esquivel-Naranjo and Alfredo Herrera-Estrella
    Citation: BMC Genomics 2016 17:327
    Content type: Research article Published on:

  21. Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the c...

    Authors: Jordane Despres, Evelyne Forano, Pascale Lepercq, Sophie Comtet-Marre, Gregory Jubelin, Christophe Chambon, Carl J. Yeoman, Margaret E. Berg Miller, Christopher J. Fields, Eric Martens, Nicolas Terrapon, Bernard Henrissat, Bryan A. White and Pascale Mosoni
    Citation: BMC Genomics 2016 17:326
    Content type: Research article Published on:

  22. The presence of population structure in a sample may confound the search for important genetic loci associated with disease. Our four samples in the Family Investigation of Nephropathy and Diabetes (FIND), Eur...

    Authors: Robert C. Williams, Robert C. Elston, Pankaj Kumar, William C. Knowler, Hanna E. Abboud, Sharon Adler, Donald W. Bowden, Jasmin Divers, Barry I. Freedman, Robert P. Igo Jr., Eli Ipp, Sudha K. Iyengar, Paul L. Kimmel, Michael J. Klag, Orly Kohn, Carl D. Langefeld…
    Citation: BMC Genomics 2016 17:325
    Content type: Research article Published on:

  23. Genomic prediction (GP) allows breeders to select plants and animals based on their breeding potential for desirable traits, without lengthy and expensive field trials or progeny testing. We have proposed to u...

    Authors: Priyanka Singh, Jasper Engel, Jeroen Jansen, Jorn de Haan and Lutgarde Maria Celina Buydens
    Citation: BMC Genomics 2016 17:324
    Content type: Methodology article Published on:

  24. In oviparous species accidental variation of incubation temperatures may occur under natural conditions and mechanisms may have evolved by natural selection that facilitate coping with these stressors. However...

    Authors: Watcharapong Naraballobh, Nares Trakooljul, Eduard Muráni, Ronald Brunner, Carsten Krischek, Sabine Janisch, Michael Wicke, Siriluck Ponsuksili and Klaus Wimmers
    Citation: BMC Genomics 2016 17:323
    Content type: Research article Published on:

  25. Thymus is the crucial site for T cell development and once believed to be immune privileged. Recently, thymus has gained special attention as it is commonly targeted by infectious agents which may cause pathog...

    Authors: Haibo Huang, An Liu, Hui Wu, Abdur Rahman Ansari, Jixiang Wang, Xiyao Huang, Xing Zhao, Kemei Peng, Juming Zhong and Huazhen Liu
    Citation: BMC Genomics 2016 17:322
    Content type: Research article Published on:

  26. Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for...

    Authors: Francisco J. Herraiz, José Blanca, Pello Ziarsolo, Pietro Gramazio, Mariola Plazas, Gregory J. Anderson, Jaime Prohens and Santiago Vilanova
    Citation: BMC Genomics 2016 17:321
    Content type: Research article Published on:

  27. More than 2,500 breeds of chicken are reared throughout the world as a source of eggs or meat and as pets. The primary ancestor of the present domestic chicken is widely believed to be the red junglefowl, alth...

    Authors: Maria Ulfah, Ryouka Kawahara-Miki, Achmad Farajalllah, Muladno Muladno, Ben Dorshorst, Alison Martin and Tomohiro Kono
    Citation: BMC Genomics 2016 17:320
    Content type: Research article Published on:

  28. Low iron bioavailability is a common feature of ocean surface water and therefore micro-algae developed original strategies to optimize iron uptake and metabolism. The marine picoeukaryotic green alga Ostreococcu...

    Authors: Gaëlle Lelandais, Ivo Scheiber, Javier Paz-Yepes, Jean-Claude Lozano, Hugo Botebol, Jana Pilátová, Vojtěch Žárský, Thibaut Léger, Pierre-Louis Blaiseau, Chris Bowler, François-Yves Bouget, Jean-Michel Camadro, Robert Sutak and Emmanuel Lesuisse
    Citation: BMC Genomics 2016 17:319
    Content type: Research article Published on:

  29. Bardet-Biedl Syndrome (BBS) and Alström Syndrome are two pleiotropic ciliopathies with significant phenotypic overlap between them across many tissues. Although BBS and Alström genes are necessary for the prop...

    Authors: Timothy L. Hostelley, Sukanya Lodh and Norann A. Zaghloul
    Citation: BMC Genomics 2016 17:318
    Content type: Research article Published on:

  30. Plants develop sustainable defence responses to pathogen attacks through resistance (R) genes contributing to effector-triggered immunity (ETI). TIR-NB-LRR genes (TNL genes) constitute a major family of ETI R gen...

    Authors: Cyril Van Ghelder and Daniel Esmenjaud
    Citation: BMC Genomics 2016 17:317
    Content type: Research article Published on:

  31. Cyclospora cayetanensis is an apicomplexan that causes diarrhea in humans. The investigation of foodborne outbreaks of cyclosporiasis has been hampered by a lack of genetic data and po...

    Authors: Shiyou Liu, Lin Wang, Huajun Zheng, Zhixiao Xu, Dawn M. Roellig, Na Li, Michael A. Frace, Kevin Tang, Michael J. Arrowood, Delynn M. Moss, Longxian Zhang, Yaoyu Feng and Lihua Xiao
    Citation: BMC Genomics 2016 17:316
    Content type: Research article Published on:

  32. Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which hav...

    Authors: Diego César Batista Mariano, Thiago de Jesus Sousa, Felipe Luiz Pereira, Flávia Aburjaile, Debmalya Barh, Flávia Rocha, Anne Cybelle Pinto, Syed Shah Hassan, Tessália Diniz Luerce Saraiva, Fernanda Alves Dorella, Alex Fiorini de Carvalho, Carlos Augusto Gomes Leal, Henrique César Pereira Figueiredo, Artur Silva, Rommel Thiago Jucá Ramos and Vasco Ariston Carvalho Azevedo
    Citation: BMC Genomics 2016 17:315
    Content type: Research article Published on:

  34. Opioids are a mainstay for the treatment of chronic pain. Unfortunately, therapy-limiting maladaptations such as loss of treatment effect (tolerance), and paradoxical opioid-induced hyperalgesia (OIH) can occu...

    Authors: Robin Donaldson, Yuan Sun, De-Yong Liang, Ming Zheng, Peyman Sahbaie, David L. Dill, Gary Peltz, Kari J. Buck and J. David Clark
    Citation: BMC Genomics 2016 17:313
    Content type: Research article Published on:

  35. Plant response mechanisms to heat and drought stresses have been considered in strategies for generating stress tolerant genotypes, but with limited success. Here, we analyzed the transcriptome and improved to...

    Authors: José A. Casaretto, Ashraf El-kereamy, Bin Zeng, Suzy M. Stiegelmeyer, Xi Chen, Yong-Mei Bi and Steven J. Rothstein
    Citation: BMC Genomics 2016 17:312
    Content type: Research article Published on:

  36. Authors: Pamela A. Alexandre, Lisette J. A. Kogelman, Miguel H. A. Santana, Danielle Passarelli, Lidia H. Pulz, Paulo Fantinato-Neto, Saulo Luz Silva, Paulo R. Leme, Ricardo F. Strefezzi, Luiz L. Coutinho, José B. S. Ferraz, Joanir P. Eler, Haja N. Kadarmideen and Heidge Fukumasu
    Citation: BMC Genomics 2016 17:311
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2015 16:1073

  38. Hearing loss is the most common sensory defect afflicting several hundred million people worldwide. In most cases, regardless of the original cause, hearing loss is related to the degeneration and death of hai...

    Authors: Sabrina Riccardi, Sebastian Bergling, Frederic Sigoillot, Martin Beibel, Annick Werner, Juliet Leighton-Davies, Judith Knehr, Tewis Bouwmeester, Christian N. Parker, Guglielmo Roma and Bernd Kinzel
    Citation: BMC Genomics 2016 17:309
    Content type: Research article Published on:

  39. Oenococcus oeni is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermen...

    Authors: Peter R. Sternes and Anthony R. Borneman
    Citation: BMC Genomics 2016 17:308
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:813

  40. The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to addres...

    Authors: I-Min A. Chen, Victor M. Markowitz, Krishna Palaniappan, Ernest Szeto, Ken Chu, Jinghua Huang, Anna Ratner, Manoj Pillay, Michalis Hadjithomas, Marcel Huntemann, Natalia Mikhailova, Galina Ovchinnikova, Natalia N. Ivanova and Nikos C. Kyrpides
    Citation: BMC Genomics 2016 17:307
    Content type: Software Published on:

  41. Trypanosoma brucei is a unicellular parasite which multiplies in mammals (bloodstream form) and Tsetse flies (procyclic form). Trypanosome RNA polymerase II transcription is polycistro...

    Authors: Enoch B. Antwi, Jurgen R. Haanstra, Gowthaman Ramasamy, Bryan Jensen, Dorothea Droll, Federico Rojas, Igor Minia, Monica Terrao, Clémentine Mercé, Keith Matthews, Peter J. Myler, Marilyn Parsons and Christine Clayton
    Citation: BMC Genomics 2016 17:306
    Content type: Research article Published on:

  42. Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell o...

    Authors: Jessica M. Vera and Robin D. Dowell
    Citation: BMC Genomics 2016 17:305
    Content type: Research article Published on:

  43. cAMP signaling produces dramatic changes in astrocyte morphology and physiology. However, its involvement in phenotype acquisition and the transcriptionally mediated mechanisms of action are largely unknown.

    Authors: Sonia Paco, Manuela Hummel, Virginia Plá, Lauro Sumoy and Fernando Aguado
    Citation: BMC Genomics 2016 17:304
    Content type: Research article Published on:

  44. Valeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots ...

    Authors: Yun Ji Park, Xiaohua Li, Seung Jae Noh, Jae Kwang Kim, Soon Sung Lim, Nam Il Park, Soonok Kim, Yeon Bok Kim, Young Ock Kim, Sang Won Lee, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi and Sang Un Park
    Citation: BMC Genomics 2016 17:303
    Content type: Research article Published on:

  45. Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinf...

    Authors: Jelena Čuklina, Julia Hahn, Maxim Imakaev, Ulrich Omasits, Konrad U. Förstner, Nikolay Ljubimov, Melanie Goebel, Gabriella Pessi, Hans-Martin Fischer, Christian H. Ahrens, Mikhail S. Gelfand and Elena Evguenieva-Hackenberg
    Citation: BMC Genomics 2016 17:302
    Content type: Research article Published on:

  46. Pine wilt disease (PWD) is a worldwide threat to pine forests, and is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus. Bacteria are known to be associated with PWN and may have an important role...

    Authors: Claudia S. L. Vicente, Francisco X. Nascimento, Yoriko Ikuyo, Peter J. A. Cock, Manuel Mota and Koichi Hasegawa
    Citation: BMC Genomics 2016 17:301
    Content type: Research article Published on:

  47. Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatib...

    Authors: P. Gramazio, J. Blanca, P. Ziarsolo, F. J. Herraiz, M. Plazas, J. Prohens and S. Vilanova
    Citation: BMC Genomics 2016 17:300
    Content type: Research article Published on:

  48. Dissecting the role copy number variants (CNVs) play in disease pathogenesis is directly reliant on accurate methods for quantification. The Shar-Pei dog breed is predisposed to a complex autoinflammatory dise...

    Authors: M. Olsson, M. Kierczak, Å. Karlsson, J. Jabłońska, P. Leegwater, M. Koltookian, J. Abadie, C. Dufaure De Citres, A. Thomas, Å. Hedhammar, L. Tintle, K. Lindblad-Toh and J. R. S. Meadows
    Citation: BMC Genomics 2016 17:299
    Content type: Research article Published on:

  49. Nonalcoholic fatty liver disease (NAFLD) is a major health problem and a leading cause of chronic liver disease in the United States and Western countries. In humans, genetic factors greatly influence individu...

    Authors: Volodymyr P. Tryndyak, Tao Han, James C. Fuscoe, Sharon A. Ross, Frederick A. Beland and Igor P. Pogribny
    Citation: BMC Genomics 2016 17:298
    Content type: Research article Published on:

  50. Non-heading Chinese cabbage (NHCC, Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, little is known about the molecular mechanisms underlying tolerance for extreme temperatur...

    Authors: Xiaoming Song, Gaofeng Liu, Zhinan Huang, Weike Duan, Huawei Tan, Ying Li and Xilin Hou
    Citation: BMC Genomics 2016 17:297
    Content type: Research article Published on:

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BMC Genomics

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