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  1. MicroRNAs (miRNAs) are short non-coding RNAs that are emerging as important post-transcriptional regulators of neuronal and synaptic development. The precise impact of miRNAs on presynaptic function and neurot...

    Authors: Vivian Y. Poon, Minxia Gu, Fang Ji, Antonius M. VanDongen and Marc Fivaz
    Citation: BMC Genomics 2016 17:777
    Content type: Research article Published on:

  2. MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known...

    Authors: Christian Wake, Adam Labadorf, Alexandra Dumitriu, Andrew G. Hoss, Joli Bregu, Kenneth H. Albrecht, Anita L. DeStefano and Richard H. Myers
    Citation: BMC Genomics 2016 17:776
    Content type: Research article Published on:

  3. Manganese (Mn) has several essential functions in plants, including a role as cofactor in the oxygen evolving complex (OEC) of photosystem II (PSII). Manganese deficiency is a major plant nutritional disorder ...

    Authors: Florian Leplat, Pai Rosager Pedas, Søren Kjærsgaard Rasmussen and Søren Husted
    Citation: BMC Genomics 2016 17:775
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:805

  4. Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for im...

    Authors: Sofía P. Brandariz, Agustín González Reymúndez, Bettina Lado, Marcos Malosetti, Antonio Augusto Franco Garcia, Martín Quincke, Jarislav von Zitzewitz, Marina Castro, Iván Matus, Alejandro del Pozo, Ariel J. Castro and Lucía Gutiérrez
    Citation: BMC Genomics 2016 17:773
    Content type: Research article Published on:

  5. Symbioses throughout the animal kingdom are known to extend physiological and ecological capabilities to hosts. Insect-microbe associations are extremely common and are often related to novel niche exploitatio...

    Authors: Brittany F. Peterson and Michael E. Scharf
    Citation: BMC Genomics 2016 17:772
    Content type: Research article Published on:

  6. The parasitic flowering plant dwarf mistletoe (Arceuthobium spp., Viscaceae) is one of the most destructive forest pests, posing a major threat to numerous conifer species worldwide. Arceuthobium sichuanense (spr...

    Authors: Yonglin Wang, Xuewu Li, Weifen Zhou, Tao Li and Chengming Tian
    Citation: BMC Genomics 2016 17:771
    Content type: Research article Published on:

  7. The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an afforda...

    Authors: Maria G. Onyango, Nicola C. Aitken, Cameron Jack, Aaron Chuah, James Oguya, Appolinaire Djikeng, Steve Kemp, Glenn A. Bellis, Adrian Nicholas, Peter J. Walker and Jean-Bernard Duchemin
    Citation: BMC Genomics 2016 17:769
    Content type: Research article Published on:

  8. Bidirectional gene pairs are highly abundant and mostly co-regulated in eukaryotic genomes. The structural features of bidirectional promoters (BDPs) have been well studied in yeast, humans and plants. However...

    Authors: Yuan Fang, Lei Wang, Ximeng Wang, Qi You, Xiucai Pan, Jin Xiao, Xiu-e Wang, Yufeng Wu, Zhen Su and Wenli Zhang
    Citation: BMC Genomics 2016 17:768
    Content type: Research article Published on:

  9. The genus Bordetella consists of nine species that include important respiratory pathogens such as the ‘classical’ species B. bronchiseptica, B. pertussis and B. parapertussis and six more distantly related and l...

    Authors: Bodo Linz, Yury V. Ivanov, Andrew Preston, Lauren Brinkac, Julian Parkhill, Maria Kim, Simon R. Harris, Laura L. Goodfield, Norman K. Fry, Andrew R. Gorringe, Tracy L. Nicholson, Karen B. Register, Liliana Losada and Eric T. Harvill
    Citation: BMC Genomics 2016 17:767
    Content type: Research article Published on:

  10. A-to-I RNA-editing mediated by ADAR (adenosine deaminase acting on RNA) enzymes that converts adenosine to inosine in RNA sequence can generate mutations and alter gene regulation in metazoans. Previous studies h...

    Authors: Si Qiu, Wenhui Li, Heng Xiong, Dongbing Liu, Yali Bai, Kui Wu, Xiuqing Zhang, Huanming Yang, Kun Ma, Yong Hou and Bo Li
    Citation: BMC Genomics 2016 17:766
    Content type: Research article Published on:

  11. The ascomycetous family Chaetomiaceae (class Sordariomycetes) includes numerous soilborn, saprophytic, endophytic and pathogenic fungi which can adapt to various growth conditions and living niches by providing a...

    Authors: Marcel Zámocký, Hakim Tafer, Katarína Chovanová, Ksenija Lopandic, Anna Kamlárová and Christian Obinger
    Citation: BMC Genomics 2016 17:763
    Content type: Research article Published on:

  13. Remarkable advances in Next Generation Sequencing (NGS) technologies, bioinformatics algorithms and computational technologies have significantly accelerated genomic research. However, complicated NGS data ana...

    Authors: Weizhong Li, R. Alexander Richter, Yunsup Jung, Qiyun Zhu and Robert W. Li
    Citation: BMC Genomics 2016 17:761
    Content type: Software Published on:

  14. ATP-binding cassette (ABC) transporters are one of the major transmembrane protein families found in all organisms and play important roles in transporting a variety of compounds across intra and extra cellula...

    Authors: Weiping Qi, Xiaoli Ma, Weiyi He, Wei Chen, Mingmin Zou, Geoff M. Gurr, Liette Vasseur and Minsheng You
    Citation: BMC Genomics 2016 17:760
    Content type: Research article Published on:

  15. Sainfoin (Onobrychis viciifolia) is a highly nutritious tannin-containing forage legume. In the diet of ruminants sainfoin can have anti-parasitic effects and reduce methane emissions under in vitro conditions. M...

    Authors: Marina Mora-Ortiz, Martin T. Swain, Martin J. Vickers, Matthew J. Hegarty, Rhys Kelly, Lydia M. J. Smith and Leif Skøt
    Citation: BMC Genomics 2016 17:756
    Content type: Research article Published on:

  16. Drug-induced liver injury (DILI) is a well-recognized adverse event of anti tuberculosis drugs (ATD) possibly associated with genetic variations. The objective of this study was to perform genome-wide associat...

    Authors: Zelalem Petros, Ming-Ta Michael Lee, Atsushi Takahashi, Yanfei Zhang, Getnet Yimer, Abiy Habtewold, Wondwossen Amogne, Getachew Aderaye, Ina Schuppe-Koistinen, Taisei Mushiroda, Eyasu Makonnen, Michiaki Kubo and Eleni Aklillu
    Citation: BMC Genomics 2016 17:755
    Content type: Research article Published on:

  17. The identification of genomic biomarkers is a key step towards improving diagnostic tests and therapies. We present a reference-free method for this task that relies on a k-mer representation of genomes and a mac...

    Authors: Alexandre Drouin, Sébastien Giguère, Maxime Déraspe, Mario Marchand, Michael Tyers, Vivian G. Loo, Anne-Marie Bourgault, François Laviolette and Jacques Corbeil
    Citation: BMC Genomics 2016 17:754
    Content type: Methodology Article Published on:

  18. Linkage of DNA markers with phenotypic traits provides essential information to dissect clustered genes with potential phenotypic contributions in a target genome region. Pinus flexilis E. James (limber pine) is ...

    Authors: Jun-Jun Liu, Anna W. Schoettle, Richard A. Sniezko, Rona N. Sturrock, Arezoo Zamany, Holly Williams, Amanda Ha, Danelle Chan, Bob Danchok, Douglas P. Savin and Angelia Kegley
    Citation: BMC Genomics 2016 17:753
    Content type: Research article Published on:

  20. Differences between cattle production systems can influence the nutritional and sensory characteristics of beef, in particular its fatty acid (FA) composition. As beef products derived from pasture-based syste...

    Authors: Torres Sweeney, Alex Lejeune, Aidan P. Moloney, Frank J. Monahan, Paul Mc Gettigan, Gerard Downey, Stephen D. E. Park and Marion T. Ryan
    Citation: BMC Genomics 2016 17:746
    Content type: Research article Published on:

  21. Genome-wide association studies have revealed associations between single-nucleotide polymorphisms (SNPs) and phenotypes such as disease symptoms and drug tolerance. To address the small sample size for rare v...

    Authors: Takanori Hasegawa, Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori and Masao Nagasaki
    Citation: BMC Genomics 2016 17:745
    Content type: Software Published on:

  22. Bayesian mixture models in which the effects of SNP are assumed to come from normal distributions with different variances are attractive for simultaneous genomic prediction and QTL mapping. These models are u...

    Authors: Tingting Wang, Yi-Ping Phoebe Chen, Phil J. Bowman, Michael E. Goddard and Ben J. Hayes
    Citation: BMC Genomics 2016 17:744
    Content type: Research article Published on:

  24. Brucellosis is a bacterial disease caused by Brucella infection. In the late fifties, Brucella suis vaccine strain S2 with reduced virulence was obtained by serial transfer of a virulent B. suis biovar 1 strain i...

    Authors: Dong-dong Di, Hai Jiang, Li-li Tian, Jing-li Kang, Wen Zhang, Xin-ping Yi, Feng Ye, Qi Zhong, Bo Ni, You-yu He, Lin Xia, Yao Yu, Bu-yun Cui, Xiang Mao and Wei-xing Fan
    Citation: BMC Genomics 2016 17:741
    Content type: Research article Published on:

  25. Isothiocyanates (ITCs) are degradation products of the plant secondary metabolites glucosinolates (GSLs) and are known to affect human health as well as plant herbivores and pathogens. To investigate the proce...

    Authors: Ralph Kissen, Anders Øverby, Per Winge and Atle M. Bones
    Citation: BMC Genomics 2016 17:740
    Content type: Research article Published on:

  27. Alterations in gene expression are key events in disease etiology and risk. Poor reproducibility in detecting differentially expressed genes across studies suggests individual genes may not be sufficiently inf...

    Authors: Katherine Hartmann, Michał Seweryn, Samuel K. Handleman, Grzegorz A. Rempała and Wolfgang Sadee
    Citation: BMC Genomics 2016 17:738
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:988

  28. Various small RNA (sRNA) sizes and varieties have been identified, but their relationship as well as relationship with their origins and allocations have not been well understood or investigated.

    Authors: Michael Hackenberg, Antonio Rueda, Perry Gustafson, Peter Langridge and Bu-Jun Shi
    Citation: BMC Genomics 2016 17:735
    Content type: Research article Published on:

  29. The Borrelia burgdorferi sensu lato (s.l.) species complex consists of tick-transmitted bacteria and currently comprises approximately 20 named and proposed genospecies some of which are known to cause Lyme Borre...

    Authors: Noémie S. Becker, Gabriele Margos, Helmut Blum, Stefan Krebs, Alexander Graf, Robert S. Lane, Santiago Castillo-Ramírez, Andreas Sing and Volker Fingerle
    Citation: BMC Genomics 2016 17:734
    Content type: Research article Published on:

  31. Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatm...

    Authors: Afreenish Hassan, Anam Naz, Ayesha Obaid, Rehan Zafar Paracha, Kanwal Naz, Faryal Mehwish Awan, Syed Aun Muhmmad, Hussnain Ahmed Janjua, Jamil Ahmad and Amjad Ali
    Citation: BMC Genomics 2016 17:732
    Content type: Research article Published on:

  32. Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequ...

    Authors: Mengmeng Lu, Konstantin V. Krutovsky, C. Dana Nelson, Tomasz E. Koralewski, Thomas D. Byram and Carol A. Loopstra
    Citation: BMC Genomics 2016 17:730
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:869

  33. The protozoan parasite Trypanosoma cruzi, causative agent of Chagas disease, depends upon a cell surface-expressed trans-sialidase (ts) to avoid activation of complement-mediated lysis and to enhance intracellula...

    Authors: D. Brent Weatherly, Duo Peng and Rick L. Tarleton
    Citation: BMC Genomics 2016 17:729
    Content type: Research article Published on:

  34. Hydrallantois is the excessive accumulation of fluid within the allantoic cavity in pregnant animals and is associated with fetal mortality. Although the incidence of hydrallantois is very low in artificial in...

    Authors: Shinji Sasaki, Kiyotoshi Hasegawa, Tomoko Higashi, Yutaka Suzuki, Sumio Sugano, Yasuaki Yasuda and Yoshikazu Sugimoto
    Citation: BMC Genomics 2016 17:724
    Content type: Research article Published on:

  35. Genome-wide CRISPR-Cas9 dropout screens can identify genes whose knockout affects cell viability. Recent CRISPR screens detected thousands of essential genes required for cellular survival and key cellular pro...

    Authors: Michael K. Kiessling, Sven Schuierer, Silke Stertz, Martin Beibel, Sebastian Bergling, Judith Knehr, Walter Carbone, Cheryl de Vallière, Joelle Tchinda, Tewis Bouwmeester, Klaus Seuwen, Gerhard Rogler and Guglielmo Roma
    Citation: BMC Genomics 2016 17:723
    Content type: Methodology article Published on:

  36. Human diseases are commonly the result of multidimensional changes at molecular, cellular, and systemic levels. Recent advances in genomic technologies have enabled an outpour of omics datasets that capture th...

    Authors: Douglas Arneson, Anindya Bhattacharya, Le Shu, Ville-Petteri Mäkinen and Xia Yang
    Citation: BMC Genomics 2016 17:722
    Content type: Software Published on:

  37. Authors: Peter Petschner, Viola Tamasi, Csaba Adori, Eszter Kirilly, Romeo D. Ando, Laszlo Tothfalusi and Gyorgy Bagdy
    Citation: BMC Genomics 2016 17:721
    Content type: Retraction Note Published on:

    The original article was published in BMC Genomics 2013 14:930

  38. The blood transcriptome can reflect both systemic exposures and pathological changes in other organs of the body because immune cells recirculate through the blood, lymphoid tissues, and affected sites. In hum...

    Authors: Jeanine S. Morey, Marion G. Neely, Denise Lunardi, Paul E. Anderson, Lori H. Schwacke, Michelle Campbell and Frances M. Van Dolah
    Citation: BMC Genomics 2016 17:720
    Content type: Research article Published on:

  39. The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well...

    Authors: Takashi P. Satoh, Masaki Miya, Kohji Mabuchi and Mutsumi Nishida
    Citation: BMC Genomics 2016 17:719
    Content type: Research article Published on:

  40. The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies great...

    Authors: Amos A. Schaffer, Michael Bazarsky, Karine Levy, Vered Chalifa-Caspi and Uri Gat
    Citation: BMC Genomics 2016 17:718
    Content type: Research article Published on:

  41. The transcriptional response to many widely used drugs and its modulation by genetic variability is poorly understood. Here we present an analysis of RNAseq profiles from heart tissue of 18 inbred mouse strain...

    Authors: Andrea Prunotto, Brian J. Stevenson, Corinne Berthonneche, Fanny Schüpfer, Jacques S. Beckmann, Fabienne Maurer and Sven Bergmann
    Citation: BMC Genomics 2016 17:717
    Content type: Research article Published on:

  42. Spiders are known for their predatory efficiency and for their high capacity of digesting relatively large prey. They do this by combining both extracorporeal and intracellular digestion. Whereas many high thr...

    Authors: Felipe J. Fuzita, Martijn W. H. Pinkse, José S. L. Patane, Peter D. E. M. Verhaert and Adriana R. Lopes
    Citation: BMC Genomics 2016 17:716
    Content type: Research article Published on:

  45. Campylobacter fetus (C. fetus) can cause disease in both humans and animals. C. fetus has been divided into three subspecies: C. fetus subsp. fetus (Cff), C. fetus subsp. venerealis (C...

    Authors: Linda van der Graaf–van Bloois, Birgitta Duim, William G. Miller, Ken J. Forbes, Jaap A. Wagenaar and Aldert Zomer
    Citation: BMC Genomics 2016 17:713
    Content type: Research article Published on:

  46. Understanding the genetic basis of novel traits is a central topic in evolutionary biology. Two novel pigmentation phenotypes, egg-spots and blotches, emerged during the rapid diversification of East African c...

    Authors: M. Emília Santos, Laura Baldo, Langyu Gu, Nicolas Boileau, Zuzana Musilova and Walter Salzburger
    Citation: BMC Genomics 2016 17:712
    Content type: Research article Published on:

  47. Rhizobia are soil bacteria that establish symbiotic relationships with legumes and fix nitrogen in root nodules. We recently reported that several nitrogen-fixing rhizobial strains, belonging to Rhizobium phaseol...

    Authors: Humberto Peralta, Alejandro Aguilar, Rafael Díaz, Yolanda Mora, Gabriel Martínez-Batallar, Emmanuel Salazar, Carmen Vargas-Lagunas, Esperanza Martínez, Sergio Encarnación, Lourdes Girard and Jaime Mora
    Citation: BMC Genomics 2016 17:711
    Content type: Research article Published on:

  48. Deep sequencing makes it possible to observe low-frequency viral variants and sub-populations with greater accuracy and sensitivity than ever before. Existing platforms can be used to multiplex a large number ...

    Authors: Samuel S. Shepard, Sarah Meno, Justin Bahl, Malania M. Wilson, John Barnes and Elizabeth Neuhaus
    Citation: BMC Genomics 2016 17:708
    Content type: Methodology article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:801

  49. The evolution of animal mitochondrial (mt) genomes has resulted in a highly conserved structure: a single compact circular chromosome approximately 14 to 20 kb long. Within the last two decades exceptions to t...

    Authors: Wendy S. Phillips, Amanda M. V. Brown, Dana K. Howe, Amy B. Peetz, Vivian C. Blok, Dee R. Denver and Inga A. Zasada
    Citation: BMC Genomics 2016 17:706
    Content type: Research article Published on:

  50. Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected by the unexpected behavior of marker linkage disequilibrium (LD) decay. We developed a heuristic p...

    Authors: Adam T. H. Utsunomiya, Daniel J. A. Santos, Solomon A. Boison, Yuri T. Utsunomiya, Marco Milanesi, Derek M. Bickhart, Paolo Ajmone-Marsan, Johann Sölkner, José F. Garcia, Ricardo da Fonseca and Marcos V. G. B. da Silva
    Citation: BMC Genomics 2016 17:705
    Content type: Research article Published on:

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BMC Genomics

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