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  1. Quality control (QC) analysis is an important component in maize breeding and seed systems. Genotyping by next-generation sequencing (GBS) is an emerging method of SNP genotyping, which is being increasingly a...

    Authors: Berhanu Tadesse Ertiro, Veronica Ogugo, Mosisa Worku, Biswanath Das, Michael Olsen, Maryke Labuschagne and Kassa Semagn
    Citation: BMC Genomics 2015 16:908
    Content type: Research article Published on:

  2. Down syndrome (DS) or trisomy 21 is the result of a genetic dosage imbalance that translates in a broad clinical spectrum. A major challenge in the study of DS is the identification of functional genetic eleme...

    Authors: Xavier Bofill-De Ros, Mónica Santos, Maria Vila-Casadesús, Eneko Villanueva, Nuria Andreu, Mara Dierssen and Cristina Fillat
    Citation: BMC Genomics 2015 16:907
    Content type: Research article Published on:

  3. Adult neurogenesis and the incorporation of adult-born neurons into functional circuits requires precise spatiotemporal coordination across molecular networks regulating a wide array of processes, including ce...

    Authors: Tracy A. Larson, Karin L. Lent, Theo K. Bammler, James W. MacDonald, William E. Wood, Melissa L. Caras, Nivretta M. Thatra, Agata Budzillo, David J. Perkel and Eliot A. Brenowitz
    Citation: BMC Genomics 2015 16:905
    Content type: Research article Published on:

  4. Transcriptional enhancers are frequently bound by a set of transcription factors that collaborate to activate lineage-specific gene expression. Recently, it was appreciated that a subset of enhancers comprise ...

    Authors: Steven Witte, Allan Bradley, Anton J. Enright and Stefan A. Muljo
    Citation: BMC Genomics 2015 16:903
    Content type: Research article Published on:

  5. Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this spe...

    Authors: Tifeng Shan, Shaojun Pang, Jing Li, Xia Li and Li Su
    Citation: BMC Genomics 2015 16:902
    Content type: Research article Published on:

  6. Auxin and auxin signaling are involved in a series of developmental processes in plants. Auxin Response Factors (ARFs) is reported to modulate the expression of target genes by binding to auxin response elemen...

    Authors: Kaidong Liu, Changchun Yuan, Haili Li, Wanhuang Lin, Yanjun Yang, Chenjia Shen and Xiaolin Zheng
    Citation: BMC Genomics 2015 16:901
    Content type: Research article Published on:

  8. Mammalian aging is a highly complex process, a full mechanistic understanding of which is still lacking. One way to help understand the molecular changes underlying aging is through a comprehensive analysis of...

    Authors: Ryan R. White, Brandon Milholland, Sheila L. MacRae, Mingyan Lin, Deyou Zheng and Jan Vijg
    Citation: BMC Genomics 2015 16:899
    Content type: Research article Published on:

  9. Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiolog...

    Authors: Xianjun Peng, Linhong Teng, Xueqing Yan, Meiling Zhao and Shihua Shen
    Citation: BMC Genomics 2015 16:898
    Content type: Research article Published on:

  10. Streptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencep...

    Authors: Rui Wang, Liping Li, Yan Huang, Fuguang Luo, Wanwen Liang, Xi Gan, Ting Huang, Aiying Lei, Ming Chen and Lianfu Chen
    Citation: BMC Genomics 2015 16:897
    Content type: Research article Published on:

  11. Paulownia witches’ broom (PaWB) is a fatal disease of Paulownia caused by a phytoplasma. In previous studies, we found that plants with PaWB symptoms would revert to a healthy morphology after methyl methane s...

    Authors: Guoqiang Fan, Xibing Cao, Suyan Niu, Minjie Deng, Zhenli Zhao and Yanpeng Dong
    Citation: BMC Genomics 2015 16:896
    Content type: Research article Published on:

  12. FNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species. Since FNR homologues are some of the most ...

    Authors: Joseph E. Kumka and Carl E. Bauer
    Citation: BMC Genomics 2015 16:895
    Content type: Research article Published on:

  13. Copy number variations (CNVs) are modifications in DNA structure comprising of deletions, duplications, insertions and complex multi-site variants. Although CNVs are proven to be involved in a variety of pheno...

    Authors: Magretha Diane Wang, Kennedy Dzama, Charles A. Hefer and Farai C. Muchadeyi
    Citation: BMC Genomics 2015 16:894
    Content type: Research article Published on:

  14. Chlamydia pecorum is a globally recognised pathogen of livestock and koalas. To date, comparative genomics of C. pecorum strains from sheep, cattle and koalas has revealed that only si...

    Authors: Martina Jelocnik, Nathan L. Bachmann, Bernhard Kaltenboeck, Courtney Waugh, Lucy Woolford, K. Natasha Speight, Amber Gillett, Damien P. Higgins, Cheyne Flanagan, Garry S. A. Myers, Peter Timms and Adam Polkinghorne
    Citation: BMC Genomics 2015 16:893
    Content type: Research article Published on:

  15. Next generation sequencing (NGS) technology has been rapidly introduced into basic and translational research in oncology, but the reduced availability of fresh frozen (FF) tumor tissues and the poor quality o...

    Authors: Annalisa Astolfi, Milena Urbini, Valentina Indio, Margherita Nannini, Chiara Giusy Genovese, Donatella Santini, Maristella Saponara, Anna Mandrioli, Giorgio Ercolani, Giovanni Brandi, Guido Biasco and Maria A. Pantaleo
    Citation: BMC Genomics 2015 16:892
    Content type: Research article Published on:

  16. Copy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contri...

    Authors: Diego Forni, Diana Martin, Razan Abujaber, Andrew J. Sharp, Manuela Sironi and Edward J. Hollox
    Citation: BMC Genomics 2015 16:891
    Content type: Research article Published on:

  17. The malaria parasites in the genus Plasmodium have a very complicated life cycle involving an invertebrate vector and a vertebrate host. RNA-binding proteins (RBPs) are critical factors involved in every aspect o...

    Authors: BP Niranjan Reddy, Sony Shrestha, Kevin J. Hart, Xiaoying Liang, Karen Kemirembe, Liwang Cui and Scott E. Lindner
    Citation: BMC Genomics 2015 16:890
    Content type: Research article Published on:

  19. Toxoplasma gondii is an intracellular protozoan that affects most species of endothermic animals including humans with a great infection rate. The vertical transmission of T. gondii ca...

    Authors: Weisheng Cheng, Fang Liu, Man Li, Xiaodong Hu, He Chen, Faustina Pappoe, Qingli Luo, Huiqin Wen, Tian Xing, Yuanhong Xu and Jilong Shen
    Citation: BMC Genomics 2015 16:888
    Content type: Research article Published on:

  20. Leishmaniasis is a neglected parasitic disease with diverse clinical manifestations and a complex epidemiology. It has been shown that its parasite-related traits vary between species and that they modulate in...

    Authors: Hugo O. Valdivia, Larissa L. S. Scholte, Guilherme Oliveira, Toni Gabaldón and Daniella C. Bartholomeu
    Citation: BMC Genomics 2015 16:887
    Content type: Research article Published on:

  21. Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the tra...

    Authors: Wenyan An, Wenfang Gong, Shoupu He, Zhaoe Pan, Junling Sun and Xiongming Du
    Citation: BMC Genomics 2015 16:886
    Content type: Research article Published on:

  22. Environmental factors such as pesticides can cause phenotypic changes in various organisms, including mammals. We studied the effects of the widely used herbicide atrazine (ATZ) on meiosis, a key step of gamet...

    Authors: Aurore Gely-Pernot, Chunxiang Hao, Emmanuelle Becker, Igor Stuparevic, Christine Kervarrec, Frédéric Chalmel, Michael Primig, Bernard Jégou and Fatima Smagulova
    Citation: BMC Genomics 2015 16:885
    Content type: Research article Published on:

  23. Bovine milk fat composition is responsive to dietary manipulation providing an avenue to modify the content of fatty acids and especially some specific unsaturated fatty acid (USFA) isomers of benefit to human...

    Authors: Ran Li, Frédéric Beaudoin, Adolf A. Ammah, Nathalie Bissonnette, Chaouki Benchaar, Xin Zhao, Chuzhao Lei and Eveline M. Ibeagha-Awemu
    Citation: BMC Genomics 2015 16:884
    Content type: Research article Published on:

  24. Pseudomonas aeruginosa is an environmentally ubiquitous Gram-negative bacterium and important opportunistic human pathogen, causing severe chronic respiratory infections in patients wi...

    Authors: John J. Varga, Mariette Barbier, Xavier Mulet, Piotr Bielecki, Jennifer A. Bartell, Joshua P. Owings, Inmaculada Martinez-Ramos, Lauren E. Hittle, Michael R. Davis Jr., F. Heath Damron, George W. Liechti, Jacek Puchałka, Vitor A. P. Martins dos Santos, Robert K. Ernst, Jason A. Papin, Sebastian Albertí…
    Citation: BMC Genomics 2015 16:883
    Content type: Research article Published on:

  25. To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate spe...

    Authors: Song Yang, Nir Oksenberg, Sachiko Takayama, Seok-Jin Heo, Alexander Poliakov, Nadav Ahituv, Inna Dubchak and Dario Boffelli
    Citation: BMC Genomics 2015 16:882
    Content type: Research article Published on:

  26. Ophiocordyceps unilateralis is an outstanding insect fungus for its biology to manipulate host ants’ behavior and for its extreme host-specificity. Through the sequencing and annotatio...

    Authors: Duangdao Wichadakul, Noppol Kobmoo, Supawadee Ingsriswang, Sithichoke Tangphatsornruang, Duriya Chantasingh, Janet Jennifer Luangsa-ard and Lily Eurwilaichitr
    Citation: BMC Genomics 2015 16:881
    Content type: Research article Published on:

  28. Among teleosts, the South American genus Austrolebias (Cyprinodontiformes: Rivulidae) includes 42 taxa of annual fishes divided into five different species groups. It is a monophyletic genus, but morphological an...

    Authors: Verónica Gutiérrez, Natalia Rego, Hugo Naya and Graciela García
    Citation: BMC Genomics 2015 16:879
    Content type: Research article Published on:

  29. The 7B-1 tomato line (Solanum lycopersicum cv. Rutgers) is a photoperiod-sensitive male-sterile mutant, with potential application in hybrid seed production. Small RNAs (sRNAs) in tomato have been mainly characte...

    Authors: Vahid Omidvar, Irina Mohorianu, Tamas Dalmay and Martin Fellner
    Citation: BMC Genomics 2015 16:878
    Content type: Research article Published on:

  30. Bixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of Bixa orellana L. An enzymatic pathway for bixin biosynthesis was inferred from...

    Authors: Yair Cárdenas-Conejo, Víctor Carballo-Uicab, Meric Lieberman, Margarita Aguilar-Espinosa, Luca Comai and Renata Rivera-Madrid
    Citation: BMC Genomics 2015 16:877
    Content type: Research article Published on:

  31. Parkinson’s disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the syste...

    Authors: Raffaella Calligaris, Mihaela Banica, Paola Roncaglia, Elisa Robotti, Sara Finaurini, Christina Vlachouli, Lucia Antonutti, Francesco Iorio, Annamaria Carissimo, Tatiana Cattaruzza, Andrea Ceiner, Dejan Lazarevic, Alberto Cucca, Nicola Pangher, Emilio Marengo, Diego di Bernardo…
    Citation: BMC Genomics 2015 16:876
    Content type: Research article Published on:

  32. The low concordance between different variant calling methods still poses a challenge for the wide-spread application of next-generation sequencing in research and clinical practice. A wide range of variant an...

    Authors: András Gézsi, Bence Bolgár, Péter Marx, Peter Sarkozy, Csaba Szalai and Péter Antal
    Citation: BMC Genomics 2015 16:875
    Content type: Methodology Article Published on:

  33. Francisella infection attenuates immune cell infiltration and expression of selected pro-inflammatory cytokines in response to endogenous LPS, suggesting the bacteria is actively antag...

    Authors: Kathie-Anne Walters, Rachael Olsufka, Rolf E. Kuestner, Xiagang Wu, Kai Wang, Shawn J. Skerrett and Adrian Ozinsky
    Citation: BMC Genomics 2015 16:874
    Content type: Research article Published on:

  35. Asian buffaloes (Bubalus bubalis) have an important socio-economic role. The majority of the population is situated in developing countries. Due to the scarce resources in these countries, very few species-specif...

    Authors: GMF de Camargo, RR Aspilcueta-Borquis, MRS Fortes, R. Porto-Neto, DF Cardoso, DJA Santos, SA Lehnert, A. Reverter, SS Moore and H. Tonhati
    Citation: BMC Genomics 2015 16:872
    Content type: Research article Published on:

  36. In Europe, Ixodes ricinus ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information is missing and functional annot...

    Authors: Wibke J. Cramaro, Dominique Revets, Oliver E. Hunewald, Regina Sinner, Anna L. Reye and Claude P. Muller
    Citation: BMC Genomics 2015 16:871
    Content type: Research article Published on:

  37. Although posttranscriptional modification of mitochondrial (mt) transcripts plays key roles in completion of the coding information and in the expression of mtDNA-encoded genes, there is little experimental ev...

    Authors: Silvia Marková, Karolína Filipi, Jeremy B. Searle and Petr Kotlík
    Citation: BMC Genomics 2015 16:870
    Content type: Research article Published on:

  38. Idiopathic interstitial pneumonias (IIPs) are a group of heterogeneous, somewhat unpredictable diseases characterized by progressive scarring of the interstitium. Since lung function is a key determinant of su...

    Authors: Mark P. Steele, Leah G. Luna, Christopher D. Coldren, Elissa Murphy, Corinne E. Hennessy, David Heinz, Christopher M. Evans, Steve Groshong, Carlyne Cool, Gregory P. Cosgrove, Kevin K. Brown, Tasha E. Fingerlin, Marvin I. Schwarz, David A. Schwartz and Ivana V. Yang
    Citation: BMC Genomics 2015 16:869
    Content type: Research article Published on:

  39. Trichomes, developing from the epidermis of nearly all terrestrial plants, provide good structural resistance against insect herbivores and an excellent model for studying the molecular mechanisms underlying c...

    Authors: Changxian Yang, Yanna Gao, Shenghua Gao, Gang Yu, Cheng Xiong, Jiang Chang, Hanxia Li and Zhibiao Ye
    Citation: BMC Genomics 2015 16:868
    Content type: Research article Published on:

  40. The migratory locust, Locusta migratoria manilensis, is an immensely destructive agricultural pest that forms a devastating and voracious gregarious phase. The fungal insect pathogen, Metarhizium acridum, is a sp...

    Authors: Wei Zhang, Jianhong Chen, Nemat O. Keyhani, Zhengyi Zhang, Sai Li and Yuxian Xia
    Citation: BMC Genomics 2015 16:867
    Content type: Research article Published on:

  41. N-ethyl-N-nitrosourea (ENU) mutagen has become the method of choice for inducing random mutations for forward genetics applications. However, distinguishing induced mutations from sequencing errors or sporadic...

    Authors: Denis C. Bauer, Brendan J. McMorran, Simon J. Foote and Gaetan Burgio
    Citation: BMC Genomics 2015 16:866
    Content type: Research Article Published on:

  42. Alcohol abuse and alcoholism are significant public health problems, but the genetic basis for individual variation in alcohol sensitivity remains poorly understood. Drosophila melanogaster presents a powerful mo...

    Authors: Tatiana V. Morozova, Wen Huang, Victoria A. Pray, Thomas Whitham, Robert R. H. Anholt and Trudy F. C. Mackay
    Citation: BMC Genomics 2015 16:865
    Content type: Research article Published on:

  43. Transcription of nodulation genes in rhizobial species is orchestrated by the regulatory nodD gene. Rhizobium tropici strain CIAT 899 is an intriguing species in possessing features such as broad host range, high...

    Authors: Pablo del Cerro, Amanda Alves Paiva Rolla-Santos, Douglas Fabiano Gomes, Bettina Berquó Marks, María del Rosario Espuny, Miguel Ángel Rodríguez-Carvajal, María Eugenia Soria-Díaz, André Shigueyoshi Nakatani, Mariangela Hungria, Francisco Javier Ollero and Manuel Megías
    Citation: BMC Genomics 2015 16:864
    Content type: Research article Published on:

  44. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements ...

    Authors: Yury V. Ivanov, Nikki Shariat, Karen B. Register, Bodo Linz, Israel Rivera, Kai Hu, Edward G. Dudley and Eric T. Harvill
    Citation: BMC Genomics 2015 16:863
    Content type: Research article Published on:

  46. Methicillin-resistant Staphylococcus aureus (MRSA)-USA300 is notorious for its ability to cause community- and healthcare-acquired infections, which are even more difficult to treat when associated with a biofilm...

    Authors: J. S. Sabirova, J-P Hernalsteens, S. De Backer, B. B. Xavier, P. Moons, A. Turlej-Rogacka, H. De Greve, H. Goossens and S. Malhotra-Kumar
    Citation: BMC Genomics 2015 16:861
    Content type: Research article Published on:

  47. Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human u...

    Authors: Amir Ariff, Michael J. Wise, Charlene M. Kahler, Chin Yen Tay, Fanny Peters, Timothy T. Perkins and Barbara J. Chang
    Citation: BMC Genomics 2015 16:860
    Content type: Research article Published on:

  48. The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics ap...

    Authors: Robert M. Bowers, Alicia Clum, Hope Tice, Joanne Lim, Kanwar Singh, Doina Ciobanu, Chew Yee Ngan, Jan-Fang Cheng, Susannah G. Tringe and Tanja Woyke
    Citation: BMC Genomics 2015 16:856
    Content type: Methodology article Published on:

  49. Penicillium digitatum is one of the most destructive postharvest pathogen of citrus fruits, causing fruit decay and economic loss. The emergence of fungicide-resistant strains made the...

    Authors: Jing Liu, Shengqiang Wang, Tingting Qin, Na Li, Yuhui Niu, Dandan Li, Yongze Yuan, Hui Geng, Li Xiong and Deli Liu
    Citation: BMC Genomics 2015 16:855
    Content type: Research article Published on:

  50. Exposure to dichlorvos (DDVP), an organophosphorus pesticide, is known to result in neurotoxicity as well as other metabolic perturbations. However, the molecular causes of DDVP toxicity are poorly understood,...

    Authors: Tri M. Bui-Nguyen, Christine E. Baer, John A. Lewis, Dongren Yang, Pamela J. Lein and David A. Jackson
    Citation: BMC Genomics 2015 16:853
    Content type: Research article Published on:

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BMC Genomics

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