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  1. Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and sal...

    Authors: Qiaojun Jia, Cong Tan, Junmei Wang, Xiao-Qi Zhang, Jinghuan Zhu, Hao Luo, Jianming Yang, Sharon Westcott, Sue Broughton, David Moody and Chengdao Li
    Citation: BMC Genomics 2016 17:911
    Content type: Research article Published on:

  2. Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this...

    Authors: Bianca Baccili Zanotto Vigna, Fernanda Ancelmo de Oliveira, Guilherme de Toledo-Silva, Carla Cristina da Silva, Cacilda Borges do Valle and Anete Pereira de Souza
    Citation: BMC Genomics 2016 17:910
    Content type: Research article Published on:

  3. The TALLYHO/Jng (TH) mouse is a polygenic model for obesity and type 2 diabetes first described in the literature in 2001. The origin of the TH strain is an outbred colony of the Theiler Original strain and mi...

    Authors: James Denvir, Goran Boskovic, Jun Fan, Donald A. Primerano, Jacaline K. Parkman and Jung Han Kim
    Citation: BMC Genomics 2016 17:907
    Content type: Research article Published on:

  4. The diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in...

    Authors: Adriana Muñoz, Daniella Santos Muñoz, Aleksey Zimin and James A. Yorke
    Citation: BMC Genomics 2016 17(Suppl 10):826
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 10

  5. Phylogenetic networks are leaf-labeled graphs used to model and display complex evolutionary relationships that do not fit a single tree. There are two classes of phylogenetic networks: Data-display networks a...

    Authors: Yun Yu, Christopher Jermaine and Luay Nakhleh
    Citation: BMC Genomics 2016 17(Suppl 10):784
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 10

  6. Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon ide...

    Authors: Nam-phuong Nguyen, Michael Nute, Siavash Mirarab and Tandy Warnow
    Citation: BMC Genomics 2016 17(Suppl 10):765
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 10

  8. Mollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal fo...

    Authors: A. L. De Oliveira, T. Wollesen, A. Kristof, M. Scherholz, E. Redl, C. Todt, C. Bleidorn and A. Wanninger
    Citation: BMC Genomics 2016 17:905
    Content type: Research article Published on:

  9. Authors: Ana Carolina Vieira Araujo, Viviana Morillo, Jefferson Cypriano, Lia Cardoso Rocha Saraiva Teixeira, Pedro Leão, Sidcley Lyra, Luiz Gonzaga de Almeida, Dennis A. Bazylinski, Ana Tereza Ribeiro de Vasconcelos, Fernanda Abreu and Ulysses Lins
    Citation: BMC Genomics 2016 17:904
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2016 17:726

  10. Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders’ ability to improve these traits simultaneously...

    Authors: Md Sariful Islam, Gregory N. Thyssen, Johnie N. Jenkins, Linghe Zeng, Christopher D. Delhom, Jack C. McCarty, Dewayne D. Deng, Doug J. Hinchliffe, Don C. Jones and David D. Fang
    Citation: BMC Genomics 2016 17:903
    Content type: Research article Published on:

  11. We had previously identified Ctr9, the key scaffold subunit of the human RNA polymerase II (RNAPII) associated factor complex (PAFc), as a key factor regulating a massive ERα target gene expression and ERα-pos...

    Authors: Hao Zeng, Li Lu, Ngai Ting Chan, Mark Horswill, Paul Ahlquist, Xuehua Zhong and Wei Xu
    Citation: BMC Genomics 2016 17:902
    Content type: Research article Published on:

  12. The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Pha...

    Authors: Nicolás Bellora, Martín Moliné, Márcia David-Palma, Marco A. Coelho, Chris Todd Hittinger, José P. Sampaio, Paula Gonçalves and Diego Libkind
    Citation: BMC Genomics 2016 17:901
    Content type: Research article Published on:

  13. Genomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. A highly diverse immune gene family of the sea urchin (Strongylocentrotus purpuratus), called Sp...

    Authors: Matan Oren, Megan A. Barela Hudgell, Brian D’Allura, Jacob Agronin, Alexandra Gross, Daniele Podini and L. Courtney Smith
    Citation: BMC Genomics 2016 17:900
    Content type: Research article Published on:

  14. Cancer microenvironment plays a vital role in cancer development and progression, and cancer-stromal interactions have been recognized as important targets for cancer therapy. However, identifying relevant and...

    Authors: Daisuke Komura, Takayuki Isagawa, Kazuki Kishi, Ryohei Suzuki, Reiko Sato, Mariko Tanaka, Hiroto Katoh, Shogo Yamamoto, Kenji Tatsuno, Masashi Fukayama, Hiroyuki Aburatani and Shumpei Ishikawa
    Citation: BMC Genomics 2016 17:899
    Content type: Methodology article Published on:

  15. Seedlessness in grape (Vitis vinifera) is of considerable commercial importance for both the table grape and processing industries. Studies to date of grape seed development have been made certain progress, but m...

    Authors: Li Wang, Xiaoyan Hu, Chen Jiao, Zhi Li, Zhangjun Fei, Xiaoxiao Yan, Chonghuai Liu, Yuejin Wang and Xiping Wang
    Citation: BMC Genomics 2016 17:898
    Content type: Research article Published on:

  16. Waterlily (Nymphaea spp.), a perennial herbaceous aquatic plant, is divided into two ecological groups: hardy waterlily and tropical waterlily. Although the hardy waterlily has no attractive blue flower cultivar,...

    Authors: Qian Wu, Jie Wu, Shan-Shan Li, Hui-Jin Zhang, Cheng-Yong Feng, Dan-Dan Yin, Ru-Yan Wu and Liang-Sheng Wang
    Citation: BMC Genomics 2016 17:897
    Content type: Research article Published on:

  17. MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initi...

    Authors: Bin Wang, Ni Ye, San-jie Cao, Xin-tian Wen, Yong Huang and Qi-gui Yan
    Citation: BMC Genomics 2016 17:896
    Content type: Research article Published on:

  19. Maize requires more water than most other crops; therefore, the water use efficiency of this crop must be improved for maize production under undesirable land and changing environmental conditions.

    Authors: Chunhui Li, Baocheng Sun, Yongxiang Li, Cheng Liu, Xun Wu, Dengfeng Zhang, Yunsu Shi, Yanchun Song, Edward S. Buckler, Zhiwu Zhang, Tianyu Wang and Yu Li
    Citation: BMC Genomics 2016 17:894
    Content type: Research article Published on:

  20. Intraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples i...

    Authors: Agnieszka Zmienko, Anna Samelak-Czajka, Piotr Kozlowski, Maja Szymanska and Marek Figlerowicz
    Citation: BMC Genomics 2016 17:893
    Content type: Research article Published on:

  21. Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significan...

    Authors: Taylor P. Frazier, Nathan A. Palmer, Fuliang Xie, Christian M. Tobias, Teresa J. Donze-Reiner, Aureliano Bombarely, Kevin L. Childs, Shengqiang Shu, Jerry W. Jenkins, Jeremy Schmutz, Baohong Zhang, Gautam Sarath and Bingyu Zhao
    Citation: BMC Genomics 2016 17:892
    Content type: Research article Published on:

  22. Consumers are becoming increasingly conscientious about the nutritional value of their food. Consumption of some fatty acids has been associated with human health traits such as blood pressure and cardiovascul...

    Authors: L. M. Kramer, M. A. Abdel Ghaffar, J. E. Koltes, E. R. Fritz-Waters, M. S. Mayes, A. D. Sewell, N. T. Weeks, D. J. Garrick, R. L. Fernando, L. Ma and J. M. Reecy
    Citation: BMC Genomics 2016 17:891
    Content type: Research article Published on:

  23. The atyid shrimp Paratya australiensis occurs in surface freshwater habitats throughout eastern Australia and has been used to study the ecotoxicology of contaminants such as pesticides and metals. The acidificat...

    Authors: Peter A. Bain, Adrienne L. Gregg and Anupama Kumar
    Citation: BMC Genomics 2016 17:890
    Content type: Research article Published on:

  24. Tibetan wild barley (Hordeum spontaneum L.) has been confirmed to contain elite accessions in tolerance to abiotic stresses, including salinity. However, molecular mechanisms underlying genotypic difference of sa...

    Authors: Qiufang Shen, Liangbo Fu, Fei Dai, Lixi Jiang, Guoping Zhang and Dezhi Wu
    Citation: BMC Genomics 2016 17:889
    Content type: Research article Published on:

  25. Babesia microti is an emerging tick-borne apicomplexan parasite with increasing geographic range and incidence in the United States. The rapid expansion of B. microti into its current ...

    Authors: Giovanna Carpi, Katharine S. Walter, Choukri Ben Mamoun, Peter J. Krause, Andrew Kitchen, Timothy J. Lepore, Ankit Dwivedi, Emmanuel Cornillot, Adalgisa Caccone and Maria A. Diuk-Wasser
    Citation: BMC Genomics 2016 17:888
    Content type: Research article Published on:

  26. The transcription factor SOX10 is essential for all stages of Schwann cell development including myelination. SOX10 cooperates with other transcription factors to activate the expression of key myelin genes in...

    Authors: Chetna Gopinath, William D. Law, José F. Rodríguez-Molina, Arjun B. Prasad, Lingyun Song, Gregory E. Crawford, James C. Mullikin, John Svaren and Anthony Antonellis
    Citation: BMC Genomics 2016 17:887
    Content type: Research article Published on:

  27. Reconstructing three-dimensional structures of chromosomes is useful for visualizing their shapes in a cell and interpreting their function. In this work, we reconstruct chromosomal structures from Hi-C data b...

    Authors: Badri Adhikari, Tuan Trieu and Jianlin Cheng
    Citation: BMC Genomics 2016 17:886
    Content type: Research article Published on:

  28. Chromium (Cr) being multifarious industrial used element, is considered a potential environmental threat. Cr found to be a prospective water and soil pollutant, and thus it is a current area of concern. Oilsee...

    Authors: Rafaqat A. Gill, Basharat Ali, Peng Cui, Enhui Shen, Muhammad A. Farooq, Faisal Islam, Shafaqat Ali, Bizeng Mao and Weijun Zhou
    Citation: BMC Genomics 2016 17:885
    Content type: Research article Published on:

  29. Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive ...

    Authors: Julie Ferreira de Carvalho, Victor de Jager, Thomas P. van Gurp, Niels C. A. M. Wagemaker and Koen J. F. Verhoeven
    Citation: BMC Genomics 2016 17:884
    Content type: Research article Published on:

  30. Sex chromosomes change more frequently in fish than in mammals or birds. However, certain chromosomes or genes are repeatedly used as sex determinants in different members of the teleostean lineage. East Afric...

    Authors: Astrid Böhne, Catherine A. Wilson, John H. Postlethwait and Walter Salzburger
    Citation: BMC Genomics 2016 17:883
    Content type: Research article Published on:

  31. Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genom...

    Authors: Xin Zhao and Oscar P. Kuipers
    Citation: BMC Genomics 2016 17:882
    Content type: Research article Published on:

  33. Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into t...

    Authors: Christopher A. Miller, Joshua McMichael, Ha X. Dang, Christopher A. Maher, Li Ding, Timothy J. Ley, Elaine R. Mardis and Richard K. Wilson
    Citation: BMC Genomics 2016 17:880
    Content type: Software Published on:

  34. Mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase that is a central regulator of cell growth and metabolism. CCI-779 is a specific inhibitor of the mTORC1 signaling pa...

    Authors: Yuting Fu, Xu Zheng, Xiaoyang Jia, Uyanga Binderiya, Yanfeng Wang, Wenlei Bao, Lili Bao, Keyu Zhao, Yu Fu, Huifang Hao and Zhigang Wang
    Citation: BMC Genomics 2016 17:879
    Content type: Research article Published on:

  36. Verticillium wilt (VW) caused by Verticillium dahliae (Kleb) is one of the most destructive diseases of cotton. The identification of highly resistant QTLs or genes in the whole cotton...

    Authors: Yuzhen Shi, Baocai Zhang, Aiying Liu, Wentan Li, Junwen Li, Quanwei Lu, Zhen Zhang, Shaoqi Li, Wankui Gong, Haihong Shang, Juwu Gong, Tingting Chen, Qun Ge, Tao Wang, Heqin Zhu, Zhi Liu…
    Citation: BMC Genomics 2016 17:877
    Content type: Research article Published on:

  38. Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In m...

    Authors: Lin Li, Roman Briskine, Robert Schaefer, Patrick S. Schnable, Chad L. Myers, Lex E. Flagel, Nathan M. Springer and Gary J. Muehlbauer
    Citation: BMC Genomics 2016 17:875
    Content type: Research article Published on:

  39. Complex diseases are characterized by multiple subtle perturbations to biological processes. New omics platforms can detect these perturbations, but translating the diverse molecular and statistical informatio...

    Authors: Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean Geoffrey Byars, Taru Tukiainen, Johannes Kettunen, Luz D. Orozco, Matteo Pellegrini, Aldons J. Lusis, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville-Petteri Mäkinen and Xia Yang
    Citation: BMC Genomics 2016 17:874
    Content type: Methodology article Published on:

  40. ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal us...

    Authors: Peter Hansen, Jochen Hecht, Jonas Ibn-Salem, Benjamin S. Menkuec, Sebastian Roskosch, Matthias Truss and Peter N. Robinson
    Citation: BMC Genomics 2016 17:873
    Content type: Research Article Published on:

  41. The differentiation of human bone marrow derived skeletal stem cells (known as human bone marrow stromal or mesenchymal stem cells, hMSCs) into osteoblasts involves the activation of a small number of well-des...

    Authors: Natalie A. Twine, Linda Harkness, Moustapha Kassem and Marc R. Wilkins
    Citation: BMC Genomics 2016 17:872
    Content type: Research article Published on:

  42. The developmental cycle of Dictyostelid amoebae represents an early form of multicellularity with cell type differentiation. Mutant studies in the model Dictyostelium discoideum revealed that its developmental pr...

    Authors: Christina Schilde, Hajara M. Lawal, Angelika A. Noegel, Ludwig Eichinger, Pauline Schaap and Gernot Glöckner
    Citation: BMC Genomics 2016 17:871
    Content type: Research article Published on:

  45. Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adopt...

    Authors: Adam J. Northcutt, Kawasi M. Lett, Virginia B. Garcia, Clare M. Diester, Brian J. Lane, Eve Marder and David J. Schulz
    Citation: BMC Genomics 2016 17:868
    Content type: Research article Published on:

  46. Obesity-related diseases are major contributors to morbidity and mortality in the developed world. Molecular diagnostics and targets of therapies to combat nutritional imbalance are urgently needed in the clin...

    Authors: Christopher S. Nelson, Jennifer N. Beck, Kenneth A. Wilson, Elijah R. Pilcher, Pankaj Kapahi and Rachel B. Brem
    Citation: BMC Genomics 2016 17:867
    Content type: Research article Published on:

  47. Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few e...

    Authors: Thomas Pauli, Lucia Vedder, Daniel Dowling, Malte Petersen, Karen Meusemann, Alexander Donath, Ralph S. Peters, Lars Podsiadlowski, Christoph Mayer, Shanlin Liu, Xin Zhou, Peter Heger, Thomas Wiehe, Lars Hering, Georg Mayer, Bernhard Misof…
    Citation: BMC Genomics 2016 17:861
    Content type: Research article Published on:

  48. Polymorphisms underlying complex traits often explain a small part (less than 1 %) of the phenotypic variance (σ2 P). This makes identification of mutations underling complex traits dif...

    Authors: K. E. Kemper, M. D. Littlejohn, T. Lopdell, B. J. Hayes, L. E. Bennett, R. P. Williams, X. Q. Xu, P. M. Visscher, M. J. Carrick and M. E. Goddard
    Citation: BMC Genomics 2016 17:858
    Content type: Research article Published on:

  49. Iron deficiency is a common childhood micronutrient deficiency that results in altered hippocampal function and cognitive disorders. However, little is known about the mechanisms through which neonatal iron de...

    Authors: Kyle M. Schachtschneider, Yingkai Liu, Laurie A. Rund, Ole Madsen, Rodney W. Johnson, Martien A. M. Groenen and Lawrence B. Schook
    Citation: BMC Genomics 2016 17:856
    Content type: Research article Published on:

  50. Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem...

    Authors: Anneke Frerichs, Rahere Thoma, Ali Taleb Abdallah, Peter Frommolt, Wolfgang Werr and John William Chandler
    Citation: BMC Genomics 2016 17:855
    Content type: Research article Published on:

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BMC Genomics

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