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  1. Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsat...

    Authors: Aitor Serres-Armero, Inna S. Povolotskaya, Javier Quilez, Oscar Ramirez, Gabriel Santpere, Lukas F. K. Kuderna, Jessica Hernandez-Rodriguez, Marcos Fernandez-Callejo, Daniel Gomez-Sanchez, Adam H. Freedman, Zhenxin Fan, John Novembre, Arcadi Navarro, Adam Boyko, Robert Wayne, Carles Vilà…
    Citation: BMC Genomics 2017 18:977
    Content type: Research article Published on:

  2. Understanding the consequences of thermal and chemical variations in aquatic habitats is of importance in a scenario of global change. In ecology, the sex ratio is a major population demographic parameter. So ...

    Authors: Noelia Díaz and Francesc Piferrer
    Citation: BMC Genomics 2017 18:973
    Content type: Research article Published on:

  3. The Sertoli cells act to induce testis differentiation and subsequent development in fetal and post-natal life which makes them key to an understanding of testis biology. As a major step towards characterisati...

    Authors: U. Soffientini, D. Rebourcet, M. H. Abel, S. Lee, G. Hamilton, P. A. Fowler, L. B. Smith and P. J. O’Shaughnessy
    Citation: BMC Genomics 2017 18:972
    Content type: Research article Published on:

  4. Farmed and wild Atlantic salmon are exposed to many infectious and non-infectious challenges that can cause mortality when they enter the sea. Exercise before transfer promotes growth, health and survival in t...

    Authors: Nicholas A. Robinson, Gerrit Timmerhaus, Matthew Baranski, Øivind Andersen, Harald Takle and Aleksei Krasnov
    Citation: BMC Genomics 2017 18:971
    Content type: Research article Published on:

  5. Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to asse...

    Authors: Gina L. Conte, Kathryn A. Hodgins, Sam Yeaman, Jon C. Degner, Sally N. Aitken, Loren H. Rieseberg and Michael C. Whitlock
    Citation: BMC Genomics 2017 18:970
    Content type: Research article Published on:

  6. Drought is a lifestyle disease. Plant metabolomics has been exercised for understanding the fine-tuning of the potential pathways to surmount the adverse effects of drought stress. A broad spectrum of morpholo...

    Authors: Naimat Ullah, Meral Yüce, Z. Neslihan Öztürk Gökçe and Hikmet Budak
    Citation: BMC Genomics 2017 18:969
    Content type: Research article Published on:

  7. Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to...

    Authors: Thomas J. Lopdell, Kathryn Tiplady, Maksim Struchalin, Thomas J. J. Johnson, Michael Keehan, Ric Sherlock, Christine Couldrey, Stephen R. Davis, Russell G. Snell, Richard J. Spelman and Mathew D. Littlejohn
    Citation: BMC Genomics 2017 18:968
    Content type: Research article Published on:

  8. Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and f...

    Authors: T. Maroilley, G. Lemonnier, J. Lecardonnel, D. Esquerré, Y. Ramayo-Caldas, M. J. Mercat, C. Rogel-Gaillard and J. Estellé
    Citation: BMC Genomics 2017 18:967
    Content type: Research Article Published on:

  9. Cytosine methylation is a stable epigenetic modification of DNA that plays an important role in both normal physiology and disease. Most diseases exhibit some degree of sexual dimorphism, but the extent to whi...

    Authors: Helen McCormick, Paul E. Young, Suzy S. J. Hur, Keith Booher, Hunter Chung, Jennifer E. Cropley, Eleni Giannoulatou and Catherine M. Suter
    Citation: BMC Genomics 2017 18:966
    Content type: Research Article Published on:

  10. The chemosensory system plays an important role in orchestrating sexual behaviors in mammals. Pheromones trigger sexually dimorphic behaviors and different mouse strains exhibit differential responses to phero...

    Authors: Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson and C. Ron Yu
    Citation: BMC Genomics 2017 18:965
    Content type: Research article Published on:

  11. DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is ex...

    Authors: Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand and Marcos J. Araúzo-Bravo
    Citation: BMC Genomics 2017 18:964
    Content type: Research Article Published on:

  12. The lytic cycle of the protozoan parasite Toxoplasma gondii, which involves a brief sojourn in the extracellular space, is characterized by defined transcriptional profiles. For an obligate intracellular parasite...

    Authors: Musa A. Hassan, Juan J. Vasquez, Chew Guo-Liang, Markus Meissner and T. Nicolai Siegel
    Citation: BMC Genomics 2017 18:961
    Content type: Research article Published on:

  13. Transcriptomic analyses were performed to compare the molecular responses of two potato varieties previously shown to differ in the severity of disease symptoms due to infection by “Candidatus Liberibacter solana...

    Authors: Julien G. Levy, Azucena Mendoza, J. Creighton Miller Jr., Cecilia Tamborindeguy and Elizabeth A. Pierson
    Citation: BMC Genomics 2017 18:960
    Content type: Research article Published on:

  14. The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species,...

    Authors: Chao-Nan Fu, Hong-Tao Li, Richard Milne, Ting Zhang, Peng-Fei Ma, Jing Yang, De-Zhu Li and Lian-Ming Gao
    Citation: BMC Genomics 2017 18:956
    Content type: Research article Published on:

  15. Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds an...

    Authors: Nguyen-Phuong Pham, Séverine Layec, Eric Dugat-Bony, Marie Vidal, Françoise Irlinger and Christophe Monnet
    Citation: BMC Genomics 2017 18:955
    Content type: Research article Published on:

  16. After publication of the original article [1] the authors noted that the following errors had occurred:

    Authors: Katsutomo Sasaki, Nobutaka Mitsuda, Kenji Nashima, Kyutaro Kishimoto, Yuichi Katayose, Hiroyuki Kanamori and Akemi Ohmiya
    Citation: BMC Genomics 2017 18:954
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2017 18:683

  17. Asia minor bluegrass (Polypogon fugax, P. fugax), a weed that is both distributed across China and associated with winter crops, has evolved resistance to acetyl-CoA carboxylase (ACCase) herbicides, but the resis...

    Authors: Fengyan Zhou, Yong Zhang, Wei Tang, Mei Wang and Tongchun Gao
    Citation: BMC Genomics 2017 18:953
    Content type: Research article Published on:

  18. Chlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens. Demonstration of C. gallinacea in human atypical pneumonia suggests its zoonotic pot...

    Authors: Weina Guo, Martina Jelocnik, Jing Li, Konrad Sachse, Adam Polkinghorne, Yvonne Pannekoek, Bernhard Kaltenboeck, Jiansen Gong, Jinfeng You and Chengming Wang
    Citation: BMC Genomics 2017 18:949
    Content type: Research article Published on:

  20. Avian poxviruses are important pathogens of both wild and domestic birds. To date, seven isolates from subclades A and B and one from proposed subclade E, have had their genomes completely sequenced. The genom...

    Authors: Olivia Carulei, Nicola Douglass and Anna-Lise Williamson
    Citation: BMC Genomics 2017 18:947
    Content type: Research Article Published on:

  21. RNA viruses such as HCV and HIV mutate at extremely high rates, and as a result, they exist in infected hosts as populations of genetically related variants. Recent advances in sequencing technologies make pos...

    Authors: Olga Glebova, Sergey Knyazev, Andrew Melnyk, Alexander Artyomenko, Yury Khudyakov, Alex Zelikovsky and Pavel Skums
    Citation: BMC Genomics 2017 18(Suppl 10):918
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  22. In recent years several different fields, such as ecology, medicine and microbiology, have experienced an unprecedented development due to the possibility of direct sequencing of microbioimic samples. Among pr...

    Authors: Samuele Girotto, Matteo Comin and Cinzia Pizzi
    Citation: BMC Genomics 2017 18(Suppl 10):917
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  23. Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures ...

    Authors: Atkinson G. Longmire, Seth Sims, Inna Rytsareva, David S. Campo, Pavel Skums, Zoya Dimitrova, Sumathi Ramachandran, Magdalena Medrzycki, Hong Thai, Lilia Ganova-Raeva, Yulin Lin, Lili T. Punkova, Amanda Sue, Massimo Mirabito, Silver Wang, Robin Tracy…
    Citation: BMC Genomics 2017 18(Suppl 10):916
    Content type: Software Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  24. Identification of common genes associated with comorbid diseases can be critical in understanding their pathobiological mechanism. This work presents a novel method to predict missing common genes associated w...

    Authors: Pakeeza Akram and Li Liao
    Citation: BMC Genomics 2017 18(Suppl 10):902
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  25. While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de no...

    Authors: Sing-Hoi Sze, Jonathan J. Parrott and Aaron M. Tarone
    Citation: BMC Genomics 2017 18(Suppl 10):895
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  26. Intra-host hepatitis C virus (HCV) populations are genetically heterogeneous and organized in subpopulations. With the exception of blood transfusions, transmission of HCV occurs via a small number of genetic ...

    Authors: David S. Campo, June Zhang, Sumathi Ramachandran and Yury Khudyakov
    Citation: BMC Genomics 2017 18(Suppl 10):881
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  27. Identification of acute or recent hepatitis C virus (HCV) infections is important for detecting outbreaks and devising timely public health interventions for interruption of transmission. Epidemiological inves...

    Authors: James Lara, Mahder Teka and Yury Khudyakov
    Citation: BMC Genomics 2017 18(Suppl 10):880
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  28. Although single molecule sequencing is still improving, the lengths of the generated sequences are inevitably an advantage in genome assembly. Prior work that utilizes long reads to conduct genome assembly has...

    Authors: Shenglong Zhu, Danny Z. Chen and Scott J. Emrich
    Citation: BMC Genomics 2017 18(Suppl 10):879
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  29. Since the introduction of microarrays in 1995, researchers world-wide have used both commercial and custom-designed microarrays for understanding differential expression of transcribed genes. Public databases ...

    Authors: Ernur Saka, Benjamin J. Harrison, Kirk West, Jeffrey C. Petruska and Eric C. Rouchka
    Citation: BMC Genomics 2017 18(Suppl 10):875
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  30. The differentiation and maturation trajectories of fetal liver stem/progenitor cells (LSPCs) are not fully understood at single-cell resolution, and a priori knowledge of limited biomarkers could restrict traj...

    Authors: Xianbin Su, Yi Shi, Xin Zou, Zhao-Ning Lu, Gangcai Xie, Jean Y. H. Yang, Chong-Chao Wu, Xiao-Fang Cui, Kun-Yan He, Qing Luo, Yu-Lan Qu, Na Wang, Lan Wang and Ze-Guang Han
    Citation: BMC Genomics 2017 18:946
    Content type: Research article Published on:

  31. Meat tenderness is the consumer’s most preferred sensory attribute. This trait is affected by a number of factors, including genotype, age, animal sex, and pre- and post-slaughter management. In view of the hi...

    Authors: Larissa Fernanda Simielli Fonseca, Daniele Fernanda Jovino Gimenez, Danielly Beraldo dos Santos Silva, Roger Barthelson, Fernando Baldi, Jesus Aparecido Ferro and Lucia Galvão Albuquerque
    Citation: BMC Genomics 2017 18:945
    Content type: Research article Published on:

  32. Significant human diseases/phenotypes exist which require both an environmental trigger event and a genetic predisposition before the disease/phenotype emerges, e.g. Carbamazepine with the rare SNP allele of r...

    Authors: Kaitlin Stouffer, Michael Nahorski, Pablo Moreno, Nivedita Sarveswaran, David Menon, Michael Lee and C. Geoffrey Woods
    Citation: BMC Genomics 2017 18:944
    Content type: Methodology article Published on:

  33. Some populations of West African Aedes aegypti, the dengue and zika vector, are reproductively incompatible; our earlier study showed that divergence and rearrangements of genes on chromosome 1, which bears the s...

    Authors: Corey L. Campbell, Laura B. Dickson, Saul Lozano-Fuentes, Punita Juneja, Francis M. Jiggins and William C. Black IV
    Citation: BMC Genomics 2017 18:943
    Content type: Research article Published on:

  34. Aspergillus fumigatus is a human fungal pathogen that causes aspergillosis in immunocompromised hosts. A. fumigatus is believed to be exposed to diverse environmental stresses in the h...

    Authors: Hiroki Takahashi, Yoko Kusuya, Daisuke Hagiwara, Azusa Takahashi-Nakaguchi, Kanae Sakai and Tohru Gonoi
    Citation: BMC Genomics 2017 18:942
    Content type: Research article Published on:

  35. Spinach is a useful source of dietary vitamins and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identificati...

    Authors: Jun Qin, Ainong Shi, Beiquan Mou, Michael A. Grusak, Yuejin Weng, Waltram Ravelombola, Gehendra Bhattarai, Lingdi Dong and Wei Yang
    Citation: BMC Genomics 2017 18:941
    Content type: Research article Published on:

  36. Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers a...

    Authors: Héctor Cordero, Monica F. Brinchmann, Alberto Cuesta and María A. Esteban
    Citation: BMC Genomics 2017 18:939
    Content type: Research article Published on:

  37. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression of target mRNAs involved in plant growth, development, and abiotic stress. As one of the most important model plants, peach (Prunus persi...

    Authors: Shaoxuan Li, Zhanru Shao, Xiling Fu, Wei Xiao, Ling Li, Ming Chen, Mingyue Sun, Dongmei Li and Dongsheng Gao
    Citation: BMC Genomics 2017 18:938
    Content type: Research article Published on:

  38. The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work ...

    Authors: Zachary N. Harris, Laszlo G. Kovacs and Jason P. Londo
    Citation: BMC Genomics 2017 18:937
    Content type: Research article Published on:

  39. Lactation is extremely important for dairy cows; however, the understanding of the underlying metabolic mechanisms is very limited. This study was conducted to investigate the inherent metabolic patterns durin...

    Authors: Hui-Zeng Sun, Kai Shi, Xue-Hui Wu, Ming-Yuan Xue, Zi-Hai Wei, Jian-Xin Liu and Hong-Yun Liu
    Citation: BMC Genomics 2017 18:936
    Content type: Research article Published on:

  40. Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computati...

    Authors: Yuki Kato, Jan Gorodkin and Jakob Hull Havgaard
    Citation: BMC Genomics 2017 18:935
    Content type: Methodology article Published on:

  41. Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aim...

    Authors: Emma Whittington, Desiree Forsythe, Kirill Borziak, Timothy L. Karr, James R. Walters and Steve Dorus
    Citation: BMC Genomics 2017 18:931
    Content type: Research Published on:

  42. Genomic selection (GS) can offer unprecedented gains, in terms of cost efficiency and generation turnover, to forest tree selective breeding; especially for late expressing and low heritability traits. Here, w...

    Authors: Frances R. Thistlethwaite, Blaise Ratcliffe, Jaroslav Klápště, Ilga Porth, Charles Chen, Michael U. Stoehr and Yousry A. El-Kassaby
    Citation: BMC Genomics 2017 18:930
    Content type: Research article Published on:

  43. Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importan...

    Authors: Alexandra Blant, Michelle Kwong, Zachary A. Szpiech and Trevor J. Pemberton
    Citation: BMC Genomics 2017 18:928
    Content type: Methodology article Published on:

  44. Xenorhabdus innexi is a bacterial symbiont of Steinernema scapterisci nematodes, which is a cricket-specialist parasite and together the nematode and bacteria infect and kill crickets....

    Authors: Il-Hwan Kim, Sudarshan K. Aryal, Dariush T. Aghai, Ángel M. Casanova-Torres, Kai Hillman, Michael P. Kozuch, Erin J. Mans, Terra J. Mauer, Jean-Claude Ogier, Jerald C. Ensign, Sophie Gaudriault, Walter G. Goodman, Heidi Goodrich-Blair and Adler R. Dillman
    Citation: BMC Genomics 2017 18:927
    Content type: Research article Published on:

  45. Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molec...

    Authors: Yingchun Xu, Yanjie Wang, Neil Mattson, Liu Yang and Qijiang Jin
    Citation: BMC Genomics 2017 18:926
    Content type: Research article Published on:

  46. Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential....

    Authors: Bhavya Papudeshi, J. Matthew Haggerty, Michael Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano Thompson, Robert A. Edwards and Elizabeth A. Dinsdale
    Citation: BMC Genomics 2017 18:915
    Content type: Methodology article Published on:

  47. Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic...

    Authors: Hidenobu Segawa, Yoji Kukita and Kikuya Kato
    Citation: BMC Genomics 2017 18:914
    Content type: Methodology article Published on:

  48. It is often difficult to obtain sufficient quantity of RNA molecules for gene expression profiling under many practical situations. Amplification from low-input samples may induce artificial signals.

    Authors: Huaping Liu, Yawei Li, Jun He, Qingzhou Guan, Rou Chen, Haidan Yan, Weicheng Zheng, Kai Song, Hao Cai, You Guo, Xianlong Wang and Zheng Guo
    Citation: BMC Genomics 2017 18:913
    Content type: Research article Published on:

  50. Single-cell genome sequencing provides high-resolution details of the clonal genomic modifications that occur during cancer initiation, progression, and ongoing evolution as patients undergo treatment. One lim...

    Authors: John Easton, Veronica Gonzalez-Pena, Donald Yergeau, Xiaotu Ma and Charles Gawad
    Citation: BMC Genomics 2017 18:906
    Content type: Methodology article Published on:

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BMC Genomics

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