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  1. Content type: Research article

    The genus Helicobacter are gram-negative, microaerobic, flagellated, mucus-inhabiting bacteria associated with gastrointestinal inflammation and classified as gastric or enterohepatic Helicobacter species (EHS) a...

    Authors: Anthony Mannion, Zeli Shen and James G. Fox

    Citation: BMC Genomics 2018 19:830

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  2. Content type: Research article

    Antimicrobial peptides (AMPs) are multifunctional effector molecules that often combine direct antimicrobial activities with signaling or immunomodulatory functions. The skin secretions of anurans contain a va...

    Authors: Tomislav Rončević, Marco Gerdol, Francesca Spazzali, Fiorella Florian, Stjepan Mekinić, Alessandro Tossi and Alberto Pallavicini

    Citation: BMC Genomics 2018 19:827

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  3. Content type: Research article

    Porcine Circovirus Type 2 (PCV2) is a pathogen that has the ability to cause often devastating disease manifestations in pig populations with major economic implications. How PCV2 establishes subclinical persi...

    Authors: Nicolaas Van Renne, Ruifang Wei, Nathalie Pochet and Hans J. Nauwynck

    Citation: BMC Genomics 2018 19:831

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  4. Content type: Research article

    The marine alga Ulva compressa is the dominant species in coastal areas receiving effluents from copper mines. The alga can accumulate high amounts of copper and possesses a strong antioxidant system. Here, we pe...

    Authors: Felipe E. Rodríguez, Daniel Laporte, Alberto González, Katterinne N. Mendez, Eduardo Castro-Nallar, Claudio Meneses, Juan Pablo Huidobro-Toro and Alejandra Moenne

    Citation: BMC Genomics 2018 19:829

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  5. Content type: Research article

    Pigeon crop has the unique ability to produce a nutrient rich substance termed pigeon ‘milk’ (PM), which has functional resemblance with the mammalian milk. Previous researches have demonstrated that a large n...

    Authors: Yao Ma, Siyuan Feng, Xun Wang, Izhar Hyder Qazi, Keren Long, Yi Luo, Guojun Li, Chunyou Ning, Yixin Wang, Silu Hu, Juan Xiao, Xiaokai Li, Dan Lan, Yaodong Hu, Qianzi Tang, Jideng Ma…

    Citation: BMC Genomics 2018 19:828

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  6. Content type: Research article

    The CHRNA5/A3/B4 gene locus is associated with nicotine dependence and other smoking related disorders. While the non-synonymous CHRNA5 variant rs16969968 appears to be the main risk factor, linkage disequilibriu...

    Authors: Sung-Ha Lee, Woo-Young Ahn, Michał Seweryn and Wolfgang Sadee

    Citation: BMC Genomics 2018 19:826

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  7. Content type: Research article

    Despite its relevance, almost no studies account for the genetic control in the early stages of tree development, i.e. from germination on. This study seeks to make a quite complete transcriptome for olive dev...

    Authors: Jaime Jiménez-Ruiz, María de la O Leyva-Pérez, Isabel Vidoy-Mercado, Araceli Barceló and Francisco Luque

    Citation: BMC Genomics 2018 19:824

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  8. Content type: Database

    MicroRNAs (miRNAs) regulate gene expression and have been targeted as indicators of environmental/toxicologic stressors. Using the data from our deep sequencing of miRNAs in an extensive sampling of rat tissue...

    Authors: Pierre R. Bushel, Florian Caiment, Han Wu, Raegan O’Lone, Frank Day, John Calley, Aaron Smith and Jianying Li

    Citation: BMC Genomics 2018 19:825

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  9. Content type: Research article

    The nuclear envelope (NE) that encapsulates the nuclear genome is a double lipid bilayer with several integral and peripherally associated proteins. It is a characteristic feature of the eukaryotes and acts as...

    Authors: Hita Sony Garapati and Krishnaveni Mishra

    Citation: BMC Genomics 2018 19:823

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  10. Content type: Research article

    PAX6 is a homeodomain transcription factor that acts in a highly dosage-sensitive manner to regulate the development and function of the eyes, nose, central nervous system, gut, and endocrine pancreas. Several...

    Authors: Bridget C. Ryan, Kieran Lowe, Laura Hanson, Talveen Gil, Lauren Braun, Perry L. Howard and Robert L. Chow

    Citation: BMC Genomics 2018 19:820

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  11. Content type: Research article

    The three superfamilies of Long Terminal Repeat (LTR) retrotransposons are a widespread kind of transposable element and a major factor in eukaryotic genome evolution. In metazoans, recent studies suggested th...

    Authors: Camille Thomas-Bulle, Mathieu Piednoël, Tifenn Donnart, Jonathan Filée, Didier Jollivet and Éric Bonnivard

    Citation: BMC Genomics 2018 19:821

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  12. Content type: Research article

    The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the mos...

    Authors: Xiaohui Zhang, Yunsong Lai, Wei Zhang, Jalil Ahmad, Yang Qiu, Xiaoxue Zhang, Mengmeng Duan, Tongjin Liu, Jiangping Song, Haiping Wang and Xixiang Li

    Citation: BMC Genomics 2018 19:819

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  13. Content type: Research article

    Pseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae (Psa) initiated a worldwide pandemic in 2008 on cult...

    Authors: Peter A. McAtee, Lara Brian, Ben Curran, Otto van der Linden, Niels J. Nieuwenhuizen, Xiuyin Chen, Rebecca A. Henry-Kirk, Erin A. Stroud, Simona Nardozza, Jay Jayaraman, Erik H. A. Rikkerink, Cris G. Print, Andrew C. Allan and Matthew D. Templeton

    Citation: BMC Genomics 2018 19:822

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  14. Content type: Research article

    Solea senegalensis (Kaup, 1858) is a commercially important flatfish species, belonging to the Pleuronectiformes order. The taxonomy of this group has long been controversial, and the karyotype of the order prese...

    Authors: Aglaya García-Angulo, Manuel A. Merlo, Silvia Portela-Bens, María E. Rodríguez, Emilio García, Ahmed Al-Rikabi, Thomas Liehr and Laureana Rebordinos

    Citation: BMC Genomics 2018 19:818

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  15. Content type: Software

    A widely applied approach to extract knowledge from high-throughput genomic data is clustering of gene expression profiles followed by functional enrichment analysis. This type of analysis, when done manually,...

    Authors: Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo and Hedi Peterson

    Citation: BMC Genomics 2018 19:817

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  16. Content type: Research article

    Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. TcII is among the major DTUs enrolled in human infections in South America sou...

    Authors: João Luís Reis-Cunha, Rodrigo P. Baptista, Gabriela F. Rodrigues-Luiz, Anderson Coqueiro-dos-Santos, Hugo O. Valdivia, Laila Viana de Almeida, Mariana Santos Cardoso, Daniella Alchaar D’Ávila, Fernando Hugo Cunha Dias, Ricardo Toshio Fujiwara, Lúcia M. C. Galvão, Egler Chiari, Gustavo Coutinho Cerqueira and Daniella C. Bartholomeu

    Citation: BMC Genomics 2018 19:816

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  17. Content type: Research article

    The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative ...

    Authors: E. Jurak, H. Suzuki, G. van Erven, J. A. Gandier, P. Wong, K. Chan, C. Y. Ho, Y. Gong, E. Tillier, M.-N. Rosso, M. A. Kabel, S. Miyauchi and E. R. Master

    Citation: BMC Genomics 2018 19:815

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  18. Content type: Research article

    Current heart failure (HF) treatment is based on targeting symptoms and left ventricle dysfunction severity, relying on a common HF pathway paradigm to justify common treatments for HF patients. This common st...

    Authors: Mary E. Sweet, Andrea Cocciolo, Dobromir Slavov, Kenneth L. Jones, Joseph R. Sweet, Sharon L. Graw, T. Brett Reece, Amrut V. Ambardekar, Michael R. Bristow, Luisa Mestroni and Matthew R. G. Taylor

    Citation: BMC Genomics 2018 19:812

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  19. Content type: Research article

    Fertility is a complex trait that has a major impact on the development of the buffalo industry. Genome-wide association study (GWAS) has increased the ability to detect genes influencing complex traits, and m...

    Authors: Jun Li, Jiajia Liu, Giuseppe Campanile, Graham Plastow, Chunyan Zhang, Zhiquan Wang, Martino Cassandro, Bianca Gasparrini, Angela Salzano, Guohua Hua, Aixin Liang and Liguo Yang

    Citation: BMC Genomics 2018 19:814

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  20. Content type: Research article

    The cellular response to ionizing radiation involves activation of p53-dependent pathways and activation of the atypical NF-κB pathway. The crosstalk between these two transcriptional networks include (co)regu...

    Authors: Katarzyna Szołtysek, Patryk Janus, Gracjana Zając, Tomasz Stokowy, Anna Walaszczyk, Wiesława Widłak, Bartosz Wojtaś, Bartłomiej Gielniewski, Simon Cockell, Neil D. Perkins, Marek Kimmel and Piotr Widlak

    Citation: BMC Genomics 2018 19:813

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  21. Content type: Research article

    The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can...

    Authors: Emilien Peltier, Vikas Sharma, Maria Martí Raga, Miguel Roncoroni, Margaux Bernard, Vladimir Jiranek, Yves Gibon and Philippe Marullo

    Citation: BMC Genomics 2018 19:772

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  22. Content type: Software

    Translatomics data, particularly genome-wide ribosome profiling and polysome profiling, provide multiple levels of gene regulatory information that can be used to assess general transcription and translation, ...

    Authors: Amanda W. Ernlund, Robert J. Schneider and Kelly V. Ruggles

    Citation: BMC Genomics 2018 19:809

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  23. Content type: Research article

    Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix–lo...

    Authors: Miyako Kodama, Henrik Brinch-Pedersen, Shrikant Sharma, Inger Bæksted Holme, Bjarne Joernsgaard, Tsaneta Dzhanfezova, Daniel Buchvaldt Amby, Filipe Garrett Vieira, Shanlin Liu and M Thomas P Gilbert

    Citation: BMC Genomics 2018 19:811

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  24. Content type: Research article

    Staphylococcus caprae is an animal-associated bacterium regarded as part of goats’ microflora. Recently, S. caprae has been reported to cause human nosocomial infections such as bacteremia and bone and joint infe...

    Authors: Shinya Watanabe, Yoshifumi Aiba, Xin-Ee Tan, Feng-Yu Li, Tanit Boonsiri, Kanate Thitiananpakorn, Bintao Cui, Yusuke Sato’o, Kotaro Kiga, Teppei Sasahara and Longzhu Cui

    Citation: BMC Genomics 2018 19:810

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  25. Content type: Research article

    Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of t...

    Authors: Qiming Cheng, Shiqie Bai, Gentu Ge, Ping Li, Liying Liu, Chengdong Zhang and Yushan Jia

    Citation: BMC Genomics 2018 19:807

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  26. Content type: Research article

    Animal studies show that high fat (HF) diet-induced gut microbiota contributes to the development of obesity. Oil composition of high-fat diet affects metabolic inflammation differently with deleterious effect...

    Authors: Vania Patrone, Andrea Minuti, Michela Lizier, Francesco Miragoli, Franco Lucchini, Erminio Trevisi, Filippo Rossi and Maria Luisa Callegari

    Citation: BMC Genomics 2018 19:808

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  27. Content type: Research article

    Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of th...

    Authors: Luyun Ning, Zhiwei Lin, Jianwei Gu, Lu Gan, Yonghong Li, Hao Wang, Liyun Miao, Libin Zhang, Baoshan Wang and Maoteng Li

    Citation: BMC Genomics 2018 19:806

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  28. Content type: Research article

    Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DN...

    Authors: Sven Warris, Elio Schijlen, Henri van de Geest, Rahulsimham Vegesna, Thamara Hesselink, Bas te Lintel Hekkert, Gabino Sanchez Perez, Paul Medvedev, Kateryna D. Makova and Dick de Ridder

    Citation: BMC Genomics 2018 19:798

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  29. Content type: Research article

    WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modi...

    Authors: Rui Hu, Jie Xiao, Ting Gu, Xiaofen Yu, Yang Zhang, Junli Chang, Guangxiao Yang and Guangyuan He

    Citation: BMC Genomics 2018 19:803

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  30. Content type: Research article

    A change in the environment may impair development or survival of living organisms leading them to adapt to the change. The resulting adaptation trait may reverse, or become fixed in the population leading to ...

    Authors: Yves Moné, Sandra Nhim, Sylvie Gimenez, Fabrice Legeai, Imène Seninet, Hugues Parrinello, Nicolas Nègre and Emmanuelle d’Alençon

    Citation: BMC Genomics 2018 19:804

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  31. Content type: Research article

    Calanthe masuca and C. sinica are two genetically closely related species in Orchidaceae. C. masuca is widely distributed in Asia, whereas C. sinica is restricted to Yunnan and Guangxi Provinces in southwest Chin...

    Authors: Chao Hu, Hongxing Yang, Kai Jiang, Ling Wang, Boyun Yang, Tungyu Hsieh, Siren Lan and Weichang Huang

    Citation: BMC Genomics 2018 19:800

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  32. Content type: Research article

    Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the...

    Authors: Suchawan Pornsukarom, Arnoud H M van Vliet and Siddhartha Thakur

    Citation: BMC Genomics 2018 19:801

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  33. Content type: Methodology article

    Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count dat...

    Authors: M. Senthil Kumar, Eric V. Slud, Kwame Okrah, Stephanie C. Hicks, Sridhar Hannenhalli and Héctor Corrada Bravo

    Citation: BMC Genomics 2018 19:799

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  34. Content type: Research article

    Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embry...

    Authors: Yan Chen, Xue Li, Liyao Su, Xu Chen, Shuting Zhang, Xiaoping Xu, Zihao Zhang, Yukun Chen, Xu XuHan, Yuling Lin and Zhongxiong Lai

    Citation: BMC Genomics 2018 19:805

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  35. Content type: Research article

    Ornamental cabbage (Brassica oleracea var. acephala) is an attractive landscape plant that remains colorful at low temperatures during winter. Its key feature is its inner leaf coloration, which can include red, ...

    Authors: Si-Won Jin, Md Abdur Rahim, Khandker Shazia Afrin, Jong-In Park, Jong-Goo Kang and Ill-Sup Nou

    Citation: BMC Genomics 2018 19:797

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  36. Content type: Research article

    Epithelial–mesenchymal transition (EMT) is regarded as a critical event during tumor metastasis. Recent studies have revealed changes and the contributions of proteins in/on exosomes during EMT. Besides protei...

    Authors: Yue-Ting Tang, Yi-Yao Huang, Jing-Huan Li, Si-Hua Qin, Yong Xu, Tai-Xue An, Chun-Chen Liu, Qian Wang and Lei Zheng

    Citation: BMC Genomics 2018 19:802

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  37. Content type: Research article

    Development of the face and mouth is orchestrated by a large number of transcription factors, signaling pathways and epigenetic regulators. While we know many of these regulators, our understanding of how they...

    Authors: Stacey E. Wahl, Brent H. Wyatt, Stephen D. Turner and Amanda J. G. Dickinson

    Citation: BMC Genomics 2018 19:795

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  38. Content type: Research article

    Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-whi...

    Authors: Juan Carlos Higareda-Almaraz, Michael Karbiener, Maude Giroud, Florian M. Pauler, Teresa Gerhalter, Stephan Herzig and Marcel Scheideler

    Citation: BMC Genomics 2018 19:794

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  39. Content type: Research article

    Dependence on marine natural resources threatens the sustainability of Atlantic salmon aquaculture. In the present study, Atlantic salmon fed for 14 weeks with an experimental diet based on animal by-products ...

    Authors: Albert Caballero-Solares, Xi Xue, Christopher C. Parrish, Maryam Beheshti Foroutani, Richard G. Taylor and Matthew L. Rise

    Citation: BMC Genomics 2018 19:796

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  40. Content type: Research article

    The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple indivi...

    Authors: Majid Khansefid, Jennie E. Pryce, Sunduimijid Bolormaa, Yizhou Chen, Catriona A. Millen, Amanda J. Chamberlain, Christy J. Vander Jagt and Michael E. Goddard

    Citation: BMC Genomics 2018 19:793

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  41. Content type: Research article

    Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptatio...

    Authors: Billie A. Gould, Juan Diego Palacio-Mejia, Jerry Jenkins, Sujan Mamidi, Kerrie Barry, Jeremy Schmutz, Thomas E. Juenger and David B. Lowry

    Citation: BMC Genomics 2018 19:792

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  42. Content type: Research article

    Hypsizygus marmoreus (Beech mushroom) is a popular ingredient in Asian cuisine. The medicinal effects of its bioactive compounds such as hypsin and hypsiziprenol have been reported, but the genetic basis or biosy...

    Authors: Byoungnam Min, Seunghwan Kim, Youn-Lee Oh, Won-Sik Kong, Hongjae Park, Heejung Cho, Kab-Yeul Jang, Jeong-Gu Kim and In-Geol Choi

    Citation: BMC Genomics 2018 19:789

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  43. Content type: Research article

    Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to ...

    Authors: Justyna Horodyska, Klaus Wimmers, Henry Reyer, Nares Trakooljul, Anne Maria Mullen, Peadar G. Lawlor and Ruth M. Hamill

    Citation: BMC Genomics 2018 19:791

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  44. Content type: Methodology article

    Although human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) da...

    Authors: Shuto Hayashi, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa and Seiya Imoto

    Citation: BMC Genomics 2018 19:790

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  45. Content type: Methodology article

    Fusion genes are known to be drivers of many common cancers, so they are potential markers for diagnosis, prognosis or therapy response. The advent of paired-end RNA sequencing enhances our ability to discover...

    Authors: Trung Nghia Vu, Wenjiang Deng, Quang Thinh Trac, Stefano Calza, Woochang Hwang and Yudi Pawitan

    Citation: BMC Genomics 2018 19:786

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  46. Content type: Research article

    The insect olfactory system is a highly specific and sensitive chemical detector, which plays important roles in feeding, mating and finding an appropriate oviposition site. The ecological niche of Bombyx mori ha...

    Authors: Chuan-Zhen Qiu, Qiu-Zhong Zhou, Ting-Ting Liu, Shou-Min Fang, Ya-Wang Wang, Xin Fang, Chun-Li Huang, Quan-You Yu, Chun-Hong Chen and Ze Zhang

    Citation: BMC Genomics 2018 19:788

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  47. Content type: Research article

    Macaca fascicularis (M. fascicularis) is a primate model organism that played important role in studying human health. It is vital to better understand the similarity and differences of gene regulation between M....

    Authors: Tao Tan, Lin Xia, Kailing Tu, Jie Tang, Senlin Yin, Lunzhi Dai, Peng Lei, Biao Dong, Hongbo Hu, Yong Fan, Yang Yu and Dan Xie

    Citation: BMC Genomics 2018 19:787

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  48. Content type: Research article

    The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is pred...

    Authors: Lin-sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-gang Sun, Irfan Ullah and Yin-cang Han

    Citation: BMC Genomics 2018 19:785

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  50. Content type: Research article

    Our previous study showed that (+)-cholesten-3-one (CN) has the potential to induce the osteoblastic differentiation of mesenchymal stem cells (MSCs). However, the roles of CN in targeting miRNA-mRNA-lncRNA in...

    Authors: Qiuke Hou, Yongquan Huang, Yamei Liu, Yiwen Luo, Bin Wang, Rudong Deng, Saixia Zhang, Fengbin Liu and Dongfeng Chen

    Citation: BMC Genomics 2018 19:783

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