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  1. Content type: Research article

    Nicotiana rustica (Aztec tobacco), like common tobacco (Nicotiana tabacum), is an allotetraploid formed through a recent hybridization event; however, it originated from completely different progenitor species. H...

    Authors: N. Sierro, J. N. D. Battey, L. Bovet, V. Liedschulte, S. Ouadi, J. Thomas, H. Broye, H. Laparra, A. Vuarnoz, G. Lang, S. Goepfert, M. C. Peitsch and N. V. Ivanov

    Citation: BMC Genomics 2018 19:855

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  2. Content type: Research article

    Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide app...

    Authors: Clémentine Dressaire, Vânia Pobre, Sandrine Laguerre, Laurence Girbal, Cecilia Maria Arraiano and Muriel Cocaign-Bousquet

    Citation: BMC Genomics 2018 19:848

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  3. Content type: Research article

    Chemosensation is a critical signalling process for all organisms and is achieved through the interaction between chemosensory receptors and their ligands. The Crown-of-thorns starfish, Acanthaster planci species...

    Authors: R. E. Roberts, D. Powell, T. Wang, M. H. Hall, C. A. Motti and S. F. Cummins

    Citation: BMC Genomics 2018 19:853

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  4. Content type: Research article

    The green peach aphid (GPA), Myzus persicae (Sülzer), is a widespread phloem-feeding insect that significantly influences the yield and visual quality of peach [Prunus persica (L.) Batsch]. Single dominant gene (

    Authors: Liang Niu, Lei Pan, Wenfang Zeng, Zhenhua Lu, Guochao Cui, Meili Fan, Qiang Xu, Zhiqiang Wang and Guohuai Li

    Citation: BMC Genomics 2018 19:846

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  5. Content type: Research article

    Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishma...

    Authors: Sumudu R. Samarasinghe, Nilakshi Samaranayake, Udeshika L. Kariyawasam, Yamuna D. Siriwardana, Hideo Imamura and Nadira D. Karunaweera

    Citation: BMC Genomics 2018 19:843

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  6. Content type: Research article

    Increased attention is being paid to breast muscle yield and meat quality in the duck breeding industry. Our previous report has demonstrated that dietary Clostridium butyricum (C. butyricum) can improve meat qua...

    Authors: Yanhan Liu, Yaxiong Jia, Cun Liu, Limin Ding and Zhaofei Xia

    Citation: BMC Genomics 2018 19:844

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  7. Content type: Research article

    Pyropia yezoensis is an important marine crop which, due to its high protein content, is widely used as a seafood in China. Unfortunately, red rot disease, caused by Pythium porphyrae, seriously damages P. yezoen...

    Authors: Sohrab Khan, Yunxiang Mao, Dong Gao, Sadaf Riaz, Zeeshan Niaz, Lei Tang, Sohaib Khan and Dongmei Wang

    Citation: BMC Genomics 2018 19:842

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  8. Content type: Methodology article

    Copy Number Alternations (CNAs) is defined as somatic gain or loss of DNA regions. The profiles of CNAs may provide a fingerprint specific to a tumor type or tumor grade. Low-coverage sequencing for reporting ...

    Authors: Sangdi Lin, Chen Wang, Shabnam Zarei, Debra A. Bell, Sarah E. Kerr, George C. Runger and Jean-Pierre A. Kocher

    Citation: BMC Genomics 2018 19:841

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  9. Content type: Research article

    Skeletal muscle satellite cells (MSC) are crucial for postnatal growth and regeneration of skeletal muscle. An interaction exists between MSC and intramuscular preadipocytes (IMPA). This study is the first to ...

    Authors: Liping Guo, Huanxian Cui, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng, Yuming Guo and Jie Wen

    Citation: BMC Genomics 2018 19:838

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  10. Content type: Research article

    An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective abso...

    Authors: Qi Zhao, Qian Mao, Zheng Zhao, Tongyi Dou, Zhiguo Wang, Xiaoyu Cui, Yuanning Liu and Xiaoya Fan

    Citation: BMC Genomics 2018 19:839

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  11. Content type: Research article

    Nε-Acetylation of lysine residues, a frequently occurring post-translational modification, plays important functions in regulating physiology and metabolism. However, the information of global overview of protei....

    Authors: Jutang Jiang, Zhongshuai Gai, Yu Wang, Kai Fan, Litao Sun, Hui Wang and Zhaotang Ding

    Citation: BMC Genomics 2018 19:840

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  12. Content type: Research article

    Acetogenic bacteria constitute promising biocatalysts for the conversion of CO2/H2 or synthesis gas (H2/CO/CO2) into biofuels and value-added biochemicals. These microorganisms are naturally capable of autotrophi...

    Authors: Yoseb Song, Jongoh Shin, Sangrak Jin, Jung-Kul Lee, Dong Rip Kim, Sun Chang Kim, Suhyung Cho and Byung-Kwan Cho

    Citation: BMC Genomics 2018 19:837

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  13. Content type: Research article

    Gene ontology analysis using the microarray database generated in a previous study by this laboratory was used to further evaluate how maternal dietary supplementation with pyridoxine combined with different s...

    Authors: Danyel Bueno Dalto, Stephen Tsoi, Michael K. Dyck and Jean-Jacques Matte

    Citation: BMC Genomics 2018 19:836

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  14. Content type: Research article

    Helicobacter pylori is a human stomach pathogen, naturally-competent for DNA uptake, and prone to homologous recombination. Extensive homoplasy (i.e., phylogenetically-unlinked identical variations) observed in H...

    Authors: Sujay Chattopadhyay, Peter B. Chi, Vladimir N. Minin, Douglas E. Berg and Evgeni V. Sokurenko

    Citation: BMC Genomics 2018 19:835

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  15. Content type: Research article

    Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecolo...

    Authors: David Armisén, Rajendhran Rajakumar, Markus Friedrich, Joshua B. Benoit, Hugh M. Robertson, Kristen A. Panfilio, Seung-Joon Ahn, Monica F. Poelchau, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Richard A. Gibbs, Daniel S. T. Hughes, Yi Han, Sandra L. Lee…

    Citation: BMC Genomics 2018 19:832

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  16. Content type: Research article

    Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the Eur...

    Authors: Huabai Xue, Suke Wang, Jia-Long Yao, Cecilia H. Deng, Long Wang, Yanli Su, Huirong Zhang, Huangkai Zhou, Minshan Sun, Xiugen Li and Jian Yang

    Citation: BMC Genomics 2018 19:833

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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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