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  1. Content type: Research article

    Economically important growth and meat quality traits in pigs are controlled by cascading molecular events occurring during development and continuing throughout the conversion of muscle to meat. However, litt...

    Authors: Deborah Velez-Irizarry, Sebastian Casiro, Kaitlyn R. Daza, Ronald O. Bates, Nancy E. Raney, Juan P. Steibel and Catherine W. Ernst

    Citation: BMC Genomics 2019 20:3

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  2. Content type: Research article

    The Tibetan highland fish, Gymnocypris przewalskii, migrates from Lake Qinghai to its spawning grounds every summer. This seasonal reproduction is critically regulated by intrinsic and extrinsic signals. However,...

    Authors: Fei Tian, Sijia Liu, Jianquan Shi, Hongfang Qi, Kai Zhao and Baosheng Xie

    Citation: BMC Genomics 2019 20:2

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  3. Content type: Research

    The evolution of influenza A viruses leads to the antigenic changes. Serological diagnosis of the antigenicity is usually labor-intensive, time-consuming and not suitable for early-stage detection. Computation...

    Authors: Xinrui Zhou, Rui Yin, Chee-Keong Kwoh and Jie Zheng

    Citation: BMC Genomics 2018 19(Suppl 10):936

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    This article is part of a Supplement: Volume 19 Supplement 10

  4. Content type: Research

    Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace, whereas IR29 is a salt-sensitive but widely cultivated genotype. Comparative analysis of t...

    Authors: Yong-Fang Li, Yun Zheng, Lakshminarayana R. Vemireddy, Sanjib Kumar Panda, Smitha Jose, Alok Ranjan, Piyalee Panda, Ganesan Govindan, Junxia Cui, Kangning Wei, Mahmoud W. Yaish, Gnanambal Charmaine Naidoo and Ramanjulu Sunkar

    Citation: BMC Genomics 2018 19(Suppl 10):935

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    This article is part of a Supplement: Volume 19 Supplement 10

  5. Content type: Research

    Interactions among transcription factors (TFs) and histone modifications (HMs) play an important role in the precise regulation of gene expression. The context specificity of those interactions and further its...

    Authors: Lirong Zhang, Gaogao Xue, Junjie Liu, Qianzhong Li and Yong Wang

    Citation: BMC Genomics 2018 19(Suppl 10):914

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    This article is part of a Supplement: Volume 19 Supplement 10

  6. Content type: Research

    Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially regulate many aspects o...

    Authors: Robert Pokoo, Shuchao Ren, Qingyi Wang, Christy M. Motes, Timothy D. Hernandez, Sayvan Ahmadi, Maria J. Monteros, Yun Zheng and Ramanjulu Sunkar

    Citation: BMC Genomics 2018 19(Suppl 10):913

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    This article is part of a Supplement: Volume 19 Supplement 10

  7. Content type: Research

    NGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads. The o...

    Authors: Liang Zhao, Jin Xie, Lin Bai, Wen Chen, Mingju Wang, Zhonglei Zhang, Yiqi Wang, Zhe Zhao and Jinyan Li

    Citation: BMC Genomics 2018 19(Suppl 10):912

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    This article is part of a Supplement: Volume 19 Supplement 10

  8. Content type: Research

    In the process of post-transcription, microRNAs (miRNAs) are closely related to various complex human diseases. Traditional verification methods for miRNA-disease associations take a lot of time and expense, s...

    Authors: Limin Jiang, Yongkang Xiao, Yijie Ding, Jijun Tang and Fei Guo

    Citation: BMC Genomics 2018 19(Suppl 10):911

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    This article is part of a Supplement: Volume 19 Supplement 10

  9. Content type: Research

    With the increasing number of annotated long noncoding RNAs (lncRNAs) from the genome, researchers are continually updating their understanding of lncRNAs. Recently, thousands of lncRNAs have been reported to ...

    Authors: Chao Zeng and Michiaki Hamada

    Citation: BMC Genomics 2018 19(Suppl 10):906

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    This article is part of a Supplement: Volume 19 Supplement 10

  10. Content type: Research

    The DNase I hypersensitive sites (DHSs) are associated with the cis-regulatory DNA elements. An efficient method of identifying DHSs can enhance the understanding on the accessibility of chromatin. Despite a m...

    Authors: Chuqiao Lyu, Lei Wang and Juhua Zhang

    Citation: BMC Genomics 2018 19(Suppl 10):905

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    This article is part of a Supplement: Volume 19 Supplement 10

  11. Content type: Research

    Human gut microbiome has an essential role in human health and disease. Although the major dominant microbiota within individuals have been reported, the change of gut microbiome caused by external factors, su...

    Authors: Hui-Mei Chen, Chung-Chu Chen, Chien-Chi Chen, Shen-Chih Wang, Chun-Lin Wang, Chien-Hsun Huang, Jong-Shian Liou, Ta-Wei Liu, Hwei-Ling Peng, Feng-Mao Lin, Chia-Yuan Liu, Shun-Long Weng, Chieh-Jen Cheng, Yi-Fang Hung, Chii-Cherng Liao and Hsien-Da Huang

    Citation: BMC Genomics 2018 19(Suppl 10):904

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  12. Content type: Research

    With the maturity of next generation sequencing technology, a huge amount of epigenomic data have been generated by several large consortia in the last decade. These plenty resources leave us the opportunity a...

    Authors: Can Wang and Shihua Zhang

    Citation: BMC Genomics 2018 19(Suppl 10):903

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    This article is part of a Supplement: Volume 19 Supplement 10

  13. Content type: Research

    Recent advances in sequencing technologies have enabled parallel assays of chromatin accessibility and gene expression for major human cell lines. Such innovation provides a great opportunity to decode phenoty...

    Authors: Shining Ma, Tao Jiang and Rui Jiang

    Citation: BMC Genomics 2018 19(Suppl 10):884

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  14. Content type: Research

    Proteins are a kind of macromolecules and the main component of a cell, and thus it is the most essential and versatile material of life. The research of protein functions is of great significance in decoding ...

    Authors: Lin Liu, Lin Tang, Mingjing Tang and Wei Zhou

    Citation: BMC Genomics 2018 19(Suppl 10):883

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  15. Content type: Research

    Species of Paris Sect. Marmorata are valuable medicinal plants to synthesize steroidal saponins with effective pharmacological therapy. However, the wild resources of the species are threatened by plundering expl...

    Authors: Xiaoyang Gao, Xuan Zhang, Honghu Meng, Jing Li, Di Zhang and Changning Liu

    Citation: BMC Genomics 2018 19(Suppl 10):878

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  16. Content type: Research

    One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the “normal” vaginal microbiome; however, the normal microbiome appears to differ accor...

    Authors: Hui-Mei Chen, Tzu-Hao Chang, Feng-Mao Lin, Chao Liang, Chih-Min Chiu, Tzu-Ling Yang, Ting Yang, Chia-Yen Huang, Yeong-Nan Cheng, Yi-An Chang, Po-Ya Chang and Shun-Long Weng

    Citation: BMC Genomics 2018 19(Suppl 10):876

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  17. Content type: Research article

    Mud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is ...

    Authors: Xi Shi, Khor Waiho, Xincang Li, Mhd Ikhwanuddin, Guidong Miao, Fan Lin, Yueling Zhang, Shengkang Li, Huaiping Zheng, Wenhua Liu, Jude Juventus Aweya, Ghazali Azmie, Juliana C. Baylon, Emilia T. Quinitio and Hongyu Ma

    Citation: BMC Genomics 2018 19:981

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  18. Content type: Research article

    The parthenogenetic Caucasian rock lizard Darevskia armeniaca, like most other parthenogenetic vertebrate species, originated through interspecific hybridization between the closely related sexual Darevskia mixta

    Authors: Anastasiya E. Girnyk, Andrey A. Vergun, Seraphima K. Semyenova, Andrei S. Guliaev, Marine S. Arakelyan, Felix D. Danielyan, Irena A. Martirosyan, Robert W. Murphy and Alexey P. Ryskov

    Citation: BMC Genomics 2018 19:979

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  19. Content type: Research article

    Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a traditional Chinese herbal medicine with high medicinal value in China. Polysaccharides and alkaloids are its main active ingredients. To understand the differe...

    Authors: Yingdan Yuan, Maoyun Yu, Zhaohui Jia, Xue’er Song, Yingquan Liang and Jinchi Zhang

    Citation: BMC Genomics 2018 19:978

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  20. Content type: Methodology article

    Chloroplasts are organelles that conduct photosynthesis in plant and algal cells. The information chloroplast genome contained is widely used in agriculture and studies of evolution and ecology. Correctly asse...

    Authors: Weiwen Wang, Miriam Schalamun, Alejandro Morales-Suarez, David Kainer, Benjamin Schwessinger and Robert Lanfear

    Citation: BMC Genomics 2018 19:977

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  21. Content type: Research article

    Caleosin/peroxygenases, CLO/PXG, (designated PF05042 in Pfam) are a group of genes/proteins with anomalous distributions in eukaryotic taxa. We have previously characterised CLO/PXGs in the Viridiplantae. The aim...

    Authors: Farzana Rahman, Mehedi Hassan, Abdulsamie Hanano, David A. Fitzpatrick, Charley G. P. McCarthy and Denis J. Murphy

    Citation: BMC Genomics 2018 19:976

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  22. Content type: Research article

    MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important roles in the regulation of gene expression. However, the role of miRNAs in bovine mammary gland responses to heat stress is not well u...

    Authors: Qiuling Li, Chunhong Yang, Juan Du, Baogui Zhang, Ying He, Qimeng Hu, Meiru Li, Yiming Zhang, Changfa Wang and Jifeng Zhong

    Citation: BMC Genomics 2018 19:975

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  23. Content type: Review

    Numerous different types of variations can occur in DNA and have diverse effects and consequences. The Variation Ontology (VariO) was developed for systematic descriptions of variations and their effects at DN...

    Authors: Mauno Vihinen

    Citation: BMC Genomics 2018 19:974

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  24. Content type: Research article

    The ability of bacteria to acquire resistance to antibiotics relies to a large extent on their capacity for genome modification. Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer,...

    Authors: Marloes Hoeksema, Martijs J. Jonker, Keshia Bel, Stanley Brul and Benno H. ter Kuile

    Citation: BMC Genomics 2018 19:973

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  25. Content type: Research article

    Paratuberculosis is a contagious, chronic and enteric disease in ruminants, which is caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection, resulting in enormous economic losses worldwide. The...

    Authors: Yahui Gao, Jianping Jiang, Shaohua Yang, Jie Cao, Bo Han, Yachun Wang, Yi Zhang, Ying Yu, Shengli Zhang, Qin Zhang, Lingzhao Fang, Bonnie Cantrell and Dongxiao Sun

    Citation: BMC Genomics 2018 19:972

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  26. Content type: Research article

    The insect gustatory system plays a central role in the regulation of multiple physiological behaviors and the co-evolution between insects and their hosts. The gustatory receptors (Gr) are important to allow ...

    Authors: Kui Kang, Pan Yang, Li-E Chen, Rui Pang, Lu-Jun Yu, Wen-Wu Zhou, Zeng-Rong Zhu and Wen-Qing Zhang

    Citation: BMC Genomics 2018 19:970

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  27. Content type: Research article

    Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in t...

    Authors: Alexander V. Tyakht, Alexander I. Manolov, Alexandra V. Kanygina, Dmitry S. Ischenko, Boris A. Kovarsky, Anna S. Popenko, Alexander V. Pavlenko, Anna V. Elizarova, Daria V. Rakitina, Julia P. Baikova, Valentina G. Ladygina, Elena S. Kostryukova, Irina Y. Karpova, Tatyana A. Semashko, Andrei K. Larin, Tatyana V. Grigoryeva…

    Citation: BMC Genomics 2018 19:968

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  28. Content type: Research article

    Heart development is a relatively fragile process in which many transcription factor genes show dose-sensitive characteristics such as haploinsufficiency and lower penetrance. Despite efforts to unravel the ge...

    Authors: Yutaro Hori, Yoko Tanimoto, Satoru Takahashi, Tetsushi Furukawa, Kazuko Koshiba-Takeuchi and Jun K. Takeuchi

    Citation: BMC Genomics 2018 19:967

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  29. Content type: Research article

    The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, re...

    Authors: Olga O. Bochkareva, Elena V. Moroz, Iakov I. Davydov and Mikhail S. Gelfand

    Citation: BMC Genomics 2018 19:965

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  30. Content type: Software

    Studies that aim at explaining phenotypes or disease susceptibility by genetic or epigenetic variants often rely on clustering methods to stratify individuals or samples. While statistical associations may poi...

    Authors: Jiangning Gao, Görel Sundström, Behrooz Torabi Moghadam, Neda Zamani and Manfred G. Grabherr

    Citation: BMC Genomics 2018 19:964

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  31. Content type: Research article

    A-to-I RNA editing is a co−/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, ...

    Authors: Edoardo Giacopuzzi, Massimo Gennarelli, Chiara Sacco, Alice Filippini, Jessica Mingardi, Chiara Magri and Alessandro Barbon

    Citation: BMC Genomics 2018 19:963

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  32. Content type: Research article

    Somatic embryogenesis receptor-like kinases (SERKs) are leucine-rich repeat receptor-like kinases associated with various signaling pathways. These kinases have a relationship with stress signals, and they are...

    Authors: Liwei Zheng, Juanjuan Ma, Jiangping Mao, Sheng Fan, Dong Zhang, Caiping Zhao, Na An and Mingyu Han

    Citation: BMC Genomics 2018 19:962

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  33. Content type: Research article

    Cosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of e...

    Authors: Tianjuan Su, Bo He, Kui Li and Aiping Liang

    Citation: BMC Genomics 2018 19:961

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  34. Content type: Software

    New single-cell isolation technologies are facilitating studies on the transcriptomics of individual cells. Bio-Rad ddSEQ is a droplet-based microfluidic system that, when coupled with downstream Illumina libr...

    Authors: Dario Romagnoli, Giulia Boccalini, Martina Bonechi, Chiara Biagioni, Paola Fassan, Roberto Bertorelli, Veronica De Sanctis, Angelo Di Leo, Ilenia Migliaccio, Luca Malorni and Matteo Benelli

    Citation: BMC Genomics 2018 19:960

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  35. Content type: Research article

    Both human and mouse fibroblasts can be reprogrammed to pluripotency with Oct4, Sox2, Klf4, and c-Myc (OSKM) transcription factors. While both systems generate pluripotency, human reprogramming takes considera...

    Authors: Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Stephen T. Smale, Kenneth S. Zaret, Kathrin Plath and Matteo Pellegrini

    Citation: BMC Genomics 2018 19:956

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  36. Content type: Research article

    Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content ...

    Authors: Li-Yi Xu, Li-Yuan Wang, Kang Wei, Li-Qiang Tan, Jing-Jing Su and Hao Cheng

    Citation: BMC Genomics 2018 19:955

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  37. Content type: Research article

    The human chromosome 14 microRNA cluster (C14MC) is a conserved microRNA (miRNA) cluster across eutherian mammals, reported to play an important role in placental development. However, the expression kinetics ...

    Authors: Pouya Dini, Peter Daels, Shavahn C. Loux, Alejandro Esteller-Vico, Mariano Carossino, Kirsten E. Scoggin and Barry A. Ball

    Citation: BMC Genomics 2018 19:954

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  38. Content type: Methodology article

    When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and resea...

    Authors: John R. Stevens, Jennifer S. Herrick, Roger K. Wolff and Martha L. Slattery

    Citation: BMC Genomics 2018 19:953

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  39. Content type: Research article

    Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to sear...

    Authors: Ning Li, Lisui Bao, Tao Zhou, Zihao Yuan, Shikai Liu, Rex Dunham, Yuanning Li, Kun Wang, Xiaoyan Xu, Yulin Jin, Qifan Zeng, Sen Gao, Qiang Fu, Yang Liu, Yujia Yang, Qi Li…

    Citation: BMC Genomics 2018 19:952

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  40. Content type: Research article

    Guar [Cyamopsis tetragonoloba, L. Taub.] is an important industrial crop because of the commercial applications of the galactomannan gum contained in its seeds. Plant breeding programmes based on marker-assisted ...

    Authors: Omika Thakur and Gursharn Singh Randhawa

    Citation: BMC Genomics 2018 19:951

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  41. Content type: Research article

    Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primar...

    Authors: Sui Wang, Chuanping Yang, Xiyang Zhao, Su Chen and Guan-Zheng Qu

    Citation: BMC Genomics 2018 19:950

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  42. Content type: Research article

    Bovine papillomavirus (BPV) belongs to the Papillomaviridae family and infects epithelial cells of bovines and closely related animals, causing hyperproliferative lesions known as warts or papillomas, which ma...

    Authors: Débora M. Barreto, Gerlane S. Barros, Lucas A. B. O. Santos, Rosilene C. Soares and Marcus V. A. Batista

    Citation: BMC Genomics 2018 19:949

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  43. Content type: Research article

    Genome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional annota...

    Authors: Marc Griesemer, Jeffrey A. Kimbrel, Carol E. Zhou, Ali Navid and Patrik D’haeseleer

    Citation: BMC Genomics 2018 19:948

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  44. Content type: Software

    Recent advances in sequencing technology have allowed us to investigate personal genomes to find structural variations, which have been studied extensively to identify their association with the physiology of ...

    Authors: Junwoo Bae, Kyeong Won Lee, Mohammad Nazrul Islam, Hyung-Soon Yim, Heejin Park and Mina Rho

    Citation: BMC Genomics 2018 19:944

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  45. Content type: Research article

    Root-knot nematodes (RKN), genus Meloidogyne, are plant parasitic worms that have the ability to transform root vascular cylinder cells into hypertrophied, multinucleate and metabolically over-active feeding cell...

    Authors: Clémence Medina, Martine da Rocha, Marc Magliano, Alizée Raptopoulo, Nathalie Marteu, Kevin Lebrigand, Pierre Abad, Bruno Favery and Stéphanie Jaubert-Possamai

    Citation: BMC Genomics 2018 19:943

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