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  1. Whole-genome sequencing (WGS) plays an increasingly important role in clinical practice and public health. Due to the big data size, WGS data analysis is usually compute-intensive and IO-intensive. Currently i...

    Authors: Yiqi Wang, Gen Li, Mark Ma, Fazhong He, Zhuo Song, Wei Zhang and Chengkun Wu
    Citation: BMC Genomics 2018 19(Suppl 1):959
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  2. Emerging evidence has been experimentally confirmed the tissue-specific expression of circRNAs (circRNAs). Global identification of human tissue-specific circRNAs is crucial for the functionality study, which ...

    Authors: Yu-Chen Liu, Yu-Jung Chiu, Jian-Rong Li, Chuan-Hu Sun, Chun-Chi Liu and Hsien-Da Huang
    Citation: BMC Genomics 2018 19(Suppl 1):958
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  3. Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues,...

    Authors: Naoki Osato
    Citation: BMC Genomics 2018 19(Suppl 1):957
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  4. It has been observed that many transcription factors (TFs) can bind to different genomic loci depending on the cell type in which a TF is expressed in, even though the individual TF usually binds to the same c...

    Authors: Xin Wang, Peijie Lin and Joshua W. K. Ho
    Citation: BMC Genomics 2018 19(Suppl 1):929
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  5. RNA editing is an important mechanism that expands the diversity and complexity of genetic codes. The conversions of adenosine (A) to inosine (I) and cytosine (C) to uridine (U) are two prominent types of RNA ...

    Authors: Yingying Cao, Ruiyuan Cao, Yaowei Huang, Hongxia Zhou, Yuanhua Liu, Xuan Li, Wu Zhong and Pei Hao
    Citation: BMC Genomics 2018 19(Suppl 1):925
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  6. The advances in target control of complex networks not only can offer new insights into the general control dynamics of complex systems, but also be useful for the practical application in systems biology, suc...

    Authors: Wei-Feng Guo, Shao-Wu Zhang, Qian-Qian Shi, Cheng-Ming Zhang, Tao Zeng and Luonan Chen
    Citation: BMC Genomics 2018 19(Suppl 1):924
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  7. Post-translational modification is considered an important biological mechanism with critical impact on the diversification of the proteome. Although a long list of such modifications has been studied, succiny...

    Authors: Yosvany López, Alok Sharma, Abdollah Dehzangi, Sunil Pranit Lal, Ghazaleh Taherzadeh, Abdul Sattar and Tatsuhiko Tsunoda
    Citation: BMC Genomics 2018 19(Suppl 1):923
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  8. Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-gener...

    Authors: Yuko Makita, Mika Kawashima, Nyok Sean Lau, Ahmad Sofiman Othman and Minami Matsui
    Citation: BMC Genomics 2018 19(Suppl 1):922
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  9. Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively use...

    Authors: Liang Cheng, Yue Jiang, Hong Ju, Jie Sun, Jiajie Peng, Meng Zhou and Yang Hu
    Citation: BMC Genomics 2018 19(Suppl 1):919
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  10. The immunoglobulin (Ig) superfamily receptor Down syndrome cell adhesion molecule (Dscam) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for both nervous and immune s...

    Authors: Guozheng Cao, Yang Shi, Jian Zhang, Hongru Ma, Shouqing Hou, Haiyang Dong, Weiling Hong, Shuo Chen, Hao Li, Yandan Wu, Pengjuan Guo, Xu Shao, Bingbing Xu, Feng Shi, Yijun Meng and Yongfeng Jin
    Citation: BMC Genomics 2018 19:66
    Content type: Research article Published on:

  12. Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemp...

    Authors: Jean P. Elbers, Mary B. Brown and Sabrina S. Taylor
    Citation: BMC Genomics 2018 19:64
    Content type: Research article Published on:

  13. Adenosine-to-Inosine (A-to-I) RNA editing is catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes, which induces alterations in mRNA sequence. It has been shown that A-to-I RNA editing e...

    Authors: Yaowei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Wu Zhong, Xuan Li, Chen Chen and Pei Hao
    Citation: BMC Genomics 2018 19(Suppl 1):43
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  14. Ebolavirus (EBOV) is responsible for one of the most fatal diseases encountered by mankind. Cellular T-cell responses have been implicated to be important in providing protection against the virus. Antigenic vari...

    Authors: Wan Ching Lim and Asif M. Khan
    Citation: BMC Genomics 2018 19(Suppl 1):42
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  15. Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax noto...

    Authors: Kun Chen, Li Liu, Xiaotuo Zhang, Yuanyuan Yuan, Shuchao Ren, Junqiang Guo, Qingyi Wang, Peiran Liao, Shipeng Li, Xiuming Cui, Yong-Fang Li and Yun Zheng
    Citation: BMC Genomics 2018 19(Suppl 1):41
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  16. Since PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properl...

    Authors: Yongbing Zhao, Chen Sun, Dongyu Zhao, Yadong Zhang, Yang You, Xinmiao Jia, Junhui Yang, Lingping Wang, Jinyue Wang, Haohuan Fu, Yu Kang, Fei Chen, Jun Yu, Jiayan Wu and Jingfa Xiao
    Citation: BMC Genomics 2018 19(Suppl 1):36
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  18. Heat shock proteins (Hsps) are essential components in plant tolerance mechanism under various abiotic stresses. Hsp20 is the major family of heat shock proteins, but little of Hsp20 family is known in potato (So...

    Authors: Peng Zhao, Dongdong Wang, Ruoqiu Wang, Nana Kong, Chao Zhang, Chenghui Yang, Wentao Wu, Haoli Ma and Qin Chen
    Citation: BMC Genomics 2018 19:61
    Content type: Research article Published on:

  20. The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in orde...

    Authors: Nicole J. Ward, Darrell Green, Janet Higgins, Tamas Dalmay, Andrea Münsterberg, Simon Moxon and Grant N. Wheeler
    Citation: BMC Genomics 2018 19:59
    Content type: Research article Published on:

  21. The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta

    Authors: Eddy Patricia Lopez Molano, Odalys García Cabrera, Juliana Jose, Leandro Costa do Nascimento, Marcelo Falsarella Carazzolle, Paulo José Pereira Lima Teixeira, Javier Correa Alvarez, Ricardo Augusto Tiburcio, Paulo Massanari Tokimatu Filho, Gustavo Machado Alvares de Lima, Rafael Victório Carvalho Guido, Thamy Lívia Ribeiro Corrêa, Adriana Franco Paes Leme, Piotr Mieczkowski and Gonçalo Amarante Guimarães Pereira
    Citation: BMC Genomics 2018 19:58
    Content type: Research article Published on:

  22. De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera ‘Sultanina’ genome assemblies for comparis...

    Authors: Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng and Anne Y. Fennell
    Citation: BMC Genomics 2018 19:57
    Content type: Research article Published on:

  23. Technical advances in mobile devices such as smartphones and tablets have produced an extraordinary increase in their use around the world and have become part of our daily lives. The possibility of carrying t...

    Authors: Sergio Diaz-del-Pino, Oswaldo Trelles and Juan Falgueras
    Citation: BMC Genomics 2018 19:56
    Content type: Software Published on:

  24. Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been clear. In this study, a syst...

    Authors: Huanxian Cui, Maiqing Zheng, Guiping Zhao, Ranran Liu and Jie Wen
    Citation: BMC Genomics 2018 19:55
    Content type: Research article Published on:

  25. Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes...

    Authors: Luis Acuña-Amador, Aline Primot, Edouard Cadieu, Alain Roulet and Frédérique Barloy-Hubler
    Citation: BMC Genomics 2018 19:54
    Content type: Research article Published on:

  26. Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation...

    Authors: Barbara Ramos, Daniel González-Acuña, David E. Loyola, Warren E. Johnson, Patricia G. Parker, Melanie Massaro, Gisele P. M. Dantas, Marcelo D. Miranda and Juliana A. Vianna
    Citation: BMC Genomics 2018 19:53
    Content type: Research article Published on:

  27. The protean chemical properties of mercury have long made it attractive for diverse applications, but its toxicity requires great care in its use, disposal, and recycling. Mercury occurs in multiple chemical f...

    Authors: Stephen P. LaVoie and Anne O. Summers
    Citation: BMC Genomics 2018 19:52
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:268

  28. The MADS-box transcription factors are an ancient family of genes that regulate numerous physiological and biochemical processes in plants and facilitate the development of floral organs. However, the function...

    Authors: Xuanrui Zeng, Hailun Liu, Hongyang Du, Sujing Wang, Wenming Yang, Yingjun Chi, Jiao Wang, Fang Huang and Deyue Yu
    Citation: BMC Genomics 2018 19:51
    Content type: Research article Published on:

  29. Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious disease...

    Authors: Yang Jiao, Ran Li, Chao Wu, Yibin Ding, Yanning Liu, Danmei Jia, Lifeng Wang, Xiang Xu, Jing Zhu, Min Zheng and Junling Jia
    Citation: BMC Genomics 2018 19:50
    Content type: Methodology article Published on:

  30. Phycodnaviruses are widespread algae-infecting large dsDNA viruses and presently contain six genera: Chlorovirus, Prasinovirus, Prymnesiovirus, Phaeovirus, Coccolithovirus and Raphidovirus. The members in Prasino...

    Authors: Hao Chen, Weijia Zhang, Xiefei Li, Yingjie Pan, Shuling Yan and Yongjie Wang
    Citation: BMC Genomics 2018 19:49
    Content type: Research article Published on:

  31. Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white...

    Authors: Deepak K. Gupta, Martin Rühl, Bagdevi Mishra, Vanessa Kleofas, Martin Hofrichter, Robert Herzog, Marek J. Pecyna, Rahul Sharma, Harald Kellner, Florian Hennicke and Marco Thines
    Citation: BMC Genomics 2018 19:48
    Content type: Research article Published on:

  32. The increasing application of next generation sequencing technologies has led to the availability of thousands of reference genomes, often providing multiple genomes for the same or closely related species. Th...

    Authors: Christine Jandrasits, Piotr W. Dabrowski, Stephan Fuchs and Bernhard Y. Renard
    Citation: BMC Genomics 2018 19:47
    Content type: Methodology article Published on:

  33. The conventional variant calling of pathogenic alleles in exome and genome sequencing requires the presence of the non-pathogenic alleles as genome references. This hinders the correct identification of varian...

    Authors: Mahmoud Koko, Mohammed O. E. Abdallah, Mutaz Amin and Muntaser Ibrahim
    Citation: BMC Genomics 2018 19:46
    Content type: Research article Published on:

  34. Among naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link ...

    Authors: Michael A. Skinnider, Chad W. Johnston, Nishanth J. Merwin, Chris A. Dejong and Nathan A. Magarvey
    Citation: BMC Genomics 2018 19:45
    Content type: Research article Published on:

  35. Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “func...

    Authors: Matteo Chiara, Antonio Placido, Ernesto Picardi, Luigi Ruggiero Ceci, David Stephen Horner and Graziano Pesole
    Citation: BMC Genomics 2018 19:44
    Content type: Software Published on:

  36. Plant stress responses and mechanisms determining tolerance are controlled by diverse sets of genes. Transcription factors (TFs) have been implicated in conferring drought tolerance under drought stress condit...

    Authors: Pil Joong Chung, Harin Jung, Yang Do Choi and Ju-Kon Kim
    Citation: BMC Genomics 2018 19:40
    Content type: Research article Published on:

  37. The authors of the original article [1] would like to recognize the critical contribution of core members of the FANTOM5 Consortium, who played the critical role of HeliScopeCAGE sequencing experiments, qualit...

    Authors: Peter Zhang, Emmanuel Dimont, Thomas Ha, Douglas J. Swanson, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Winston Hide and Dan Goldowitz
    Citation: BMC Genomics 2018 19:39
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2017 18:461

  38. The growth of Inner Mongolian Cashmere goat skin hair follicle exhibits a periodic growth pattern. The hair growth cycle is distinguished as telogen, anagen, and catagen stages. The role of vimentin in the gro...

    Authors: Nai Rile, Zhihong Liu, Lixia Gao, Jingkai Qi, Meng Zhao, Yuchun Xie, Rui Su, Yanjun Zhang, Ruijun Wang, Jie Li, Hongmei Xiao and Jinquan Li
    Citation: BMC Genomics 2018 19:38
    Content type: Research article Published on:

  39. Senescence is a fundamental biological process implicated in various pathologies, including cancer. Regarding carcinogenesis, senescence signifies, at least in its initial phases, an anti-tumor response that n...

    Authors: Eirini-Stavroula Komseli, Ioannis S. Pateras, Thorbjørn Krejsgaard, Konrad Stawiski, Sophia V. Rizou, Alexander Polyzos, Fani-Marlen Roumelioti, Maria Chiourea, Ioanna Mourkioti, Eleni Paparouna, Christos P. Zampetidis, Sentiljana Gumeni, Ioannis P. Trougakos, Dafni-Eleftheria Pefani, Eric O’Neill, Sarantis Gagos…
    Citation: BMC Genomics 2018 19:37
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:327

  41. Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. Th...

    Authors: Elisa Peripolli, Nedenia Bonvino Stafuzza, Danísio Prado Munari, André Luís Ferreira Lima, Renato Irgang, Marco Antonio Machado, João Cláudio do Carmo Panetto, Ricardo Vieira Ventura, Fernando Baldi and Marcos Vinícius Gualberto Barbosa da Silva
    Citation: BMC Genomics 2018 19:34
    Content type: Research article Published on:

  42. Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe r...

    Authors: Silvia Arboleya, Francesca Bottacini, Mary O’Connell-Motherway, C. Anthony Ryan, R. Paul Ross, Douwe van Sinderen and Catherine Stanton
    Citation: BMC Genomics 2018 19:33
    Content type: Research article Published on:

  43. Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are...

    Authors: Madeleine Carruthers, Andrey A. Yurchenko, Julian J. Augley, Colin E. Adams, Pawel Herzyk and Kathryn R. Elmer
    Citation: BMC Genomics 2018 19:32
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:448

  44. The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for sp...

    Authors: Catherine M. Purcell, Arun S. Seetharam, Owyn Snodgrass, Sofia Ortega-García, John R. Hyde and Andrew J. Severin
    Citation: BMC Genomics 2018 19:31
    Content type: Research article Published on:

  45. Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigation...

    Authors: Laura E. MacConaill, Robert T. Burns, Anwesha Nag, Haley A. Coleman, Michael K. Slevin, Kristina Giorda, Madelyn Light, Kevin Lai, Mirna Jarosz, Matthew S. McNeill, Matthew D. Ducar, Matthew Meyerson and Aaron R. Thorner
    Citation: BMC Genomics 2018 19:30
    Content type: Research article Published on:

  46. Chicken embryos are widely used as a model for studies of obesity; however, no detailed information is available about the dynamic changes of proteins during the regulation of adipose biology and metabolism. T...

    Authors: Mengling Peng, Shengnan Li, Qianian He, Jinlong Zhao, Longlong Li and Haitian Ma
    Citation: BMC Genomics 2018 19:29
    Content type: Research article Published on:

  47. Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain. We used the highly accurate microfluid...

    Authors: Hiba Zaidan, Gokul Ramaswami, Yaela N. Golumbic, Noa Sher, Assaf Malik, Michal Barak, Dalia Galiani, Nava Dekel, Jin B. Li and Inna Gaisler-Salomon
    Citation: BMC Genomics 2018 19:28
    Content type: Research article Published on:

  48. Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cyste...

    Authors: Juan Liu, Anupma Sharma, Marie Jamille Niewiara, Ratnesh Singh, Ray Ming and Qingyi Yu
    Citation: BMC Genomics 2018 19:26
    Content type: Research article Published on:

  49. Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumouri...

    Authors: Claudia Cava, Gloria Bertoli, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi and Isabella Castiglioni
    Citation: BMC Genomics 2018 19:25
    Content type: Methodology article Published on:

  50. The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this α-proteobacterium...

    Authors: Angela Kranz, Tobias Busche, Alexander Vogel, Björn Usadel, Jörn Kalinowski, Michael Bott and Tino Polen
    Citation: BMC Genomics 2018 19:24
    Content type: Research article Published on:

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BMC Genomics

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