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  1. With the current microarray and RNA-seq technologies, two-sample genome-wide expression data have been widely collected in biological and medical studies. The related differential expression analysis and gene ...

    Authors: Yinglei Lai, Fanni Zhang, Tapan K. Nayak, Reza Modarres, Norman H. Lee and Timothy A. McCaffrey
    Citation: BMC Genomics 2017 18(Suppl 1):1050
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  2. DNA methylation is the major form of epigenetic modifications through which the cell regulates the gene expression and silencing. There have been extensive studies on the roles of DNA methylation in cancers, a...

    Authors: Jie Zhang and Kun Huang
    Citation: BMC Genomics 2017 18(Suppl 1):1045
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  3. The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning ...

    Authors: Yao-zhong Zhang, Rui Yamaguchi, Seiya Imoto and Satoru Miyano
    Citation: BMC Genomics 2017 18(Suppl 1):1044
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  4. Identifying the genes associated to human diseases is crucial for disease diagnosis and drug design. Computational approaches, esp. the network-based approaches, have been recently developed to identify diseas...

    Authors: Jiajie Peng, Kun Bai, Xuequn Shang, Guohua Wang, Hansheng Xue, Shuilin Jin, Liang Cheng, Yadong Wang and Jin Chen
    Citation: BMC Genomics 2017 18(Suppl 1):1043
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  5. Selaginella moellendorffii, a lycophyte, is a model plant to study the early evolution and development of vascular plants. As the first and only sequenced lycophyte to date, the genome...

    Authors: Yan Zhu, Longxian Chen, Chengjun Zhang, Pei Hao, Xinyun Jing and Xuan Li
    Citation: BMC Genomics 2017 18(Suppl 1):1042
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  6. Periodontitis is an inflammatory disease affecting the tissues supporting teeth (periodontium). Integrative analysis of metagenomic samples from multiple periodontitis studies is a powerful way to examine micr...

    Authors: Dongmei Ai, Ruocheng Huang, Jin Wen, Chao Li, Jiangping Zhu and Li Charlie Xia
    Citation: BMC Genomics 2017 18(Suppl 1):1041
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  7. Alternative splicing plays important roles in many regulatory processes and diseases in human. Many genetic variants contribute to phenotypic differences in gene expression and splicing that determine variatio...

    Authors: Qian Yang, Yue Hu, Jun Li and Xuegong Zhang
    Citation: BMC Genomics 2017 18(Suppl 1):963
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  8. Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial commun...

    Authors: Jifang Yan, Guohui Chuai, Tao Qi, Fangyang Shao, Chi Zhou, Chenyu Zhu, Jing Yang, Yifei Yu, Cong Shi, Ning Kang, Yuan He and Qi Liu
    Citation: BMC Genomics 2017 18(Suppl 1):962
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  9. Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining in...

    Authors: Lina Yuan, Yang Yu, Yanmin Zhu, Yulai Li, Changqing Li, Rujiao Li, Qin Ma, Gilman Kit-Hang Siu, Jun Yu, Taijiao Jiang, Jingfa Xiao and Yu Kang
    Citation: BMC Genomics 2017 18(Suppl 1):952
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  10. Lateral Organ Boundaries Domain (LBD) genes arise from charophyte algae and evolve essential functions in land plants in regulating organ development and secondary metabolism. Although...

    Authors: Yimeng Kong, Peng Xu, Xinyun Jing, Longxian Chen, Laigeng Li and Xuan Li
    Citation: BMC Genomics 2017 18(Suppl 1):951
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  11. This study is to explore the key genes and signaling transduction pathways related to the survival time of glioblastoma multiforme (GBM) patients.

    Authors: Yuan Xia, Chuanwei Yang, Nan Hu, Zhenzhou Yang, Xiaoyu He, Tingting Li and Le Zhang
    Citation: BMC Genomics 2017 18(Suppl 1):950
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  12. Corynebacterium glutamicum is a non-pathogenic bacterium widely used in industrial amino acid production and metabolic engineering research. Although the genome sequences of some C. gl...

    Authors: Junjie Yang and Sheng Yang
    Citation: BMC Genomics 2017 18(Suppl 1):940
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  13. The drug discovery and development pipeline is a long and arduous process that inevitably hampers rapid drug development. Therefore, strategies to improve the efficiency of drug development are urgently needed...

    Authors: Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang and Sok Ching Cheong
    Citation: BMC Genomics 2017 18(Suppl 1):934
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  14. Coxsackievirus A16 (CVA16) and enterovirus 71 (EV71) are two of the major causes of hand, foot and mouth disease (HFMD) world-wide. Although many studies have focused on infection and pathogenic mechanisms, th...

    Authors: Jun Jin, Rujiao Li, Chunlai Jiang, Ruosi Zhang, Xiaomeng Ge, Fang Liang, Xin Sheng, Wenwen Dai, Meili Chen, Jiayan Wu, Jingfa Xiao and Weiheng Su
    Citation: BMC Genomics 2017 18(Suppl 1):933
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  15. Gastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medi...

    Authors: Chao Liang, Han-Chi Tseng, Hui-Mei Chen, Wei-Chi Wang, Chih-Min Chiu, Jen-Yun Chang, Kuan-Yi Lu, Shun-Long Weng, Tzu-Hao Chang, Chao-Hsiang Chang, Chen-Tsung Weng, Hwei-Ming Wang and Hsien-Da Huang
    Citation: BMC Genomics 2017 18(Suppl 1):932
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  16. Meiotic recombination is a major source of genetic variation in eukaryotes. The role of recombination in evolution is recognized but little is known about how evolutionary forces affect the recombination pathw...

    Authors: Gaganpreet K. Sidhu, Tomasz Warzecha and Wojciech P. Pawlowski
    Citation: BMC Genomics 2017 18:106
    Content type: Research article Published on:

  17. Much of the morbidity associated with short bowel syndrome (SBS) is attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition (TPN). We hypothesized that acute SBS a...

    Authors: Kathy A. Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching-Ling Lien, Brendan H. Grubbs and Tracy C. Grikscheit
    Citation: BMC Genomics 2017 18:23
    Content type: Research Article Published on:

  18. Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the ho...

    Authors: T. A. Mansour, E. Y. Scott, C. J. Finno, R. R. Bellone, M. J. Mienaltowski, M. C. Penedo, P. J. Ross, S. J. Valberg, J. D. Murray and C. T. Brown
    Citation: BMC Genomics 2017 18:103
    Content type: Research Article Published on:

  19. We set out to describe the fine-scale population structure across the Eastern region of Nepal. To date there is relatively little known about the genetic structure of the Sherpa residing in Nepal and their gen...

    Authors: Amy M. Cole, Sean Cox, Choongwon Jeong, Nayia Petousi, Dhana R. Aryal, Yunden Droma, Masayuki Hanaoka, Masao Ota, Nobumitsu Kobayashi, Paolo Gasparini, Hugh Montgomery, Peter Robbins, Anna Di Rienzo and Gianpiero L. Cavalleri
    Citation: BMC Genomics 2017 18:102
    Content type: Research article Published on:

  20. Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable e...

    Authors: Kevin Maringer, Amjad Yousuf, Kate J. Heesom, Jun Fan, David Lee, Ana Fernandez-Sesma, Conrad Bessant, David A. Matthews and Andrew D. Davidson
    Citation: BMC Genomics 2017 18:101
    Content type: Research Article Published on:

  21. Contaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminat...

    Authors: Janus Borner and Thorsten Burmester
    Citation: BMC Genomics 2017 18:100
    Content type: Research article Published on:

  22. Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and te...

    Authors: Mette Lillie, Zheya Sheng, Christa F. Honaker, Ben J. Dorshorst, Christopher M. Ashwell, Paul B. Siegel and Örjan Carlborg
    Citation: BMC Genomics 2017 18:99
    Content type: Research Article Published on:

  23. Spermatozoa are stored in the oviductal functional sperm reservoir in animals with internal fertilization, including zoologically distant classes such as pigs or poultry. They are held fertile in the reservoir...

    Authors: Mohammad Atikuzzaman, Manuel Alvarez-Rodriguez, Alejandro Vicente-Carrillo, Martin Johnsson, Dominic Wright and Heriberto Rodriguez-Martinez
    Citation: BMC Genomics 2017 18:98
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2017 18:563

  24. Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a ...

    Authors: Julien Prunier, Sébastien Caron and John MacKay
    Citation: BMC Genomics 2017 18:97
    Content type: Research article Published on:

  25. Epigenetic modifications of DNA, such as 5-methylcytosine and 5-hydroxymethycytosine, play important roles in development and disease. Here, we present a cost-effective and versatile methodology for the analys...

    Authors: Gary G. Chen, Jeffrey A. Gross, Pierre-Eric Lutz, Kathryn Vaillancourt, Gilles Maussion, Alexandre Bramoulle, Jean-François Théroux, Elena S. Gardini, Ulrike Ehlert, Geneviève Bourret, Aurélie Masurel, Pierre Lepage, Naguib Mechawar, Gustavo Turecki and Carl Ernst
    Citation: BMC Genomics 2017 18:96
    Content type: methodology article Published on:

  26. The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing tec...

    Authors: Ole K. Tørresen, Bastiaan Star, Sissel Jentoft, William B. Reinar, Harald Grove, Jason R. Miller, Brian P. Walenz, James Knight, Jenny M. Ekholm, Paul Peluso, Rolf B. Edvardsen, Ave Tooming-Klunderud, Morten Skage, Sigbjørn Lien, Kjetill S. Jakobsen and Alexander J. Nederbragt
    Citation: BMC Genomics 2017 18:95
    Content type: Research Article Published on:

  27. Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simp...

    Authors: Javier Montero-Pau, José Blanca, Cristina Esteras, Eva Ma. Martínez-Pérez, Pedro Gómez, Antonio J. Monforte, Joaquín Cañizares and Belén Picó
    Citation: BMC Genomics 2017 18:94
    Content type: Research Article Published on:

  28. Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable featur...

    Authors: Emanuele Bosi, Marco Fondi, Valerio Orlandini, Elena Perrin, Isabel Maida, Donatella de Pascale, Maria Luisa Tutino, Ermenegilda Parrilli, Angelina Lo Giudice, Alain Filloux and Renato Fani
    Citation: BMC Genomics 2017 18:93
    Content type: Research article Published on:

  29. The objective of this study was to acquire a broader, more comprehensive picture of the transcriptional changes in the L. Thoracis muscle (LT) and subcutaneous fat (SF) of lambs supplemented with vitamin E. Furth...

    Authors: Laura González-Calvo, Elda Dervishi, Margalida Joy, Pilar Sarto, Roberto Martin-Hernandez, Magdalena Serrano, Jose M. Ordovás and Jorge H. Calvo
    Citation: BMC Genomics 2017 18:92
    Content type: Research Article Published on:

  30. The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amarant...

    Authors: William T. Molin, Alice A. Wright, Amy Lawton-Rauh and Christopher A. Saski
    Citation: BMC Genomics 2017 18:91
    Content type: Research article Published on:

  32. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by targeting specific mRNA species for degradation or interfering with translation. Specific miRNAs are key regulators of adi...

    Authors: Jenny C. Link, Yehudit Hasin-Brumshtein, Rita M. Cantor, Xuqi Chen, Arthur P. Arnold, Aldons J. Lusis and Karen Reue
    Citation: BMC Genomics 2017 18:89
    Content type: Research article Published on:

  35. Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium)...

    Authors: Antoine Le Quéré, Nisha Tak, Hukam Singh Gehlot, Celine Lavire, Thibault Meyer, David Chapulliot, Sonam Rathi, Ilham Sakrouhi, Guadalupe Rocha, Marine Rohmer, Dany Severac, Abdelkarim Filali-Maltouf and Jose-Antonio Munive
    Citation: BMC Genomics 2017 18:85
    Content type: Research article Published on:

  36. Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancin...

    Authors: Pawel Michalak, Lin Kang, Pernille M. Sarup, Mads F. Schou and Volker Loeschcke
    Citation: BMC Genomics 2017 18:84
    Content type: Research article Published on:

  37. Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated gene...

    Authors: Akira Kikuchi, Takeru Nakazato, Katsuhiko Ito, Yosui Nojima, Takeshi Yokoyama, Kikuo Iwabuchi, Hidemasa Bono, Atsushi Toyoda, Asao Fujiyama, Ryoichi Sato and Hiroko Tabunoki
    Citation: BMC Genomics 2017 18:83
    Content type: Research article Published on:

  38. Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive gen...

    Authors: Byung-Whi Kong, Nicholas Hudson, Dongwon Seo, Seok Lee, Bhuwan Khatri, Kentu Lassiter, Devin Cook, Alissa Piekarski, Sami Dridi, Nicholas Anthony and Walter Bottje
    Citation: BMC Genomics 2017 18:82
    Content type: Research article Published on:

  40. Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play importan...

    Authors: Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang and Cunshuan Xu
    Citation: BMC Genomics 2017 18:80
    Content type: Research Article Published on:

  41. Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, lar...

    Authors: Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T. Baldwin and Shuqing Xu
    Citation: BMC Genomics 2017 18:79
    Content type: Database Published on:

  42. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent congener of the dioxin class of environmental contaminants. Exposure to TCDD causes a wide range of toxic outcomes, ranging from chloracne to acute le...

    Authors: Stephenie D. Prokopec, Kathleen E. Houlahan, Ren X. Sun, John D. Watson, Cindy Q. Yao, Jamie Lee, Christine P’ng, Renee Pang, Alexander H. Wu, Lauren C. Chong, Ashley B. Smith, Nicholas J. Harding, Ivy D. Moffat, Jere Lindén, Sanna Lensu, Allan B. Okey…
    Citation: BMC Genomics 2017 18:78
    Content type: Software Published on:

  43. Salmonella enterica serovar Enteritidis (SE) is a food-borne pathogen and of great threat to human health through consuming the contaminated poultry products. MicroRNAs (miRNAs) play a...

    Authors: Guixian Wu, Yukai Qi, Xiaoyi Liu, Ning Yang, Guiyun Xu, Liying Liu and Xianyao Li
    Citation: BMC Genomics 2017 18:77
    Content type: Research Article Published on:

  44. In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. An...

    Authors: Ketil Malde, Bjørghild B. Seliussen, María Quintela, Geir Dahle, Francois Besnier, Hans J. Skaug, Nils Øien, Hiroko K. Solvang, Tore Haug, Rasmus Skern-Mauritzen, Naohisa Kanda, Luis A. Pastene, Inge Jonassen and Kevin A. Glover
    Citation: BMC Genomics 2017 18:76
    Content type: Research Article Published on:

  45. The food spoilage yeast species Zygosaccharomyces bailii exhibits an extraordinary capacity to tolerate weak acids, in particular acetic acid. In Saccharomyces cerevisiae, the transcription factor Haa1 (ScHaa1) i...

    Authors: Margarida Palma, Paulo Jorge Dias, Filipa de Canaveira Roque, Laura Luzia, Joana Fernandes Guerreiro and Isabel Sá-Correia
    Citation: BMC Genomics 2017 18:75
    Content type: Research Article Published on:

  46. Rose-scented geranium (Pelargonium sp.) is a perennial herb that produces a high value essential oil of fragrant significance due to the characteristic compositional blend of rose-oxide and acyclic monoterpenoids...

    Authors: Lokesh K. Narnoliya, Girija Kaushal, Sudhir P. Singh and Rajender S. Sangwan
    Citation: BMC Genomics 2017 18:74
    Content type: Research Article Published on:

  48. As the most important yield component in rapeseed (Brassica napus L.), pod number is determined by a series of successive growth and development processes. Pod number shows extensive variation in rapeseed natural...

    Authors: Jiang Ye, Yuhua Yang, Bo Chen, Jiaqin Shi, Meizhong Luo, Jiepeng Zhan, Xinfa Wang, Guihua Liu and Hanzhong Wang
    Citation: BMC Genomics 2017 18:71
    Content type: Research Article Published on:

  49. Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wid...

    Authors: Martin C. Fischer, Christian Rellstab, Marianne Leuzinger, Marie Roumet, Felix Gugerli, Kentaro K. Shimizu, Rolf Holderegger and Alex Widmer
    Citation: BMC Genomics 2017 18:69
    Content type: Research article Published on:

  50. Bone morphogenetic protein 4 (BMP4) plays an important role in cancer pathogenesis. In breast cancer, it reduces proliferation and increases migration in a cell line-dependent manner. To characterize the trans...

    Authors: M. Ampuja, T. Rantapero, A. Rodriguez-Martinez, M. Palmroth, E. L. Alarmo, M. Nykter and A. Kallioniemi
    Citation: BMC Genomics 2017 18:68
    Content type: Research article Published on:

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BMC Genomics

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