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  1. Influenza A virus (IAV) poses threats to human health and life. Many individual studies have been carried out in mice to uncover the viral factors responsible for the virulence of IAV infections. Nonetheless, ...

    Authors: Fransiskus Xaverius Ivan and Chee Keong Kwoh
    Citation: BMC Genomics 2019 20(Suppl 9):973
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  2. Adaptor proteins are carrier proteins that play a crucial role in signal transduction. They commonly consist of several modular domains, each having its own binding activity and operating by forming complexes ...

    Authors: Nguyen Quoc Khanh Le, Quang H. Nguyen, Xuan Chen, Susanto Rahardja and Binh P. Nguyen
    Citation: BMC Genomics 2019 20(Suppl 9):966
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  3. Cross-species analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved interaction patterns. Identifying such conserved substructures between PPI networks of di...

    Authors: Sawal Maskey and Young-Rae Cho
    Citation: BMC Genomics 2019 20(Suppl 9):964
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  4. Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer i...

    Authors: Quang H. Nguyen, Thanh-Hoang Nguyen-Vo, Nguyen Quoc Khanh Le, Trang T.T. Do, Susanto Rahardja and Binh P. Nguyen
    Citation: BMC Genomics 2019 20(Suppl 9):951
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  5. There are two significant problems associated with predicting protein-protein interactions using the sequences of amino acids. The first problem is representing each sequence as a feature vector, and the secon...

    Authors: Alhadi Bustamam, Mohamad I. S. Musti, Susilo Hartomo, Shirley Aprilia, Patuan P. Tampubolon and Dian Lestari
    Citation: BMC Genomics 2019 20(Suppl 9):950
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  6. A long noncoding RNA (lncRNA) can act as a competing endogenous RNA (ceRNA) to compete with an mRNA for binding to the same miRNA. Such an interplay between the lncRNA, miRNA, and mRNA is called a ceRNA crosst...

    Authors: Chaowang Lan, Hui Peng, Gyorgy Hutvagner and Jinyan Li
    Citation: BMC Genomics 2019 20(Suppl 9):943
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  7. The sequence diversity of dengue virus (DENV) is one of the challenges in developing an effective vaccine against the virus. Highly conserved, serotype-specific (HCSS), immune-relevant DENV sequences are attra...

    Authors: Li Chuin Chong and Asif M. Khan
    Citation: BMC Genomics 2019 20(Suppl 9):921
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

    The Correction to this article has been published in BMC Genomics 2021 22:219

  8. Single-cell RNA-sequencing (scRNA-seq) is a fast emerging technology allowing global transcriptome profiling on the single cell level. Cell type identification from scRNA-seq data is a critical task in a varie...

    Authors: Taiyun Kim, Kitty Lo, Thomas A. Geddes, Hani Jieun Kim, Jean Yee Hwa Yang and Pengyi Yang
    Citation: BMC Genomics 2019 20(Suppl 9):913
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  9. Module detection algorithms relying on modularity maximization suffer from an inherent resolution limit that hinders detection of small topological modules, especially in molecular networks where most biologic...

    Authors: Rama Kaalia and Jagath C. Rajapakse
    Citation: BMC Genomics 2019 20(Suppl 9):901
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  10. Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food pr...

    Authors: Yan Wang, Lijuan Luo, Qun Li, Hong Wang, Yiqian Wang, Hui Sun, Jianguo Xu, Ruiting Lan and Changyun Ye
    Citation: BMC Genomics 2019 20:1014
    Content type: Research article Published on:

  11. As a newly characterized type of noncoding RNA, circular RNA (circRNA) has been shown to have functions in diverse biological processes of animals. It has been reported that several noncoding RNAs may regulate...

    Authors: Haojie Zhang, Baoyu Hu, Jiali Xiong, Ting Chen, Qianyun Xi, Junyi Luo, Qingyan Jiang, Jiajie Sun and Yongliang Zhang
    Citation: BMC Genomics 2019 20:1013
    Content type: Research article Published on:

  13. Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Previously, we had trained an ensemble machine learning model to assign a probability of having...

    Authors: Flavio Pazos Obregón, Martín Palazzo, Pablo Soto, Gustavo Guerberoff, Patricio Yankilevich and Rafael Cantera
    Citation: BMC Genomics 2019 20:1011
    Content type: Research article Published on:

  14. Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake dive...

    Authors: Kevin Schneider, Colin E. Adams and Kathryn R. Elmer
    Citation: BMC Genomics 2019 20:1010
    Content type: Research article Published on:

  15. Agricultural insects are one of the major threats to crop yield. It is a known fact that pesticide application is an extensive approach to eliminate insect pests, and has severe adverse effects on environment ...

    Authors: Sajid Muhammad, Jingai Tan, Pingchuan Deng, Tingting Li, Haohua He, Jianmin Bian and Liang Wu
    Citation: BMC Genomics 2019 20:1009
    Content type: Research article Published on:

  16. Rumen ciliates play important roles in rumen function by digesting and fermenting feed and shaping the rumen microbiome. However, they remain poorly understood due to the lack of definitive direct evidence wit...

    Authors: Lingling Wang, Anas Abu-Doleh, Johanna Plank, Umit V. Catalyurek, Jeffrey L. Firkins and Zhongtang Yu
    Citation: BMC Genomics 2019 20:1008
    Content type: Research article Published on:

  17. Recently, a number of studies have been conducted to investigate how plants respond to stress at the cellular molecular level by measuring gene expression profiles over time. As a result, a set of time-series ...

    Authors: Dongwon Kang, Hongryul Ahn, Sangseon Lee, Chai-Jin Lee, Jihye Hur, Woosuk Jung and Sun Kim
    Citation: BMC Genomics 2019 20(Suppl 11):949
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  18. Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. However, the computation of the long sequencing reads i...

    Authors: Arghya Kusum Das, Sayan Goswami, Kisung Lee and Seung-Jong Park
    Citation: BMC Genomics 2019 20(Suppl 11):948
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  19. Knowledge Base Commons (KBCommons) v1.1 is a universal and all-inclusive web-based framework providing generic functionalities for storing, sharing, analyzing, exploring, integrating and visualizing multiple o...

    Authors: Shuai Zeng, Zhen Lyu, Siva Ratna Kumari Narisetti, Dong Xu and Trupti Joshi
    Citation: BMC Genomics 2019 20(Suppl 11):947
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  20. Researchers discover lncRNAs can act as decoys or sponges to regulate the behavior of miRNAs. Identification of lncRNA-miRNA interactions helps to understand the functions of lncRNAs, especially their roles in...

    Authors: Wen Zhang, Guifeng Tang, Shuang Zhou and Yanqing Niu
    Citation: BMC Genomics 2019 20(Suppl 11):946
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  21. Microbiomes play vital roles in shaping environments and stabilize them based on their compositions and inter-species relationships among its species. Variations in microbial properties have been reported to h...

    Authors: Suyeon Kim, Ishwor Thapa, Ling Zhang and Hesham Ali
    Citation: BMC Genomics 2019 20(Suppl 11):945
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  22. Comprehensive molecular profiling of various cancers and other diseases has generated vast amounts of multi-omics data. Each type of -omics data corresponds to one feature space, such as gene expression, miRNA...

    Authors: Tianle Ma and Aidong Zhang
    Citation: BMC Genomics 2019 20(Suppl 11):944
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  23. Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific g...

    Authors: Ruijie Liu, Wai Yee Low, Rick Tearle, Sergey Koren, Jay Ghurye, Arang Rhie, Adam M. Phillippy, Benjamin D. Rosen, Derek M. Bickhart, Timothy P. L. Smith, Stefan Hiendleder and John L. Williams
    Citation: BMC Genomics 2019 20:1000
    Content type: Research article Published on:

  24. Flammulina velutipes has been recognized as a useful basidiomycete with nutritional and medicinal values. Ergosterol, one of the main sterols of F. velutipes is an important precursor of novel anticancer and anti...

    Authors: Ruihong Wang, Pengda Ma, Chen Li, Lingang Xiao, Zongsuo Liang and Juane Dong
    Citation: BMC Genomics 2019 20:999
    Content type: Research article Published on:

  25. Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated...

    Authors: Daniela D. Moré, Fernando F. Cardoso, Maurício A. Mudadu, Wilson Malagó-Jr, Claudia C. Gulias-Gomes, Bruna P. Sollero, Adriana M. G. Ibelli, Luiz L. Coutinho and Luciana C. A. Regitano
    Citation: BMC Genomics 2019 20:998
    Content type: Research article Published on:

  27. The glasshouse whitefly, Trialeurodes vaporariorum, is a damaging crop pest and an invasive generalist capable of feeding on a broad range of host plants. As such this species has evolved mechanisms to circumvent...

    Authors: Adam Pym, Kumar Saurabh Singh, Åsa Nordgren, T. G. Emyr Davies, Christoph T. Zimmer, Jan Elias, Russell Slater and Chris Bass
    Citation: BMC Genomics 2019 20:996
    Content type: Research article Published on:

  28. Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential...

    Authors: Vera Thole, Jean-Etienne Bassard, Ricardo Ramírez-González, Martin Trick, Bijan Ghasemi Afshar, Dario Breitel, Lionel Hill, Alexandre Foito, Louise Shepherd, Sabine Freitag, Cláudia Nunes dos Santos, Regina Menezes, Pilar Bañados, Michael Naesby, Liangsheng Wang, Artem Sorokin…
    Citation: BMC Genomics 2019 20:995
    Content type: Research article Published on:

  29. Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces

    Authors: Stephen C. Heinsch, Szu-Yi Hsu, Lindsey Otto-Hanson, Linda Kinkel and Michael J. Smanski
    Citation: BMC Genomics 2019 20:994
    Content type: Research article Published on:

  30. F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S prote...

    Authors: Shulin Zhang, Zailong Tian, Haipeng Li, Yutao Guo, Yanqi Zhang, Jeremy A. Roberts, Xuebin Zhang and Yuchen Miao
    Citation: BMC Genomics 2019 20:993
    Content type: Research article Published on:

  32. Embryonic mortality is a major concern in the commercial swine industry and primarily occurs early in gestation, but also during mid-gestation (~ days 50–70). Previous reports demonstrated that the embryonic l...

    Authors: Kejun Wang, Kaijie Yang, Qiao Xu, Yufang Liu, Wenting Li, Ying Bai, Jve Wang, Cui Ding, Ximing Liu, Qiguo Tang, Yabiao Luo, Jie Zheng, Keliang Wu and Meiying Fang
    Citation: BMC Genomics 2019 20:991
    Content type: Research article Published on:

  33. Salinity has obvious effects on plant growth and crop productivity. The salinity-responsive mechanisms have been well-studied in differentiated organs (e.g., leaves, roots and stems), but not in unorganized ce...

    Authors: Yongxue Zhang, Yue Zhang, Juanjuan Yu, Heng Zhang, Liyue Wang, Sining Wang, Siyi Guo, Yuchen Miao, Sixue Chen, Ying Li and Shaojun Dai
    Citation: BMC Genomics 2019 20:990
    Content type: Research article Published on:

  34. Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variati...

    Authors: Priya Darshini Gurung, Atul Kumar Upadhyay, Pardeep Kumar Bhardwaj, Ramanathan Sowdhamini and Uma Ramakrishnan
    Citation: BMC Genomics 2019 20:989
    Content type: Research article Published on:

  35. Vibrio spp. is the major infection-producing marine bacteria in commercially important bivalve Paphia undulata. The host resistance is the major determining factor for the development of pathogenesis. To explore ...

    Authors: Mingjia Yu, Lin Zheng, Xiaobo Wang, Minfu Wu, Ming Qi, Wandong Fu and Yang Zhang
    Citation: BMC Genomics 2019 20:988
    Content type: Research article Published on:

  36. As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, w...

    Authors: Minmin Li, Ying Liu, Yahan Tao, Chongjing Xu, Xin Li, Xiaoming Zhang, Yingpeng Han, Xue Yang, Jingzhe Sun, Wenbin Li, Dongmei Li, Xue Zhao and Lin Zhao
    Citation: BMC Genomics 2019 20:987
    Content type: Research article Published on:

  37. Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one ...

    Authors: Ruibin Wang, Jingfei Ma, Qian Zhang, Chunlai Wu, Hongyan Zhao, Yanan Wu, Guangxiao Yang and Guangyuan He
    Citation: BMC Genomics 2019 20:986
    Content type: Research article Published on:

  38. Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its ...

    Authors: Roshan Sharma Poudel, Jonathan Richards, Subidhya Shrestha, Shyam Solanki and Robert Brueggeman
    Citation: BMC Genomics 2019 20:985
    Content type: Research article Published on:

  39. Pseudomonas aeruginosa (PA) is an opportunistic Gram-negative bacterium that causes serious life threatening and nosocomial infections including pneumonia. PA has the ability to alter host genome to facilitate it...

    Authors: David L. Ebenezer, Panfeng Fu, Yashaswin Krishnan, Mark Maienschein-Cline, Hong Hu, Segun Jung, Ravi Madduri, Zarema Arbieva, Anantha Harijith and Viswanathan Natarajan
    Citation: BMC Genomics 2019 20:984
    Content type: Research article Published on:

  40. Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices base...

    Authors: Yanling Hu, Aihua Tan, Lei Yu, Chenyang Hou, Haofa Kuang, Qunying Wu, Jinghan Su, Qingniao Zhou, Yuanyuan Zhu, Chenqi Zhang, Wei Wei, Lianfeng Li, Weidong Li, Yuanjie Huang, Hongli Huang, Xing Xie…
    Citation: BMC Genomics 2019 20:983
    Content type: Research article Published on:

  41. The plant homeodomain (PHD) finger is a Cys4HisCys3-type zinc finger which promotes protein-protein interactions and binds to the cis-acting elements in the promoter regions of target genes. In Medicago truncatul...

    Authors: Wenli Quan, Xun Liu, Lihua Wang, Mingzhu Yin, Li Yang and Zhulong Chan
    Citation: BMC Genomics 2019 20:982
    Content type: Research article Published on:

  42. Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering...

    Authors: Adonis D’Mello, Christian P. Ahearn, Timothy F. Murphy and Hervé Tettelin
    Citation: BMC Genomics 2019 20:981
    Content type: Methodology article Published on:

  44. The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in so...

    Authors: Jean F. Challacombe, Cedar N. Hesse, Lisa M. Bramer, Lee Ann McCue, Mary Lipton, Samuel Purvine, Carrie Nicora, La Verne Gallegos-Graves, Andrea Porras-Alfaro and Cheryl R. Kuske
    Citation: BMC Genomics 2019 20:976
    Content type: Research article Published on:

  45. Alginate is an important cell wall component and mannitol is a soluble storage carbon substance in the brown seaweed Saccharina japonica. Their contents vary with kelp developmental periods and harvesting time. A...

    Authors: Zhanru Shao, Pengyan Zhang, Chang Lu, Shaoxuan Li, Zhihang Chen, Xiuliang Wang and Delin Duan
    Citation: BMC Genomics 2019 20:975
    Content type: Research article Published on:

  46. Bud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during ...

    Authors: Noémie Vimont, Mathieu Fouché, José Antonio Campoy, Meixuezi Tong, Mustapha Arkoun, Jean-Claude Yvin, Philip A. Wigge, Elisabeth Dirlewanger, Sandra Cortijo and Bénédicte Wenden
    Citation: BMC Genomics 2019 20:974
    Content type: Research article Published on:

  47. Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fift...

    Authors: Amanda M. Vondras, Andrea Minio, Barbara Blanco-Ulate, Rosa Figueroa-Balderas, Michael A. Penn, Yongfeng Zhou, Danelle Seymour, Zirou Ye, Dingren Liang, Lucero K. Espinoza, Michael M. Anderson, M. Andrew Walker, Brandon Gaut and Dario Cantu
    Citation: BMC Genomics 2019 20:972
    Content type: Research article Published on:

  48. The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential ro...

    Authors: Wei-wei Wang, Jing Wang, Hai-jun Zhang, Shu-geng Wu and Guang-hai Qi
    Citation: BMC Genomics 2019 20:970
    Content type: Research article Published on:

  49. Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is ma...

    Authors: Shimin Fu, Jonathan Shao, Avijit Roy, Ronald H. Brlansky, Changyong Zhou and John S. Hartung
    Citation: BMC Genomics 2019 20:969
    Content type: Research article Published on:

  50. The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as...

    Authors: Paulo Rapazote-Flores, Micha Bayer, Linda Milne, Claus-Dieter Mayer, John Fuller, Wenbin Guo, Pete E. Hedley, Jenny Morris, Claire Halpin, Jason Kam, Sarah M. McKim, Monika Zwirek, M. Cristina Casao, Abdellah Barakate, Miriam Schreiber, Gordon Stephen…
    Citation: BMC Genomics 2019 20:968
    Content type: Research article Published on:

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BMC Genomics

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