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  1. Transcriptomic responses to immune stimulation were investigated in coho salmon (Oncorhynchus kisutch) with distinct growth phenotypes. Wild-type fish were contrasted to strains with accelerated growth arising ei...

    Authors: Jin-Hyoung Kim, Daniel J. Macqueen, James R. Winton, John D. Hansen, Hyun Park and Robert H. Devlin

    Citation: BMC Genomics 2019 20:1024

    Content type: Research article

    Published on:

  2. Tumor purity is the percent of cancer cells present in a sample of tumor tissue. The non-cancerous cells (immune cells, fibroblasts, etc.) have an important role in tumor biology. The ability to determine tumo...

    Authors: Yuanyuan Li, David M. Umbach, Adrienna Bingham, Qi-Jing Li, Yuan Zhuang and Leping Li

    Citation: BMC Genomics 2019 20:1021

    Content type: Research article

    Published on:

  3. RNA pseudoknot structures play an important role in biological processes. However, existing RNA secondary structure prediction algorithms cannot predict the pseudoknot structure efficiently. Although random ma...

    Authors: Zhang Kai, Wang Yuting, Lv Yulin, Liu Jun and He Juanjuan

    Citation: BMC Genomics 2019 20(Suppl 13):979

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

  4. Genomic studies demonstrate that components of virulence mechanisms in filamentous eukaryotic pathogens (FEPs, fungi and oomycetes) of plants are often highly conserved, or found in gene families that include ...

    Authors: Eswari PJ Pandaranayaka, Omer Frenkel, Yigal Elad, Dov Prusky and Arye Harel

    Citation: BMC Genomics 2019 20:1020

    Content type: Research article

    Published on:

  5. Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of ...

    Authors: Roni Tadmor-Levi, Adi Doron-Faigenboim, Evgeniya Marcos-Hadad, Jules Petit, Gideon Hulata, Maria Forlenza, Geert F. Wiegertjes and Lior David

    Citation: BMC Genomics 2019 20:1019

    Content type: Research article

    Published on:

  6. Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, on...

    Authors: Robert Bücking, Murray P Cox, Georgi Hudjashov, Lauri Saag, Herawati Sudoyo and Mark Stoneking

    Citation: BMC Genomics 2019 20:1017

    Content type: Research Article

    Published on:

    The Correction to this article has been published in BMC Genomics 2020 21:55

  7. White root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies...

    Authors: A. Zumaquero, S. Kanematsu, H. Nakayashiki, A. Matas, E. Martínez-Ferri, A. Barceló-Muñóz, F. Pliego-Alfaro, C. López-Herrera, F. M. Cazorla and C. Pliego

    Citation: BMC Genomics 2019 20:1016

    Content type: Research article

    Published on:

  8. 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

  9. 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

  10. The sensitivity of plants to ammonia is a worldwide problem that limits crop production. Excessive use of ammonium as the sole nitrogen source results in morphological and physiological disorders, and retarded...

    Authors: Xiaohong Ou, Shipeng Li, Peiran Liao, Xiuming Cui, Binglian Zheng, Ye Yang, Dahui Liu and Yun Zheng

    Citation: BMC Genomics 2019 20(Suppl 9):965

    Content type: Research

    Published on:

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

  11. 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

  12. Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas ...

    Authors: Xuan Zhang, Bang-Zhen Pan, Maosheng Chen, Wen Chen, Jing Li, Zeng-Fu Xu and Changning Liu

    Citation: BMC Genomics 2019 20(Suppl 9):958

    Content type: Database

    Published on:

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

  13. 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

  14. 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

  15. 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

  16. 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

  17. Semantic similarity between Gene Ontology (GO) terms is a fundamental measure for many bioinformatics applications, such as determining functional similarity between genes or proteins. Most previous research e...

    Authors: Xiaoshi Zhong, Rama Kaalia and Jagath C. Rajapakse

    Citation: BMC Genomics 2019 20(Suppl 9):918

    Content type: Research

    Published on:

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

  18. 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

  19. Euphorbiaceae is one of the largest families of flowering plants. Due to its exceptional growth form diversity and near-cosmopolitan distribution, it has attracted much interest since ancient times. SBP-box (SBP)...

    Authors: Jing Li, Xiaoyang Gao, Shiye Sang and Changning Liu

    Citation: BMC Genomics 2019 20(Suppl 9):912

    Content type: Research

    Published on:

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

  20. Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive ...

    Authors: Yang-Ming Lin, Ching-Tai Chen and Jia-Ming Chang

    Citation: BMC Genomics 2019 20(Suppl 9):906

    Content type: Methodology

    Published on:

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

  21. 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

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

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