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  1. Bacterial cells during many replication cycles accumulate spontaneous mutations, which result in the birth of novel clones. As a result of this clonal expansion, an evolving bacterial population has different clo...

    Authors: Wazim Mohammed Ismail and Haixu Tang

    Citation: BMC Genomics 2019 20(Suppl 12):1002

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  2. The rapid development of Next-Generation Sequencing technologies enables sequencing genomes with low cost. The dramatically increasing amount of sequencing data raised crucial needs for efficient compression a...

    Authors: Tao Tang, Yuansheng Liu, Buzhong Zhang, Benyue Su and Jinyan Li

    Citation: BMC Genomics 2019 20(Suppl 10):978

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  3. Hip dysplasia and osteoarthritis continue to be prevalent problems in veterinary and human medicine. Canine hip dysplasia is particularly problematic as it massively affects several large-sized breeds and can ...

    Authors: Lea Mikkola, Saila Holopainen, Tiina Pessa-Morikawa, Anu K. Lappalainen, Marjo K. Hytönen, Hannes Lohi and Antti Iivanainen

    Citation: BMC Genomics 2019 20:1027

    Content type: Research article

    Published on:

  4. Non-key traits (NKTs) in radiata pine (Pinus radiata D. Don) refer to traits other than growth, wood density and stiffness, but still of interest to breeders. Branch-cluster frequency, stem straightness, external...

    Authors: Yongjun Li, Jaroslav Klápště, Emily Telfer, Phillip Wilcox, Natalie Graham, Lucy Macdonald and Heidi S. Dungey

    Citation: BMC Genomics 2019 20:1026

    Content type: Research article

    Published on:

  5. Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still...

    Authors: Shenghui Zhou, Jinpeng Zhang, Haiming Han, Jing Zhang, Huihui Ma, Zhi Zhang, Yuqing Lu, Weihua Liu, Xinming Yang, Xiuquan Li and Lihui Li

    Citation: BMC Genomics 2019 20:1025

    Content type: Research article

    Published on:

  6. 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:

  7. Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic ana...

    Authors: Christopher J. Troll, Joshua Kapp, Varsha Rao, Kelly M. Harkins, Charles Cole, Colin Naughton, Jessica M. Morgan, Beth Shapiro and Richard E. Green

    Citation: BMC Genomics 2019 20:1023

    Content type: Methodology article

    Published on:

  8. In 2017, World Health Organization (WHO) published a catalogue of 12 families of antibiotic-resistant “priority pathogens” that are posing the greatest threats to human health. Six of these dreaded pathogens a...

    Authors: Tungadri Bose, K. V. Venkatesh and Sharmila S. Mande

    Citation: BMC Genomics 2019 20:1022

    Content type: Research article

    Published on:

  9. 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:

  10. The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectur...

    Authors: Wei Gan, Juan Luo, Yi Zhou Li, Jia Li Guo, Min Zhu and Meng Long Li

    Citation: BMC Genomics 2019 20(Suppl 13):980

    Content type: Research

    Published on:

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

  11. 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

  12. Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the develop...

    Authors: Jinho Im, Byungkyu Park and Kyungsook Han

    Citation: BMC Genomics 2019 20(Suppl 13):967

    Content type: Research

    Published on:

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

  13. Proteins play essential roles in almost all life processes. The prediction of protein function is of significance for the understanding of molecular function and evolution. Network alignment provides a fast an...

    Authors: Jialu Hu, Junhao He, Jing Li, Yiqun Gao, Yan Zheng and Xuequn Shang

    Citation: BMC Genomics 2019 20(Suppl 13):932

    Content type: Research

    Published on:

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

  14. To infer gene regulatory networks (GRNs) from gene-expression data is still a fundamental and challenging problem in systems biology. Several existing algorithms formulate GRNs inference as a regression proble...

    Authors: Xiang Chen, Min Li, Ruiqing Zheng, Fang-Xiang Wu and Jianxin Wang

    Citation: BMC Genomics 2019 20(Suppl 13):929

    Content type: Research

    Published on:

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

  15. Identification of protein-protein interactions (PPIs) is crucial for understanding biological processes and investigating the cellular functions of genes. Self-interacting proteins (SIPs) are those in which mo...

    Authors: Zhan-Heng Chen, Zhu-Hong You, Li-Ping Li, Yan-Bin Wang, Yu Qiu and Peng-Wei Hu

    Citation: BMC Genomics 2019 20(Suppl 13):928

    Content type: Research

    Published on:

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

  16. 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:

  17. 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:

  18. 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

  19. 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:

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

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