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Comparative and evolutionary genomics

Section edited by Igor Rogozin and Alexei Fedorov

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

Page 1 of 18

  1. Content type: Research article

    As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolate...

    Authors: Zhi Zhong, Lai-Yu Kwok, Qiangchuan Hou, Yaru Sun, Weicheng Li, Heping Zhang and Zhihong Sun

    Citation: BMC Genomics 2019 20:602

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  2. Content type: Research article

    Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target ...

    Authors: Fazhe Yan, Xuelin Yu, Zhongqu Duan, Jinyuan Lu, Ben Jia, Yuyang Qiao, Chen Sun and Chaochun Wei

    Citation: BMC Genomics 2019 20:595

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  3. Content type: Software

    During the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technolo...

    Authors: Jose V. Die, Moamen M. Elmassry, Kimberly H. LeBlanc, Olaitan I. Awe, Allissa Dillman and Ben Busby

    Citation: BMC Genomics 2019 20:591

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  4. Content type: Methodology article

    The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are mi...

    Authors: Keoni Saint-Pé, Maeva Leitwein, Laurence Tissot, Nicolas Poulet, Bruno Guinand, Patrick Berrebi, Geoffrey Marselli, Jean-Marc Lascaux, Pierre-Alexandre Gagnaire and Simon Blanchet

    Citation: BMC Genomics 2019 20:582

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  5. Content type: Research article

    The σ54 factor controls unique promoters and interacts with a specialized activator (enhancer binding proteins [EBP]) for transcription initiation. Although σ54 is present in many Clostridiales species that have ...

    Authors: Xiaoqun Nie, Wenyue Dong and Chen Yang

    Citation: BMC Genomics 2019 20:565

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  6. Content type: Research article

    The Crustacea are an evolutionarily diverse taxon which underpins marine food webs and contributes significantly to the global economy. However, our knowledge of crustacean endocrinology and development is far...

    Authors: Cameron J. Hyde, Quinn P. Fitzgibbon, Abigail Elizur, Gregory G. Smith and Tomer Ventura

    Citation: BMC Genomics 2019 20:531

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  7. Content type: Research article

    Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including Leishmania parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, ...

    Authors: Valeria Petrella, Serena Aceto, Vincenza Colonna, Giuseppe Saccone, Remo Sanges, Nikola Polanska, Petr Volf, Luigi Gradoni, Gioia Bongiorno and Marco Salvemini

    Citation: BMC Genomics 2019 20:522

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  8. Content type: Research article

    Bovine viral diarrhea virus (BVDV) is an economically important viral pathogen of domestic and wild ruminants. Apart from cattle, small ruminants (goats and sheep) are also the susceptible hosts for BVDV. BVDV...

    Authors: Wenliang Li, Li Mao, Xin Shu, Runxia Liu, Fei Hao, Jizong Li, Maojun Liu, Leilei Yang, Wenwen Zhang, Min Sun, Chunyan Zhong and Jieyuan Jiang

    Citation: BMC Genomics 2019 20:516

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  9. Content type: Research article

    Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of C...

    Authors: Min Zhou, Shigang Zheng, Rong Liu, Jing Lu, Lu Lu, Chihong Zhang, Zehou Liu, Congpei Luo, Lei Zhang, Levi Yant and Yu Wu

    Citation: BMC Genomics 2019 20:505

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  10. Content type: Research article

    Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in fi...

    Authors: Ashok Kumar Sharma, Barbora Pafčo, Klára Vlčková, Barbora Červená, Jakub Kreisinger, Samuel Davison, Karen Beeri, Terence Fuh, Steven R. Leigh, Michael B. Burns, Ran Blekhman, Klára J. Petrželková and Andres Gomez

    Citation: BMC Genomics 2019 20:493

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  11. Content type: Research article

    It is hypothesized that the highly conserved inverted repeats (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organization, whereas the mechanism of the occurren...

    Authors: Hong-Rui Zhang, Xian-Chun Zhang and Qiao-Ping Xiang

    Citation: BMC Genomics 2019 20:484

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    The Correction to this article has been published in BMC Genomics 2019 20:523

  12. Content type: Research article

    Plasmids play an vital role in driving the rapid global spread of antimicrobial resistance and adaptation to changing ambient conditions. It has been suggested that the presence of plasmids can pose tremendous...

    Authors: Dan Long, Lan-lan Zhu, Fang-ling Du, Tian-xin Xiang, La-Gen Wan, Dan-dan Wei, Wei Zhang and Yang Liu

    Citation: BMC Genomics 2019 20:480

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  13. Content type: Research article

    The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is av...

    Authors: Chaokun Li, Longxin Chen, Xuefeng Liu, Xiaoqian Shi, Yu Guo, Rui Huang, Fangyuan Nie, Changming Zheng, Chenglin Zhang and Runlin Z. Ma

    Citation: BMC Genomics 2019 20:479

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  14. Content type: Research article

    The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly ...

    Authors: J. Blommaert, S. Riss, B. Hecox-Lea, D. B. Mark Welch and C. P. Stelzer

    Citation: BMC Genomics 2019 20:466

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  15. Content type: Research article

    Isopods constitute a particular group of crustaceans that has successfully colonized all environments including marine, freshwater and terrestrial habitats. Their ability to use various food sources, especiall...

    Authors: Marius Bredon, Benjamin Herran, Baptiste Lheraud, Joanne Bertaux, Pierre Grève, Bouziane Moumen and Didier Bouchon

    Citation: BMC Genomics 2019 20:462

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  16. Content type: Methodology article

    Directed DNA methylation on N6-adenine (6mA), N4-cytosine (4mC), and C5-cytosine (5mC) can potentially increase DNA coding capacity and regulate a variety of biological functions. These modifications are relat...

    Authors: Zach K. O’Brown, Konstantinos Boulias, Jie Wang, Simon Yuan Wang, Natasha M. O’Brown, Ziyang Hao, Hiroki Shibuya, Paul-Enguerrand Fady, Yang Shi, Chuan He, Sean G. Megason, Tao Liu and Eric L. Greer

    Citation: BMC Genomics 2019 20:445

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  17. Content type: Research article

    Host genetic backgrounds affect gene functions. The genetic backgrounds of genetically engineered organisms must be identified to confirm their genetic backgrounds identity with those of recipients. Marker-ass...

    Authors: Tiantian Li, Zhiwei Fang, Hai Peng, Junfei Zhou, Pengcheng Liu, Yanyan Wang, Wenhui Zhu, Lun Li, Quanfang Zhang, Lihong Chen, Lili Li, Zhihao Liu, Weixiong Zhang, Wenxue Zhai, Long Lu and Lifen Gao

    Citation: BMC Genomics 2019 20:444

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  18. Content type: Research article

    Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environm...

    Authors: Xian Zhang, Xueduan Liu, Liangzhi Li, Guanyun Wei, Danli Zhang, Yili Liang and Bo Miao

    Citation: BMC Genomics 2019 20:438

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  19. Content type: Research article

    The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol f...

    Authors: Mari Mäkinen, Jaana Kuuskeri, Pia Laine, Olli-Pekka Smolander, Andriy Kovalchuk, Zhen Zeng, Fred O. Asiegbu, Lars Paulin, Petri Auvinen and Taina Lundell

    Citation: BMC Genomics 2019 20:430

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  20. Content type: Research article

    The role of Salmonella virulence factor (VF) allelic variation in modulating pathogenesis or host specificity has only been demonstrated in a few cases, mostly through serendipitous findings. Virulence factor (VF...

    Authors: Alexey V. Rakov, Emilio Mastriani, Shu-Lin Liu and Dieter M. Schifferli

    Citation: BMC Genomics 2019 20:429

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  21. Content type: Research article

    The golden birdwing butterfly (Troides aeacus formosanus) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared T. aeacus larvae. From the previous Kimura...

    Authors: Yu-Feng Huang, Tzu-Han Chen, Zih-Ting Chang, Tai-Chuan Wang, Se Jin Lee, Jong Cheol Kim, Jae Su Kim, Kuo-Ping Chiu and Yu-Shin Nai

    Citation: BMC Genomics 2019 20:419

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  22. Content type: Research article

    Lactobacillus brevis is a member of the lactic acid bacteria (LAB), and strains of L. brevis have been isolated from silage, as well as from fermented cabbage and other fermented foods. However, this bacterium is...

    Authors: Marine Feyereisen, Jennifer Mahony, Philip Kelleher, Richard John Roberts, Tadhg O’Sullivan, Jan-Maarten A. Geertman and Douwe van Sinderen

    Citation: BMC Genomics 2019 20:416

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  23. Content type: Research article

    Chinese giant salamander Andrias davidianus is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and mechanism of sex...

    Authors: Qiaomu Hu, Cuifang Chang, Quanhe Wang, Haifeng Tian, Zhigang Qiao, Lei Wang, Yan Meng, Cunshuan Xu and Hanbing Xiao

    Citation: BMC Genomics 2019 20:415

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  24. Content type: Research article

    Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mec...

    Authors: Yinzhao Wang, Giorgio Casaburi, Wei Lin, Ying Li, Fengping Wang and Yongxin Pan

    Citation: BMC Genomics 2019 20:407

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  25. Content type: Research article

    The three epidemiologically important Opisthorchiidae liver flukes Opisthorchis felineus, O. viverrini, and Clonorchis sinensis, are believed to harbour similar potencies to provoke hepatobiliary diseases in thei...

    Authors: Nikita I. Ershov, Viatcheslav A. Mordvinov, Egor B. Prokhortchouk, Mariya Y. Pakharukova, Konstantin V. Gunbin, Kirill Ustyantsev, Mikhail A. Genaev, Alexander G. Blinov, Alexander Mazur, Eugenia Boulygina, Svetlana Tsygankova, Ekaterina Khrameeva, Nikolay Chekanov, Guangyi Fan, An Xiao, He Zhang…

    Citation: BMC Genomics 2019 20:399

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  26. Content type: Research article

    Salmonella enterica consists of over 2500 serovars and displays dichotomy in disease manifestations and host range. Except for the enrichment of pseudogenes in genomes for human-restricted serovars, no hallmark h...

    Authors: Ye Feng, Enze Lin, Shengmei Zou, Chyi-Liang Chen and Cheng-Hsun Chiu

    Citation: BMC Genomics 2019 20:398

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  27. Content type: Research article

    Enormous variability in skin colour and patterning is a characteristic of teleost fish, including Salmonidae fishes, which present themselves as a suitable model for studying mechanisms of pigment patterning. ...

    Authors: Ida Djurdjevič, Tomasz Furmanek, Seita Miyazawa and Simona Sušnik Bajec

    Citation: BMC Genomics 2019 20:359

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  28. Content type: Research article

    Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator–prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are...

    Authors: Hugo Oliveira, Marta Sampaio, Luís D. R. Melo, Oscar Dias, Welkin H. Pope, Graham F. Hatfull and Joana Azeredo

    Citation: BMC Genomics 2019 20:357

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  29. Content type: Research article

    Cadmium (Cd)-containing chemicals can cause serious damage to biological systems. In animals and plants, Cd exposure can lead to metabolic disorders or death. However, for the most part the effects of Cd on sp...

    Authors: De-Long Guan, Rui-Rui Ding, Xiao-Yu Hu, Xing-Ran Yang, Sheng-Quan Xu, Wei Gu and Min Zhang

    Citation: BMC Genomics 2019 20:356

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  30. Content type: Research article

    Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evoluti...

    Authors: María Torres-Sánchez, David J. Gower, David Alvarez-Ponce, Christopher J. Creevey, Mark Wilkinson and Diego San Mauro

    Citation: BMC Genomics 2019 20:354

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  31. Content type: Research article

    Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mi...

    Authors: Anna I. Kolesnikova, Yuliya A. Putintseva, Evgeniy P. Simonov, Vladislav V. Biriukov, Natalya V. Oreshkova, Igor N. Pavlov, Vadim V. Sharov, Dmitry A. Kuzmin, James B. Anderson and Konstantin V. Krutovsky

    Citation: BMC Genomics 2019 20:351

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  32. Content type: Research article

    Since domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been forme...

    Authors: Dorcus Kholofelo Malomane, Henner Simianer, Annett Weigend, Christian Reimer, Armin Otto Schmitt and Steffen Weigend

    Citation: BMC Genomics 2019 20:345

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  33. Content type: Research article

    The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod...

    Authors: Han Ming Gan, Frederic Grandjean, Tom L. Jenkins and Christopher Mervyn Austin

    Citation: BMC Genomics 2019 20:335

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  34. Content type: Research article

    Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitiv...

    Authors: Rute R. da Fonseca, Irene Ureña, Sandra Afonso, Ana Elisabete Pires, Emil Jørsboe, Lounès Chikhi and Catarina Ginja

    Citation: BMC Genomics 2019 20:334

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  35. Content type: Research article

    Oenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethanol-rich environments of wine and cider fermentation, where it performs the crucial role of malolactic fermentation. It has a small gen...

    Authors: Marc P. Lorentzen, Hugo Campbell-Sills, Tue S. Jorgensen, Tue K. Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen and Patrick M. Lucas

    Citation: BMC Genomics 2019 20:330

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  36. Content type: Research article

    Growth rate is one of the most important features for aquaculture species and deciphering its regulation mechanism has great significance both in genetics and in economics. Hypothalamus-pituitary growth axis (...

    Authors: Beide Fu, Xiaomu Yu, Jingou Tong, Meixia Pang, Ying Zhou, Qingshan Liu and Wenjing Tao

    Citation: BMC Genomics 2019 20:328

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  37. Content type: Research article

    WUSCHEL-related homeobox (WOX) genes encoding plant-specific homeobox (HB) transcription factors play important roles in the growth and development of plants. To date, WOX genes has been identified and analyzed i...

    Authors: Mengdi Li, Ruihua Wang, Zhengyi Liu, Xiaoming Wu and Jianbo Wang

    Citation: BMC Genomics 2019 20:317

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  38. Content type: Research article

    The Fusarium incarnatum-equiseti species complex (FIESC) comprises 33 phylogenetically distinct species that have been recovered from diverse biological sources, but have been most often isolated from agricultura...

    Authors: Alessandra Villani, Robert H. Proctor, Hye-Seon Kim, Daren W. Brown, Antonio F. Logrieco, Maria Teresa Amatulli, Antonio Moretti and Antonia Susca

    Citation: BMC Genomics 2019 20:314

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  39. Content type: Research article

    Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the ...

    Authors: A. Santos-Zavaleta, E. Pérez-Rueda, M. Sánchez-Pérez, D. A. Velázquez-Ramírez and J. Collado-Vides

    Citation: BMC Genomics 2019 20:299

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  40. Content type: Research article

    Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress p...

    Authors: Yuhui Du, Jinjin Ma, Zhiqiu Yin, Kai Liu, Gan Yao, Wenfeng Xu, Lingchao Fan, Binghai Du, Yanqin Ding and Chengqiang Wang

    Citation: BMC Genomics 2019 20:283

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  41. Content type: Research article

    Gastrointestinal nematodes (GIN), liver flukes (Fasciola hepatica) and bovine lungworms (Dictyocaulus viviparus) are the most important parasitic agents in pastured dairy cattle. Endoparasite infections are assoc...

    Authors: Katharina May, Carsten Scheper, Kerstin Brügemann, Tong Yin, Christina Strube, Paula Korkuć, Gudrun A. Brockmann and Sven König

    Citation: BMC Genomics 2019 20:277

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  42. Content type: Software Article

    Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic classification remains challenging due to the magnitude of the datasets and the i...

    Authors: Gurjit S. Randhawa, Kathleen A. Hill and Lila Kari

    Citation: BMC Genomics 2019 20:267

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  43. Content type: Research article

    There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of...

    Authors: Diyan Li, Yan Li, Miao Li, Tiandong Che, Shilin Tian, Binlong Chen, Xuming Zhou, Guolong Zhang, Uma Gaur, Majing Luo, Kai Tian, Mengnan He, Shen He, Zhongxian Xu, Long Jin, Qianzi Tang…

    Citation: BMC Genomics 2019 20:263

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  44. Content type: Research article

    Sheep have developed the ability to store fat in their tails, which is a unique way of reserving energy to survive a harsh environment. However, the mechanism underlying this adaptive trait remains largely uns...

    Authors: Zhangyuan Pan, Shengdi Li, Qiuyue Liu, Zhen Wang, Zhengkui Zhou, Ran Di, Xuejiao An, Benpeng Miao, Xiangyu Wang, Wenping Hu, Xiaofei Guo, Shenjin Lv, Fukuan Li, Guohui Ding, Mingxing Chu and Yixue Li

    Citation: BMC Genomics 2019 20:261

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  45. Content type: Research article

    Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis ...

    Authors: You-jie Zhao, Xin-yi Liu, Ran Guo, Kun-rong Hu, Yong Cao and Fei Dai

    Citation: BMC Genomics 2019 20:253

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