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Prokaryote microbial genomics

Section edited by Theo Smits

This section covers the structure and function of the genomes of prokaryotic and archaea microorganisms.

Page 1 of 13

  1. Content type: Research article

    The human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adap...

    Authors: Isabelle Rosinski-Chupin, Elisabeth Sauvage, Agnès Fouet, Claire Poyart and Philippe Glaser

    Citation: BMC Genomics 2019 20:236

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  2. Content type: Research article

    The coordination of group behaviors in bacteria is achieved by a cell-cell signaling process called quorum sensing (QS). QS is an intercellular communication system, which synchronously controls expression of ...

    Authors: Miriam Khider, Erik Hjerde, Hilde Hansen and Nils Peder Willassen

    Citation: BMC Genomics 2019 20:220

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  3. Content type: Research article

    Halomicronema hongdechloris was the first cyanobacterium to be identified that produces chlorophyll (Chl) f. It contains Chl a and uses phycobiliproteins as its major light-harvesting components under white light...

    Authors: Min Chen, Miguel A. Hernandez-Prieto, Patrick C. Loughlin, Yaqiong Li and Robert D. Willows

    Citation: BMC Genomics 2019 20:207

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  4. Content type: Research article

    Escherichia coli O157:H7 (O157) has been linked to numerous foodborne disease outbreaks. The ability to rapidly sequence and analyze genomes is important for understanding epidemiology, virulence, survival, and e...

    Authors: Vijay K. Sharma, Suryatej Akavaram, Robert G. Schaut and Darrell O. Bayles

    Citation: BMC Genomics 2019 20:196

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  5. Content type: Research article

    Diseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe ...

    Authors: Michela Ruinelli, Jochen Blom, Theo H. M. Smits and Joël F. Pothier

    Citation: BMC Genomics 2019 20:172

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  6. Content type: Software Article

    Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseri...

    Authors: Reema Singh, Jo-Anne R. Dillon, Walter Demczuk and Anthony Kusalik

    Citation: BMC Genomics 2019 20:165

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  7. Content type: Research article

    Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothe...

    Authors: Ye Feng, Varune Rohan Ramnarine, Robert Bell, Stanislav Volik, Elai Davicioni, Vanessa M. Hayes, Shancheng Ren and Colin C. Collins

    Citation: BMC Genomics 2019 20:146

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  8. Content type: Research article

    A previous laboratory study involving wild type, mutant and devR/dosR complemented strains of Mycobacterium tuberculosis reported the attenuation phenotype of complemented strain, Comp1. This phenotype was intrig...

    Authors: Shyamasree De Majumdar, Kriti Sikri, Payel Ghosh, Neetika Jaisinghani, Malobi Nandi, Sheetal Gandotra, Shekhar Mande and Jaya Sivaswami Tyagi

    Citation: BMC Genomics 2019 20:129

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  9. Content type: Research article

    We describe the virulence factors of a methicillin-sensitive Staphylococcus aureus sequence type (ST) 45 strain, MCRF184, (spa type t917), that caused severe necrotizing fasciitis in a 72-year-old diabetic male. ...

    Authors: Vijay Aswani, Fares Najar, Madhulatha Pantrangi, Bob Mau, William R. Schwan and Sanjay K. Shukla

    Citation: BMC Genomics 2019 20:123

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  10. Content type: Research article

    Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasiv...

    Authors: Joaquín Giner-Lamia, Pablo Vinuesa, Laura Betancor, Claudia Silva, Julieta Bisio, Lorena Soleto, José A. Chabalgoity, José Luis Puente and Francisco García-del Portillo

    Citation: BMC Genomics 2019 20:99

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  11. Content type: Research article

    The genus Anaplasma is made up of organisms characterized by small genomes that are undergoing reductive evolution. Anaplasma ovis, one of the seven recognized species in this genus, is an understudied pathogen o...

    Authors: Zhijie Liu, Austin M. Peasley, Jifei Yang, Youquan Li, Guiquan Guan, Jianxun Luo, Hong Yin and Kelly A. Brayton

    Citation: BMC Genomics 2019 20:69

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  12. Content type: Research article

    Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antib...

    Authors: Bart J. F. Keijser, Valeria Agamennone, Tim J. van den Broek, Martien Caspers, Adri van de Braak, Richard Bomers, Mieke Havekes, Eric Schoen, Martin van Baak, Daniël Mioch, Lonneke Bomers and Roy C. Montijn

    Citation: BMC Genomics 2019 20:65

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  13. Content type: Research article

    The gram-negative Xanthomonas genus contains a large group of economically important plant pathogens, which cause severe diseases on many crops worldwide. The diffusible signal factor (DSF) - mediated quorum sens...

    Authors: Lei Li, Jinyun Li, Yunzeng Zhang and Nian Wang

    Citation: BMC Genomics 2019 20:55

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  14. Content type: Research article

    Co-colonization by Pseudomonas aeruginosa and Staphylococcus aureus is frequent in cystic fibrosis patients. Polymicrobial infections involve both detrimental and beneficial interactions between different bacteri...

    Authors: Mikaël Tognon, Thilo Köhler, Alexandre Luscher and Christian van Delden

    Citation: BMC Genomics 2019 20:30

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  15. Content type: Research article

    Short-read sequencing technologies have made microbial genome sequencing cheap and accessible. However, closing genomes is often costly and assembling short reads from genomes that are repetitive and/or have e...

    Authors: Sarah Goldstein, Lidia Beka, Joerg Graf and Jonathan L. Klassen

    Citation: BMC Genomics 2019 20:23

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  16. Content type: Research article

    Salmonella enterica subspecies enterica is an animal and zoonotic pathogen of global importance. Cattle are a significant reservoir of human non-typhoidal salmonellosis and can suffer enteric and systemic disease...

    Authors: Prerna Vohra, Roy R. Chaudhuri, Matthew Mayho, Christina Vrettou, Cosmin Chintoan-Uta, Nicholas R. Thomson, Jayne C. Hope, John Hopkins and Mark P. Stevens

    Citation: BMC Genomics 2019 20:20

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  17. Content type: Research article

    The ability of bacteria to acquire resistance to antibiotics relies to a large extent on their capacity for genome modification. Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer,...

    Authors: Marloes Hoeksema, Martijs J. Jonker, Keshia Bel, Stanley Brul and Benno H. ter Kuile

    Citation: BMC Genomics 2018 19:973

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  18. Content type: Research article

    Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in t...

    Authors: Alexander V. Tyakht, Alexander I. Manolov, Alexandra V. Kanygina, Dmitry S. Ischenko, Boris A. Kovarsky, Anna S. Popenko, Alexander V. Pavlenko, Anna V. Elizarova, Daria V. Rakitina, Julia P. Baikova, Valentina G. Ladygina, Elena S. Kostryukova, Irina Y. Karpova, Tatyana A. Semashko, Andrei K. Larin, Tatyana V. Grigoryeva…

    Citation: BMC Genomics 2018 19:968

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  19. Content type: Research article

    Genome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional annota...

    Authors: Marc Griesemer, Jeffrey A. Kimbrel, Carol E. Zhou, Ali Navid and Patrik D’haeseleer

    Citation: BMC Genomics 2018 19:948

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  20. Content type: Research article

    Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii wit...

    Authors: Cormac Brian Fitzgerald, Andrey N. Shkoporov, Thomas D. S. Sutton, Andrei V. Chaplin, Vimalkumar Velayudhan, R. Paul Ross and Colin Hill

    Citation: BMC Genomics 2018 19:931

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  21. Content type: Research article

    Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while s...

    Authors: I. S. Rusinov, A. S. Ershova, A. S. Karyagina, S. A. Spirin and A. V. Alexeevski

    Citation: BMC Genomics 2018 19:885

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  22. Content type: Research article

    Corynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects aga...

    Authors: Verlaine J. Timms, Trang Nguyen, Taryn Crighton, Marion Yuen and Vitali Sintchenko

    Citation: BMC Genomics 2018 19:869

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  23. Content type: Research article

    Photorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strai...

    Authors: Maria-Antonia Zamora-Lagos, Simone Eckstein, Angela Langer, Athanasios Gazanis, Friedhelm Pfeiffer, Bianca Habermann and Ralf Heermann

    Citation: BMC Genomics 2018 19:854

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  24. Content type: Research article

    Acetogenic bacteria constitute promising biocatalysts for the conversion of CO2/H2 or synthesis gas (H2/CO/CO2) into biofuels and value-added biochemicals. These microorganisms are naturally capable of autotrophi...

    Authors: Yoseb Song, Jongoh Shin, Sangrak Jin, Jung-Kul Lee, Dong Rip Kim, Sun Chang Kim, Suhyung Cho and Byung-Kwan Cho

    Citation: BMC Genomics 2018 19:837

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  25. Content type: Research article

    Helicobacter pylori is a human stomach pathogen, naturally-competent for DNA uptake, and prone to homologous recombination. Extensive homoplasy (i.e., phylogenetically-unlinked identical variations) observed in H...

    Authors: Sujay Chattopadhyay, Peter B. Chi, Vladimir N. Minin, Douglas E. Berg and Evgeni V. Sokurenko

    Citation: BMC Genomics 2018 19:835

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  26. Content type: Research article

    The genus Helicobacter are gram-negative, microaerobic, flagellated, mucus-inhabiting bacteria associated with gastrointestinal inflammation and classified as gastric or enterohepatic Helicobacter species (EHS) a...

    Authors: Anthony Mannion, Zeli Shen and James G. Fox

    Citation: BMC Genomics 2018 19:830

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  27. Content type: Research article

    Pseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae (Psa) initiated a worldwide pandemic in 2008 on cult...

    Authors: Peter A. McAtee, Lara Brian, Ben Curran, Otto van der Linden, Niels J. Nieuwenhuizen, Xiuyin Chen, Rebecca A. Henry-Kirk, Erin A. Stroud, Simona Nardozza, Jay Jayaraman, Erik H. A. Rikkerink, Cris G. Print, Andrew C. Allan and Matthew D. Templeton

    Citation: BMC Genomics 2018 19:822

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  28. Content type: Research article

    Staphylococcus caprae is an animal-associated bacterium regarded as part of goats’ microflora. Recently, S. caprae has been reported to cause human nosocomial infections such as bacteremia and bone and joint infe...

    Authors: Shinya Watanabe, Yoshifumi Aiba, Xin-Ee Tan, Feng-Yu Li, Tanit Boonsiri, Kanate Thitiananpakorn, Bintao Cui, Yusuke Sato’o, Kotaro Kiga, Teppei Sasahara and Longzhu Cui

    Citation: BMC Genomics 2018 19:810

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  29. Content type: Research article

    Animal studies show that high fat (HF) diet-induced gut microbiota contributes to the development of obesity. Oil composition of high-fat diet affects metabolic inflammation differently with deleterious effect...

    Authors: Vania Patrone, Andrea Minuti, Michela Lizier, Francesco Miragoli, Franco Lucchini, Erminio Trevisi, Filippo Rossi and Maria Luisa Callegari

    Citation: BMC Genomics 2018 19:808

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  30. Content type: Research article

    Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the...

    Authors: Suchawan Pornsukarom, Arnoud H M van Vliet and Siddhartha Thakur

    Citation: BMC Genomics 2018 19:801

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  31. Content type: Research article

    Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China. PA1 and a few other strains were grouped into a novel species, Dickeya fangzhongdai, and only...

    Authors: Jingxin Zhang, John Hu, Huifang Shen, Yucheng Zhang, Dayuan Sun, Xiaoming Pu, Qiyun Yang, Qiurong Fan and Birun Lin

    Citation: BMC Genomics 2018 19:782

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  32. Content type: Research article

    Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich f...

    Authors: Daniel G. Mediati, Catherine M. Burke, Shirin Ansari, Elizabeth J. Harry and Iain G. Duggin

    Citation: BMC Genomics 2018 19:781

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  33. Content type: Research article

    Small RNAs (sRNAs) are noncoding molecules that regulate different cellular activities in several bacteria. The role of sRNAs in gene expression regulation is poorly characterized in the etiological agent of p...

    Authors: Tiago Ebert Fritsch, Franciele Maboni Siqueira and Irene Silveira Schrank

    Citation: BMC Genomics 2018 19:767

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  34. Content type: Research article

    The cattle gastrointestinal tract (GIT) is the main enterohemorrhagic Escherichia coli (EHEC) reservoir. In order to identify nutrients required for the survival or multiplication of EHEC in the bovine GIT, we co...

    Authors: Audrey Segura, Marine Bertoni, Pauline Auffret, Christophe Klopp, Olivier Bouchez, Clémence Genthon, Alexandra Durand, Yolande Bertin and Evelyne Forano

    Citation: BMC Genomics 2018 19:766

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  35. Content type: Research article

    Gluconobacter oxydans is a strictly aerobic Gram-negative acetic acid bacterium used industrially for oxidative biotransformations due to its exceptional type of catabolism. It incompletely oxidizes a wide variet...

    Authors: Angela Kranz, Andrea Steinmann, Ursula Degner, Aliye Mengus-Kaya, Susana Matamouros, Michael Bott and Tino Polen

    Citation: BMC Genomics 2018 19:753

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  36. Content type: Research article

    Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range ...

    Authors: Filipe P Matteoli, Hemanoel Passarelli-Araujo, Régis Josué A Reis, Letícia O da Rocha, Emanuel M de Souza, L Aravind, Fabio L Olivares and Thiago M Venancio

    Citation: BMC Genomics 2018 19:750

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  37. Content type: Research article

    Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically impo...

    Authors: Peng Luo, Long Yun, Yingying Li, Yushun Tian, Qiuting Liu, Wen Huang and Chaoqun Hu

    Citation: BMC Genomics 2018 19:741

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  38. Content type: Research article

    Streptococcus agalactiae (Group B Streptococcus, GBS) is a common bacteria species infecting both human and bovine. Previous studies have shown that the GBS isolated from human and bovine are mostly unrelated and...

    Authors: Rui Wang, Liping Li, Ting Huang, Yan Huang, Weiyi Huang, Xiuying Yang, Aiying Lei and Ming Chen

    Citation: BMC Genomics 2018 19:716

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  39. Content type: Methodology article

    Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiologi...

    Authors: Nicholas D Sanderson, Teresa L Street, Dona Foster, Jeremy Swann, Bridget L Atkins, Andrew J Brent, Martin A McNally, Sarah Oakley, Adrian Taylor, Tim E A Peto, Derrick W Crook and David W Eyre

    Citation: BMC Genomics 2018 19:714

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  40. Content type: Research article

    Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. Moreover, the potential pathogenic fac...

    Authors: Furqan Awan, Yuhao Dong, Jin Liu, Nannan Wang, Muhammad Hassan Mushtaq, Chengping Lu and Yongjie Liu

    Citation: BMC Genomics 2018 19:712

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  41. Content type: Research article

    Listeria monocytogenes is a widespread foodborne pathogen that can cause listeriosis, a potentially fatal infection. L. monocytogenes is subdivided into four phylogenetic lineages, with the highest incidence of l...

    Authors: Cary Pirone-Davies, Yi Chen, Arthur Pightling, Gina Ryan, Yu Wang, Kuan Yao, Maria Hoffmann and Marc W. Allard

    Citation: BMC Genomics 2018 19:708

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  42. Content type: Research article

    JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which h...

    Authors: Jie Wang, Laiqing Song, Qiqing Jiao, Shuke Yang, Rui Gao, Xingbo Lu and Guangfang Zhou

    Citation: BMC Genomics 2018 19:689

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  43. Content type: Research article

    Enterohemorrhagic Escherichia coli (EHEC) O26:H11/H, the most common non-O157 serotype causing hemolytic uremic syndrome worldwide, are evolutionarily highly dynamic with new pathogenic clones emerging rapidly. ...

    Authors: Lucia Karnisova, Monika Marejkova, Hana Hrbackova, Alexander Mellmann, Helge Karch, Angelika Fruth, Pavel Drevinek, Kveta Blahova, Martina Bielaszewska and Jaroslav Nunvar

    Citation: BMC Genomics 2018 19:647

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  44. Content type: Research article

    Rhizobia are alpha-proteobacteria commonly found in soil and root nodules of legumes. It was recently reported that nitrogen-fixing rhizobia also inhabit legume seeds. In this study, we examined whole-genome s...

    Authors: Alejandro Aguilar, Yolanda Mora, Araceli Dávalos, Lourdes Girard, Jaime Mora and Humberto Peralta

    Citation: BMC Genomics 2018 19:645

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  45. Content type: Research article

    Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patie...

    Authors: Bryan A. Wee, Anna S. Tai, Laura J. Sherrard, Nouri L. Ben Zakour, Kirt R. Hanks, Timothy J. Kidd, Kay A. Ramsay, Iain Lamont, David M. Whiley, Scott C. Bell and Scott A. Beatson

    Citation: BMC Genomics 2018 19:644

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  46. Content type: Research article

    Pontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environ...

    Authors: Byung Cheol Cho, Stephen C. Hardies, Gwang Il Jang and Chung Yeon Hwang

    Citation: BMC Genomics 2018 19:625

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