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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 16

  1. Content type: Research article

    G-protein coupled receptors (GPCRs) are ancient, ubiquitous, constitute the largest family of transducing cell surface proteins, and are integral to cell communication via an array of ligands/neuropeptides. Mo...

    Authors: Nhut M. Tran, Donald L. Mykles, Abigail Elizur and Tomer Ventura

    Citation: BMC Genomics 2019 20:74

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  3. Content type: Research article

    The diversity of avian eggshell colour plays important biological roles in ensuring successful reproduction. Eggshell colour is also an important trait in poultry, but the mechanisms underlying it are poorly u...

    Authors: Ding-Ping Bai, Xin-Yu Lin, Yan Wu, Shi-Ye Zhou, Zhong-bin Huang, Yi-Fan Huang, Ang Li and Xiao-Hong Huang

    Citation: BMC Genomics 2019 20:66

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  4. Content type: Research article

    Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a...

    Authors: Hui Wang, Zhixin Chai, Dan Hu, Qiumei Ji, Jinwei Xin, Chengfu Zhang and Jincheng Zhong

    Citation: BMC Genomics 2019 20:61

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  5. Content type: Research article

    Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria...

    Authors: Dekang Zhu, Jiao He, Zhishuang Yang, Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Yunya Liu, Ling Zhang, Yanling Yu, Yu You, Xiaoyue Chen…

    Citation: BMC Genomics 2019 20:63

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  6. Content type: Research article

    Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adap...

    Authors: Rahul V. Rane, Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò, Philippa C. Griffin, Goujie Zhang, Siu F. Lee, Ary A. Hoffmann and John G. Oakeshott

    Citation: BMC Genomics 2019 20:52

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  7. Content type: Research article

    Differential gene expression can be translated into differing phenotypic traits. Especially during embryogenesis, specific gene expression networks regulate the development of different body structures. Cichli...

    Authors: Athimed El Taher, Nicolás Lichilín, Walter Salzburger and Astrid Böhne

    Citation: BMC Genomics 2019 20:39

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  8. Content type: Review

    The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protei...

    Authors: Shannon J. Sibbald, Julia F. Hopkins, Gina V. Filloramo and John M. Archibald

    Citation: BMC Genomics 2019 20:38

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  10. Content type: Research article

    The Dickeya genus is part of the Pectobacteriaceae family that is included in the newly described enterobacterales order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution an...

    Authors: Špela Alič, Jacques Pédron, Tanja Dreo and Frédérique Van Gijsegem

    Citation: BMC Genomics 2019 20:34

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  11. Content type: Research article

    Pathogens stimulate immune functions of macrophages. Macrophages are a key sentinel cell regulating the response to pathogenic ligands and orchestrating the direction of the immune response. Our study aimed at...

    Authors: Felix N. Toka, Kiera Dunaway, Felicia Smaltz, Lidia Szulc-Dąbrowska, Jenny Drnevich, Matylda Barbara Mielcarska, Magdalena Bossowska-Nowicka and Matthias Schweizer

    Citation: BMC Genomics 2019 20:15

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  12. Content type: Research article

    Argument remains as to whether birds have lost genes compared with mammals and non-avian vertebrates during speciation. High quality-reference gene sets are necessary for precisely evaluating gene gain and los...

    Authors: Zhong-Tao Yin, Feng Zhu, Fang-Bin Lin, Ting Jia, Zhen Wang, Dong-Ting Sun, Guang-Shen Li, Cheng-Lin Zhang, Jacqueline Smith, Ning Yang and Zhuo-Cheng Hou

    Citation: BMC Genomics 2019 20:4

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  13. Content type: Research article

    Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our know...

    Authors: Kai Kamm, Bernd Schierwater and Rob DeSalle

    Citation: BMC Genomics 2019 20:5

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  14. Content type: Research article

    The parthenogenetic Caucasian rock lizard Darevskia armeniaca, like most other parthenogenetic vertebrate species, originated through interspecific hybridization between the closely related sexual Darevskia mixta

    Authors: Anastasiya E. Girnyk, Andrey A. Vergun, Seraphima K. Semyenova, Andrei S. Guliaev, Marine S. Arakelyan, Felix D. Danielyan, Irena A. Martirosyan, Robert W. Murphy and Alexey P. Ryskov

    Citation: BMC Genomics 2018 19:979

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  15. Content type: Review

    Numerous different types of variations can occur in DNA and have diverse effects and consequences. The Variation Ontology (VariO) was developed for systematic descriptions of variations and their effects at DN...

    Authors: Mauno Vihinen

    Citation: BMC Genomics 2018 19:974

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  16. Content type: Research article

    Caleosin/peroxygenases, CLO/PXG, (designated PF05042 in Pfam) are a group of genes/proteins with anomalous distributions in eukaryotic taxa. We have previously characterised CLO/PXGs in the Viridiplantae. The aim...

    Authors: Farzana Rahman, Mehedi Hassan, Abdulsamie Hanano, David A. Fitzpatrick, Charley G. P. McCarthy and Denis J. Murphy

    Citation: BMC Genomics 2018 19:976

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  17. Content type: Research article

    Cosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of e...

    Authors: Tianjuan Su, Bo He, Kui Li and Aiping Liang

    Citation: BMC Genomics 2018 19:961

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  18. Content type: Research article

    The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, re...

    Authors: Olga O. Bochkareva, Elena V. Moroz, Iakov I. Davydov and Mikhail S. Gelfand

    Citation: BMC Genomics 2018 19:965

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  19. Content type: Research article

    Both human and mouse fibroblasts can be reprogrammed to pluripotency with Oct4, Sox2, Klf4, and c-Myc (OSKM) transcription factors. While both systems generate pluripotency, human reprogramming takes considera...

    Authors: Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Stephen T. Smale, Kenneth S. Zaret, Kathrin Plath and Matteo Pellegrini

    Citation: BMC Genomics 2018 19:956

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  20. Content type: Research article

    Dissecting the genetic basis of phenotypic diversity is one of the fundamental goals in evolutionary biology. Despite growing evidence for gene expression divergence being responsible for the evolution of comp...

    Authors: Sri Pratima Nandamuri, Matthew A. Conte and Karen L. Carleton

    Citation: BMC Genomics 2018 19:945

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  21. Content type: Software

    Recent advances in sequencing technology have allowed us to investigate personal genomes to find structural variations, which have been studied extensively to identify their association with the physiology of ...

    Authors: Junwoo Bae, Kyeong Won Lee, Mohammad Nazrul Islam, Hyung-Soon Yim, Heejin Park and Mina Rho

    Citation: BMC Genomics 2018 19:944

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  22. Content type: Research article

    Unlike the chromosome constitution of most snakes (2n=36), the cobra karyotype shows a diploid chromosome number of 38 with a highly heterochromatic W chromosome and a large morphologically different chromosom...

    Authors: Worapong Singchat, Rebecca E. O’Connor, Panupong Tawichasri, Aorarat Suntronpong, Siwapech Sillapaprayoon, Sunutcha Suntrarachun, Narongrit Muangmai, Sudarath Baicharoen, Surin Peyachoknagul, Lawan Chanhome, Darren Griffin and Kornsorn Srikulnath

    Citation: BMC Genomics 2018 19:939

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  23. Content type: Research article

    The molecular mechanisms underlying stress-influenced immune function of chicken (Gallus Gallus) are not clear. The stress models can be established effectively by feeding chickens corticosterone (CORT) hormone. ...

    Authors: Yanhua Zhang, Yanting Zhou, Guirong Sun, Kui Li, Zhuanjian Li, Aru Su, Xiaojun Liu, Guoxi Li, Ruirui Jiang, Ruili Han, Yadong Tian, Xiangtao Kang and Fengbin Yan

    Citation: BMC Genomics 2018 19:918

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  24. Content type: Research article

    Comparative genomics approaches have facilitated the discovery of many novel non-coding and structured RNAs (ncRNAs). The increasing availability of related genomes now makes it possible to systematically sear...

    Authors: Rebecca Kirsch, Stefan E. Seemann, Walter L. Ruzzo, Stephen M. Cohen, Peter F. Stadler and Jan Gorodkin

    Citation: BMC Genomics 2018 19:899

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  25. Content type: Research article

    Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, a...

    Authors: Xiaoying Li, Yali Ma, Shuqing Liang, Yu Tian, Sanjun Yin, Sisi Xie and Hua Xie

    Citation: BMC Genomics 2018 19:889

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  26. Content type: Research article

    The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H2) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehy...

    Authors: Teresa Mohr, Habibu Aliyu, Raphael Küchlin, Michaela Zwick, Don Cowan, Anke Neumann and Pieter de Maayer

    Citation: BMC Genomics 2018 19:880

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  27. Content type: Research article

    Environmental stress induced genetic polymorphisms have been suggested to arbitrate functional modifications influencing adaptations in microbes. The relationship between the genetic processes and concomitant ...

    Authors: Akanksha Jaiswar, Deepti Varshney, Alok Adholeya and Pushplata Prasad

    Citation: BMC Genomics 2018 19:868

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  28. Content type: Research article

    Rapid and accurate identification of Verotoxigenic Escherichia coli (VTEC) O157:H7 is dependent on well-established, standardized and highly discriminatory typing methods. Currently, conventional subtyping tests ...

    Authors: Jillian Rumore, Lorelee Tschetter, Ashley Kearney, Rima Kandar, Rachel McCormick, Matthew Walker, Christy-Lynn Peterson, Aleisha Reimer and Celine Nadon

    Citation: BMC Genomics 2018 19:870

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  29. Content type: Research article

    The green peach aphid (GPA), Myzus persicae (Sülzer), is a widespread phloem-feeding insect that significantly influences the yield and visual quality of peach [Prunus persica (L.) Batsch]. Single dominant gene (

    Authors: Liang Niu, Lei Pan, Wenfang Zeng, Zhenhua Lu, Guochao Cui, Meili Fan, Qiang Xu, Zhiqiang Wang and Guohuai Li

    Citation: BMC Genomics 2018 19:846

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  30. Content type: Research article

    Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecolo...

    Authors: David Armisén, Rajendhran Rajakumar, Markus Friedrich, Joshua B. Benoit, Hugh M. Robertson, Kristen A. Panfilio, Seung-Joon Ahn, Monica F. Poelchau, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Richard A. Gibbs, Daniel S. T. Hughes, Yi Han, Sandra L. Lee…

    Citation: BMC Genomics 2018 19:832

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  31. Content type: Research article

    Pigeon crop has the unique ability to produce a nutrient rich substance termed pigeon ‘milk’ (PM), which has functional resemblance with the mammalian milk. Previous researches have demonstrated that a large n...

    Authors: Yao Ma, Siyuan Feng, Xun Wang, Izhar Hyder Qazi, Keren Long, Yi Luo, Guojun Li, Chunyou Ning, Yixin Wang, Silu Hu, Juan Xiao, Xiaokai Li, Dan Lan, Yaodong Hu, Qianzi Tang, Jideng Ma…

    Citation: BMC Genomics 2018 19:828

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  32. Content type: Research article

    The nuclear envelope (NE) that encapsulates the nuclear genome is a double lipid bilayer with several integral and peripherally associated proteins. It is a characteristic feature of the eukaryotes and acts as...

    Authors: Hita Sony Garapati and Krishnaveni Mishra

    Citation: BMC Genomics 2018 19:823

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  33. Content type: Research article

    The three superfamilies of Long Terminal Repeat (LTR) retrotransposons are a widespread kind of transposable element and a major factor in eukaryotic genome evolution. In metazoans, recent studies suggested th...

    Authors: Camille Thomas-Bulle, Mathieu Piednoël, Tifenn Donnart, Jonathan Filée, Didier Jollivet and Éric Bonnivard

    Citation: BMC Genomics 2018 19:821

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  34. Content type: Research article

    Solea senegalensis (Kaup, 1858) is a commercially important flatfish species, belonging to the Pleuronectiformes order. The taxonomy of this group has long been controversial, and the karyotype of the order prese...

    Authors: Aglaya García-Angulo, Manuel A. Merlo, Silvia Portela-Bens, María E. Rodríguez, Emilio García, Ahmed Al-Rikabi, Thomas Liehr and Laureana Rebordinos

    Citation: BMC Genomics 2018 19:818

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  35. Content type: Research article

    The insect olfactory system is a highly specific and sensitive chemical detector, which plays important roles in feeding, mating and finding an appropriate oviposition site. The ecological niche of Bombyx mori ha...

    Authors: Chuan-Zhen Qiu, Qiu-Zhong Zhou, Ting-Ting Liu, Shou-Min Fang, Ya-Wang Wang, Xin Fang, Chun-Li Huang, Quan-You Yu, Chun-Hong Chen and Ze Zhang

    Citation: BMC Genomics 2018 19:788

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  36. Content type: Research article

    Macaca fascicularis (M. fascicularis) is a primate model organism that played important role in studying human health. It is vital to better understand the similarity and differences of gene regulation between M....

    Authors: Tao Tan, Lin Xia, Kailing Tu, Jie Tang, Senlin Yin, Lunzhi Dai, Peng Lei, Biao Dong, Hongbo Hu, Yong Fan, Yang Yu and Dan Xie

    Citation: BMC Genomics 2018 19:787

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  37. Content type: Research article

    The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is pred...

    Authors: Lin-sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-gang Sun, Irfan Ullah and Yin-cang Han

    Citation: BMC Genomics 2018 19:785

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  38. Content type: Methodology article

    Understanding the underlying genetic structure of human populations is of fundamental interest to both biological and social sciences. Advances in high-throughput genotyping technology have markedly improved o...

    Authors: Zoltán Maróti, Zsolt Boldogkői, Dóra Tombácz, Michael Snyder and Tibor Kalmár

    Citation: BMC Genomics 2018 19:778

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  39. Content type: Research article

    Numerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has ...

    Authors: Dan Zhang, Xiuyu Lou, Hao Yan, Junhang Pan, Haiyan Mao, Hongfeng Tang, Yan Shu, Yun Zhao, Lei Liu, Junping Li, Jiang Chen, Yanjun Zhang and Xuejun Ma

    Citation: BMC Genomics 2018 19:773

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  40. Content type: Research article

    Trypanosoma conorhini and Trypanosoma rangeli, like Trypanosoma cruzi, are kinetoplastid protist parasites of mammals displaying divergent hosts, geographic ranges and lifestyles. Largely nonpathogenic T. rangeli

    Authors: Katie R Bradwell, Vishal N Koparde, Andrey V Matveyev, Myrna G Serrano, João M P Alves, Hardik Parikh, Bernice Huang, Vladimir Lee, Oneida Espinosa-Alvarez, Paola A Ortiz, André G Costa-Martins, Marta M G Teixeira and Gregory A Buck

    Citation: BMC Genomics 2018 19:770

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  42. Content type: Research article

    Diatoms play a great role in carbon fixation with about 20% of the whole fixation in the world. However, harmful algal bloom as known as red tide is a major problem in environment and fishery industry. Even th...

    Authors: Atsushi Ogura, Yuki Akizuki, Hiroaki Imoda, Katsuhiko Mineta, Takashi Gojobori and Satoshi Nagai

    Citation: BMC Genomics 2018 19:765

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  43. Content type: Research article

    Ural genetic family is a part of the Euro-American lineage of Mycobacterium tuberculosis and is endemic in Northern Eurasia (former Soviet Union [FSU]). These strains were long described as drug susceptible and o...

    Authors: Viacheslav Sinkov, Oleg Ogarkov, Igor Mokrousov, Yuri Bukin, Svetlana Zhdanova and Scott K. Heysell

    Citation: BMC Genomics 2018 19:762

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  44. Content type: Research article

    An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to extern...

    Authors: Gaurav Sharma, Rebecca Parales and Mitchell Singer

    Citation: BMC Genomics 2018 19:757

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  46. Content type: Software

    Previous studies demonstrate the usefulness of using multiple tools and methods for improving the accuracy of motif detection. Over the past years, numerous motif discovery pipelines have been developed. Howev...

    Authors: Ngoc Tam L. Tran and Chun-Hsi Huang

    Citation: BMC Genomics 2018 19:755

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  47. Content type: Research article

    Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops ...

    Authors: S. Zoledowska, A. Motyka-Pomagruk, W. Sledz, A. Mengoni and E. Lojkowska

    Citation: BMC Genomics 2018 19:751

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  48. Content type: Research article

    Studies combining experimental evolution and next-generation sequencing have found that adaptation in sexually reproducing populations is primarily fueled by standing genetic variation. Consequently, the respo...

    Authors: Mark A Phillips, Grant A Rutledge, James N Kezos, Zachary S Greenspan, Andrew Talbott, Sara Matty, Hamid Arain, Laurence D Mueller, Michael R Rose and Parvin Shahrestani

    Citation: BMC Genomics 2018 19:743

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  49. Content type: Research article

    The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute a valuable source of dietary protein. Therefore, they are cultured wor...

    Authors: Oanh T. P. Kim, Phuong T. Nguyen, Eiichi Shoguchi, Kanako Hisata, Thuy T. B. Vo, Jun Inoue, Chuya Shinzato, Binh T. N. Le, Koki Nishitsuji, Miyuki Kanda, Vu H. Nguyen, Hai V. Nong and Noriyuki Satoh

    Citation: BMC Genomics 2018 19:733

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  50. Content type: Research article

    After a short gestation, marsupials give birth to immature neonates with lungs that are not fully developed and in early life the neonate partially relies on gas exchange through the skin. Therefore, significa...

    Authors: Vengamanaidu Modepalli, Amit Kumar, Julie A Sharp, Norman R Saunders, Kevin R Nicholas and Christophe Lefèvre

    Citation: BMC Genomics 2018 19:732

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