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  1. Content type: Research article

    Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of cellular processes in diseases such as cancer, although the functions of most remain poorly understood. To address this, here we apply a nov...

    Authors: Kevin Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, Daniel W. Lambert, Stephen Brown and James R. Bradford

    Citation: BMC Genomics 2019 20:454

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  2. Content type: Research article

    Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted...

    Authors: Belinda Wright, Katherine A. Farquharson, Elspeth A. McLennan, Katherine Belov, Carolyn J. Hogg and Catherine E. Grueber

    Citation: BMC Genomics 2019 20:453

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  3. Content type: Research article

    Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification ag...

    Authors: A. C. Picornell, I. Echavarria, E. Alvarez, S. López-Tarruella, Y. Jerez, K. Hoadley, J. S. Parker, M. del Monte-Millán, R. Ramos-Medina, J. Gayarre, I. Ocaña, M. Cebollero, T. Massarrah, F. Moreno, J. A. García Saenz, H. Gómez Moreno…

    Citation: BMC Genomics 2019 20:452

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  4. Content type: Research article

    Herpetospermum pedunculosum (Ser.) Baill is annual scandent herbs. They are used in the treatment of piles, inflammation of the stomach and the intestines. It can survive the extreme environment of the Tibetan Pl...

    Authors: Yong Zhao, Fuling Xu, Jia Liu, Fachun Guan, Hong Quan and Fanjuan Meng

    Citation: BMC Genomics 2019 20:451

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  5. Content type: Research article

    Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be ident...

    Authors: Octávio Augusto Costa Almeida, Gabriel Costa Monteiro Moreira, Fernanda Marcondes Rezende, Clarissa Boschiero, Jane de Oliveira Peixoto, Adriana Mercia Guaratini Ibelli, Mônica Corrêa Ledur, Francisco José de Novais and Luiz Lehmann Coutinho

    Citation: BMC Genomics 2019 20:449

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  6. Content type: Research article

    The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although a...

    Authors: Maria José Gonzalo, Aurora Díaz, Narinder P. S. Dhillon, Umesh K. Reddy, Belén Picó and Antonio J. Monforte

    Citation: BMC Genomics 2019 20:448

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  7. Content type: Research article

    Under caged conditions, birds are affected more severely by environmental stressors such as dietary structure, activity space, human disturbances, and pathogens, which may be reflected in the gene expression i...

    Authors: Yu Wang, Jinxin Guo, Lin Wang, Hengjiu Tian and Jinling Sui

    Citation: BMC Genomics 2019 20:447

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  8. Content type: Research article

    Circulating microRNAs (miRNAs) are attractive non-invasive biomarkers for a variety of conditions due to their stability and altered pathophysiological expression levels. Reliable detection of global expressio...

    Authors: Ryan K.Y. Wong, Meabh MacMahon, Jayne V. Woodside and David A. Simpson

    Citation: BMC Genomics 2019 20:446

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  9. 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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  10. 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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  11. Content type: Database

    Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes. However, given the complexity of the molecular mechanisms underlying phenomes, only a few hundred g...

    Authors: Qingchun Pan, Junfeng Wei, Feng Guo, Suiyong Huang, Yong Gong, Hao Liu, Jianxiao Liu and Lin Li

    Citation: BMC Genomics 2019 20:443

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  12. Content type: Research article

    Alternative splicing (AS) is a regulatory mechanism used to create many forms of mature messengers RNAs (mRNAs) from the same gene. Sequencing of RNA (RNA-Seq) is an advanced technology, which has been utilized b...

    Authors: Vishwas Sharma, Amrita Nandan, Harpreet Singh, Suyash Agarwal, Richa Tripathi, Dhirendra Narain Sinha and Ravi Mehrotra

    Citation: BMC Genomics 2019 20:442

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  13. Content type: Research article

    Cytochrome P450-dependent monooxygenases (P450s), constituting one of the largest and oldest gene superfamilies found in many organisms from bacteria to humans, play a vital role in the detoxification and inac...

    Authors: Binu Antony, Jibin Johny, Mahmoud M. Abdelazim, Jernej Jakše, Mohammed Ali Al-Saleh and Arnab Pain

    Citation: BMC Genomics 2019 20:440

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  14. 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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  15. Content type: Research article

    For spring-type Chinese cabbage production, premature bolting refers to the excessive elongation of dwarf stems before harvesting. Although quantitative trait loci (QTL) mapping for bolting-related traits have...

    Authors: Shuantao Liu, Ronghua Wang, Zhigang Zhang, Qiaoyun Li, Lihua Wang, Yongqiang Wang and Zhizhong Zhao

    Citation: BMC Genomics 2019 20:437

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  16. Content type: Research article

    Bacillus cereus sensu lato s.l.) is a group of bacteria displaying close phylogenetic relationships but a high ecological diversity. The three most studied species are Bacillus anthracis, Bacillus cereus sensu st...

    Authors: Nancy Fayad, Mireille Kallassy Awad and Jacques Mahillon

    Citation: BMC Genomics 2019 20:436

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  17. Content type: Correction

    He authors reported that one of the authors’ names was typeset incorrectly in the authorship list.

    Authors: Camus Nimmo, Liam P. Shaw, Ronan Doyle, Rachel Williams, Kayleen Brien, Carrie Burgess, Judith Breuer, Francois Balloux and Alexander S. Pym

    Citation: BMC Genomics 2019 20:433

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    The original article was published in BMC Genomics 2019 20:389

  18. Content type: Research article

    Accompanied with rapid growth and high density aquaculture, gibel carp has been seriously threatened by Carassius auratus herpesvirus (CaHV) since 2012. In previous study, distinct CaHV resistances and immune res...

    Authors: Wei-Jia Lu, Fan-Xiang Gao, Yang Wang, Qi-Ya Zhang, Zhi Li, Xiao-Juan Zhang, Li Zhou and Jian-Fang Gui

    Citation: BMC Genomics 2019 20:432

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  19. Content type: Research article

    BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its...

    Authors: Tom A. Mendum, Aneesh Chandran, Kerstin Williams, H. Martin Vordermeier, Bernardo Villarreal-Ramos, H. Wu, Albel Singh, Alex A. Smith, Rachel E. Butler, Aravind Prasad, Neeraj Bharti, Ruma Banerjee, Sunitha M. Kasibhatla, Apoorva Bhatt, Graham R. Stewart and Johnjoe McFadden

    Citation: BMC Genomics 2019 20:431

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  20. 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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  21. 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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  22. Content type: Research article

    Deciphering the molecular mechanisms mediating the chemical senses, taste, and smell has been of vital importance for understanding the nature of how insects interact with their chemical environment. Several g...

    Authors: William B. Walker III, Amit Roy, Peter Anderson, Fredrik Schlyter, Bill S. Hansson and Mattias C. Larsson

    Citation: BMC Genomics 2019 20:428

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  23. Content type: Research article

    The two Caenorhabditis elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic tissues of the adult reproductive system. The sister cells of the SGPs are two head mesoderma...

    Authors: Laura D. Mathies, Surjyendu Ray, Kayla Lopez-Alvillar, Michelle N. Arbeitman, Andrew G. Davies and Jill C. Bettinger

    Citation: BMC Genomics 2019 20:427

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  24. Content type: Research article

    Cotton is the most essential textile crop worldwide, and phytohormones are critical for cotton fiber development. One example is the role of auxin in fiber initiation, but we know little molecular basis. Micro...

    Authors: Tianlun Zhao, Xiaojian Xu, Min Wang, Cheng Li, Cong Li, Rubing Zhao, Shuijin Zhu, Qiuling He and Jinhong Chen

    Citation: BMC Genomics 2019 20:421

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  25. Content type: Research article

    The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subse...

    Authors: Elizabeth A. Cooper, Zachary W. Brenton, Barry S. Flinn, Jerry Jenkins, Shengqiang Shu, Dave Flowers, Feng Luo, Yunsheng Wang, Penny Xia, Kerrie Barry, Chris Daum, Anna Lipzen, Yuko Yoshinaga, Jeremy Schmutz, Christopher Saski, Wilfred Vermerris…

    Citation: BMC Genomics 2019 20:420

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  26. 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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  27. Content type: Research article

    To control the osmotic pressure in the body, physiological adjustments to salinity fluctuations require the fish to regulate body fluid homeostasis in relation to environmental change via osmoregulation. Previ...

    Authors: Maoliang Su, Jianan Zhou, Zhengyu Duan and Junbin Zhang

    Citation: BMC Genomics 2019 20:418

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  28. Content type: Research article

    Mutations in the transcription factor, KLF1, are common within certain populations of the world. Heterozygous missense mutations in KLF1 mostly lead to benign phenotypes, but a heterozygous mutation in a DNA-bind...

    Authors: Melissa D. Ilsley, Stephen Huang, Graham W. Magor, Michael J. Landsberg, Kevin R. Gillinder and Andrew C. Perkins

    Citation: BMC Genomics 2019 20:417

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  29. 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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  30. 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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  31. Content type: Research article

    Immediately after birth, the porcine intestine rapidly develops morphologically, functionally, and immunologically. The jejunum, the second part of the small intestine, is of importance for nutrient uptake and...

    Authors: Dirkjan Schokker, Ina Hulsegge, Henri Woelders and Johanna M. J. Rebel

    Citation: BMC Genomics 2019 20:414

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  32. Content type: Research article

    Parts of Europe and the United States have witnessed dramatic losses in commercially managed honey bees over the past decade to what is considered an unsustainable extent. The large-scale loss of bees has cons...

    Authors: Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth and Adam G. Dolezal

    Citation: BMC Genomics 2019 20:412

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  33. Content type: Research article

    Trichophyton rubrum is the main etiological agent of skin and nail infections worldwide. Because of its keratinolytic activity and anthropophilic nature, infection models based on the addition of protein substrat...

    Authors: Tamires Aparecida Bitencourt, Claudia Macedo, Matheus Eloy Franco, Marina Campos Rocha, Igor Sawasaki Moreli, Bruna Aline Micheloto Cantelli, Pablo Rodrigo Sanches, Rene Oliveira Beleboni, Iran Malavazi, Geraldo Aleixo Passos, Mozart Marins and Ana Lúcia Fachin

    Citation: BMC Genomics 2019 20:411

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  34. Content type: Methodology article

    China has the richest local chicken breeding resources in the world and is the world’s second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chicken...

    Authors: Ranran Liu, Siyuan Xing, Jie Wang, Maiqing Zheng, Huanxian Cui, Richard P. M. A. Crooijmans, Qinghe Li, Guiping Zhao and Jie Wen

    Citation: BMC Genomics 2019 20:410

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  35. Content type: Research article

    Our previous study described the crucial role of Rho-associated coiled-coil containing-kinases (ROCK) in hepatocellular carcinoma (HCC). However, the potential significance of long noncoding RNA downstream of ...

    Authors: He-Ming Zhou, Ji-Gang Zhang, Xue Zhang, Guo-Rong Fan, Gao-Lin Liu and Qin Li

    Citation: BMC Genomics 2019 20:409

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  36. Content type: Research article

    Overfeeding reduces laying performance in broiler breeder hens, which is associated with obesity, hepatic steatosis and systemic inflammation. To unravel the underlying mechanisms governing the effect of feedi...

    Authors: Zehui Wei, Pengcheng Li, Sijia Huang, Purevsuren Lkhagvagarav, Mengqi Zhu, Chuanyu Liang and Cunling Jia

    Citation: BMC Genomics 2019 20:408

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  37. 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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  38. Content type: Research article

    Cryptosporidiosis is a major cause of gastrointestinal diseases in humans and other vertebrates. Previous analyses of invasion-related proteins revealed that Cryptosporidium parvum, Cryptosporidium hominis, and C...

    Authors: Zhixiao Xu, Yaqiong Guo, Dawn M. Roellig, Yaoyu Feng and Lihua Xiao

    Citation: BMC Genomics 2019 20:406

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  39. Content type: Research article

    Fertility in dairy cows depends on ovarian cyclicity and on uterine involution. Ovarian cyclicity and uterine involution are delayed when there is uterine dysbiosis (overgrowth of pathogenic bacteria). Fertili...

    Authors: Stephen G. Moore, Aaron C. Ericsson, Susanta K. Behura, William R. Lamberson, Timothy J. Evans, Matthew S. McCabe, Scott E. Poock and Matthew C. Lucy

    Citation: BMC Genomics 2019 20:405

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  40. Content type: Research article

    Human milk oligosaccharides (OS) play a key role in brain and gut microbiota development of the neonate, but the underlying biosynthetic steps of OS in the mammary gland are still largely unknown. As bovine mi...

    Authors: Nina A. Poulsen, Randall C. Robinson, Daniela Barile, Lotte B. Larsen and Bart Buitenhuis

    Citation: BMC Genomics 2019 20:404

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  41. Content type: Research article

    Cotton (Gossypium spp.) is the most important natural fiber crop worldwide, and cottonseed oil is its most important byproduct. Phospholipid: diacylglycerol acyltransferase (PDAT) is important in TAG biosynthesis...

    Authors: Xinshan Zang, Xiaoli Geng, Lei Ma, Nuohan Wang, Wenfeng Pei, Man Wu, Jinfa Zhang and Jiwen Yu

    Citation: BMC Genomics 2019 20:402

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  42. Content type: Research article

    Through precise implementation of distinct cell type specification programs, differentially regulated in both space and time, complex patterns emerge during organogenesis. Thanks to its easy experimental acces...

    Authors: Christian Feregrino, Fabio Sacher, Oren Parnas and Patrick Tschopp

    Citation: BMC Genomics 2019 20:401

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  43. Content type: Research article

    In the mammary gland transcriptome of lactating dairy cows genes encoding milk proteins are highly abundant, which can impair the detection of lowly expressed transcripts and can bias the outcome in global tra...

    Authors: Johanna Brodhagen, Rosemarie Weikard, Ulrike Thom, Annika Heimes, Juliane Günther, Frieder Hadlich, Holm Zerbe, Wolfgang Petzl, Marie M. Meyerholz, Martina Hoedemaker, Hans-Joachim Schuberth, Susanne Engelmann and Christa Kühn

    Citation: BMC Genomics 2019 20:400

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  44. 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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  45. 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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