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Proteomics

This section covers all aspects of high-throughput proteomics, experimental and analytical approaches to proteome analysis, mass spectrometry, and also metabolomics.

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  1. Low-temperature severely affects the growth and development of chrysanthemum which is one kind of ornamental plant well-known and widely used in the world. Lysine crotonylation is a recently identified post-tr...

    Authors: Ping Lin, Hui-ru Bai, Ling He, Qiu-xiang Huang, Qin-han Zeng, Yuan-zhi Pan, Bei-bei Jiang, Fan Zhang, Lei Zhang and Qing-Lin Liu

    Citation: BMC Genomics 2021 22:51

    Content type: Research article

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  3. Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is ...

    Authors: Johannes Balkenhol, Kristin V. Kaltdorf, Elmina Mammadova-Bach, Attila Braun, Bernhard Nieswandt, Marcus Dittrich and Thomas Dandekar

    Citation: BMC Genomics 2020 21:897

    Content type: Research article

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  4. Ophiocordyceps sinensis is an important traditional Chinese medicine for its comprehensive active ingredients, such as cordycepin, cordycepic acid, and Cordyceps polysaccharide. O. sinensis zjut, a special strain...

    Authors: Bo Zhang, Bo Li, Xiao-Hui Men, Zhe-Wen Xu, Hui Wu, Xiang-Tian Qin, Feng Xu, Yi Teng, Shui-Jin Yuan, Li-Qun Jin, Zhi-Qiang Liu and Yu-Guo Zheng

    Citation: BMC Genomics 2020 21:886

    Content type: Research article

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  5. Late blight disease (LBD) caused by the pathogen Phytophthora infestans (PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emergi...

    Authors: Chunfang Xiao, Mengling Huang, Jianhua Gao, Zhen Wang, Denghong Zhang, Yuanxue Zhang, Lei Yan, Xiao Yu, Bo Li and Yanfen Shen

    Citation: BMC Genomics 2020 21:880

    Content type: Research article

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  6. Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge,

    Authors: Haiyan Zhao, Jianshe Wang, Yunfang Qu, Renhai Peng, Richard Odongo Magwanga, Fang Liu and Jinling Huang

    Citation: BMC Genomics 2020 21:859

    Content type: Research article

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  7. Information on protein-protein interactions affected by mutations is very useful for understanding the biological effect of mutations and for developing treatments targeting the interactions. In this study, we...

    Authors: Jinchan Qu, Albert Steppi, Dongrui Zhong, Jie Hao, Jian Wang, Pei-Yau Lung, Tingting Zhao, Zhe He and Jinfeng Zhang

    Citation: BMC Genomics 2020 21:773

    Content type: Methodology article

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  8. Abiotic stress, including heat, is one of the major factors that affect alfalfa growth and forage yield. The small RNA, microRNA156 (miR156), regulates multiple traits in alfalfa during abiotic stress. The aim...

    Authors: Muhammad Arshad, Alpa Puri, Aaron J. Simkovich, Justin Renaud, Margaret Y. Gruber, Frédéric Marsolais and Abdelali Hannoufa

    Citation: BMC Genomics 2020 21:758

    Content type: Research article

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  9. Recent advances in single-cell RNA sequencing have allowed researchers to explore transcriptional function at a cellular level. In particular, single-cell RNA sequencing reveals that there exist clusters of ce...

    Authors: Florian Klimm, Enrique M. Toledo, Thomas Monfeuga, Fang Zhang, Charlotte M. Deane and Gesine Reinert

    Citation: BMC Genomics 2020 21:756

    Content type: Research article

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  10. Protein expression patterns underlie physiological processes and phenotypic differences including those occurring during early development. The Pacific oyster (Crassostrea gigas) undergoes a major phenotypic chan...

    Authors: Shelly A. Trigg, Kaitlyn R. Mitchell, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma B. Timmins-Schiffman and Steven B. Roberts

    Citation: BMC Genomics 2020 21:723

    Content type: Research article

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  11. Amylose accumulation in rice grains is controlled by genetic and environmental factors. Amylose content is a determinant factor of rice quality in terms of cooking and eating. Great variations in amylose conte...

    Authors: Hengdong Zhang, Jiana Chen, Shuanglü Shan, Fangbo Cao, Guanghui Chen, Yingbin Zou, Min Huang and Salah F. Abou-Elwafa

    Citation: BMC Genomics 2020 21:714

    Content type: Research article

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  12. The process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrom...

    Authors: Michal Levin, Marion Scheibe and Falk Butter

    Citation: BMC Genomics 2020 21:690

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:790

  13. The Fujian oyster Crassostrea angulata is an economically important species that has typical settlement and metamorphosis stages. The development of the oyster involves complex morphological and physiological cha...

    Authors: Guilan Di, Xiaohuo Xiao, Ming Him Tong, Xinhua Chen, Li Li, Miaoqin Huang, Long Zhou and Caihuan Ke

    Citation: BMC Genomics 2020 21:675

    Content type: Research article

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  14. Antimicrobial resistance is one of our most serious health threats. Antimicrobial peptides (AMPs), effecter molecules of innate immune system, can defend host organisms against microbes and most have shown a l...

    Authors: Haoyi Fu, Zicheng Cao, Mingyuan Li and Shunfang Wang

    Citation: BMC Genomics 2020 21:597

    Content type: Research article

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  15. Prolonged exposure to elevated free fatty acids induces β-cell failure (lipotoxicity) and contributes to the pathogenesis of type 2 diabetes. In vitro exposure of β-cells to the saturated free fatty acid palmi...

    Authors: Maria Lytrivi, Kassem Ghaddar, Miguel Lopes, Victoria Rosengren, Anthony Piron, Xiaoyan Yi, Henrik Johansson, Janne Lehtiö, Mariana Igoillo-Esteve, Daniel A. Cunha, Lorella Marselli, Piero Marchetti, Henrik Ortsäter, Decio L. Eizirik and Miriam Cnop

    Citation: BMC Genomics 2020 21:590

    Content type: Research article

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  16. Queen failure is a persistent problem in beekeeping operations, but in the absence of overt symptoms it is often difficult, if not impossible, to ascertain the root cause. Stressors like heat-shock, cold-shock...

    Authors: Alison McAfee, Joseph Milone, Abigail Chapman, Leonard J. Foster, Jeffery S. Pettis and David R. Tarpy

    Citation: BMC Genomics 2020 21:571

    Content type: Research article

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  19. Fatty liver is a high incidence of perinatal disease in dairy cows caused by negative energy balance, which seriously threatens the postpartum health and milk production. It has been reported that lysine acety...

    Authors: Zhang Le-tian, Hu Cheng-zhang, Zhang Xuan, Qin Zhang, Yan Zhen-gui, Wei Qing-qing, Wang Sheng-xuan, Xu Zhong-jin, Li Ran-ran, Liu Ting-jun, Su Zhong-qu, Wang Zhong-hua and Shi Ke-rong

    Citation: BMC Genomics 2020 21:435

    Content type: Research article

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  20. Cantaloupe is susceptible to cold stress when it is stored at low temperatures, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of low temperatures resistance in c...

    Authors: Wen Song, Fengxian Tang, Wenchao Cai, Qin Zhang, Fake Zhou, Ming Ning, Huan Tian and Chunhui Shan

    Citation: BMC Genomics 2020 21:390

    Content type: Research article

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  21. Lysine succinylation, an important protein posttranslational modification (PTM), is widespread and conservative. The regulatory functions of succinylation in leaf color has been reported. The chimeric leaves of A...

    Authors: Meiqin Mao, Yanbin Xue, Yehua He, Xuzixing Zhou, Fatima Rafique, Hao Hu, Jiawen Liu, Lijun Feng, Wei Yang, Xi Li, Lingxia Sun, Zhuo Huang and Jun Ma

    Citation: BMC Genomics 2020 21:383

    Content type: Research article

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  22. Post-database search is a key procedure in peptide identification with tandem mass spectrometry (MS/MS) strategies for refining peptide-spectrum matches (PSMs) generated by database search engines. Although ma...

    Authors: Xijun Liang, Zhonghang Xia, Ling Jian, Yongxiang Wang, Xinnan Niu and Andrew J. Link

    Citation: BMC Genomics 2020 21:324

    Content type: Methodology Article

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  23. Aquaculture is a fast-growing industry and therefore welfare and environmental impact have become of utmost importance. Preventing stress associated to common aquaculture practices and optimizing the fish stre...

    Authors: Cláudia Raposo de Magalhães, Denise Schrama, Ana Paula Farinha, Dominique Revets, Annette Kuehn, Sébastien Planchon, Pedro Miguel Rodrigues and Marco Cerqueira

    Citation: BMC Genomics 2020 21:309

    Content type: Research article

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  24. Phytopathogens secreted effectors during host colonization to suppress or trigger plant immunity. Identification of new effectors is one of the research focuses in recent years. There is only a limited knowled...

    Authors: Shixue Zhao, Bang An, Yanhua Guo, Xingrong Hou, Hongli Luo, Chaozu He and Qiannan Wang

    Citation: BMC Genomics 2020 21:275

    Content type: Research article

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  25. Exploration of the bioactive components of bovine milk has gained global interest due to their potential applications in human nutrition and health promotion. Despite advances in proteomics profiling, limited ...

    Authors: Shakil A. Bhat, Syed M. Ahmad, Eveline M. Ibeagha-Awemu, Mohammad Mobashir, Mashooq A. Dar, Peerzada T. Mumtaz, Riaz A. Shah, Tanveer A. Dar, Nadeem Shabir, Hina F. Bhat and Nazir A. Ganai

    Citation: BMC Genomics 2020 21:161

    Content type: Research article

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  26. Microbes play important roles in kanef-degumming. This study aims at identifying the key candidate microbes and proteins responsible for the degumming of kenaf bast (Hibiscus cannabinus). Kenaf bast was cut into ...

    Authors: Sheng Wen Duan, Li Feng Cheng, Xiang Yuan Feng, Qi Yang, Zhi Yuan Liu, Ke Zheng and Yuan De Peng

    Citation: BMC Genomics 2020 21:121

    Content type: Research article

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  27. Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Prima...

    Authors: Federico Vita, Beatrice Giuntoli, Edoardo Bertolini, Cosimo Taiti, Elettra Marone, Chiara D’Ambrosio, Emanuela Trovato, Danilo Sciarrone, Mariosimone Zoccali, Raffaella Balestrini, Andrea Scaloni, Luigi Mondello, Stefano Mancuso, Massimo Alessio and Amedeo Alpi

    Citation: BMC Genomics 2020 21:90

    Content type: Research article

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  28. Lactoferrampin (LFampin), Lactoferricin (LFcin), and LFchimera are three well-known antimicrobial peptides derived from Lactoferrin and proposed as alternatives for antibiotics. Although the intracellular acti...

    Authors: Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi and Mohammad Hadi Sekhavati

    Citation: BMC Genomics 2020 21:60

    Content type: Research article

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  29. Candida albicans is an opportunistic pathogenic yeast, which could become pathogenic in various stressful environmental factors including the spaceflight environment. In this study, we aim to explore the phenotyp...

    Authors: Jiaping Wang, Yu Liu, Guangxian Zhao, Jianyi Gao, Junlian Liu, Xiaorui Wu, Chong Xu and Yongzhi Li

    Citation: BMC Genomics 2020 21:57

    Content type: Research article

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  30. Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the ...

    Authors: Jiyong Xie, Jiaqi Li, Yucheng Jie, Deyu Xie, Di Yang, Huazhong Shi and Yingli Zhong

    Citation: BMC Genomics 2020 21:40

    Content type: Research article

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  32. Embryonic mortality is a major concern in the commercial swine industry and primarily occurs early in gestation, but also during mid-gestation (~ days 50–70). Previous reports demonstrated that the embryonic l...

    Authors: Kejun Wang, Kaijie Yang, Qiao Xu, Yufang Liu, Wenting Li, Ying Bai, Jve Wang, Cui Ding, Ximing Liu, Qiguo Tang, Yabiao Luo, Jie Zheng, Keliang Wu and Meiying Fang

    Citation: BMC Genomics 2019 20:991

    Content type: Research article

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  33. Salinity has obvious effects on plant growth and crop productivity. The salinity-responsive mechanisms have been well-studied in differentiated organs (e.g., leaves, roots and stems), but not in unorganized ce...

    Authors: Yongxue Zhang, Yue Zhang, Juanjuan Yu, Heng Zhang, Liyue Wang, Sining Wang, Siyi Guo, Yuchen Miao, Sixue Chen, Ying Li and Shaojun Dai

    Citation: BMC Genomics 2019 20:990

    Content type: Research article

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  34. Understanding the mechanisms by which organisms adapt to unfavourable conditions is a fundamental question in ecology and evolutionary biology. One such mechanism is diapause, a period of dormancy typically fo...

    Authors: Thomas J. Colgan, Sive Finlay, Mark J. F. Brown and James C. Carolan

    Citation: BMC Genomics 2019 20:959

    Content type: Research article

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  35. Fusarium graminearum is a destructive fungal pathogen of wheat, barley and other small grain cereals. During plant infection, the pathogen produces trichothecene mycotoxin deoxynivalenol (DON), which is harmful t...

    Authors: Shanyue Zhou and Chunlan Wu

    Citation: BMC Genomics 2019 20:841

    Content type: Research article

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  36. Tail-anchored membrane proteins (TAMPs) differ from other integral membrane proteins, because they contain a single transmembrane domain at the extreme carboxyl-terminus and are therefore obliged to target to ...

    Authors: Glauber Costa Brito, Wiebke Schormann, Satinder K. Gidda, Robert T. Mullen and David W. Andrews

    Citation: BMC Genomics 2019 20:835

    Content type: Research article

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  37. Small ungulates (sheep and goat) display a seasonal breeding, characterised by two successive periods, sexual activity (SA) and sexual rest (SR). Odours emitted by a sexually active male can reactivate the ovu...

    Authors: Paul Cann, Malika Chabi, Aliénor Delsart, Chrystelle Le Danvic, Jean-Michel Saliou, Manon Chasles, Matthieu Keller and Patricia Nagnan-Le Meillour

    Citation: BMC Genomics 2019 20:794

    Content type: Research article

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  38. Rhizome is the storage underground stem of lotus (Nelumbo nucifera), which is enlarged before winter season and could be used for asexual propagation. In addition, the enlarged rhizome is a nutritional vegetable ...

    Authors: Dingding Cao, Rebecca Njeri Damaris, Yue Zhang, Meihui Liu, Ming Li and Pingfang Yang

    Citation: BMC Genomics 2019 20:766

    Content type: Research article

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  39. The mesocotyl connects the coleoptilar node and the basal part of the seminal root of maize (Zea mays) seedling. The mesocotyl pushes the shoot of the seedling out of the soil during seed germination; thus, its g...

    Authors: Liangjie Niu, Zhaokun Wu, Hui Liu, Xiaolin Wu and Wei Wang

    Citation: BMC Genomics 2019 20:758

    Content type: Research article

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  40. While DNA and RNA methods are routine to disrupt the expression of specific genes, complete understanding of developmental processes requires also protein methods, because: oocytes and early embryos accumulate...

    Authors: Steffen Israel, Ellen Casser, Hannes C.A. Drexler, Georg Fuellen and Michele Boiani

    Citation: BMC Genomics 2019 20:755

    Content type: Research article

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  41. The underlying physiological mechanisms associated with aging are still complex and unclear. As a very important tissue of human body, the circulatory system also plays a very important role in the process of ...

    Authors: Hao Wang, Xiaoqi Zhu, Junyan Shen, En-Feng Zhao, Dajun He, Haitao Shen, Hailiang Liu and Yongxin Zhou

    Citation: BMC Genomics 2019 20:725

    Content type: Research article

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  42. Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft as...

    Authors: Jiorgos Kourelis, Farnusch Kaschani, Friederike M. Grosse-Holz, Felix Homma, Markus Kaiser and Renier A. L. van der Hoorn

    Citation: BMC Genomics 2019 20:722

    Content type: Research article

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  43. Bermudagrass (Cynodon dactylon L.) is an important turfgrass species with two types of stems, shoots and stolons. Despite their importance in determining the morphological variance and plasticity of bermudagrass,...

    Authors: Bing Zhang, Jibiao Fan and Jianxiu Liu

    Citation: BMC Genomics 2019 20:708

    Content type: Research article

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  44. The crop growth compensation effect is a naturally biological phenomenon, and nitrogen (N) is essential for crop growth and development, especially for yield formation. Little is known about the molecular mech...

    Authors: Qiangqiang Xiong, Lei Zhong, Tianhua Shen, Chaohao Cao, Haohua He and Xiaorong Chen

    Citation: BMC Genomics 2019 20:681

    Content type: Research article

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  45. The hard tick Hyalomma dromedarii is one of the most injurious ectoparasites affecting camels and apparently best adapted to deserts. As long-term blood feeders, ticks are threatened by host defense system compou...

    Authors: Chaima Bensaoud, Hajer Aounallah, Juliana Mozer Sciani, Fernanda Faria, Ana Marisa Chudzinski-Tavassi, Ali Bouattour and Youmna M’ghirbi

    Citation: BMC Genomics 2019 20:675

    Content type: Research article

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  46. Adrenocortical adenomas (ACAs) can lead to the autonomous secretion of aldosterone responsible for primary aldosteronism (PA), which is the most common form of secondary arterial hypertension. However, the aut...

    Authors: He Ma, Ranwei Li, Xin Di, Xin Jin, Yan Wang, Bingjie Lai, Cailian Shi, Mingxin Ji, Xinran Zhu and Ke Wang

    Citation: BMC Genomics 2019 20:655

    Content type: Research article

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  47. The detection of protein complexes is of great significance for researching mechanisms underlying complex diseases and developing new drugs. Thus, various computational algorithms have been proposed for protei...

    Authors: Rongquan Wang, Caixia Wang, Liyan Sun and Guixia Liu

    Citation: BMC Genomics 2019 20:637

    Content type: Methodology article

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  48. Cell contain diverse array of proteins with different molecular weight and isoelectric point (pI). The molecular weight and pI of protein play important role in determining the molecular biochemical function. ...

    Authors: Tapan Kumar Mohanta, Abdullatif Khan, Abeer Hashem, Elsayed Fathi Abd_Allah and Ahmed Al-Harrasi

    Citation: BMC Genomics 2019 20:631

    Content type: Research article

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  49. Pre-slaughter stress (PSS) impairs animal welfare and meat quality. Dark, firm and dry (DFD) are terms used to designate poor quality meats induced by PSS. Protein phosphorylation can be a potentially signific...

    Authors: Ariadna Mato, Raquel Rodríguez-Vázquez, María López-Pedrouso, Susana Bravo, Daniel Franco and Carlos Zapata

    Citation: BMC Genomics 2019 20:590

    Content type: Research article

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  50. Maturation of oocytes under in vitro conditions (IVM) results in impaired developmental competence compared to oocytes matured in vivo. As oocytes are closely coupled to their cumulus complex, elucidating aber...

    Authors: Jasmin Walter, Fabian Huwiler, Claudia Fortes, Jonas Grossmann, Bernd Roschitzki, Junmin Hu, Hanspeter Naegeli, Endre Laczko and Ulrich Bleul

    Citation: BMC Genomics 2019 20:588

    Content type: Research article

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