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Proteomics

Section edited by Scott Hemby

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

Page 1 of 4

  1. Content type: Research article

    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

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  2. Content type: Research article

    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

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  3. Content type: Research article

    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

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  4. Content type: Research article

    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

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  5. Content type: Research article

    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

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  6. Content type: Research article

    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

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  7. Content type: Methodology article

    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

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  8. Content type: Research article

    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

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  9. Content type: Research article

    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

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  10. Content type: Research article

    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

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  12. Content type: Research article

    Intercellular adhesion and biofilm production by Staphylococcus aureus makes these bacteria resistant to antimicrobial therapy. Here, Methicillin-resistant Staphylococcus aureus (MRSA) strains were characterized ...

    Authors: Kifaya Azmi, Walaa Qrei and Ziad Abdeen

    Citation: BMC Genomics 2019 20:578

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  13. Content type: Research article

    To illuminate the mechanisms underlying the high-altitude tolerance of Tibetan pig spermatozoa, proteomes of spermatozoa from Tibetan pigs raised in high and low altitudes were compared using a tandem mass tag...

    Authors: Yanling Zhao, Xiaoli Lu, Zhipeng Cheng, Mengfang Tian, Yangzong Qiangba, Qiang Fu and Zili Ren

    Citation: BMC Genomics 2019 20:569

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    The Correction to this article has been published in BMC Genomics 2019 20:626

  14. Content type: Research article

    T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large ...

    Authors: Xin Wen, Yadong Hu, Xinyu Zhang, Xiaozhen Wei, Tao Wang and Shaowu Yin

    Citation: BMC Genomics 2019 20:563

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  15. Content type: Research article

    Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information re...

    Authors: Elisa B. Carvalho, Mateus P. Gionbelli, Rafael T. S. Rodrigues, Sarah F. M. Bonilha, Charles J. Newbold, Simone E. F. Guimarães, Walmir Silva, Lucas L. Verardo, Fabyano F. Silva, Edenio Detmann and Marcio S. Duarte

    Citation: BMC Genomics 2019 20:501

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  16. Content type: Research article

    The pearl oyster Pinctada fucata martensii (Pfu.), widely cultured in the South China Sea, is a precious source of sea pearls and calcifying materials. A yellow shell variety of Pfu. was obtained after years of a...

    Authors: Meng Xu, Jing Huang, Yu Shi, Hua Zhang and Maoxian He

    Citation: BMC Genomics 2019 20:469

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  17. 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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  18. Content type: Research article

    Salinization seriously threatens land use efficiency and crop yields across the world. Understanding the mechanisms plants use to protect against salt stress will help breeders develop salt-tolerant vegetable ...

    Authors: Yihua Zhan, Qingfei Wu, Yue Chen, Mengling Tang, Chendong Sun, Junwei Sun and Chenliang Yu

    Citation: BMC Genomics 2019 20:381

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  20. Content type: Research article

    Lysine crotonylation, as a novel evolutionarily conserved type of post-translational modifications, is ubiquitous and essential in cell biology. However, its functions in tea plants are largely unknown, and th...

    Authors: Jianhao Sun, Chen Qiu, Wenjun Qian, Yu Wang, Litao Sun, Yusheng Li and Zhaotang Ding

    Citation: BMC Genomics 2019 20:340

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  21. Content type: Methodology article

    Two-dimensional electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are widely used in plant proteomics research. However, these two techniques cannot be simultaneously satisfi...

    Authors: Xiang Jin, Liping Zhu, Chengcheng Tao, Quanliang Xie, Xinyang Xu, Lili Chang, Yanhua Tan, Guohua Ding, Hongbin Li and Xuchu Wang

    Citation: BMC Genomics 2019 20:285

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  22. Content type: Research article

    Cotton leaf curl disease (CLCuD), caused by begomoviruses in association with satellite molecules, is a major threat to cotton production causing enormous losses to cotton crop in most of the cotton growing co...

    Authors: Razia Qadir, Zainul A. Khan, Dilip Monga and Jawaid A. Khan

    Citation: BMC Genomics 2019 20:274

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  23. Content type: Research article

    Triple negative breast cancer (TNBC) is a malignancy with very poor prognosis, due to its aggressive clinical characteristics and lack of response to receptor-targeted drug therapy. In TNBC, immune-related pat...

    Authors: Fernando J. Velloso, Alexandre R. Campos, Mari C. Sogayar and Ricardo G. Correa

    Citation: BMC Genomics 2019 20:152

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  24. Content type: Research article

    Colonization of deep-sea hydrothermal vents by most invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers in these ecosystems. A...

    Authors: Camille Détrée, Iman Haddad, Emmanuelle Demey-Thomas, Joëlle Vinh, François H. Lallier, Arnaud Tanguy and Jean Mary

    Citation: BMC Genomics 2019 20:109

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  25. Content type: Research article

    Bakanae disease, caused by the fungus Fusarium fujikuroi, occurs widely throughout Asia and Europe and sporadically in other rice production areas. Recent changes in climate and cropping patterns have aggravated ...

    Authors: Zhijuan Ji, Yuxiang Zeng, Yan Liang, Qian Qian and Changdeng Yang

    Citation: BMC Genomics 2019 20:91

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  26. Content type: Research article

    Waterlogging is one of the main abiotic stresses that limit wheat production. Quantitative proteomics analysis has been applied in the study of crop abiotic stress as an effective way in recent years (e.g. sal...

    Authors: Rui Pan, Dongli He, Le Xu, Meixue Zhou, Chengdao Li, Chu Wu, Yanhao Xu and Wenying Zhang

    Citation: BMC Genomics 2019 20:60

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  27. Content type: Software

    Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is oft...

    Authors: Laetitia Guillot, Ludovic Delage, Alain Viari, Yves Vandenbrouck, Emmanuelle Com, Andrés Ritter, Régis Lavigne, Dominique Marie, Pierre Peterlongo, Philippe Potin and Charles Pineau

    Citation: BMC Genomics 2019 20:56

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  28. Content type: Research article

    Streptococcus agalactiae (GBS) is a major pathogen of Nile tilapia, a global commodity of the aquaculture sector. The aims of this study were to evaluate protein expression in the main genotypes of GBS isolated f...

    Authors: Guilherme Campos Tavares, Felipe Luiz Pereira, Gustavo Morais Barony, Cristiana Perdigão Rezende, Wanderson Marques da Silva, Gustavo Henrique Martins Ferreira de Souza, Thiago Verano-Braga, Vasco Ariston de Carvalho Azevedo, Carlos Augusto Gomes Leal and Henrique César Pereira Figueiredo

    Citation: BMC Genomics 2019 20:11

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  30. Content type: Research article

    Thiazolidinone derivatives show inhibitory activity (IC50) against the Toxoplasma gondii parasite, as well as high selectivity with high therapeutic index. To disclose the target proteins of the thiazolidinone co...

    Authors: Diego Molina, Rodrigo Cossio-Pérez, Cristian Rocha-Roa, Lina Pedraza, Edwar Cortes, Alejandro Hernández and Jorge E. Gómez-Marín

    Citation: BMC Genomics 2018 19:856

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  31. Content type: Research article

    Pyropia yezoensis is an important marine crop which, due to its high protein content, is widely used as a seafood in China. Unfortunately, red rot disease, caused by Pythium porphyrae, seriously damages P. yezoen...

    Authors: Sohrab Khan, Yunxiang Mao, Dong Gao, Sadaf Riaz, Zeeshan Niaz, Lei Tang, Sohaib Khan and Dongmei Wang

    Citation: BMC Genomics 2018 19:842

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  33. Content type: Research article

    Wheat (Triticum aestivum L.) is one of the world’s most important grain crops. The amyloplast, a specialized organelle, is the major site for starch synthesis and storage in wheat grain. Understanding the metabol...

    Authors: Dongyun Ma, Xin Huang, Junfeng Hou, Ying Ma, Qiaoxia Han, Gege Hou, Chenyang Wang and Tiancai Guo

    Citation: BMC Genomics 2018 19:768

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  34. Content type: Research article

    Databases of literature-curated protein-protein interactions (PPIs) are often used to interpret high-throughput interactome mapping studies and estimate error rates. These databases combine interactions across...

    Authors: R. Greg Stacey, Michael A. Skinnider, Jenny H. L. Chik and Leonard J. Foster

    Citation: BMC Genomics 2018 19:758

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  35. Content type: Research article

    High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection. This was done using a rainbow trout (Oncorhynchus mykiss) model following infection with Ae...

    Authors: Dwight R Causey, Moritz A N Pohl, David A Stead, Samuel A M Martin, Christopher J Secombes and Daniel J Macqueen

    Citation: BMC Genomics 2018 19:719

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  37. Content type: Research article

    Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental stu...

    Authors: Suyu Mei, Erik K. Flemington and Kun Zhang

    Citation: BMC Genomics 2018 19:505

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  38. Content type: Methodology article

    Apoptosis is associated with some human diseases, including cancer, autoimmune disease, neurodegenerative disease and ischemic damage, etc. Apoptosis proteins subcellular localization information is very impor...

    Authors: Bin Yu, Shan Li, Wenying Qiu, Minghui Wang, Junwei Du, Yusen Zhang and Xing Chen

    Citation: BMC Genomics 2018 19:478

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  39. Content type: Research article

    Eukaryotic cells contain a huge variety of internally specialized subcellular compartments. Stoichiogenomics aims to reveal patterns of elements usage in biological macromolecules. However, the stoichiogenomic...

    Authors: Yu-Juan Zhang, Chengxu Zhu, Yiran Ding, Zheng-Wen Yan, Gong-Hua Li, Yang Lan, Jian-Fan Wen and Bin Chen

    Citation: BMC Genomics 2018 19:469

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  40. Content type: Research article

    Genome wide association studies (GWAS) have helped identify large numbers of genetic loci that significantly associate with increased risk of developing diseases. However, translating genetic knowledge into un...

    Authors: Raffaele Ferrari, Demis A. Kia, James E. Tomkins, John Hardy, Nicholas W. Wood, Ruth C. Lovering, Patrick A. Lewis and Claudia Manzoni

    Citation: BMC Genomics 2018 19:452

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  41. Content type: Research article

    Coexistence and transition of diverse sex determination strategies have been revealed in some ectothermic species, but the variation between males caused by different sex determination strategies and the under...

    Authors: Yao-Jun Zhu, Xi-Yin Li, Jun Zhang, Zhi Li, Miao Ding, Xiao-Juan Zhang, Li Zhou and Jian-Fang Gui

    Citation: BMC Genomics 2018 19:437

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  42. Content type: Research article

    Rapid evolution of phosphorylation sites could provide raw materials of natural selection to fit the environment by rewiring the regulation of signal pathways. However, a large part of phosphorylation sites wa...

    Authors: Benpeng Miao, Qingyu Xiao, Weiran Chen, Yixue Li and Zhen Wang

    Citation: BMC Genomics 2018 19:431

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  43. Content type: Research article

    Azadirachtin, one of the most promising botanical insecticides, has been widely used for pest control. Azadirachtin induces apoptosis in insect cell lines, including Sf9, SL-1 and BTI-Tn-5B1–4. Mitochondrial a...

    Authors: Benshui Shu, Jianwen Jia, Jingjing Zhang, Veeran Sethuraman, Xin Yi and Guohua Zhong

    Citation: BMC Genomics 2018 19:413

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  44. Content type: Research article

    In avian species, liver is the main site of de novo lipogenesis, and hepatic lipid metabolism relates closely to adipose fat deposition. Using our fat and lean chicken lines of striking differences in abdomina...

    Authors: Wei Na, Yuan-Yuan Wu, Peng-Fei Gong, Chun-Yan Wu, Bo-Han Cheng, Yu-Xiang Wang, Ning Wang, Zhi-Qiang Du and Hui Li

    Citation: BMC Genomics 2018 19:384

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  45. Content type: Research article

    Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can kee...

    Authors: Xiujun Sun, Zhihong Liu, Biao Wu, Liqing Zhou, Qi Wang, Wei Wu and Aiguo Yang

    Citation: BMC Genomics 2018 19:377

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  47. Content type: Research article

    Midgut invasion, a major bottleneck for malaria parasites transmission is considered as a potential target for vector-parasite interaction studies. New intervention strategies are required to explore the midgu...

    Authors: Sonam Vijay, Ritu Rawal, Kavita Kadian, Jagbir Singh, Tridibesh Adak and Arun Sharma

    Citation: BMC Genomics 2018 19:337

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  48. Content type: Research article

    Spike architecture mutants in tetraploid wheat (Triticum turgidum L., 2n = 28, AABB) have a distinct morphology, with parts of the rachis node producing lateral meristems that develop into ramified spikelete (RSs...

    Authors: Shulin Chen, Juan Chen, Fu Hou, Yigao Feng and Ruiqi Zhang

    Citation: BMC Genomics 2018 19:228

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  49. Content type: Research article

    Protein lysine malonylation, a newly discovered post-translational modification (PTM), plays an important role in diverse metabolic processes in both eukaryotes and prokaryotes. Common wheat is a major global ...

    Authors: Jiabin Liu, Guangyuan Wang, Qi Lin, Wenxing Liang, Zhiqiang Gao, Ping Mu, Guiquan Li and Limin Song

    Citation: BMC Genomics 2018 19:209

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  50. Content type: Research article

    Atlantic salmon production in Tasmania (Southern Australia) occurs near the upper limits of the species thermal tolerance. Summer water temperatures can average over 19 °C over several weeks and have negative eff...

    Authors: Waldo G. Nuez-Ortín, Chris G. Carter, Peter D. Nichols, Ira R. Cooke and Richard Wilson

    Citation: BMC Genomics 2018 19:133

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