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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

    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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. Content type: Research article

    The growth of Inner Mongolian Cashmere goat skin hair follicle exhibits a periodic growth pattern. The hair growth cycle is distinguished as telogen, anagen, and catagen stages. The role of vimentin in the gro...

    Authors: Nai Rile, Zhihong Liu, Lixia Gao, Jingkai Qi, Meng Zhao, Yuchun Xie, Rui Su, Yanjun Zhang, Ruijun Wang, Jie Li, Hongmei Xiao and Jinquan Li

    Citation: BMC Genomics 2018 19:38

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  26. Content type: Research article

    Chicken embryos are widely used as a model for studies of obesity; however, no detailed information is available about the dynamic changes of proteins during the regulation of adipose biology and metabolism. T...

    Authors: Mengling Peng, Shengnan Li, Qianian He, Jinlong Zhao, Longlong Li and Haitian Ma

    Citation: BMC Genomics 2018 19:29

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  27. Content type: Research article

    Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers a...

    Authors: Héctor Cordero, Monica F. Brinchmann, Alberto Cuesta and María A. Esteban

    Citation: BMC Genomics 2017 18:939

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  28. Content type: Research article

    Lactation is extremely important for dairy cows; however, the understanding of the underlying metabolic mechanisms is very limited. This study was conducted to investigate the inherent metabolic patterns durin...

    Authors: Hui-Zeng Sun, Kai Shi, Xue-Hui Wu, Ming-Yuan Xue, Zi-Hai Wei, Jian-Xin Liu and Hong-Yun Liu

    Citation: BMC Genomics 2017 18:936

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  29. Content type: Research article

    Parthenocarpy is an excellent agronomic trait that enables crops to set fruit in the absence of pollination and fertilization, and therefore to produce seedless fruit. Although parthenocarpy is widely recogniz...

    Authors: Ji Li, Jian Xu, Qin-Wei Guo, Zhe Wu, Ting Zhang, Kai-Jing Zhang, Chun-yan Cheng, Pin-yu Zhu, Qun-Feng Lou and Jin-Feng Chen

    Citation: BMC Genomics 2017 18:896

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  30. Content type: Research article

    Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics resu...

    Authors: J. Michael Proffitt, Jeremy Glenn, Anthony J. Cesnik, Avinash Jadhav, Michael R. Shortreed, Lloyd M. Smith, Kylie Kavanagh, Laura A. Cox and Michael Olivier

    Citation: BMC Genomics 2017 18:877

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  31. Content type: Research article

    Skeletal muscle development is closely linked to meat production and its quality. This study is the first to quantify the proteomes and metabolomes of breast muscle in two distinct chicken breeds at embryonic ...

    Authors: Ranran Liu, Hongyang Wang, Jie Liu, Jie Wang, Maiqing Zheng, Xiaodong Tan, Siyuan Xing, Huanxian Cui, Qinghe Li, Guiping Zhao and Jie Wen

    Citation: BMC Genomics 2017 18:816

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  32. Content type: Research article

    Haliotis diversicolor is commercially important species. The trochophore and veliger are distinct larval stages in gastropod development. Their development involves complex morphologic...

    Authors: Guilan Di, Xianghui Kong, Xiulian Miao, Yifang Zhang, Miaoqin Huang, Yuting Gu, Weiwei You, Jianxin Zhang and Caihuan Ke

    Citation: BMC Genomics 2017 18:809

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  33. Content type: Database

    Nanobodies are single-domain antibodies that contain the unique structural and functional properties of naturally-occurring heavy chain in camelidae. As a novel class of antibody, they show many advantages com...

    Authors: Jing Zuo, Jian Li, Rongxin Zhang, Longsheng Xu, Hanhan Chen, Xiaohuan Jia, Zhipeng Su, Linhong Zhao, Xing Huang and Wei Xie

    Citation: BMC Genomics 2017 18:797

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  34. Content type: Research article

    Salamanders regenerate their limbs after amputation. However, the molecular mechanism of this unique regeneration remains unclear. In this study, isobaric tags for relative and absolute quantification (iTRAQ) ...

    Authors: Jie Tang, Yuan Yu, Hanxue Zheng, Lu Yin, Mei Sun, Wenjun Wang, Jihong Cui, Wenguang Liu, Xin Xie and Fulin Chen

    Citation: BMC Genomics 2017 18:750

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  35. Content type: Research article

    Polyploidy is an important phenomenon in plants because of its roles in agricultural and forestry production as well as in plant tolerance to environmental stresses. Tetraploid black locust (Robinia pseudoacacia ...

    Authors: Qiuxiang Luo, Mu Peng, Xiuli Zhang, Pei Lei, Ximei Ji, Wahsoon Chow, Fanjuan Meng and Guanyu Sun

    Citation: BMC Genomics 2017 18:648

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  36. Content type: Research article

    Human hepatitis B virus (HBV) infection is an important public health issue in the Asia-Pacific region and is associated with chronic hepatitis, liver fibrosis, cirrhosis and even liver cancer. However, the un...

    Authors: Fangming Kan, Lei Ye, Tao Yan, Jiaqi Cao, Jianhua Zheng and Wuping Li

    Citation: BMC Genomics 2017 18:641

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  37. Content type: Research article

    Aedes albopictus is a vector of arboviruses that cause severe diseases in humans such as Chikungunya, Dengue and Zika fevers. The vector competence of Ae. albopictus varies depending o...

    Authors: Yoann Saucereau, Claire Valiente Moro, Cindy Dieryckx, Jean-William Dupuy, Florence-Hélène Tran, Vincent Girard, Patrick Potier and Patrick Mavingui

    Citation: BMC Genomics 2017 18:635

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  38. Content type: Research article

    Nelson Bay orthoreovirus (NBV) is a fusogenic bat borne virus with an unknown zoonotic potential. Previous studies have shown that NBV can infect and replicate in a wide variety of cell types derived from thei...

    Authors: Lawrence Mok, James W. Wynne, Mary Tachedjian, Brian Shiell, Kris Ford, David A. Matthews, Antony Bacic and Wojtek P. Michalski

    Citation: BMC Genomics 2017 18:615

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  39. Content type: Research article

    Spiders are predaceous arthropods that are capable of subduing and consuming relatively large prey items compared to their own body size. For this purpose, spiders have evolved potent venoms to immobilise prey...

    Authors: André Walter, Jesper Bechsgaard, Carsten Scavenius, Thomas S. Dyrlund, Kristian W. Sanggaard, Jan J. Enghild and Trine Bilde

    Citation: BMC Genomics 2017 18:600

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  40. Content type: Research article

    Lysine succinylation is a ubiquitous and important protein post-translational modification in various eukaryotic and prokaryotic cells. However, its functions in Dendrobium officinale, an important traditional Ch...

    Authors: Shangguo Feng, Kaili Jiao, Hong Guo, Mengyi Jiang, Juan Hao, Huizhong Wang and Chenjia Shen

    Citation: BMC Genomics 2017 18:598

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  41. Content type: Research article

    Dermatophytes, the most common cause of fungal infections, affect millions of individuals worldwide. They pose a major threat to public health because of the severity and longevity of infections caused by derm...

    Authors: Xingye Xu, Tao Liu, Jian Yang, Lihong Chen, Bo Liu, Candong Wei, Lingling Wang and Qi Jin

    Citation: BMC Genomics 2017 18:577

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  42. Content type: Research article

    The monovalent anions formate, nitrite and hydrosulphide are main metabolites of bacterial respiration during anaerobic mixed-acid fermentation. When accumulated in the cytoplasm, these anions become cytotoxic...

    Authors: Mishtu Mukherjee, Manu Vajpai and Ramasubbu Sankararamakrishnan

    Citation: BMC Genomics 2017 18:560

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  43. Content type: Research article

    Corynebacterium pseudotuberculosis is a pathogen classified into two biovars: C. pseudotuberculosis biovar ovis, the etiologic agent of caseous lymphadenitis and C. pseudotuberculosis ...

    Authors: Wanderson M. Silva, Edson L. Folador, Siomar C. Soares, Gustavo H. M. F. Souza, Agenor V. Santos, Cassiana S. Sousa, Henrique Figueiredo, Anderson Miyoshi, Yves Le Loir, Artur Silva and Vasco Azevedo

    Citation: BMC Genomics 2017 18:451

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  44. Content type: Methodology article

    Recombinant peptide chips could constitute a versatile complementation to state-of-the-art in situ (chemical on-chip) synthesis, particle-based printing, or pre-manufactured peptide spotting. Bottlenecks still im...

    Authors: Harald Hundsberger, Kamil Önder, Peter Schuller-Götzburg, Dezso P. Virok, Julia Herzog and Raphaela Rid

    Citation: BMC Genomics 2017 18:450

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