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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 3

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. Content type: Research article

    Lamprosema indicate is a major leaf feeding insect pest to soybean, which has caused serious yield losses in central and southern China. To explore the defense mechanisms of soybean resistance to Lamprosema indic...

    Authors: Weiying Zeng, Zudong Sun, Zhaoyan Cai, Huaizhu Chen, Zhenguang Lai, Shouzhen Yang and Xiangmin Tang

    Citation: BMC Genomics 2017 18:444

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  37. Content type: Research article

    This study characterises the molecular processes altered by both elevated CO2 and increasing temperature in oysters. Differences in resilience of marine organisms against the environmental stressors associated wi...

    Authors: Priscila Goncalves, Emma L. Thompson and David A. Raftos

    Citation: BMC Genomics 2017 18:431

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  38. Content type: Research article

    Brucella spp. are Gram-negative, facultative intracellular pathogens that cause brucellosis in both humans and animals. The B. abortus vaccine strain 104 M is the only vaccine availabl...

    Authors: Xiaodong Zai, Qiaoling Yang, Kun Liu, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Ying Yin, Dayong Dong, Ling Fu, Shanhu Li, Junjie Xu and Wei Chen

    Citation: BMC Genomics 2017 18:402

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  39. Content type: Research article

    The function of the prion protein, involved in the so-called prion diseases, remains a subject of intense debate and the possibility that it works as a pleiotropic protein through the interaction with multiple...

    Authors: J. A. Macedo, D. Schrama, I. Duarte, E. Tavares, J. Renaut, M. E. Futschik, P. M. Rodrigues and E. P. Melo

    Citation: BMC Genomics 2017 18:319

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  40. Content type: Research Article

    Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological functi...

    Authors: Colin W. Brown, Viswanadham Sridhara, Daniel R. Boutz, Maria D. Person, Edward M. Marcotte, Jeffrey E. Barrick and Claus O. Wilke

    Citation: BMC Genomics 2017 18:301

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  41. Content type: Research article

    Intra-uterine growth restriction (IUGR) and fetal overgrowth increase risks to postnatal health. Maternal nutrition is the major intrauterine environmental factor that alters fetal weight. However, the mechani...

    Authors: Long Che, ZhenGuo Yang, MengMeng Xu, ShengYu Xu, LianQiang Che, Yan Lin, ZhengFeng Fang, Bin Feng, Jian Li, DaiWen Chen and De Wu

    Citation: BMC Genomics 2017 18:213

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  42. Content type: Research article

    Intermuscular bones (IBs) and ribs both are a part of skeletal system in teleosts, but with different developing process. The chemical composition of fish IBs and ribs as well as the underlying mechanism about...

    Authors: Chun-Hong Nie, Shi-Ming Wan, Tea Tomljanovic, Tomislav Treer, Chung-Der Hsiao, Wei-Min Wang and Ze-Xia Gao

    Citation: BMC Genomics 2017 18:147

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  43. Content type: Research Article

    Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable e...

    Authors: Kevin Maringer, Amjad Yousuf, Kate J. Heesom, Jun Fan, David Lee, Ana Fernandez-Sesma, Conrad Bessant, David A. Matthews and Andrew D. Davidson

    Citation: BMC Genomics 2017 18:101

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  44. Content type: Research Article

    Barley seed proteins are of prime importance to the brewing industry, human and animal nutrition and in plant breeding for cultivar identification. To obtain comprehensive proteomic data from seeds, total prot...

    Authors: Ramamurthy Mahalingam

    Citation: BMC Genomics 2017 18:44

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  45. Content type: Research article

    Lysine acetylation in proteins is a ubiquitous and conserved post-translational modification, playing a critical regulatory role in almost every aspect of living cells. Although known for many years, its funct...

    Authors: Shanyue Zhou, Qianqian Yang, Changfa Yin, Lin Liu and Wenxing Liang

    Citation: BMC Genomics 2016 17:1019

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