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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. The filamentous actinomycete Microbispora ATCC-PTA-5024 produces the lantibiotic NAI-107, which is an antibiotic peptide effective against multidrug-resistant Gram-positive bacteria. In actinomycetes, antibiotic ...

    Authors: Giuseppe Gallo, Giovanni Renzone, Emilia Palazzotto, Paolo Monciardini, Simona Arena, Teresa Faddetta, Anna Giardina, Rosa Alduina, Tilmann Weber, Fabio Sangiorgi, Alessandro Russo, Giovanni Spinelli, Margherita Sosio, Andrea Scaloni and Anna Maria Puglia

    Citation: BMC Genomics 2016 17:42

    Content type: Research article

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  2. Francisella tularensis is a select bio-threat agent and one of the most virulent intracellular pathogens known, requiring just a few organisms to establish an infection. Although sever...

    Authors: Anders Wallqvist, Vesna Memišević, Nela Zavaljevski, Rembert Pieper, Seesandra V. Rajagopala, Keehwan Kwon, Chenggang Yu, Timothy A. Hoover and Jaques Reifman

    Citation: BMC Genomics 2015 16:1106

    Content type: Research article

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  3. Comparison between multiple protein datasets requires the choice of an appropriate reference system and a number of variables to describe their differences. Here we introduce an innovative approach to discrimi...

    Authors: Petr Klus, Riccardo Delli Ponti, Carmen Maria Livi and Gian Gaetano Tartaglia

    Citation: BMC Genomics 2015 16:1071

    Content type: Software

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  4. The barnacle Balanus amphitrite is widely distributed in marine shallow and tidal waters, and has significant economic and ecological importance. Nauplii, the first larval stage of most crustaceans, are extremely...

    Authors: Kondethimmanahalli H. Chandramouli, Sarah Al-Aqeel, Taewoo Ryu, Huoming Zhang, Loqmane Seridi, Yanal Ghosheh, Pei-Yuan Qian and Timothy Ravasi

    Citation: BMC Genomics 2015 16:1063

    Content type: Research article

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  5. To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical ...

    Authors: Núria Casas-Vila, Marion Scheibe, Anja Freiwald, Dennis Kappei and Falk Butter

    Citation: BMC Genomics 2015 16:965

    Content type: Research article

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  6. Limited information is available on aluminum (Al)-toxicity-responsive proteins in woody plant roots. Seedlings of ‘Xuegan’ (Citrus sinensis) and ‘Sour pummelo’ (Citrus grandis) were treated for 18 weeks with nutr...

    Authors: Huan-Xin Jiang, Lin-Tong Yang, Yi-Ping Qi, Yi-Bin Lu, Zeng-Rong Huang and Li-Song Chen

    Citation: BMC Genomics 2015 16:949

    Content type: Research article

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  7. Gene duplication followed by adaptive selection is a well-accepted process leading to toxin diversification in venoms. However, emergent genomic, transcriptomic and proteomic evidence now challenges this role ...

    Authors: Ranko Gacesa, Ray Chung, Simon R. Dunn, Andrew J. Weston, Adrian Jaimes-Becerra, Antonio C. Marques, André C. Morandini, Daslav Hranueli, Antonio Starcevic, Malcolm Ward and Paul F. Long

    Citation: BMC Genomics 2015 16:774

    Content type: Research article

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  8. Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understa...

    Authors: Rima Chaudhuri, Arash Sadrieh, Nolan J. Hoffman, Benjamin L. Parker, Sean J. Humphrey, Jacqueline Stöckli, Adam P. Hill, David E. James and Jean Yee Hwa Yang

    Citation: BMC Genomics 2015 16:617

    Content type: Software

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  9. A systems toxicology investigation comparing and integrating transcriptomic and proteomic results was conducted to develop holistic effects characterizations for the wildlife bird model, Northern bobwhite (Colinu...

    Authors: Kurt A. Gust, Bindu Nanduri, Arun Rawat, Mitchell S. Wilbanks, Choo Yaw Ang, David R. Johnson, Ken Pendarvis, Xianfeng Chen, Michael J. Quinn Jr., Mark S. Johnson, Shane C. Burgess and Edward J. Perkins

    Citation: BMC Genomics 2015 16:587

    Content type: Research article

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  10. Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most abundant resource of archived human specimens in pathology. Such tissue specimens are emerging as a highly valuable resource for translationa...

    Authors: J. Weißer, Z. W. Lai, P. Bronsert, M. Kuehs, V. Drendel, S. Timme, S. Kuesters, C. A. Jilg, U. F. Wellner, S. Lassmann, M. Werner, M. L. Biniossek and O. Schilling

    Citation: BMC Genomics 2015 16:559

    Content type: Methodology article

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  11. Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains...

    Authors: Li-Ling Lin, Chia-Lang Hsu, Chia-Wei Hu, Shiao-Yun Ko, Hsu-Liang Hsieh, Hsuan-Cheng Huang and Hsueh-Fen Juan

    Citation: BMC Genomics 2015 16:533

    Content type: Research article

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  12. Metabolic syndrome is a multi-component disorder associated to a high risk of cardiovascular disease. Its etiology is the result of a complex interaction between genetic and environmental factors, including di...

    Authors: Oriol Alberto Rangel-Zúñiga, Antonio Camargo, Carmen Marin, Patricia Peña-Orihuela, Pablo Pérez-Martínez, Javier Delgado-Lista, Lorena González-Guardia, Elena M. Yubero-Serrano, Francisco J. Tinahones, María M. Malagón, Francisco Pérez-Jiménez, Helen M. Roche and José López-Miranda

    Citation: BMC Genomics 2015 16:509

    Content type: Research article

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  13. Muscle ageing contributes to both loss of functional autonomy and increased morbidity. Muscle atrophy accelerates after 50 years of age, but the mechanisms involved are complex and likely result from the alter...

    Authors: Marine Gueugneau, Cécile Coudy-Gandilhon, Ophélie Gourbeyre, Christophe Chambon, Lydie Combaret, Cécile Polge, Daniel Taillandier, Didier Attaix, Bertrand Friguet, Andrea B Maier, Gillian Butler-Browne and Daniel Béchet

    Citation: BMC Genomics 2014 15:1165

    Content type: Research article

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  14. Small secreted proteins (SSPs) are employed by plant pathogenic fungi as essential strategic tools for their successful colonization. SSPs are often species-specific and so far only a few widely phylogenetical...

    Authors: Qiang Cheng, Haoran Wang, Bin Xu, Sheng Zhu, Lanxi Hu and Minren Huang

    Citation: BMC Genomics 2014 15:1151

    Content type: Research article

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  15. Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isot...

    Authors: Qiang Kou, Si Wu and Xiaowen Liu

    Citation: BMC Genomics 2014 15:1140

    Content type: Research article

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  16. Proteins are composed of one or more amino acid chains and exhibit several structure levels. IDPs (intrinsically disordered proteins) represent a class of proteins that do not fold into any particular conforma...

    Authors: Patrícia de Cássia Ruy, Raul Torrieri, Juliano Simões Toledo, Viviane de Souza Alves, Angela Kaysel Cruz and Jeronimo Conceição Ruiz

    Citation: BMC Genomics 2014 15:1100

    Content type: Research article

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  17. Corynebacterium pseudotuberculosis biovar ovis is a facultative intracellular pathogen, and the etiological agent of caseous lymphadenitis in small ruminants. During the infection process, the bacterium is subjec...

    Authors: Wanderson M Silva, Rodrigo D Carvalho, Siomar C Soares, Isabela FS Bastos, Edson L Folador, Gustavo HMF Souza, Yves Le Loir, Anderson Miyoshi, Artur Silva and Vasco Azevedo

    Citation: BMC Genomics 2014 15:1065

    Content type: Research article

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  18. In the filamentous cyanobacterium Nostoc punctiforme ATCC 29133, removal of combined nitrogen induces the differentiation of heterocysts, a cell-type specialized in N2 fixation. The differentiation involves genom...

    Authors: Gustaf Sandh, Margareta Ramström and Karin Stensjö

    Citation: BMC Genomics 2014 15:1064

    Content type: Research article

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  19. The in vivo gene response associated with hyperthermia is poorly understood. Here, we perform a global, multiorgan characterization of the gene response to heat stress using an in vivo conscious rat model.

    Authors: Jonathan D Stallings, Danielle L Ippolito, Vineet Rakesh, Christine E Baer, William E Dennis, Bryan G Helwig, David A Jackson, Lisa R Leon, John A Lewis and Jaques Reifman

    Citation: BMC Genomics 2014 15:1058

    Content type: Research article

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  20. Wheat (Triticum aestivum L.) is an economically important grain crop. Two-dimensional gel-based approaches are limited by the low identification rate of proteins and lack of accurate protein quantitation. The rec...

    Authors: Chaoying Ma, Jianwen Zhou, Guanxing Chen, Yanwei Bian, Dongwen Lv, Xiaohui Li, Zhimin Wang and Yueming Yan

    Citation: BMC Genomics 2014 15:1029

    Content type: Research article

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  21. Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH...

    Authors: Emma Timmins-Schiffman, William D Coffey, Wilber Hua, Brook L Nunn, Gary H Dickinson and Steven B Roberts

    Citation: BMC Genomics 2014 15:951

    Content type: Research article

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  22. Vascular wilt caused by Fusarium oxysporum f. sp. ciceri Race 1 (Foc1) is a serious disease of chickpea (Cicer arietinum L.) accounting for approximately 10-15% annual crop loss. The fungus invades the plant via ...

    Authors: Moniya Chatterjee, Sumanti Gupta, Anirban Bhar, Dipankar Chakraborti, Debabrata Basu and Sampa Das

    Citation: BMC Genomics 2014 15:949

    Content type: Research article

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  23. Osteochondrosis (OC(D)) is a juvenile osteo-articular disorder affecting several mammalian species. In horses, OC(D) is considered as a multifactorial disease and has been described as a focal disruption of en...

    Authors: Clémence Desjardin, Julie Riviere, Anne Vaiman, Caroline Morgenthaler, Mathieu Diribarne, Michel Zivy, Céline Robert, Laurence Le Moyec, Laurence Wimel, Olivier Lepage, Claire Jacques, Edmond Cribiu and Laurent Schibler

    Citation: BMC Genomics 2014 15:947

    Content type: Research article

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  24. Bone destruction is a feature of multiple myeloma, characterised by osteolytic bone destruction due to increased osteoclast activity and suppressed or absent osteoblast activity. Almost all multiple myeloma pa...

    Authors: Paul Dowling, Catriona Hayes, Kay Reen Ting, Abdul Hameed, Justine Meiller, Constantine Mitsiades, Kenneth C Anderson, Martin Clynes, Colin Clarke, Paul Richardson and Peter O’Gorman

    Citation: BMC Genomics 2014 15:904

    Content type: Research article

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  25. Current practice in mass spectrometry (MS)-based proteomics is to identify peptides by comparison of experimental mass spectra with theoretical mass spectra derived from a reference protein database; however, ...

    Authors: Gloria M Sheynkman, James E Johnson, Pratik D Jagtap, Michael R Shortreed, Getiria Onsongo, Brian L Frey, Timothy J Griffin and Lloyd M Smith

    Citation: BMC Genomics 2014 15:703

    Content type: Methodology article

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  26. Most of the proteins contained in royal jelly (RJ) are secreted from the hypopharyngeal glands (HG) of young bees. Although generic protein composition of RJ has been investigated, little is known about how ag...

    Authors: Ting Ji, Zhenguo Liu, Jie Shen, Fang Shen, Qin Liang, Liming Wu, Guohong Chen and Miguel Corona

    Citation: BMC Genomics 2014 15:665

    Content type: Research article

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  27. The major Gram-positive coccoid pathogens cause similar invasive diseases and show high rates of antimicrobial resistance. Uncharacterised proteins shared by these organisms may be involved in virulence or be ...

    Authors: Antonio J Martín-Galiano, José Yuste, María I Cercenado and Adela G de la Campa

    Citation: BMC Genomics 2014 15:652

    Content type: Research article

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  28. The Homeobox (Hox) family complex contains 39 genes, clustered into four groups (A-D) all expressing in sequential manner. The HOX proteins are transcriptional factors involved in regulation of pattern formation ...

    Authors: Monal Sharma, Leena Rawal, Deepak Panwar, Neeta Sehgal and Sher Ali

    Citation: BMC Genomics 2014 15:638

    Content type: Research article

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  29. Mycoplasma hyopneumoniae causes respiratory disease in swine and contributes to the porcine respiratory disease complex, a major disease problem in the swine industry. The M. hyopneumoniae strain 232 genome is on...

    Authors: Ken Pendarvis, Matthew P Padula, Jessica L Tacchi, Andrew C Petersen, Steven P Djordjevic, Shane C Burgess and F Chris Minion

    Citation: BMC Genomics 2014 15:576

    Content type: Research article

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  30. Hemolymph plays key roles in honey bee molecule transport, immune defense, and in monitoring the physiological condition. There is a lack of knowledge regarding how the proteome achieves these biological missi...

    Authors: Mao Feng, Haitham Ramadan, Bin Han, Yu Fang and Jianke Li

    Citation: BMC Genomics 2014 15:563

    Content type: Research article

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  31. Multiple tick saliva proteins, the majority of which are unknown, confer tick resistance in repeatedly infested animals. The objective of this study was to identify the 24-48 h fed Amblyomma americanum tick saliv...

    Authors: Željko M Radulović, Tae K Kim, Lindsay M Porter, Sing-Hoi Sze, Lauren Lewis and Albert Mulenga

    Citation: BMC Genomics 2014 15:518

    Content type: Research article

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  32. In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tub...

    Authors: Ashfaq Ali, Erik Alexandersson, Marianne Sandin, Svante Resjö, Marit Lenman, Pete Hedley, Fredrik Levander and Erik Andreasson

    Citation: BMC Genomics 2014 15:497

    Content type: Research article

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  33. The cotton (Gossypium spp.) fiber cell is an important unicellular model for studying cell differentiation. There is evidence suggesting that phosphorylation is a critical post-translational modification involved...

    Authors: Qifeng Ma, Man Wu, Wenfeng Pei, Haijing Li, Xingli Li, Jinfa Zhang, Jiwen Yu and Shuxun Yu

    Citation: BMC Genomics 2014 15:466

    Content type: Research article

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  34. Protein phosphorylation is one of the most important post-translational modifications involved in the regulation of plant growth and development as well as diverse stress response. As a member of the Poaceae, Bra...

    Authors: Dong-Wen Lv, Xin Li, Ming Zhang, Ai-Qin Gu, Shou-Min Zhen, Chang Wang, Xiao-Hui Li and Yue-Ming Yan

    Citation: BMC Genomics 2014 15:375

    Content type: Research article

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  35. Efficient light acclimation of photosynthetic cells is a basic and important property of plants. The process of acclimation depends on transformation of retrograde signals in gene expression, transcript accumu...

    Authors: Marie-Luise Oelze, Meenakumari Muthuramalingam, Marc Oliver Vogel and Karl-Josef Dietz

    Citation: BMC Genomics 2014 15:320

    Content type: Research article

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  36. Phenotypic plasticity in defensive traits occurs in many species when facing heterogeneous predator regimes. The waterflea Daphnia is well-known for showing a variety of these so called inducible defences. Howeve...

    Authors: Kathrin A Otte, Thomas Fröhlich, Georg J Arnold and Christian Laforsch

    Citation: BMC Genomics 2014 15:306

    Content type: Research article

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  37. Ralstonia solanacearum, the causal agent of bacterial wilt, is a genetically diverse bacterial plant pathogen present in tropical and subtropical regions of the world that infects more than 200 plant species, inc...

    Authors: Ana M Bocsanczy, Ute CM Achenbach, Arianna Mangravita-Novo, Marjorie Chow and David J Norman

    Citation: BMC Genomics 2014 15:280

    Content type: Research article

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  38. Plant and animal pathogenic fungus Cochliobolus lunatus cause great economic damages worldwide every year. C. lunatus displays an increased temperature dependent-virulence to a wide range of hosts. Nonetheless, t...

    Authors: Bengyella Louis, Sayanika Devi Waikhom, Pranab Roy, Pardeep Kumar Bhardwaj, Mohendro Wakambam Singh, Sailendra Goyari, Chandradev K Sharma and Narayan Chandra Talukdar

    Citation: BMC Genomics 2014 15:213

    Content type: Research article

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    The Erratum to this article has been published in BMC Genomics 2015 16:347

  39. Semiochemical is a generic term used for a chemical substance that influences the behaviour of an organism. It is a common term used in the field of chemical ecology to encompass pheromones, allomones, kairomo...

    Authors: Kamala Jayanthi P D, Vivek Kempraj, Ravindra M Aurade, Tapas Kumar Roy, Shivashankara K S and Abraham Verghese

    Citation: BMC Genomics 2014 15:209

    Content type: Methodology article

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  40. Royal jelly (RJ) is a proteinaceous secretion produced from the hypopharyngeal and mandibular glands of nurse bees. It plays vital roles in honeybee biology and in the improvement of human health. However, som...

    Authors: Lan Zhang, Bin Han, Rongli Li, Xiaoshan Lu, Aiying Nie, Lihai Guo, Yu Fang, Mao Feng and Jianke Li

    Citation: BMC Genomics 2014 15:135

    Content type: Research article

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  41. Microglial cells are resident macrophages of the central nervous system and important cellular mediators of the immune response and neuroinflammatory processes. In particular, microglial activation and communi...

    Authors: Dohyun Han, Sungyoon Moon, Yikwon Kim, Hophil Min and Youngsoo Kim

    Citation: BMC Genomics 2014 15:95

    Content type: Research article

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  42. A lack of competence to form adventitious roots by cuttings of Chrysanthemum (Chrysanthemum morifolium) is an obstacle for the rapid fixation of elite genotypes. We performed a proteomic analysis of cutting bases...

    Authors: Ruixia Liu, Sumei Chen, Jiafu Jiang, Lu Zhu, Chen Zheng, Shuang Han, Jing Gu, Jing Sun, Huiyun Li, Haibin Wang, Aiping Song and Fadi Chen

    Citation: BMC Genomics 2013 14:919

    Content type: Research article

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  43. The marine annelid Platynereis dumerilii is emerging as a powerful lophotrochozoan experimental model for evolutionary developmental biology (evo-devo) and neurobiology. Recent studies revealed the presence of co...

    Authors: Markus Conzelmann, Elizabeth A Williams, Karsten Krug, Mirita Franz-Wachtel, Boris Macek and Gáspár Jékely

    Citation: BMC Genomics 2013 14:906

    Content type: Research article

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  44. Recently, questions have been raised regarding the ability of animal models to recapitulate human disease at the molecular level. It has also been demonstrated that cellular kinases, individually or as a colle...

    Authors: Brett Trost, Jason Kindrachuk, Erin Scruten, Philip Griebel, Anthony Kusalik and Scott Napper

    Citation: BMC Genomics 2013 14:854

    Content type: Research article

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  45. Fungal pathogens cause devastating losses in economically important cereal crops by utilising pathogen proteins to infect host plants. Secreted pathogen proteins are referred to as effectors and have thus far ...

    Authors: Jana Sperschneider, Donald M Gardiner, Jennifer M Taylor, James K Hane, Karam B Singh and John M Manners

    Citation: BMC Genomics 2013 14:807

    Content type: Research article

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  46. Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of bio...

    Authors: Jianhua Zheng, Liguo Liu, Jin Wang and Qi Jin

    Citation: BMC Genomics 2013 14:777

    Content type: Research article

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  47. Honeybee venom is a complicated defensive toxin that has a wide range of pharmacologically active compounds. Some of these compounds are useful for human therapeutics. There are two major forms of honeybee ven...

    Authors: Rongli Li, Lan Zhang, Yu Fang, Bin Han, Xiaoshan Lu, Tiane Zhou, Mao Feng and Jianke Li

    Citation: BMC Genomics 2013 14:766

    Content type: Research article

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  48. The transport of sugars, hormones, amino acids, proteins, sugar alcohols, and other organic compounds from the sites of synthesis to the sites of use or storage occurs through the conducting cells of the phloe...

    Authors: James A Anstead, Steven D Hartson and Gary A Thompson

    Citation: BMC Genomics 2013 14:764

    Content type: Research article

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