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  1. Vascular endothelial growth factor (VEGF) is a critical pro-angiogenic factor, found in a number of cancers, and a target of therapy. It is typically assessed by immunohistochemistry (IHC) in clinical research...

    Authors: Joon-Yong Chung, Till Braunschweig, Seung-Mo Hong, David S Kwon, Soo-Heang Eo, HyungJun Cho and Stephen M Hewitt
    Citation: Proteome Science 2014 12:27
    Content type: Methodology Published on:

  3. The myotendinous junction is a specialized structure of the muscle fibre enriched in mechanosensing complexes, including costameric proteins and core elements of the z-disc. Here, laser capture microdissection...

    Authors: Tugba Can, Laura Faas, David A Ashford, Adam Dowle, Jerry Thomas, Peter O’Toole and Gonzalo Blanco
    Citation: Proteome Science 2014 12:25
    Content type: Research Published on:

  4. Lipid lowering agent such as agonists of peroxisome proliferator-activated receptors (PPAR) are suggested as neuroprotective agents and may protect from the sequelae of brain ischemic stroke. Although the demo...

    Authors: Patrick Gelé, Valérie Vingtdeux, Camille Potey, Hervé Drobecq, Antoine Ghestem, Patricia Melnyk, Luc Buée, Nicolas Sergeant and Régis Bordet
    Citation: Proteome Science 2014 12:24
    Content type: Research Published on:

  5. Tight spatio-temporal signaling of cytoskeletal and adhesion dynamics is required for localized membrane protrusion that drives directed cell migration. Different ensembles of proteins are therefore likely to ...

    Authors: Georgios Fengos, Alexander Schmidt, Katrin Martin, Erika Fluri, Ruedi Aebersold, Dagmar Iber and Olivier Pertz
    Citation: Proteome Science 2014 12:23
    Content type: Research Published on:

  6. Hepatic resection is the preferred treatment for huge hepatocellular carcinoma (>10 cm in diameter; H-HCC). However, the patients with H-HCC suffer from poor prognosis due to the early recurrence/metastasis. T...

    Authors: Xinhui Huang, Yongyi Zeng, Xiaohua Xing, Jinhua Zeng, Yunzhen Gao, Zhixiong Cai, Bo Xu, Xiaolong Liu, Aimin Huang and Jingfeng Liu
    Citation: Proteome Science 2014 12:22
    Content type: Research Published on:

  7. The biofilm forming bacterium Staphylococcus aureus is responsible for maladies ranging from severe skin infection to major diseases such as bacteremia, endocarditis and osteomyelitis. A flow displacement system ...

    Authors: Nazrul Islam, Yonghyun Kim, Julia M Ross and Mark R Marten
    Citation: Proteome Science 2014 12:21
    Content type: Research Published on:

  8. Idiopathic Parkinson’s disease is marked by degeneration of dopamine neurons projecting from the substantia nigra to the striatum. Although proteins expressed by the target striatum can positively affect the v...

    Authors: Heidi R Fuller, Maica Llavero Hurtado, Thomas M Wishart and Monte A Gates
    Citation: Proteome Science 2014 12:20
    Content type: Research Published on:

  9. Milk contains a range of proteins of moderate or low abundance that contribute to host defence. Characterisation of these proteins, the extent to which their abundance is regulated by pathogenic stimuli, and t...

    Authors: Grant A Smolenski, Marita K Broadhurst, Kerst Stelwagen, Brendan J Haigh and Thomas T Wheeler
    Citation: Proteome Science 2014 12:19
    Content type: Research Published on:

  11. Allergies are nearly always triggered by protein molecules and the majority of individuals with documented immunologic reactions to foods exhibit IgE hypersensitivity reactions. In this study we aimed to under...

    Authors: Cátia Fonseca, Sébastien Planchon, Carla Pinheiro, Jenny Renaut, Cândido Pinto Ricardo, M Margarida Oliveira and Rita Batista
    Citation: Proteome Science 2014 12:17
    Content type: Research Published on:

  13. Despite extensive research on hepatic cells precursors and their differentiated states, much remains to be learned about the mechanism underlying the self-renewal and differentiation.

    Authors: Claudia Montaldo, Carmine Mancone, Alice Conigliaro, Angela Maria Cozzolino, Valeria de Nonno and Marco Tripodi
    Citation: Proteome Science 2014 12:15
    Content type: Research Published on:

  14. The length of time that a protein remains available to perform its function is significantly influenced by its turnover rate. Knowing the turnover rate of proteins involved in different processes is important ...

    Authors: Marie-Laure A Sauer, Bing Xu and Fedora Sutton
    Citation: Proteome Science 2014 12:14
    Content type: Methodology Published on:

  16. Scientists have injected endotoxin into animals to investigate and understand various pathologies and novel therapies for several decades. Recent observations have shown that there is selective susceptibility to

    Authors: Saul Chemonges, John-Paul Tung and John F Fraser
    Citation: Proteome Science 2014 12:12
    Content type: Review Published on:

  17. Proteomic analysis was performed in post-nuclear supernatant (PNS) and Percoll-purified membranes (PM) prepared from fore brain cortex of rats exposed to increasing doses of morphine (10–50 mg/kg) for 10 days.

    Authors: Hana Ujcikova, Adam Eckhardt, Dmytro Kagan, Lenka Roubalova and Petr Svoboda
    Citation: Proteome Science 2014 12:11
    Content type: Research Published on:

  18. Blast wounds often involve diverse tissue types and require substantial time and treatment for appropriate healing. Some of these subsequent wounds become colonized with bacteria requiring a better understandi...

    Authors: Brett A Chromy, Angela Eldridge, Jonathan A Forsberg, Trevor S Brown, Benjamin C Kirkup, Eric Elster and Paul Luciw
    Citation: Proteome Science 2014 12:10
    Content type: Methodology Published on:

  20. Certain wheat gluten proteins form large protein polymers that are extractable in 0.5% SDS only after sonication. Although there is a strong relationship between the amounts of these polymers in the flour and ...

    Authors: William H Vensel, Charlene K Tanaka and Susan B Altenbach
    Citation: Proteome Science 2014 12:8
    Content type: Research Published on:

  21. Apple, an invaluable fruit crop worldwide, is often prone to infection by pathogenic fungi. Identification of potentially resistance-conferring apple proteins is one of the most important aims for studying app...

    Authors: Miaomiao Li, Jianhua Xu, Zonghao Qiu, Juan Zhang, Fengwang Ma and Junke Zhang
    Citation: Proteome Science 2014 12:7
    Content type: Research Published on:

  22. Fast Fixation is necessary to study real-time protein-protein interactions under physiological conditions. Fast formaldehyde cross-linking can fix transient and weak protein interactions, thereby reducing the ...

    Authors: Lisi Zhu, Menglin Li, Lilong Wei, Xuejiao Liu, Jianrui Yin and Youhe Gao
    Citation: Proteome Science 2014 12:6
    Content type: Research Published on:

  23. With the promise of disease modifying treatments, there is a need for more specific diagnosis and prognosis of Alzheimer’s disease (AD) and mild cognitive impairment (MCI). Plasma biomarkers are likely to be u...

    Authors: Fei Song, Anne Poljak, Nicole A Kochan, Mark Raftery, Henry Brodaty, George A Smythe and Perminder S Sachdev
    Citation: Proteome Science 2014 12:5
    Content type: Research Published on:

  24. The complexity of protein glycosylation makes it difficult to characterize glycosylation patterns on a proteomic scale. In this study, we developed an integrated strategy for comparatively analyzing N-glycosyl...

    Authors: Ji Wang, Chuang Zhou, Wei Zhang, Jun Yao, Haojie Lu, Qiongzhu Dong, Haijun Zhou and Lunxiu Qin
    Citation: Proteome Science 2014 12:4
    Content type: Research Published on:

  25. A limiting factor in performing proteomics analysis on cancerous cells is the difficulty in obtaining sufficient amounts of starting material. Cell lines can be used as a simplified model system for studying c...

    Authors: Saiful Anuar Karsani, Nor Afiza Saihen, Rosnah Binti Zain, Sok-Ching Cheong and Mariati Abdul Rahman
    Citation: Proteome Science 2014 12:3
    Content type: Research Published on:

  29. Profiling technologies allow the simultaneous measurement and comparison of thousands of cell components without prior knowledge of their identity. In the present study, we used two-dimensional gel electrophor...

    Authors: Sarah Zanon Agapito-Tenfen, Miguel Pedro Guerra, Odd-Gunnar Wikmark and Rubens Onofre Nodari
    Citation: Proteome Science 2013 11:46
    Content type: Research Published on:

  30. Pathogenic mycobacteria are important agents causing human disease. Mycobacterium avium subsp. hominissuis (M. avium) is a species of recalcitrant environmental pathogen. The bacterium forms robust biofilms that ...

    Authors: Michael McNamara, Shin-Cheng Tzeng, Claudia Maier, Martin Wu and Luiz E Bermudez
    Citation: Proteome Science 2013 11:45
    Content type: Research Published on:

  31. Many computational approaches have been developed to detect protein complexes from protein-protein interaction (PPI) networks. However, these PPI networks are always built from high-throughput experiments. The...

    Authors: Bo Xu, Hongfei Lin, Kavishwar B Wagholikar, Zhihao Yang and Hongfang Liu
    Citation: Proteome Science 2013 11(Suppl 1):S21
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  32. Protein interaction networks (PINs) are known to be useful to detect protein complexes. However, most available PINs are static, which cannot reflect the dynamic changes in real networks. At present, some rese...

    Authors: Qianghua Xiao, Jianxin Wang, Xiaoqing Peng and Fang-Xiang Wu
    Citation: Proteome Science 2013 11(Suppl 1):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  33. Proteins are essential biological molecules which play vital roles in nearly all biological processes. It is the tertiary structure of a protein that determines its functions. Therefore the prediction of a pro...

    Authors: Jyh-Jong Tsay and Shih-Chieh Su
    Citation: Proteome Science 2013 11(Suppl 1):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  34. Recently, large data sets of protein-protein interactions (PPI) which can be modeled as PPI networks are generated through high-throughput methods. And locally dense regions in PPI networks are very likely to ...

    Authors: Shuliang Wang and Fang Wu
    Citation: Proteome Science 2013 11(Suppl 1):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  35. Biomedical extraction based on supervised machine learning still faces the problem that a limited labeled dataset does not saturate the learning method. Many supervised learning algorithms for bio-event extrac...

    Authors: Jian Wang, Qian Xu, Hongfei Lin, Zhihao Yang and Yanpeng Li
    Citation: Proteome Science 2013 11(Suppl 1):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  36. Tandem affinity purification coupled with mass-spectrometry (TAP/MS) analysis is a popular method for the identification of novel endogenous protein-protein interactions (PPIs) in large-scale. Computational an...

    Authors: Xiaoyun Sun, Pengyu Hong, Meghana Kulkarni, Young Kwon and Norbert Perrimon
    Citation: Proteome Science 2013 11(Suppl 1):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  37. Phosphorylation site assignment of high throughput tandem mass spectrometry (LC-MS/MS) data is one of the most common and critical aspects of phosphoproteomics. Correctly assigning phosphorylated residues help...

    Authors: Fahad Saeed, Trairak Pisitkun, Jason D Hoffert, Sara Rashidian, Guanghui Wang, Marjan Gucek and Mark A Knepper
    Citation: Proteome Science 2013 11(Suppl 1):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  38. Differences in sample collection, biomolecule extraction, and instrument variability introduce bias to data generated by liquid chromatography coupled with mass spectrometry (LC-MS). Normalization is used to a...

    Authors: Mohammad R Nezami Ranjbar, Yi Zhao, Mahlet G Tadesse, Yue Wang and Habtom W Ressom
    Citation: Proteome Science 2013 11(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  39. Many problems in protein modeling require obtaining a discrete representation of the protein conformational space as an ensemble of conformations. In ab-initio structure prediction, in particular, where the go...

    Authors: Brian S Olson and Amarda Shehu
    Citation: Proteome Science 2013 11(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  40. Prediction and analysis of protein-protein interactions (PPI) and specifically types of PPIs is an important problem in life science research because of the fundamental roles of PPIs in many biological process...

    Authors: Mina Maleki, Gokul Vasudev and Luis Rueda
    Citation: Proteome Science 2013 11(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  41. The sequence database searching has been the dominant method for peptide identification, in which a large number of peptide spectra generated from LC/MS/MS experiments are searched using a search engine agains...

    Authors: Xijun Liang, Zhonghang Xia, Xinnan Niu, Andrew J Link, Liping Pang, Fang-Xiang Wu and Hongwei Zhang
    Citation: Proteome Science 2013 11(Suppl 1):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  42. To understand the function of protein complexes and their association with biological processes, a lot of studies have been done towards analyzing the protein-protein interaction (PPI) networks. However, the a...

    Authors: Chengwei Lei, Saleh Tamim, Alexander JR Bishop and Jianhua Ruan
    Citation: Proteome Science 2013 11(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  43. Discovering sequence patterns with variation can unveil functions of a protein family that are important for drug discovery. Exploring protein families using existing methods such as multiple sequence alignmen...

    Authors: En-Shiun Annie Lee and Andrew KC Wong
    Citation: Proteome Science 2013 11(Suppl 1):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  44. Membrane proteins perform essential roles in diverse cellular functions and are regarded as major pharmaceutical targets. The significance of membrane proteins has led to the developing dozens of resources rel...

    Authors: Min-Sung Kim and Gwan-Su Yi
    Citation: Proteome Science 2013 11(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  45. Elucidating the three-dimensional structure of a higher-order molecular assembly formed by interacting molecular units, a problem commonly known as docking, is central to unraveling the molecular basis of cell...

    Authors: Irina Hashmi and Amarda Shehu
    Citation: Proteome Science 2013 11(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  46. β-turns are secondary structure type that have essential role in molecular recognition, protein folding, and stability. They are found to be the most common type of non-repetitive structures since 25% of amino ....

    Authors: Murtada Khalafallah Elbashir, Jianxin Wang, Fang-Xiang Wu and Lusheng Wang
    Citation: Proteome Science 2013 11(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  47. Independent of the approach used, the ability to correctly interpret tandem MS data depends on the quality of the original spectra. Even in the case of the highest quality spectra, the majority of spectral pea...

    Authors: James P Cleveland and John R Rose
    Citation: Proteome Science 2013 11(Suppl 1):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  48. Protein-protein interactions (PPIs) play a key role in understanding the mechanisms of cellular processes. The availability of interactome data has catalyzed the development of computational approaches to eluc...

    Authors: Young-Rae Cho, Marco Mina, Yanxin Lu, Nayoung Kwon and Pietro H Guzzi
    Citation: Proteome Science 2013 11(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  49. Detecting protein complexes in protein-protein interaction (PPI) networks plays an important role in improving our understanding of the dynamic of cellular organisation. However, protein interaction data gener...

    Authors: Bingjing Cai, Haiying Wang, Huiru Zheng and Hui Wang
    Citation: Proteome Science 2013 11(Suppl 1):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  50. Today large scale genome sequencing technologies are uncovering an increasing amount of new genes and proteins, which remain uncharacterized. Experimental procedures for protein function prediction are low thr...

    Authors: Alfredo Benso, Stefano Di Carlo, Hafeez ur Rehman, Gianfranco Politano, Alessandro Savino and Prashanth Suravajhala
    Citation: Proteome Science 2013 11(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

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