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  1. 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

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

  2. 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

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

  3. 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

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

  4. 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

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

  5. The immune system must detect a wide variety of microbial pathogens, such as viruses, bacteria, fungi and parasitic worms, to protect the host against disease. Antigenic peptides displayed by MHC II (class II ...

    Authors: Wen-Jun Shen, Shaohong Zhang and Hau-San Wong
    Citation: Proteome Science 2013 11(Suppl 1):S15

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

  6. 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

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

  7. 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

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

  8. 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

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

  9. 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

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

  10. 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

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

  11. 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

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

  12. 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

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

  13. 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

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

  14. 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

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

  15. 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

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

  16. 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

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

  17. 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

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

  18. 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

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

  19. 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

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

  20. Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Despite the identification of several virulence factors the pathogenesis is still poorly...

    Authors: Philippe Vanden Bergh, Manfred Heller, Sophie Braga-Lagache and Joachim Frey
    Citation: Proteome Science 2013 11:44
  21. Osteoarthritis (OA) is a destructive joint disease and there are no known biomarkers available for an early diagnosis. To identify potential disease biomarkers and gain further insight into the disease mechani...

    Authors: Johan Stenberg, Ulla Rüetschi, Eva Skiöldebrand, Johan Kärrholm and Anders Lindahl
    Citation: Proteome Science 2013 11:43
  22. Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Several virulence factors have been described, but the type-three secretion system (T3SS...

    Authors: Philippe Vanden Bergh, Manfred Heller, Sophie Braga-Lagache and Joachim Frey
    Citation: Proteome Science 2013 11:42
  23. Fusarium wilt of banana is one of the most destructive diseases in the world. This disease has caused heavy losses in major banana production areas. Except for molecular breeding methods based on plant defense...

    Authors: Xingshen Li, Tingting Bai, Yunfeng Li, Xiaolei Ruan and Huaping Li
    Citation: Proteome Science 2013 11:41
  24. Post treatment minimal residual disease (MRD) determination contributes to impending relapse prediction, chemotherapy response and clinical outcomes assessment, guiding clinicians to develop reasonable and eff...

    Authors: Ju Bai, Aili He, Wanggang Zhang, Chen Huang, Juan Yang, Yun Yang, Jianli Wang and Yang Zhang
    Citation: Proteome Science 2013 11:39
  25. Cell surface glycoprotein sialylation is one of the most ubiquitous glycan modifications found on higher eukaryotes. The surface sialylation pattern of cells is influenced by the cellular environment but also ...

    Authors: Ville I Parviainen, Sakari Joenväärä, Niina Tohmola and Risto Renkonen
    Citation: Proteome Science 2013 11:38
  26. Liver perfusates exhibit theoretical advantages regarding the discovery of disease biomarkers because they contain proteins that readily enter the blood-stream, and perfusion preserves the disease state in its...

    Authors: Yang Zhang, Menglin Li, Lilong Wei, Lisi Zhu, Siqi Hu, Shuzhen Wu, Sucan Ma and Youhe Gao
    Citation: Proteome Science 2013 11:37
  27. Two-dimensional gel electrophoresis (2DE) is one of the most popular methods in proteomics. Currently, most 2DE experiments are performed using immobilized pH gradient (IPG) in the first dimension; however, so...

    Authors: Rimantas Slibinskas, Raimundas Ražanskas, Rūta Zinkevičiūtė and Evaldas Čiplys
    Citation: Proteome Science 2013 11:36
  28. Aims of the research were to devise a proteome map of the chicken Pectoralis superficialis muscle, as resolved by two-dimensional gel electrophoresis, and to characterize protein expression changes in the soluble...

    Authors: Enrico Zanetti, Antonio Masi, Micaela Pivato, Serena Tolin, Anna Rita Trentin, Cem Guler, Servet Yalçin and Martino Cassandro
    Citation: Proteome Science 2013 11:34
  29. We report here a new type of protein chip to detect antibodies in sera. This chip method was used to a prototype created to detect hepatocellular carcinoma (HCC) -related autoantibodies in the sera of hepatiti...

    Authors: Junko Akada, Shuichi Kamei, Akane Ito, Moe Ito, Takao Kitagawa, Hiroko Furumoto, Yukari Kato, Michiko Tamesa, Motonari Takashima, Mutsunori Shirai, Hirofumi Yamano, Masaaki Oka, Yasuhiro Kuramitsu and Kazuyuki Nakamura
    Citation: Proteome Science 2013 11:33
  30. (−)-Epigallocatechin-3-gallate (EGCG), the most abundant catechin found in green tea, effectively reduces body weight and tissue and blood lipid accumulation. To explore the mechanism by which EGCG inhibits ce...

    Authors: Zhonghua Liu, Qin Li, Jianan Huang, Qionglin Liang, Yujun Yan, Haiyan Lin, Wenjun Xiao, Yong Lin, Sheng Zhang, Bin Tan and Guoan Luo
    Citation: Proteome Science 2013 11:32
  31. Transmissible gastroenteritis coronavirus (TGEV) is an enteropathogenic coronavirus that causes diarrhea in pigs, which is correlated with high morbidity and mortality in suckling piglets. Information remains ...

    Authors: Xin Zhang, Hong-Yan Shi, Jian-Fei Chen, Da Shi, Hong-Wu Lang, Zhong-Tian Wang and Li Feng
    Citation: Proteome Science 2013 11:31
  32. Hepatic fibrosis is an inevitable process in the progression of chronic HBV infection to hepatic cirrhosis, but its detailed mechanism is still unknown. Clinic serum biomarkers of HBV hepatic cirrhosis were sc...

    Authors: Bin Zhang, Zi Wang, Bin Deng, Xiaoqiong Wu, Jing Liu and Xueping Feng
    Citation: Proteome Science 2013 11:30
  33. A.BY/SnJ mice are used to study pathological alterations in the heart due to enteroviral infections. Since age is a well-known factor influencing the susceptibility of mice to infection, response to stress and...

    Authors: Krishnatej Nishtala, Truong Quoc Phong, Leif Steil, Martina Sauter, Manuela Gesell Salazar, Reinhard Kandolf, Stephan B Felix, Uwe Völker, Karin Klingel and Elke Hammer
    Citation: Proteome Science 2013 11:29
  34. The spore-bearing alkaliphilic Bacillus species constitute a large, heterogeneous group of microorganisms, important for their ability to produce enzymes, antibodies and metabolites of potential medical use. Some...

    Authors: Rosa Lippolis, Rosa Anna Siciliano, Maria Fiorella Mazzeo, Anna Abbrescia, Antonio Gnoni, Anna Maria Sardanelli and Sergio Papa
    Citation: Proteome Science 2013 11:28
  35. Aortic aneurysm is an increasingly common vascular disorder with fatal implication. However, there is no established diagnosis other than that based on aneurysmal size. For this purpose, serum protein biomarke...

    Authors: Kazumi Satoh, Tomoko Maniwa, Teiji Oda and Ken-ichi Matsumoto
    Citation: Proteome Science 2013 11:27
  36. Plant cells are routinely exposed to various pathogens and environmental stresses that cause cell wall perturbations. Little is known of the mechanisms that plant cells use to sense these disturbances and tran...

    Authors: Hana Mujahid, Feng Tan, Jian Zhang, Babi Ramesh Reddy Nallamilli, Ken Pendarvis and Zhaohua Peng
    Citation: Proteome Science 2013 11:26
  37. Salvia splendens Ker-Gawl, most commonly used in China to add a splash of brilliant color to the surroundings during the warm season, is subject to heat stress, which can greatly affect its growth and yield.

    Authors: Hui Liu, Guozheng Shen, Xianping Fang, Qiaojuan Fu, Kangkang Huang, Yi Chen, Hong Yu, Yun Zhao, Le Zhang, Liang Jin and Songlin Ruan
    Citation: Proteome Science 2013 11:25

    The Erratum to this article has been published in Proteome Science 2013 11:35

  38. There is great interest in the design of small molecules that selectively target minor grooves of duplex DNA for controlling specific gene expression implicated in a disease. The design of chiral small molecul...

    Authors: Ya-ting Yang, Chun-Yu Lin, Jingyueh Jeng and Chi-Wi Ong
    Citation: Proteome Science 2013 11:23
  39. Mapping of proteins involved in normal eye functions is a prerequisite to identify pathological changes during eye disease processes. We therefore analysed the proteome of human vitreous by applying in-depth p...

    Authors: Sebastian Aretz, Tim U Krohne, Kerstin Kammerer, Uwe Warnken, Agnes Hotz-Wagenblatt, Marion Bergmann, Boris V Stanzel, Tore Kempf, Frank G Holz, Martina Schnölzer and Jürgen Kopitz
    Citation: Proteome Science 2013 11:22
  40. Here we describe a novel approach used to identify the constituents of protein complexes with high fidelity, using the integrin-associated scaffolding protein PINCH as a test case. PINCH is comprised of five L...

    Authors: Masaaki Yoshigi, Stephen M Pronovost and Julie L Kadrmas
    Citation: Proteome Science 2013 11:21
  41. Bee venom has been used to relieve pain and to treat inflammatory diseases, including rheumatoid arthritis, in humans. To better understand the mechanisms of the anti-inflammatory and anti-atherosclerosis effe...

    Authors: Hyun-Ji Cho, Jeong-Han Kang, Kwan-Kyu Park, Jung-Yoon Choe, Yoon-Yub Park, Yong-Suk Moon, Il-Kyung Chung, Hyeun-Wook Chang, Cheorl-Ho Kim, Yung Hyun Choi, Wun-Jae Kim, Sung-Kwon Moon and Young-Chae Chang
    Citation: Proteome Science 2013 11:20
  42. Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears...

    Authors: Sausan Azzam, Laurie Broadwater, Shuo Li, Ernest J Freeman, Jennifer McDonough and Roger B Gregory
    Citation: Proteome Science 2013 11:19
  43. Neural Stem Cells (NSCs) are a distinct group of cells present in the embryonic and adult mammalian central nervous system (CNS) that are able to differentiate into neurons, astrocytes and oligodendrocytes. As...

    Authors: Ariel B Abraham, Robert Bronstein, Emily I Chen, Antonius Koller, Lorenza Ronfani, Mirjana Maletic-Savatic and Stella E Tsirka
    Citation: Proteome Science 2013 11:18
  44. SDS-PAGE followed by in-gel digestion (IGD) is a popular workflow in mass spectrometry-based proteomics. In GeLC-MS/MS, a protein lysate of a biological sample is separated by SDS-PAGE and each gel lane is sli...

    Authors: Sander R Piersma, Marc O Warmoes, Meike de Wit, Inge de Reus, Jaco C Knol and Connie R Jiménez
    Citation: Proteome Science 2013 11:17
  45. Vigna mungo, a tropical leguminous plant, highly susceptible to yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus (MYMIV) resulting in high yield penalty. The molecular events occurring during c...

    Authors: Subrata Kundu, Dipjyoti Chakraborty, Anirban Kundu and Amita Pal
    Citation: Proteome Science 2013 11:15
  46. The comprehensive analysis of human kidney glomerulus we previously performed using highly purified glomeruli, provided a dataset of 6,686 unique proteins representing 2,966 distinct genes. This dataset, howev...

    Authors: Zenyui Cui, Yutaka Yoshida, Bo Xu, Ying Zhang, Masaaki Nameta, Sameh Magdeldin, Tomoo Makiguchi, Toshikazu Ikoma, Hidehiko Fujinaka, Eishin Yaoita and Tadashi Yamamoto
    Citation: Proteome Science 2013 11:13

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