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  1. Similarity search in protein databases is one of the most essential issues in computational proteomics. With the growing number of experimentally resolved protein structures, the focus shifted from sequences t...

    Authors: Jakub Galgonek, David Hoksza and Tomáš Skopal
    Citation: Proteome Science 2011 9(Suppl 1):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  2. Proteins play fundamental and crucial roles in nearly all biological processes, such as, enzymatic catalysis, signaling transduction, DNA and RNA synthesis, and embryonic development. It has been a long-standi...

    Authors: Shih-Chieh Su, Cheng-Jian Lin and Chuan-Kang Ting
    Citation: Proteome Science 2011 9(Suppl 1):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  3. Identifying biologically relevant protein complexes from a large protein-protein interaction (PPI) network, is essential to understand the organization of biological systems. However, high-throughput experimen...

    Authors: Shikui Tu, Runsheng Chen and Lei Xu
    Citation: Proteome Science 2011 9(Suppl 1):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  4. There is a growing interest in the identification of proteins on the proteome wide scale. Among different kinds of protein structure identification methods, graph-theoretic methods are very sharp ones. Due to ...

    Authors: Yan Yan, Shenggui Zhang and Fang-Xiang Wu
    Citation: Proteome Science 2011 9(Suppl 1):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  5. Protein-RNA interactions play an important role in numbers of fundamental cellular processes such as RNA splicing, transport and translation, protein synthesis and certain RNA-mediated enzymatic processes. The...

    Authors: Wei Chen, Shao-Wu Zhang, Yong-Mei Cheng and Quan Pan
    Citation: Proteome Science 2011 9(Suppl 1):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  6. Protein complexes are important for understanding principles of cellular organization and functions. With the availability of large amounts of high-throughput protein-protein interactions (PPI), many algorithm...

    Authors: Guimei Liu, Chern Han Yong, Hon Nian Chua and Limsoon Wong
    Citation: Proteome Science 2011 9(Suppl 1):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  7. Protein complexes are important entities to organize various biological processes in the cell, like signal transduction, gene expression, and molecular transmission. In most cases, proteins perform their intri...

    Authors: Osamu Maruyama and Ayaka Chihara
    Citation: Proteome Science 2011 9(Suppl 1):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  8. Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long stan...

    Authors: M Michael Gromiha, N Saranya, S Selvaraj, B Jayaram and Kazuhiko Fukui
    Citation: Proteome Science 2011 9(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  9. Studies of intrinsically disordered proteins that lack a stable tertiary structure but still have important biological functions critically rely on computational methods that predict this property based on seq...

    Authors: Ping Zhang and Zoran Obradovic
    Citation: Proteome Science 2011 9(Suppl 1):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  10. DNA-binding proteins perform their functions through specific or non-specific sequence recognition. Although many sequence- or structure-based approaches have been proposed to identify DNA-binding residues on ...

    Authors: Chien-Chih Wang and Chien-Yu Chen
    Citation: Proteome Science 2011 9(Suppl 1):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  11. In proteomics studies, liquid chromatography coupled to mass spectrometry (LC-MS) has proven to be a powerful technology to investigate differential expression of proteins/peptides that are characterized by th...

    Authors: Zhiqun Tang, Lihua Zhang, Amrita K Cheema and Habtom W Ressom
    Citation: Proteome Science 2011 9(Suppl 1):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  12. Transcriptional regulation by transcription factor (TF) controls the time and abundance of mRNA transcription. Due to the limitation of current proteomics technologies, large scale measurements of protein leve...

    Authors: Jia Meng, Jianqiu (Michelle) Zhang, Yidong Chen and Yufei Huang
    Citation: Proteome Science 2011 9(Suppl 1):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  13. The functions of proteins are closely related to their subcellular locations. In the post-genomics era, the amount of gene and protein data grows exponentially, which necessitates the prediction of subcellular...

    Authors: Man-Wai Mak, Wei Wang and Sun-Yuan Kung
    Citation: Proteome Science 2011 9(Suppl 1):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  14. Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the...

    Authors: Bo Xu, Hongfei Lin and Zhihao Yang
    Citation: Proteome Science 2011 9(Suppl 1):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  15. Complex intracellular signaling networks monitor diverse environmental inputs to evoke appropriate and coordinated effector responses. Defective signal transduction underlies many pathologies, including cancer...

    Authors: Javad Safaei, Ján Maňuch, Arvind Gupta, Ladislav Stacho and Steven Pelech
    Citation: Proteome Science 2011 9(Suppl 1):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  16. Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes. The systematic analysis of PPI networks can enable a great understanding of cellular organization, processes and f...

    Authors: Lei Shi, Xiujuan Lei and Aidong Zhang
    Citation: Proteome Science 2011 9(Suppl 1):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  17. ATP is a ubiquitous nucleotide that provides energy for cellular activities, catalyzes chemical reactions, and is involved in cellular signalling. The knowledge of the ATP-protein interactions helps with annot...

    Authors: Ke Chen, Marcin J Mizianty and Lukasz Kurgan
    Citation: Proteome Science 2011 9(Suppl 1):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  18. Charge states of tandem mass spectra from low-resolution collision induced dissociation can not be determined by mass spectrometry. As a result, such spectra with multiple charges are usually searched multiple...

    Authors: Jinhong Shi and Fang-Xiang Wu
    Citation: Proteome Science 2011 9(Suppl 1):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  19. Fourier Transform Mass Spectrometry coupled with Liquid Chromatography(LC-FTMS) has been widely used in proteomics. Past investigation has revealed that there exists an intensity dependent random suppression i...

    Authors: Xuepo Ma, Jian Cui and Jianqiu Zhang
    Citation: Proteome Science 2011 9(Suppl 1):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  20. Previous studies on protein-DNA interaction mostly focused on the bound structure of DNA-binding proteins but few paid enough attention to the unbound structures. As more new proteins are discovered, it is use...

    Authors: Weiqiang Zhou and Hong Yan
    Citation: Proteome Science 2011 9(Suppl 1):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  21. Proteome analysis is frequently applied in identifying the proteins or biomarkers in knee synovial fluids (SF) that are associated with osteoarthritis and other arthritic disorders. The 2-dimensional gel elect...

    Authors: Carl PC Chen, Chih-Chin Hsu, Wen-Lin Yeh, Hsiu-Chu Lin, Sen-Yung Hsieh, Shih-Cherng Lin, Tai-Tzung Chen, Max JL Chen and Simon FT Tang
    Citation: Proteome Science 2011 9:65
    Content type: Research Published on:

  22. Refractory cytopenia with multilineage dysplasia (RCMD) is a subgroup of myelodysplastic syndrome (MDS), which belongs to oncohematological diseases, occurring particularly in elderly patients, and represents ...

    Authors: Pavel Májek, Zuzana Reicheltová, Jiří Suttnar, Jaroslav Čermák and Jan E Dyr
    Citation: Proteome Science 2011 9:64
    Content type: Research Published on:

  23. Hodgkin lymphoma (HL) represents a category of lymphoid neoplasms with unique features, notably the usual scarcity of tumour cells in involved tissues. The most common subtype of classical HL, nodular sclerosi...

    Authors: Philippe Kischel, David Waltregny, Yannick Greffe, Gabriel Mazzucchelli, Edwin De Pauw, Laurence de Leval and Vincent Castronovo
    Citation: Proteome Science 2011 9:63
    Content type: Research Published on:

  24. Protein enrichment by sub-cellular fractionation was combined with differential-in-gel-electrophoresis (DIGE) to address the detection of the low abundance chromatin proteins in the budding yeast proteome. Com...

    Authors: Dong Ryoung Kim, Rohan D Gidvani, Brian P Ingalls, Bernard P Duncker and Brendan J McConkey
    Citation: Proteome Science 2011 9:62
    Content type: Research Published on:

  26. A recent epidemiological study demonstrated a reduced risk of lung cancer mortality in breast cancer patients using antiestrogens. These and other data implicate a role for estrogens in lung cancer, particular...

    Authors: MM Ivanova, SM Abner, WM Pierce Jr and CM Klinge
    Citation: Proteome Science 2011 9:60
    Content type: Research Published on:

  27. Parkinson's disease (PD) is histologically well defined by its characteristic degeneration of dopaminergic neurons in the substantia nigra pars compacta. Remarkably, divergent PD-related mutations can generate co...

    Authors: Madeleine Diedrich, Tohru Kitada, Grit Nebrich, Andrea Koppelstaetter, Jie Shen, Claus Zabel, Joachim Klose and Lei Mao
    Citation: Proteome Science 2011 9:59
    Content type: Research Published on:

  28. Xylella fastidiosa is limited to the xylem of the plant host and the foregut of insect vectors (sharpshooters). The mechanism of pathogenicity of this bacterium differs from other plant pathogens, since it does ...

    Authors: Mariana S Silva, Alessandra A De Souza, Marco A Takita, Carlos A Labate and Marcos A Machado
    Citation: Proteome Science 2011 9:58
    Content type: Research Published on:

  29. Mycophenolic acid (MPA) is widely used as a post transplantation medicine to prevent acute organ rejection. In the present study we used proteomics approach to identify proteome alterations in human embryonic ...

    Authors: Muhammad Qasim, Hazir Rahman, Michael Oellerich and Abdul R Asif
    Citation: Proteome Science 2011 9:57
    Content type: Research Published on:

  30. Prenatal screening for Down Syndrome (DS) would benefit from an increased number of biomarkers to improve sensitivity and specificity. Improving sensitivity and specificity would decrease the need for potentia...

    Authors: Wendy E Heywood, Tracey E Madgett, Darrell Wang, Amanda Wallington, Julie Hogg, Kevin Mills and Neil D Avent
    Citation: Proteome Science 2011 9:56
    Content type: Research Published on:

  31. Non Small Cell Lung Cancer (NSCLC) is the major cause of cancer related-death. Many patients receive diagnosis at advanced stage leading to a poor prognosis. At present, no satisfactory screening tests are ava...

    Authors: Emanuela Monari, Christian Casali, Aurora Cuoghi, Jessica Nesci, Elisa Bellei, Stefania Bergamini, Luca I Fantoni, Pamela Natali, Uliano Morandi and Aldo Tomasi
    Citation: Proteome Science 2011 9:55
    Content type: Research Published on:

  32. Follicular fluid accumulates into the antrum of follicle from the early stage of follicle development. Studies on its components may contribute to a better understanding of the mechanisms underlying follicular...

    Authors: Somayyeh Fahiminiya, Valérie Labas, Stéphane Roche, Jean-Louis Dacheux and Nadine Gérard
    Citation: Proteome Science 2011 9:54
    Content type: Research Published on:

  33. An improved version of quantitative protein array platform utilizing linear Quantum dot signaling for systematically measuring protein levels and phosphorylation states is presented. The signals are amplified ...

    Authors: Xiaoyu Wang, Ying Dong, Ameena J Jiwani, Yonglong Zou, Johanne Pastor, Makoto Kuro-o, Amyn A Habib, Minzi Ruan, David A Boothman and Chin-Rang Yang
    Citation: Proteome Science 2011 9:53
    Content type: Methodology Published on:

  34. Phytophthora sojae causes soybean root and stem rot, resulting in an annual loss of 1-2 billion US dollars in soybean production worldwide. A proteomic technique was used to determine the effects on soybean hypo...

    Authors: YuMei Zhang, JinMing Zhao, Yang Xiang, XiaoChun Bian, QiaoMei Zuo, Qi Shen, JunYi Gai and Han Xing
    Citation: Proteome Science 2011 9:52
    Content type: Research Published on:

  35. The spontaneous metamorphosis of the polychaete Capitella sp. I larvae into juveniles requires minor morphological changes, including segment formation, body elongation, and loss of cilia. In this study, we inves...

    Authors: Kondethimmanahalli H Chandramouli, Lisa Soo and Pei-Yuan Qian
    Citation: Proteome Science 2011 9:51
    Content type: Research Published on:

  36. Identification of secreted proteins of low abundance is often limited by abundant and high molecular weight (MW) proteins. We have optimised a procedure to overcome this limitation.

    Authors: Sarah Paule, Katie Meehan, Adam Rainczuk, Andrew N Stephens and Guiying Nie
    Citation: Proteome Science 2011 9:50
    Content type: Methodology Published on:

  37. We and others have previously reported that resveratrol (RSV) suppresses colon cancer cell proliferation and elevates apoptosis in vitro and/or in vivo, however molecular mechanisms are not fully elucidated. Part...

    Authors: Jairam Vanamala, Sridhar Radhakrishnan, Lavanya Reddivari, Vadiraja B Bhat and Andrey Ptitsyn
    Citation: Proteome Science 2011 9:49
    Content type: Research Published on:

  38. The anaerobe Clostridium difficile produces two major virulence factors toxin A and B that inactivate Rho proteins by glucosylation of a pivotal threonine residue. Purified toxins induce reorganization of the cyt...

    Authors: Nelli Jochim, Ralf Gerhard, Ingo Just and Andreas Pich
    Citation: Proteome Science 2011 9:48
    Content type: Research Published on:

  39. We have previously constructed an in-depth human glomerulus proteome database from a large amount of sample for understanding renal disease pathogenesis and aiding the biomarker exploration. However, it is usu...

    Authors: Ying Zhang, Yutaka Yoshida, Bo Xu, Sameh Magdeldin, Hidehiko Fujinaka, Zan Liu, Masahito Miyamoto, Eishin Yaoita and Tadashi Yamamoto
    Citation: Proteome Science 2011 9:47
    Content type: Research Published on:

  40. Mineral nutrition during wheat grain development has large effects on wheat flour protein content and composition, which in turn affect flour quality and immunogenic potential for a commodity of great economic...

    Authors: Susan B Altenbach, Charlene K Tanaka, William J Hurkman, Linda C Whitehand, William H Vensel and Frances M Dupont
    Citation: Proteome Science 2011 9:46
    Content type: Research Published on:

  41. Immunoprecipitation and subsequent 2D-PAGE/mass spectrometry are powerful tools to study post-translational protein modifications. Often disregarded in this workflow is the impact of the chemical cross-linker ...

    Authors: Mirta ML Sousa, Kristian W Steen, Lars Hagen and Geir Slupphaug
    Citation: Proteome Science 2011 9:45
    Content type: Methodology Published on:

  42. White leaf No.1 is a typical albino tea cultivar grown in China and it has received increased attention in recent years due to the fact that white leaves containing a high level of amino acids, which are very ...

    Authors: Qin Li, Jianan Huang, Shuoqian Liu, Juan Li, Xinhe Yang, Yisong Liu and Zhonghua Liu
    Citation: Proteome Science 2011 9:44
    Content type: Research Published on:

  43. The similarly in plant physiology and the difficulty of plant classification, in some medicinal plant species, especially plants of the Zingiberaceae family, are a major problem for pharmacologists, leading to...

    Authors: Apaporn Boonmee, Chantragan Srisomsap, Daranee Chokchaichamnankit, Aphichart Karnchanatat and Polkit Sangvanich
    Citation: Proteome Science 2011 9:43
    Content type: Research Published on:

  44. The inflammatory disease periodontitis results in tooth loss and can even lead to diseases of the whole body if not treated. Gingival crevicular fluid (GCF) reflects the condition of the gingiva and contains p...

    Authors: Young-Jin Choi, Sun-Hee Heo, Jae-Mok Lee and Je-Yoel Cho
    Citation: Proteome Science 2011 9:42
    Content type: Research Published on:

  45. Many important molecular events associated with implantation and development occur within the female reproductive tract, especially within the uterus endometrium, during pregnancy periods. The endometrium incl...

    Authors: Jung-Il Chae, Jumi Kim, Seong G Lee, Young-Joo Jeon, Dong-Wook Kim, Yunjo Soh, Kang S Seo, Hak K Lee, Nag-Jin Choi, Joohyun Ryu, Sunghyun Kang, Seong-Keun Cho, Dong-Seok Lee, Hyung M Chung and and Deog-Bon Koo
    Citation: Proteome Science 2011 9:41
    Content type: Research Published on:

  46. Saccharopolyspora spinosa produces the environment-friendly biopesticide spinosad, a mixture of two polyketide-derived macrolide active ingredients called spinosyns A and D. Therefore considerable interest is in...

    Authors: Yushuang Luo, Xuezhi Ding, Liqiu Xia, Fan Huang, Wenping Li, Shaoya Huang, Ying Tang and Yunjun Sun
    Citation: Proteome Science 2011 9:40
    Content type: Research Published on:

  47. The present study focused on comparative proteome analyses of low- and high-temperature stresses and potential protein-protein interaction networks, constructed by using a bioinformatics approach, in response ...

    Authors: Pavinee Kurdrid, Jittisak Senachak, Matura Sirijuntarut, Rayakorn Yutthanasirikul, Phuttawadee Phuengcharoen, Wattana Jeamton, Sittiruk Roytrakul, Supapon Cheevadhanarak and Apiradee Hongsthong
    Citation: Proteome Science 2011 9:39
    Content type: Research Published on:

  49. High temperature is a critical abiotic stress that reduces crop yield and quality. Rice (Oryza sativa L.) plants remodel their proteomes in response to high temperature stress. Moreover, phosphorylation is the mo...

    Authors: Xinhai Chen, Wenfeng Zhang, Baoqian Zhang, Jiechao Zhou, Yongfei Wang, Qiaobin Yang, Yuqin Ke and Huaqin He
    Citation: Proteome Science 2011 9:37
    Content type: Research Published on:

  50. The epidermal growth factor receptor (EGFR) is usually overexpressed in nasopharyngeal carcinoma (NPC) and is associated with pathogenesis of NPC. However, the downstream signaling proteins of EGFR in NPC have...

    Authors: Lin Ruan, Xin-Hui Li, Xun-Xun Wan, Hong Yi, Cui Li, Mao-Yu Li, Peng-Fei Zhang, Gu-Qing Zeng, Jia-Quan Qu, Qiu-Yan He, Jian-Huang Li, Yu Chen, Zhu-Chu Chen and Zhi-Qiang Xiao
    Citation: Proteome Science 2011 9:35
    Content type: Research Published on:
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