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  2. Coxiella burnetii is Gram-negative bacterium responsible for the zoonosis Q-fever. While it has an obligate intracellular growth habit, it is able to persist for extended periods outside of a host cell and can r...

    Authors: Gabriela Flores-Ramirez, Stefan Janecek, Ján A Miernyk and Ludovit Skultety

    Citation: Proteome Science 2012 10:67

    Content type: Research

    Published on:

  3. The process of protein-DNA binding has an essential role in the biological processing of genetic information. We use relational machine learning to predict DNA-binding propensity of proteins from their structu...

    Authors: Andrea Szabóová, Ondřej Kuželka, Filip Železný and Jakub Tolar

    Citation: Proteome Science 2012 10:66

    Content type: Research

    Published on:

  4. The thymus is an immune organ essential for life and plays a crucial role in the development of T cells. It undergoes a fetal to adult developmental maturation process occurring in mouse during the postnatal m...

    Authors: Xinze Cai, Wenyue Huang, Ying Qiao, Yang Chen, Shuyan Du, Dong Chen, Shuang Yu, Ruichao Che and Yi Jiang

    Citation: Proteome Science 2012 10:65

    Content type: Research

    Published on:

  5. Serum proteins carry out several functions in the circulation, including transfer, immunological functions, messenger functions, coagulation, and regulation of homeostasis. To investigate changes in serum prot...

    Authors: Lilong Wei, Lulu Jia, Lisi Zhu, Sucan Ma, Dan Zhang, Chen Shao, Wei Sun and Youhe Gao

    Citation: Proteome Science 2012 10:64

    Content type: Research

    Published on:

  6. Patients with periodontitis seek periodontal-orthodontic treatment to address certain functional and aesthetic problems. However, little is known of the effect of periodontitis on orthodontic treatment. Thus, ...

    Authors: Jieni Zhang, Shaonan Zhou, Ruoxuan Li, Tian Cao, Hui Zheng, Xuedong Wang, Yanheng Zhou, Ning Du, Feng Chen and Jiuxiang Lin

    Citation: Proteome Science 2012 10:63

    Content type: Research

    Published on:

  7. Genome-wide statistics established that long intrinsically disordered regions (over 30 residues) are predicted in a large part of proteins in all eukaryotes, with a higher ratio in trans-membrane proteins. At ...

    Authors: Claude Nespoulous, Valérie Rofidal, Nicolas Sommerer, Sonia Hem and Michel Rossignol

    Citation: Proteome Science 2012 10:62

    Content type: Research

    Published on:

  9. Dengue fever is the most important arthropod born viral disease of public health significance. Although most patients suffer only from flu-like symptoms, a small group of patient experiences more severe forms ...

    Authors: Romain Fragnoud, Javier Yugueros-Marcos, Alexandre Pachot and Frederic Bedin

    Citation: Proteome Science 2012 10:60

    Content type: Research

    Published on:

  10. Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. P...

    Authors: Dinesh Kumar Jaiswal, Doel Ray, Pratigya Subba, Poonam Mishra, Saurabh Gayali, Asis Datta, Subhra Chakraborty and Niranjan Chakraborty

    Citation: Proteome Science 2012 10:59

    Content type: Research

    Published on:

  11. Sesamia nonagrioides is a noctuid that feeds on maize, sugar cane and sorghum in North Africa and Southern Europe. Larvae reared under long day conditions pupate after 5 or 6 larval instars, whereas larvae reare...

    Authors: Meritxell Pérez-Hedo, Isabel Sánchez-López and Matilde Eizaguirre

    Citation: Proteome Science 2012 10:58

    Content type: Research

    Published on:

  12. MYC2, a basic helix-loop-helix (bHLH) domain-containing transcription factor, participates in the jasmonate (JA) signaling pathway and is involved in the modulation of diverse JA functions. However, a comprehe...

    Authors: Jing Guo, Qiuying Pang, Lihua Wang, Ping Yu, Nan Li and Xiufeng Yan

    Citation: Proteome Science 2012 10:57

    Content type: Research

    Published on:

  13. Protein extraction from formalin-fixed paraffin-embedded (FFPE) tissues is challenging due to extensive molecular crosslinking that occurs upon formalin fixation. Reverse-phase protein array (RPPA) is a high-t...

    Authors: Huifang Guo, Wenbin Liu, Zhenlin Ju, Pheroze Tamboli, Eric Jonasch, Gordon B Mills, Yiling Lu, Bryan T Hennessy and Dimitra Tsavachidou

    Citation: Proteome Science 2012 10:56

    Content type: Methodology

    Published on:

  14. The field of biomarker discovery, development and application has been the subject of intense interest and activity, especially with the recent emergence of new technologies, such as proteomics-based approache...

    Authors: Carolina Fernández-Costa, Valentina Calamia, Patricia Fernández-Puente, José-Luis Capelo-Martínez, Cristina Ruiz-Romero and Francisco J Blanco

    Citation: Proteome Science 2012 10:55

    Content type: Research

    Published on:

  16. The most frequent and malignant brain cancer is glioblastoma multiforme (GBM). In gliomas, tumor progression and poor prognosis are associated with the tumorigenic ability of the cells. U87MG cells (wild-type ...

    Authors: Anelisa Ramão, Marcela Gimenez, Helen Julie Laure, Clarice Izumi, Rodrigo Cesar dos Santos Vida, Sueli Oba-Shinjo, Suely Kazue Nagahashi Marie and Jose Cesar Rosa

    Citation: Proteome Science 2012 10:53

    Content type: Research

    Published on:

  17. Protein phosphatase 1 (PP1) is one of the major phosphatases responsible for protein dephosphorylation in eukaryotes. Protein phosphatase 1 regulatory subunit 12B (PPP1R12B), one of the regulatory subunits of ...

    Authors: Kimberly Pham, Paul Langlais, Xiangmin Zhang, Alex Chao, Morgan Zingsheim and Zhengping Yi

    Citation: Proteome Science 2012 10:52

    Content type: Research

    Published on:

  19. A giant congenital melanocytic nevus (GCMN) is a malformation of the pigment cells. It is a distress to the patients for two reasons: one is disfigurement, and the other is the possibility of malignant changes...

    Authors: Hyoung Kyu Kim, Yong Kyu Kim, In-Sung Song, Sung-Ryul Lee, Seung Hun Jeong, Min Hee Kim, Dae Yun Seo, Nari Kim, Byoung Doo Rhee, Kyoung Soo Ko, Kwan Chul Tark, Chul Gyoo Park, Je-Yoel Cho and Jin Han

    Citation: Proteome Science 2012 10:50

    Content type: Research

    Published on:

  20. Odontogenic myxoma (OM) is a benign, but locally invasive, neoplasm occurring in the jaws. However, the molecules implicated in its development are unknown. OM as well as Dental Follicle (DF), an odontogenic t...

    Authors: Alejandro García-Muñoz, Mario A Rodríguez, Ronell Bologna-Molina, Febe E Cázares-Raga, Fidel C Hernández-Hernández, J Eduardo Farfán-Morales, Juan J Trujillo, Carlos Licéaga-Escalera and Guillermo Mendoza-Hernández

    Citation: Proteome Science 2012 10:49

    Content type: Research

    Published on:

  21. Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine diseases worldwide. Despite its relevance, serum biomarkers associated with early-onset viral infection, when clinical ...

    Authors: Sem Genini, Thomas Paternoster, Alessia Costa, Sara Botti, Mario Vittorio Luini, Andrea Caprera and Elisabetta Giuffra

    Citation: Proteome Science 2012 10:48

    Content type: Research

    Published on:

  22. Liver infection with hepatitis B virus (HBV), a DNA virus of the Hepadnaviridae family, leads to severe disease, such as fibrosis, cirrhosis and hepatocellular carcinoma. The early steps of the viral life cycle a...

    Authors: Izabela Sokolowska, Cristina Dorobantu, Alisa G Woods, Alina Macovei, Norica Branza-Nichita and Costel C Darie

    Citation: Proteome Science 2012 10:47

    Content type: Research

    Published on:

  23. Human mesenchymal stem cells (hMSC) have recently raised the attention because of their therapeutic potential in the novel context of regenerative medicine. However, the safety of these new and promising cellu...

    Authors: Emanuele Capra, Riccardo Beretta, Valentina Parazzi, Mariele Viganò, Lorenza Lazzari, Antonella Baldi and Rosaria Giordano

    Citation: Proteome Science 2012 10:46

    Content type: Research

    Published on:

  24. Less than 25% of patients with a pelvic mass who are presented to a gynecologist will eventually be diagnosed with epithelial ovarian cancer. Since there is no reliable test to differentiate between different ...

    Authors: Wouter Wegdam, Perry D Moerland, Danielle Meijer, Shreyas M de Jong, Huub C J Hoefsloot, Gemma G Kenter, Marrije R Buist and Johannes MF G Aerts

    Citation: Proteome Science 2012 10:45

    Content type: Research

    Published on:

  25. Male wild type (WT) C57BL/6 mice are less capable of clearing bacteria and surviving from bacterial pneumonia than females. However, if an oxidative stress (acute ozone exposure) occurs before infection, the a...

    Authors: David S Phelps, Todd M Umstead and Joanna Floros

    Citation: Proteome Science 2012 10:44

    Content type: Research

    Published on:

  26. The pleiotropic effects of 3-Hydroxy-3-methylglutaryl coenzyme A reductase inhibitors (statins), which are independent from their cholesterol-lowering action, have been widely recognized in various biological ...

    Authors: Bin Huang, Fu An Li, Chien Hsing Wu and Danny Ling Wang

    Citation: Proteome Science 2012 10:43

    Content type: Research

    Published on:

  27. Hypoxia acts as a plant stress factor, particularly in cucumbers plants under hydroponic culture. Calcium is involved in stress signal transmission and in the growth of plants. To determine the effect of exoge...

    Authors: Lizhong He, Xiaomin Lu, Jing Tian, Yanjuan Yang, Bin Li, Jing Li and Shirong Guo

    Citation: Proteome Science 2012 10:42

    Content type: Research

    Published on:

  28. The heme-protein interactions are essential for various biological processes such as electron transfer, catalysis, signal transduction and the control of gene expression. The knowledge of heme binding residues...

    Authors: Yi Xiong, Juan Liu, Wen Zhang and Tao Zeng

    Citation: Proteome Science 2012 10(Suppl 1):S20

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  30. Many biological processes recognize in particular the importance of protein complexes, and various computational approaches have been developed to identify complexes from protein-protein interaction (PPI) netw...

    Authors: Jian Wang, Dong Xie, Hongfei Lin, Zhihao Yang and Yijia Zhang

    Citation: Proteome Science 2012 10(Suppl 1):S18

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  31. Protein-DNA docking is a very challenging problem in structural bioinformatics and has important implications in a number of applications, such as structure-based prediction of transcription factor binding sit...

    Authors: Jiadong Wu, Bo Hong, Takako Takeda and Jun-tao Guo

    Citation: Proteome Science 2012 10(Suppl 1):S17

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  32. Network alignment is one of the most common biological network comparison methods. Aligning protein-protein interaction (PPI) networks of different species is of great important to detect evolutionary conserve...

    Authors: Bingbo Wang and Lin Gao

    Citation: Proteome Science 2012 10(Suppl 1):S16

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  33. Transcription factors and microRNAs act in concert to regulate gene expression in eukaryotes. Numerous computational methods based on sequence information are available for the prediction of target genes of tr...

    Authors: Damian Roqueiro, Lei Huang and Yang Dai

    Citation: Proteome Science 2012 10(Suppl 1):S15

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  34. Recent advances in next-generation sequencing technologies have resulted in an exponential increase in the rate at which protein sequence data are being acquired. The k-gram feature representation, commonly used ...

    Authors: Cornelia Caragea, Adrian Silvescu and Prasenjit Mitra

    Citation: Proteome Science 2012 10(Suppl 1):S14

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  35. The goal of personalized medicine is to provide patients optimal drug screening and treatment based on individual genomic or proteomic profiles. Reverse-Phase Protein Array (RPPA) technology offers proteomic i...

    Authors: Dong-Chul Kim, Xiaoyu Wang, Chin-Rang Yang and Jean X Gao

    Citation: Proteome Science 2012 10(Suppl 1):S13

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  36. In a single proteomic project, tandem mass spectrometers can produce hundreds of millions of tandem mass spectra. However, majority of tandem mass spectra are of poor quality, it wastes time to search them for...

    Authors: Wenjun Lin, Jianxin Wang, Wen-Jun Zhang and Fang-Xiang Wu

    Citation: Proteome Science 2012 10(Suppl 1):S12

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  37. The regulatory mechanism of recombination is a fundamental problem in genomics, with wide applications in genome-wide association studies, birth-defect diseases, molecular evolution, cancer research, etc. In m...

    Authors: Min Wu, Chee-Keong Kwoh, Teresa M Przytycka, Jing Li and Jie Zheng

    Citation: Proteome Science 2012 10(Suppl 1):S11

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  38. Microarrays are widely used to investigate the blood stage of Plasmodium falciparum infection. Starting with synchronized cells, gene expression levels are continually measured over the 48-hour intra-erythrocytic...

    Authors: Wei Zhao, Justin Dauwels, Jacquin C Niles and Jianshu Cao

    Citation: Proteome Science 2012 10(Suppl 1):S10

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  39. Deciphering protein-protein interaction (PPI) in domain level enriches valuable information about binding mechanism and functional role of interacting proteins. The 3D structures of complex proteins are reliab...

    Authors: Yul Kim, Bumki Min and Gwan-Su Yi

    Citation: Proteome Science 2012 10(Suppl 1):S9

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  40. Analysis of multiple LC-MS based metabolomic studies is carried out to determine overlaps and differences among various experiments. For example, in large metabolic biomarker discovery studies involving hundre...

    Authors: Rency S Varghese, Bin Zhou, Mohammad R Nezami Ranjbar, Yi Zhao and Habtom W Ressom

    Citation: Proteome Science 2012 10(Suppl 1):S8

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  41. Identification of phosphorylation sites by computational methods is becoming increasingly important because it reduces labor-intensive and costly experiments and can improve our understanding of the common pro...

    Authors: Shan Gao, Shuo Xu, Yaping Fang and Jianwen Fang

    Citation: Proteome Science 2012 10(Suppl 1):S7

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  42. Identifying elements of protein structures that create differences in protein-ligand binding specificity is an essential method for explaining the molecular mechanisms underlying preferential binding. In some ...

    Authors: Brian Y Chen and Soutir Bandyopadhyay

    Citation: Proteome Science 2012 10(Suppl 1):S6

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  43. Despite computational challenges, elucidating conformations that a protein system assumes under physiologic conditions for the purpose of biological activity is a central problem in computational structural bi...

    Authors: Brian S Olson and Amarda Shehu

    Citation: Proteome Science 2012 10(Suppl 1):S5

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  44. Protein synthetic lethal genetic interactions are useful to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interactions remains uncl...

    Authors: Yuehua Zhang, Bo Li, Pradip K Srimani, Xuewen Chen and Feng Luo

    Citation: Proteome Science 2012 10(Suppl 1):S4

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  45. Recent computational techniques have facilitated analyzing genome-wide protein-protein interaction data for several model organisms. Various graph-clustering algorithms have been applied to protein interaction...

    Authors: Tak Chien Chiam and Young-Rae Cho

    Citation: Proteome Science 2012 10(Suppl 1):S3

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  46. Phenotypes exhibited by microorganisms can be useful for several purposes, e.g., ethanol as an alternate fuel. Sometimes, the target phenotype maybe required in combination with other phenotypes, in order to b...

    Authors: Kanchana Padmanabhan, Kevin Wilson, Andrea M Rocha, Kuangyu Wang, James R Mihelcic and Nagiza F Samatova

    Citation: Proteome Science 2012 10(Suppl 1):S2

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  47. Protein structures are better conserved than protein sequences, and consequently more functional information is available in structures than in sequences. However, proteins generally interact with other protei...

    Authors: Heng Yang, Rehman Qureshi and Ahmet Sacan

    Citation: Proteome Science 2012 10(Suppl 1):S1

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  48. Lymph node status is not part of the staging system for cervical cancer, but provides important information for prognosis and treatment. We investigated whether lymph node status can be predicted with proteomi...

    Authors: Toon Van Gorp, Isabelle Cadron, Anneleen Daemen, Bart De Moor, Etienne Waelkens and Ignace Vergote

    Citation: Proteome Science 2012 10:41

    Content type: Research

    Published on:

  49. When glucose is added to Saccharomyces cerevisiae grown in non-fermentable carbon sources, genes encoding ribosomal, cell-cycle, and glycolytic proteins are induced. By contrast, genes involved in mitochondrial f...

    Authors: Bennett J Giardina, Bruce A Stanley and Hui-Ling Chiang

    Citation: Proteome Science 2012 10:40

    Content type: Research

    Published on:

  50. Alcohol-induced injury has become one of the major causes for liver cirrhosis. However, the molecular mechanisms of ethanol-induced injury are not fully understood. To this end, we performed a dynamic plasma m...

    Authors: Xiaofang Jia, Lin Yin, Yanling Feng, Xia Peng, Fang Ma, Yamin Yao, Xiaoqian Liu, Zhiyong Zhang, Zhenghong Yuan and Lijun Zhang

    Citation: Proteome Science 2012 10:39

    Content type: Research

    Published on:

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