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  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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:

  14. 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:

  15. 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:

  16. Microcystis aeruginosa is a species of cyanobacteria commonly found in a number of countries and frequently related to animal poisoning episodes due to its capacity to produce the cyanotoxin known as microcystin...

    Authors: Ângela Tonietto, Bernardo A Petriz, Wérika C Araújo, Ângela Mehta, Beatriz S Magalhães and Octávio L Franco
    Citation: Proteome Science 2012 10:38
    Content type: Research Published on:

  17. Shotgun proteomics represents an attractive technical framework for the study of membrane proteins that are generally difficult to resolve using two-dimensional gel electrophoresis. The use of iTRAQ, a set of ...

    Authors: Cosette Abdallah, Kjell Sergeant, Christelle Guillier, Eliane Dumas-Gaudot, Céline C Leclercq and Jenny Renaut
    Citation: Proteome Science 2012 10:37
    Content type: Research Published on:

  18. Although osteoarthritis (OA) is a highly prevalent joint disease, to date, no reliable biomarkers have been found for the disease. In this study, we attempted to identify factors the amounts of which significa...

    Authors: Isao Fukuda, Takeshi Ishihara, Shigeki Ohmachi, Ikue Sakikawa, Atsushi Morita, Minoru Ikeda, Shoji Yamane, Tomoko Toyosaki-Maeda, Yoshihiko Takinami, Hiroyuki Okamoto, Yoshito Numata and Naoshi Fukui
    Citation: Proteome Science 2012 10:36
    Content type: Research Published on:

  20. Podophyllotoxin (PTOX), the precursor for semi-synthesis of cancer therapeutics like etoposide, teniposide and etophos, is primarily obtained from an endangered medicinal herb, Podophyllum hexandrum Royle. PTOX, ...

    Authors: Dipto Bhattacharyya, Ragini Sinha, Srijani Ghanta, Amrita Chakraborty, Saptarshi Hazra and Sharmila Chattopadhyay
    Citation: Proteome Science 2012 10:34
    Content type: Research Published on:

  21. Signal peptide peptidase (SPP), a member of the presenilin-like intra-membrane cleaving aspartyl protease family, migrates on Blue Native (BN) gels as 100 kDa, 200 kDa and 450 kDa species. SPP has recently bee...

    Authors: Stephen Hsueh-Jeng Lu, Amy Hye Won Jeon, Gerold Schmitt-Ulms, Seema Qamar, Roger Dodd, Beth McDonald, Yi Li, William Meadows, Katie Cox, Christopher Bohm, Fusheng Chen, Paul Fraser and Peter St George-Hyslop
    Citation: Proteome Science 2012 10:33
    Content type: Research Published on:

  22. Newcastle disease virus (NDV) is an enveloped RNA virus, bearing severe economic losses to the poultry industry worldwide. Previous virion proteomic studies have shown that enveloped viruses carry multiple hos...

    Authors: Xiangpeng Ren, Chunyi Xue, Qingming Kong, Chengwen Zhang, Yingzuo Bi and Yongchang Cao
    Citation: Proteome Science 2012 10:32
    Content type: Research Published on:

  23. Refractory anemia with excess blasts subtype 1 (RAEB-1) is a subgroup of myelodysplastic syndrome. It represents a heterogeneous group of oncohematological bone marrow diseases, which occur particularly in eld...

    Authors: Pavel Májek, Zuzana Reicheltová, Jiří Suttnar, Jaroslav Čermák and Jan E Dyr
    Citation: Proteome Science 2012 10:31
    Content type: Research Published on:

  24. The pathogenic mold Aspergillus fumigatus is the most frequent infectious cause of death in severely immunocompromised individuals such as leukemia and bone marrow transplant patients. Germination of inhaled coni...

    Authors: Moo-Jin Suh, Natalie D Fedorova, Steven E Cagas, Susan Hastings, Robert D Fleischmann, Scott N Peterson, David S Perlin, William C Nierman, Rembert Pieper and Michelle Momany
    Citation: Proteome Science 2012 10:30
    Content type: Research Published on:

  25. Binge ethanol in rats after chronic ethanol exposure augments necrosis and steatosis in the liver. In this study, two-dimensional gel electrophoresis proteomic profiles of liver of control, chronic ethanol, co...

    Authors: Annayya R Aroor, Lowery J Roy, Ricardo J Restrepo, Brian P Mooney and Shivendra D Shukla
    Citation: Proteome Science 2012 10:29
    Content type: Research Published on:

  26. Invertebrate biominerals are characterized by their extraordinary functionality and physical properties, such as strength, stiffness and toughness that by far exceed those of the pure mineral component of such...

    Authors: Karlheinz Mann, Eric Edsinger-Gonzales and Matthias Mann
    Citation: Proteome Science 2012 10:28
    Content type: Research Published on:

  28. The hypothalamus plays a pivotal role in numerous mechanisms highly relevant to the maintenance of body homeostasis, such as the control of food intake and energy expenditure. Impairment of these mechanisms ha...

    Authors: Amanda P Pedroso, Regina L H Watanabe, Kelse T Albuquerque, Mônica M Telles, Maria C C Andrade, Juliana D Perez, Maísa M Sakata, Mariana L Lima, Debora Estadella, Cláudia M O Nascimento, Lila M Oyama, José C Rosa, Dulce E Casarini and Eliane B Ribeiro
    Citation: Proteome Science 2012 10:26
    Content type: Research Published on:

  29. The rice roots are highly salt-sensitive organ and primary root growth is rapidly suppressed by salt stress. Sucrose nonfermenting 1-related protein kinase2 (SnRK2) family is one of the key regulator of hyper-...

    Authors: Myung Hee Nam, Sun Mi Huh, Kyung Mi Kim, Woong Woong Park, Jong Bok Seo, Kun Cho, Dool Yi Kim, Beom Gi Kim and In In Yoon
    Citation: Proteome Science 2012 10:25
    Content type: Research Published on:

  30. Infectious bronchitis virus (IBV) is first to be discovered coronavirus which is probably endemic in all regions with intensive impact on poultry production. In this study, we used two-dimensional gel electrop...

    Authors: Zhongzan Cao, Zongxi Han, Yuhao Shao, Xiaoli Liu, Junfeng Sun, Demin Yu, Xiangang Kong and Shengwang Liu
    Citation: Proteome Science 2012 10:24
    Content type: Research Published on:

  31. Although chronic myeloid leukemia (CML) treatment has improved since the introduction of imatinib mesylate (IM), cases of resistance have been reported. This resistance has been associated with the emergence o...

    Authors: Stephany Corrêa, Luciana Pizzatti, Bárbara Du Rocher, André Mencalha, Daniela Pinto and Eliana Abdelhay
    Citation: Proteome Science 2012 10:23
    Content type: Research Published on:

  32. Effective diagnosis of Johne's disease (JD), particularly at the stage of early subclinical infection, remains one of the greatest challenges for the control of JD worldwide. The IFN-γ test of cell mediated im...

    Authors: James W Wynne, Brian J Shiell, Michelle L Colgrave, Jill A Vaughan, Gary Beddome and Wojtek P Michalski
    Citation: Proteome Science 2012 10:22
    Content type: Research Published on:

  33. Biomarkers released from the heart at early stage of ischemia are very important to diagnosis of ischemic heart disease and salvage myocytes from death. Known specific markers for blood tests including CK-MB, ...

    Authors: Hong Li, Jiyuan Li, Ying Wang and Tiande Yang
    Citation: Proteome Science 2012 10:21
    Content type: Research Published on:

  34. Schwann cells (SCs) are the principal glial cells of the peripheral nervous system with a wide range of biological functions. SCs play a key role in peripheral nerve regeneration and are involved in several he...

    Authors: Mi Shen, Yuhua Ji, Shuqiang Zhang, Haiyan Shi, Gang Chen, Xiaosong Gu and Fei Ding
    Citation: Proteome Science 2012 10:20
    Content type: Research Published on:

  35. We describe a novel antigen-retrieval method using a micro-sized chamber for mass spectrometry (MS) analysis to identify proteins that are preferentially eluted from formalin-fixed paraffin-embedded (FFPE) sam...

    Authors: Keiichi Hatakeyama, Kanako Wakabayashi-Nakao, Yutaka Aoki, Shun-ichiro Ogura, Ken Yamaguchi, Takashi Nakajima, Taka-Aki Sato, Tohru Mochizuki and Isamu Hayashi
    Citation: Proteome Science 2012 10:19
    Content type: Methodology Published on:

  36. There are currently no reliable markers of acute domoic acid toxicosis (DAT) for California sea lions. We investigated whether patterns of serum peptides could diagnose acute DAT. Serum peptides were analyzed ...

    Authors: Benjamin A Neely, Jennifer L Soper, Denise J Greig, Kevin P Carlin, Elizabeth G Favre, Frances MD Gulland, Jonas S Almeida and Michael G Janech
    Citation: Proteome Science 2012 10:18
    Content type: Research Published on:

  37. Proteins that are associated with hypertension may be identified by comparing the 2-dimensional gel electrophoresis (2-DE) profiles of the sera of spontaneously hypertensive rats (SHR) with those generated fro...

    Authors: Norhaniza Aminudin, Nur-Atiqah H Abdullah, Hasni Misbah, Saiful A Karsani, Ruby Husain, See Z Hoe and Onn H Hashim
    Citation: Proteome Science 2012 10:17
    Content type: Research Published on:

  40. Tuberculosis (TB) is the most threatening infectious disease globally. Although progress has been made to reduce global incidence of TB, emergence of multidrug resistant (MDR) TB threatens to undermine these a...

    Authors: Neelja Singhal, Prashant Sharma, Manish Kumar, Beenu Joshi and Deepa Bisht
    Citation: Proteome Science 2012 10:14
    Content type: Research Published on:

  41. Recent advances in liquid chromatography-mass spectrometry (LC-MS) technology have led to more effective approaches for measuring changes in peptide/protein abundances in biological samples. Label-free LC-MS m...

    Authors: Leepika Tuli, Tsung-Heng Tsai, Rency S Varghese, Jun Feng Xiao, Amrita Cheema and Habtom W Ressom
    Citation: Proteome Science 2012 10:13
    Content type: Research Published on:

  42. Early diagnosis and treatment of Mycobacterium tuberculosis infection can prevent most deaths resulting from this pathogen; however, multidrug-resistant strains present serious threats to global tuberculosis cont...

    Authors: Lu Zhang, Qingzhong Wang, Wenjie Wang, Yanyan Liu, Jie Wang, Jun Yue, Ying Xu, Wenxi Xu, ZhenLing Cui, Xuelian Zhang and Honghai Wang
    Citation: Proteome Science 2012 10:12
    Content type: Research Published on:

  43. A contemporary view of the cancer genome reveals extensive rearrangement compared to normal cells. Yet how these genetic alterations translate into specific proteomic changes that underpin acquiring the hallma...

    Authors: Yogesh M Kulkarni and David J Klinke II
    Citation: Proteome Science 2012 10:11
    Content type: Research Published on:

  44. Trichinellosis is a zoonotic disease in humans caused by Trichinella spp. The present study was undertaken to discover excretory-secretory (E-S) proteins from T. spiralis and T. britovi muscle larvae (ML) that ho...

    Authors: Justyna Bien, Anu Näreaho, Pekka Varmanen, Katarzyna Gozdzik, Bozena Moskwa, Wladyslaw Cabaj, Tuula A Nyman and Kirsi Savijoki
    Citation: Proteome Science 2012 10:10
    Content type: Research Published on:

  45. Protein expression profiles throughout 28 days of peripheral nerve regeneration were characterized using an established rat sciatic nerve transection injury model. Reverse phase protein microarrays were used t...

    Authors: David J Bryan, C Robert Litchfield, Jeffrey V Manchio, Tanya Logvinenko, Antonia H Holway, John Austin, Ian C Summerhayes and Kimberly M Rieger-Christ
    Citation: Proteome Science 2012 10:9
    Content type: Research Published on:

  46. Electron Transfer Dissociation [ETD] can dissociate multiply charged precursor polypeptides, providing extensive peptide backbone cleavage. ETD spectra contain charge reduced precursor peaks, usually of high i...

    Authors: Viswanadham Sridhara, Dina L Bai, An Chi, Jeffrey Shabanowitz, Donald F Hunt, Stephen H Bryant and Lewis Y Geer
    Citation: Proteome Science 2012 10:8
    Content type: Methodology Published on:

  47. Naturally occurring native peptides provide important information about physiological states of an organism and its changes in disease conditions but protocols and methods for assessing their abundance are not...

    Authors: Juraj Lenco, Renny Lan, Nathan Edwards and Radoslav Goldman
    Citation: Proteome Science 2012 10:7
    Content type: Methodology Published on:

  48. Salmonella enterica serovar Hadar (S. Hadar) is a highly prevalent foodborne pathogen and therefore a major cause of human gastroenteritis worldwide. Outer membrane proteins whose production is often regulated b...

    Authors: Sarra Snoussi, Alya El May, Laurent Coquet, Philippe Chan, Thierry Jouenne, Ahmed Landoulsi and Emmanuelle DÉ
    Citation: Proteome Science 2012 10:6
    Content type: Research Published on:

  49. Three dimensional (3D) growths of cancer cells in vitro are more reflective of in situ cancer cell growth than growth in monolayer (2D). The present study is designed to determine changes in protein and phosph...

    Authors: Victor A Levin, Sonali Panchabhai, Li Shen and Keith A Baggerly
    Citation: Proteome Science 2012 10:5
    Content type: Research Published on:

  50. Somatic embryogenesis (SE) is a complex biological process that occurs under inductive conditions and causes fully differentiated cells to be reprogrammed to an embryo like state. In order to get a better insi...

    Authors: Golandam Sharifi, Hassan Ebrahimzadeh, Behzad Ghareyazie, Javad Gharechahi and Elaheh Vatankhah
    Citation: Proteome Science 2012 10:3
    Content type: Research Published on:
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ISSN: 1477-5956