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Section edited by John Garavelli

This section incorporates all aspects of proteomic analysis including but not limited to: methods and applications for the analysis of post-translational modifications, proteomic, mass spectroscopic, and chemoinformatic data.

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  1. Content type: Methodology article

    Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides muc...

    Authors: Seongho Kim, Imhoi Koo, Aiqin Fang and Xiang Zhang

    Citation: BMC Bioinformatics 2011 12:235

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  2. Content type: Research article

    Diabetes like many diseases and biological processes is not mono-causal. On the one hand multi-factorial studies with complex experimental design are required for its comprehensive analysis. On the other hand,...

    Authors: Chris Bauer, Frank Kleinjung, Celia J Smith, Mark W Towers, Ali Tiss, Alexandra Chadt, Tanja Dreja, Dieter Beule, Hadi Al-Hasani, Knut Reinert, Johannes Schuchhardt and Rainer Cramer

    Citation: BMC Bioinformatics 2011 12:140

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  3. Content type: Research article

    The goal of metabolomics analyses is a comprehensive and systematic understanding of all metabolites in biological samples. Many useful platforms have been developed to achieve this goal. Gas chromatography co...

    Authors: Hiroshi Tsugawa, Yuki Tsujimoto, Masanori Arita, Takeshi Bamba and Eiichiro Fukusaki

    Citation: BMC Bioinformatics 2011 12:131

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  4. Content type: Software

    High-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generatio...

    Authors: William S Sanders, Nan Wang, Susan M Bridges, Brandon M Malone, Yoginder S Dandass, Fiona M McCarthy, Bindu Nanduri, Mark L Lawrence and Shane C Burgess

    Citation: BMC Bioinformatics 2011 12:115

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  5. Content type: Software

    Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are al...

    Authors: Mi-Youn K Brusniak, Sung-Tat Kwok, Mark Christiansen, David Campbell, Lukas Reiter, Paola Picotti, Ulrike Kusebauch, Hector Ramos, Eric W Deutsch, Jingchun Chen, Robert L Moritz and Ruedi Aebersold

    Citation: BMC Bioinformatics 2011 12:78

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  6. Content type: Software

    The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary sig...

    Authors: Harald Barsnes, Marc Vaudel, Niklaas Colaert, Kenny Helsens, Albert Sickmann, Frode S Berven and Lennart Martens

    Citation: BMC Bioinformatics 2011 12:70

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  7. Content type: Research article

    Metal-containing proteins comprise a diverse and sizable category within the proteomes of organisms, ranging from proteins that use metals to catalyze reactions to proteins in which metals play key structural ...

    Authors: W Andrew Lancaster, Jeremy L Praissman, Farris L Poole II, Aleksandar Cvetkovic, Angeli Lal Menon, Joseph W Scott, Francis E Jenney Jr, Michael P Thorgersen, Ewa Kalisiak, Junefredo V Apon, Sunia A Trauger, Gary Siuzdak, John A Tainer and Michael W W Adams

    Citation: BMC Bioinformatics 2011 12:64

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  8. Content type: Methodology article

    The rapid identification of Bacillus spores and bacterial identification are paramount because of their implications in food poisoning, pathogenesis and their use as potential biowarfare agents. Many automated an...

    Authors: Elon Correa and Royston Goodacre

    Citation: BMC Bioinformatics 2011 12:33

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  9. Content type: Research article

    Most predictive methods currently available for the identification of protein secretion mechanisms have focused on classically secreted proteins. In fact, only two methods have been reported for predicting non...

    Authors: Daniel Restrepo-Montoya, Camilo Pino, Luis F Nino, Manuel E Patarroyo and Manuel A Patarroyo

    Citation: BMC Bioinformatics 2011 12:21

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  10. Content type: Software

    Proton Magnetic Resonance (MR) Spectroscopy (MRS) is a widely available technique for those clinical centres equipped with MR scanners. Unlike the rest of MR-based techniques, MRS yields not images but spectra...

    Authors: Alexander Pérez-Ruiz, Margarida Julià-Sapé, Guillem Mercadal, Iván Olier, Carles Majós and Carles Arús

    Citation: BMC Bioinformatics 2010 11:581

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  11. Content type: Research article

    Tandem mass spectrometry-based database searching has become an important technology for peptide and protein identification. One of the key challenges in database searching is the remarkable increase in comput...

    Authors: Chen Zhou, Hao Chi, Le-Heng Wang, You Li, Yan-Jie Wu, Yan Fu, Rui-Xiang Sun and Si-Min He

    Citation: BMC Bioinformatics 2010 11:577

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  12. Content type: Methodology article

    Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA...

    Authors: Gift Nyamundanda, Lorraine Brennan and Isobel Claire Gormley

    Citation: BMC Bioinformatics 2010 11:571

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  13. Content type: Methodology article

    Bioinformatics data analysis often deals with additive mixtures of signals for which only class labels are known. Then, the overall goal is to estimate class related signals for data mining purposes. A conveni...

    Authors: Carsten Henneges, Pavel Laskov, Endang Darmawan, Jürgen Backhaus, Bernd Kammerer and Andreas Zell

    Citation: BMC Bioinformatics 2010 11:561

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  14. Content type: Research article

    While occurring enzymatically in biological systems, O-linked glycosylation affects protein folding, localization and trafficking, protein solubility, antigenicity, biological activity, as well as cell-cell in...

    Authors: Shu-An Chen, Tzong-Yi Lee and Yu-Yen Ou

    Citation: BMC Bioinformatics 2010 11:536

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  15. Content type: Research article

    Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cle...

    Authors: Ilenia Giangreco, Orazio Nicolotti, Angelo Carotti, Francesco De Carlo, Gianfranco Gargano and Roberto Bellotti

    Citation: BMC Bioinformatics 2010 11:500

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  16. Content type: Software

    Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'o...

    Authors: Harriet J Muncey, Rebecca Jones, Maria De Iorio and Timothy MD Ebbels

    Citation: BMC Bioinformatics 2010 11:496

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  17. Content type: Methodology article

    Mass spectrometry (MS) is an essential analytical tool in proteomics. Many existing algorithms for peptide detection are based on isotope template matching and usually work at different charge states separatel...

    Authors: Youting Sun, Jianqiu Zhang, Ulisses Braga-Neto and Edward R Dougherty

    Citation: BMC Bioinformatics 2010 11:490

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  18. Content type: Research article

    Establishing the relationship between an organism's genome sequence and its phenotype is a fundamental challenge that remains largely unsolved. Accurately predicting microbial phenotypes solely based on genomi...

    Authors: Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cedric Notredame and Peter Meinicke

    Citation: BMC Bioinformatics 2010 11:481

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  19. Content type: Research article

    Proteasomes play a central role in the major histocompatibility class I (MHCI) antigen processing pathway. They conduct the proteolytic degradation of proteins in the cytosol, generating the C-terminus of CD8 ...

    Authors: Carmen M Diez-Rivero, Esther M Lafuente and Pedro A Reche

    Citation: BMC Bioinformatics 2010 11:479

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  20. Content type: Research article

    MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA levels. Computational prediction of miRNA...

    Authors: Hui Liu, Dong Yue, Yidong Chen, Shou-Jiang Gao and Yufei Huang

    Citation: BMC Bioinformatics 2010 11:476

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  21. Content type: Research article

    There is a vast need to find clinically applicable protein biomarkers as support in cancer diagnosis and tumour classification. In proteomics research, a number of methods can be used to obtain systemic inform...

    Authors: Lina Hultin Rosenberg, Bo Franzén, Gert Auer, Janne Lehtiö and Jenny Forshed

    Citation: BMC Bioinformatics 2010 11:468

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  22. Content type: Software

    Protein identification using mass spectrometry is an important tool in many areas of the life sciences, and in proteomics research in particular. Increasing the number of proteins correctly identified is depen...

    Authors: Leo C McHugh and Jonathan W Arthur

    Citation: BMC Bioinformatics 2010 11:448

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  23. Content type: Research article

    Data generated using 'omics' technologies are characterized by high dimensionality, where the number of features measured per subject vastly exceeds the number of subjects in the study. In this paper, we consi...

    Authors: Yu Guo, Armin Graber, Robert N McBurney and Raji Balasubramanian

    Citation: BMC Bioinformatics 2010 11:447

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  24. Content type: Research article

    Robust biomarkers are needed to improve microbial identification and diagnostics. Proteomics methods based on mass spectrometry can be used for the discovery of novel biomarkers through their high sensitivity ...

    Authors: Ali Al-Shahib, Raju Misra, Nadia Ahmod, Min Fang, Haroun Shah and Saheer Gharbia

    Citation: BMC Bioinformatics 2010 11:437

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  25. Content type: Methodology article

    Generally speaking, different classifiers tend to work well for certain types of data and conversely, it is usually not known a priori which algorithm will be optimal in any given classification application. I...

    Authors: Susmita Datta, Vasyl Pihur and Somnath Datta

    Citation: BMC Bioinformatics 2010 11:427

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  26. Content type: Methodology article

    MicroRNAs (miRNAs) are a class of important gene regulators. The number of identified miRNAs has been increasing dramatically in recent years. An emerging major challenge is the interpretation of the genome-sc...

    Authors: Ming Lu, Bing Shi, Juan Wang, Qun Cao and Qinghua Cui

    Citation: BMC Bioinformatics 2010 11:419

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  27. Content type: Software

    Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches...

    Authors: Tomáš Pluskal, Sandra Castillo, Alejandro Villar-Briones and Matej Orešič

    Citation: BMC Bioinformatics 2010 11:395

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  28. Content type: Software

    Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins...

    Authors: Mirva Piippo, Niina Lietzén, Olli S Nevalainen, Jussi Salmi and Tuula A Nyman

    Citation: BMC Bioinformatics 2010 11:320

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  29. Content type: Methodology article

    High resolution mass spectrometry has been employed to rapidly and accurately type and subtype influenza viruses. The detection of signature peptides with unique theoretical masses enables the unequivocal assi...

    Authors: Jason WH Wong, Alexander B Schwahn and Kevin M Downard

    Citation: BMC Bioinformatics 2010 11:266

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)


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