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Proteomics

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

    To address high-dimensional genomic data, most of the proposed prediction methods make use of genomic data alone without considering clinical data, which are often available and known to have predictive value....

    Authors: Caroline Bazzoli and Sophie Lambert-Lacroix

    Citation: BMC Bioinformatics 2018 19:314

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  2. Content type: Research Article

    The oxidation of protein-bound methionine to form methionine sulfoxide, has traditionally been regarded as an oxidative damage. However, recent evidences support the view of this reversible reaction as a regul...

    Authors: Juan C. Aledo, Francisco R. Cantón and Francisco J. Veredas

    Citation: BMC Bioinformatics 2017 18:430

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  3. Content type: Software

    Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Me...

    Authors: Jeremy P. Koelmel, Nicholas M. Kroeger, Candice Z. Ulmer, John A. Bowden, Rainey E. Patterson, Jason A. Cochran, Christopher W. W. Beecher, Timothy J. Garrett and Richard A. Yost

    Citation: BMC Bioinformatics 2017 18:331

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  4. Content type: Methodology Article

    Identifying disease correlated features early before large number of molecules are impacted by disease progression with significant abundance change is very advantageous to biologists for developing early dise...

    Authors: Sirajul Salekin, Mehrab Ghanat Bari, Itay Raphael, Thomas G. Forsthuber and Jianqiu (Michelle) Zhang

    Citation: BMC Bioinformatics 2017 18:313

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  5. Content type: Methodology article

    Characterization of mature protein N-termini by large scale proteomics is challenging. This is especially true for proteins undergoing cleavage of transit peptides when they are targeted to specific organelles...

    Authors: Willy Vincent Bienvenut, Jean-Pierre Scarpelli, Johan Dumestier, Thierry Meinnel and Carmela Giglione

    Citation: BMC Bioinformatics 2017 18:182

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  6. Content type: Research article

    Many plant pathogen secretory proteins are known to be elicitors or pathogenic factors,which play an important role in the host-pathogen interaction process. Bioinformatics approaches make possible the large s...

    Authors: Lan Jing, Dandan Guo, Wenjie Hu and Xiaofan Niu

    Citation: BMC Bioinformatics 2017 18:166

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  7. Content type: Research Article

    High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between...

    Authors: Tim O. F. Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Alexander Leichtle, Jan Vybiral, Gitta Kutyniok and Christof Schütte

    Citation: BMC Bioinformatics 2017 18:160

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  8. Content type: Software

    High-accuracy mass spectrometry enables near comprehensive quantification of the components of the cellular proteomes, increasingly including their chemically modified variants. Likewise, large-scale libraries...

    Authors: Paolo Cifani, Mojdeh Shakiba, Sagar Chhangawala and Alex Kentsis

    Citation: BMC Bioinformatics 2017 18:153

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  9. Content type: Research Article

    The classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species....

    Authors: Vera Rieder, Bernhard Blank-Landeshammer, Marleen Stuhr, Tilman Schell, Karsten Biß, Laxmikanth Kollipara, Achim Meyer, Markus Pfenninger, Hildegard Westphal, Albert Sickmann and Jörg Rahnenführer

    Citation: BMC Bioinformatics 2017 18:148

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  10. Content type: Methodology article

    High throughput metabolomics makes it possible to measure the relative abundances of numerous metabolites in biological samples, which is useful to many areas of biomedical research. However, missing values (M...

    Authors: Jasmit S. Shah, Shesh N. Rai, Andrew P. DeFilippis, Bradford G. Hill, Aruni Bhatnagar and Guy N. Brock

    Citation: BMC Bioinformatics 2017 18:114

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  11. Content type: Methodology article

    Tandem mass spectrometry (MS/MS) followed by database search is a main approach to identify peptides/proteins in proteomic studies. A lot of effort has been devoted to improve the identification accuracy and s...

    Authors: Chunwei Ma, Shaohang Xu, Geng Liu, Xin Liu, Xun Xu, Bo Wen and Siqi Liu

    Citation: BMC Bioinformatics 2017 18:109

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  12. Content type: Methodology article

    Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based o...

    Authors: Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert D. Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe Jr. and Denise M. Scholtens

    Citation: BMC Bioinformatics 2017 18:84

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  13. Content type: Software

    In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein struct...

    Authors: Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou and Jianlin Cheng

    Citation: BMC Bioinformatics 2016 17:517

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  14. Content type: Research article

    When combined with a clinical outcome variable, the size, complexity and nature of mass-spectrometry proteomics data impose great statistical challenges in the discovery of potential disease-associated biomark...

    Authors: Eleanor Stanley, Eleni Ioanna Delatola, Esther Nkuipou-Kenfack, William Spooner, Walter Kolch, Joost P. Schanstra, Harald Mischak and Thomas Koeck

    Citation: BMC Bioinformatics 2016 17:496

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  15. Content type: Research Article

    Proteomics of bacterial pathogens is a developing field exploring microbial physiology, gene expression and the complex interactions between bacteria and their hosts. One of the complications in proteomic appr...

    Authors: Dmitry Ischenko, Dmitry Alexeev, Egor Shitikov, Alexandra Kanygina, Maja Malakhova, Elena Kostryukova, Andrey Larin, Sergey Kovalchuk, Olga Pobeguts, Ivan Butenko, Nikolay Anikanov, Ilya Altukhov, Elena Ilina and Vadim Govorun

    Citation: BMC Bioinformatics 2016 17:450

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  16. Content type: Methodology Article

    Genome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challe...

    Authors: Laurence Yang, Ding Ma, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders and Bernhard O. Palsson

    Citation: BMC Bioinformatics 2016 17:391

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  17. Content type: Software

    Peptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental mass spectra with the theoretically digested peptides derived from a reference protein database....

    Authors: Bo Wen, Shaohang Xu, Ruo Zhou, Bing Zhang, Xiaojing Wang, Xin Liu, Xun Xu and Siqi Liu

    Citation: BMC Bioinformatics 2016 17:244

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  18. Content type: Research Article

    Aptamer-protein interacting pairs play a variety of physiological functions and therapeutic potentials in organisms. Rapidly and effectively predicting aptamer-protein interacting pairs is significant to desig...

    Authors: Lina Zhang, Chengjin Zhang, Rui Gao, Runtao Yang and Qing Song

    Citation: BMC Bioinformatics 2016 17:225

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  19. Content type: Research article

    Proteins are the important molecules which participate in virtually every aspect of cellular function within an organism in pairs. Although high-throughput technologies have generated considerable protein-prot...

    Authors: Yu-An Huang, Zhu-Hong You, Xing Chen, Keith Chan and Xin Luo

    Citation: BMC Bioinformatics 2016 17:184

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  20. Content type: Research Article

    Understanding the interactions between antibodies and the linear epitopes that they recognize is an important task in the study of immunological diseases. We present a novel computational method for the design...

    Authors: Rob Patro, Raquel Norel, Robert J. Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Luštrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky and Carl Kingsford

    Citation: BMC Bioinformatics 2016 17:155

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  21. Content type: Software

    Metabolomics experiments often comprise large numbers of biological samples resulting in huge amounts of data. This data needs to be inspected for plausibility before data evaluation to detect putative sources...

    Authors: Alexandra Maria Simader, Bernhard Kluger, Nora Katharina Nicole Neumann, Christoph Bueschl, Marc Lemmens, Gerald Lirk, Rudolf Krska and Rainer Schuhmacher

    Citation: BMC Bioinformatics 2015 16:341

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  22. Content type: Software

    Mass spectrometry is one of the most important techniques in the field of proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting p...

    Authors: H. López-Fernández, H. M. Santos, J. L. Capelo, F. Fdez-Riverola, D. Glez-Peña and M. Reboiro-Jato

    Citation: BMC Bioinformatics 2015 16:318

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  23. Content type: Database

    Spirulina (Arthrospira) platensis is the only cyanobacterium that in addition to being studied at the molecular level and subjected to gene manipulation, can also be mass cultivated in outdoor ponds for commerci...

    Authors: Jittisak Senachak, Supapon Cheevadhanarak and Apiradee Hongsthong

    Citation: BMC Bioinformatics 2015 16:233

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  24. Content type: Software

    Mass spectrometry analyses of complex protein samples yield large amounts of data and specific expertise is needed for data analysis, in addition to a dedicated computer infrastructure. Furthermore, the identi...

    Authors: Erik K Malm, Vaibhav Srivastava, Gustav Sundqvist and Vincent Bulone

    Citation: BMC Bioinformatics 2014 15:441

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  25. Content type: Methodology article

    Identification of individual components in complex mixtures is an important and sometimes daunting task in several research areas like metabolomics and natural product studies. NMR spectroscopy is an excellent...

    Authors: Tommy Öman, May-Britt Tessem, Tone F Bathen, Helena Bertilsson, Anders Angelsen, Mattias Hedenström and Trygve Andreassen

    Citation: BMC Bioinformatics 2014 15:413

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  26. Content type: Software

    Metabolomics is one of most recent omics technologies. It has been applied on fields such as food science, nutrition, drug discovery and systems biology. For this, gas chromatography-mass spectrometry (GC-MS) ...

    Authors: Raphael BM Aggio, Arno Mayor, Sophie Reade, Chris SJ Probert and Katya Ruggiero

    Citation: BMC Bioinformatics 2014 15:374

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  27. Content type: Research Article

    The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. Technologies like mass spectrometry are commonly being used in proteomic research. Mass spectr...

    Authors: Caroline Truntzer, Elise Mostacci, Aline Jeannin, Jean-Michel Petit, Patrick Ducoroy and Hervé Cardot

    Citation: BMC Bioinformatics 2014 15:385

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  28. Content type: Methodology article

    One of the major challenges in the field of vaccine design is identifying B-cell epitopes in continuously evolving viruses. Various tools have been developed to predict linear or conformational epitopes, each ...

    Authors: Yuh-Jyh Hu, Shun-Chien Lin, Yu-Lung Lin, Kuan-Hui Lin and Shun-Ning You

    Citation: BMC Bioinformatics 2014 15:378

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  29. Content type: Software

    A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins ...

    Authors: Christopher K Hobbs, Michelle Leung, Herbert H Tsang and H Alexander Ebhardt

    Citation: BMC Bioinformatics 2014 15:344

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  30. Content type: Methodology article

    Studies of functional modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approache...

    Authors: Jun Zhong Ji, Lang Jiao, Cui Cui Yang, Jia Wei Lv and Ai Dong Zhang

    Citation: BMC Bioinformatics 2014 15:325

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  31. Content type: Research article

    DNA-binding proteins are vital for the study of cellular processes. In recent genome engineering studies, the identification of proteins with certain functions has become increasingly important and needs to be...

    Authors: Li Song, Dapeng Li, Xiangxiang Zeng, Yunfeng Wu, Li Guo and Quan Zou

    Citation: BMC Bioinformatics 2014 15:298

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  32. Content type: Software

    In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell ...

    Authors: Pavankumar Videm, Deepika Gunasekaran, Bernd Schröder, Bettina Mayer, Martin L Biniossek and Oliver Schilling

    Citation: BMC Bioinformatics 2014 15:207

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  33. Content type: Research article

    Over the last 20 years in biotechnology, the production of recombinant proteins has been a crucial bioprocess in both biopharmaceutical and research arena in terms of human health, scientific impact and econom...

    Authors: Narjeskhatoon Habibi, Siti Z Mohd Hashim, Alireza Norouzi and Mohammed Razip Samian

    Citation: BMC Bioinformatics 2014 15:134

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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)

    Usage 
    4,129,368 downloads

    Social Media Impact
    4446 mentions

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