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Systems biology of the structural proteome

Elizabeth Brunk, Nathan Mih, Jonathan Monk, Zhen Zhang, Edward J. O'Brien, Spencer E. Bliven, Ke Chen, Roger L. Chang, Philip E. Bourne, Bernhard O. Palsson
2016 BMC Systems Biology  
systems biology and systems pharmacology.  ...  We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein  ...  This research was supported in part by the Intramural Research Program of the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (support to S.B.  ... 
doi:10.1186/s12918-016-0271-6 pmid:26969117 pmcid:PMC4787049 fatcat:7i3nenecp5eobeewh6rgvot32e

Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution and disease association

Shihab Dider, Jiadong Ji, Zheng Zhao, Lei Xie
2016 npj Systems Biology and Applications  
cellular context and on a structural proteome scale, and investigate the roles of these off-targets in impacting human physiology and pathology using text mining-based phenomics analysis.  ...  To understand the mechanisms of the side effects from FAAH inhibitors and other drugs, we develop a novel structural phenomics approach to identifying the physiological off-targets binding profile in the  ...  This research was supported by the National Library of Medicine of the National Institute of Health under the award number R01LM011986; and National Science Foundation under the award number CNS-0958379  ... 
doi:10.1038/npjsba.2016.23 pmid:28725477 pmcid:PMC5516858 fatcat:o5c7q6z2fza3bhmxvezwzxpkfm

Application of Systems Biology Technology in Research of Traditional Chinese Medicine

Ping LI, Li-ping YANG, Yue-wen GONG
2009 Journal of Traditional Chinese Medicine  
The technology platforms of systems biology, especially proteomics can provide useful tools for exploring essence of TCM syndromes and understanding principle of herbal formulation.  ...  Systems biology is an emerging science of the 21st century and its method and design of study resemble those of traditional Chinese medicine (TCM).  ...  Structural proteomics is to determine three dimensional structures of the all proteins mentioned above.  ... 
doi:10.1016/s0254-6272(09)60054-6 fatcat:thyjtqv4dffe7n77onjxjwok64

Expanding the uses of genome‐scale models with protein structures

Nathan Mih, Bernhard O Palsson
2019 Molecular Systems Biology  
In the late 2000s, a proposed interdisciplinary field of structural systems biology pitched the merger of these two approaches, with widespread applications in pharmacology, disease modeling, protein engineering  ...  Structural biology has historically taken the reductionist approach to deeply probe the inner workings of complex molecular machines.  ...  Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.15252/msb.20188601 pmid:31777175 pmcid:PMC6880182 fatcat:um26g7wm3bfojjcox5eie4f66y

Clinical Proteomics Perspective

Punit Kaur
2015 Journal of Proteomics & Bioinformatics  
The special issue Clinical Proteomics will consider studies in the area of structural biology, mass spectrometry, protein arrays, bioinformatics, cell biology, signal transduction and physiology where  ...  The journal welcomes papers in new and upcoming areas such as metabolomics, genomics, systems biology, toxicogenomics, pharmacoproteomics.  ... 
doi:10.4172/jpb.s8-e001 fatcat:gatp3tihdfbblgoghmnves3uoe

Pediatric proteomics an introduction

William L Stone
2012 Frontiers in bioscience (Scholar edition)  
Pediatric proteomics and medicine 3.1. Pediatric proteomics is a branch of clinical proteomics 3.2. Proteomics and systems biology 3.3. Clinical proteomics, proteins and biological functions 4.  ...  "Omics" and the central dogma of molecular biology 4.1. The original central dogma 4.2. The updated central dogma 4.3. Functional genomics 5. The complexity of human proteins 5.1.  ...  Proteomics and systems biology Proteomics is an integral component of systems biology (7) .  ... 
doi:10.2741/s319 pmid:22202110 fatcat:b6w37himbnakflkbdwckeqq4xm

Glyco-proteomics as compiled post-genomics insight for development of novel biomarkers: Challenges and tidings in debate

Mohamed Warda
2014 Journal of computer science and systems biology  
The dynamic proteomics, however, eventually targets the final cellular proteome outcome that structurally and functionally active with more opportunity for development of novel biomarkers of medical prognostic  ...  L ife is the outcome of interplay between genome and its expressed proteome. Last decade the human genome has been completely resolved.  ... 
doi:10.4172/0974-7230.s1.007 fatcat:g7rtvzfvebedbdni7yhysw3u6i

The Proteome of a Healthy Human during Physical Activity under Extreme Conditions

I M Larina, V A Ivanisenko, E N Nikolaev, A I Grigorev
2014 Acta Naturae  
The similarities and differences between the object and methods in systems biology, the OMICs (proteomics, transcriptomics, metabolomics) disciplines, and other related sciences have been studied.  ...  The review examines the new approaches in modern systems biology, in terms of their use for a deeper understanding of the physiological adaptation of a healthy human in extreme environments.  ...  development of the global study of the structures of genomes, proteomes, transcriptomes, metabolomes and other "-omes."  ... 
pmid:25349715 pmcid:PMC4207561 fatcat:xapdxjkiufgnrikvcj5ehmbfyi

Poster topics

2008 Journal of the American Society for Mass Spectrometry  
: Plasma Proteomics: New Approaches for Sample Preparation Proteomics: Biomarker Discovery 1 Proteomics: Clinical Applications Bioinformatics 1 Systems Biology: Quantitative TUESDAY POSTER  ...  Applications Proteomics: Biomarker Assays 1 Proteomics: New Approaches to Instrumentation Proteomics: Biomarker Discovery 3 Bioinformatics 3 Systems Biology: Interactions THURSDAY POSTER TOPICS  ... 
doi:10.1016/j.jasms.2008.04.006 fatcat:lemklubc4fhxzkjmrr4t74pgbe

Genomes, Proteomes, and the Central Dogma

S. Franklin, T. M. Vondriska
2011 Circulation: Cardiovascular Genetics  
S ystems biology, with its associated technologies of proteomics, genomics, and metabolomics, is driving the evolution of our understanding of cardiovascular physiology.  ...  We present 5 observations regarding how systems biology is guiding a revisiting of the central dogma: (1) It deemphasizes the unidirectional flow of information from genes to proteins; (2) it reveals the  ...  Sources of Funding Work in the Vondriska laboratory is supported in part by the National Heart, Lung, and Blood Institute at the NIH, the American Heart Association, and the Laubisch Endowment at UCLA.  ... 
doi:10.1161/circgenetics.110.957795 pmid:22010165 pmcid:PMC3200573 fatcat:5zcskk2tabhfdgd5mqtvso6qva

New journal on biological frontiers

Weihua Wu
2010 Frontiers in Biology  
The main topics will be bioinformatics, cell biology, developmental biology, molecular biology, molecular immunology, neurobiology, plant sciences, signal transduction, structural biology, and systems  ...  The journal will publish novel research of special significance in biology, especially in the areas of genomics, proteomics, neurobiology, genetics, developmental biology, biochemistry and molecular biology  ...  The main topics will be bioinformatics, cell biology, developmental biology, molecular biology, molecular immunology, neurobiology, plant sciences, signal transduction, structural biology, and systems  ... 
doi:10.1007/s11515-010-0199-y fatcat:uzsy3t6mhrauviv3i7jarihv2e

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology

Paolo Romano, Francesca Cordero
2016 BMC Bioinformatics  
The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology.  ...  The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics  ...  Moreover, the usage of proteomic data for structural bioinformatics and integrative systems biology is not yet sufficiently explored.  ... 
doi:10.1186/s12859-016-0907-y pmid:26960985 pmcid:PMC4896255 fatcat:az2a4fbdsvembc4aiywhxxb3me

Proteomic analysis of apoptosis induction by lariciresinol in human HepG2 cells

Zhan-Jun Ma, Xue-Xi Wang, Gang Su, Jing-Jing Yang, Ya-Juan Zhu, You-Wei Wu, Jing Li, Li Lu, Long Zeng, Hai-Xia Pei
2016 Chemico-Biological Interactions  
Proteomics is a current hot topic in the field of systems biology, and proteomics as applied to the study of complex TCM systems will undoubtedly facilitate new medical developments.  ...  Systems biology, which involves genomics, epigenomics, proteomics and metabolomics, seeks to describe the complex interactions among the components of biological systems and thus predict the behavior of  ... 
doi:10.1016/j.cbi.2016.07.011 pmid:27417256 fatcat:6o64yk5jerbctmzhzncmtfwrga

From high-throughput structural bioinformatics to integrative systems biology: NETTAB 2014

Francesca Cordero, Paolo DM Romano
2014 EMBnet journal  
The topics of the workshop will therefore relate to methods, tools, applications and perspectives on structural bioinformatics, proteomics and integrative systems biology.  ...  and management of highthroughput biological data, data integration, structural bioinformatics, functional proteomics, mass spectrometry, drug discovery, systems biology.  ... 
doi:10.14806/ej.20.0.772 fatcat:uu5cannhxjavnfh44re2sm5sue

Application of proteomics to ecology and population biology

T L Karr
2007 Heredity  
Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies  ...  Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and  ...  This work was funded in part by grants to TLK from the Royal Society (Wolfson Merit Award) and the Biotechnology and Biological Sciences Research Council (BB/C007670/1).  ... 
doi:10.1038/sj.hdy.6801008 pmid:17700638 fatcat:3wkpl4iyzjdc7lu5d24c7icupa
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