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Differential and Integral Views of Gene-Phenotype Relations: A Systems Biological Insight [chapter]

Denis Noble
2012 Lecture Notes in Computer Science  
.: Differential and Integral view of genetics in computational systems biology.  ...  This lecture uses an integrative systems biological view of the relationship between genotypes and phenotypes to clarify some conceptual problems in biological debates about causality.  ...  This lecture uses an integrative systems biological view of the relationship between genotypes and phenotypes to clarify some conceptual problems in biological debates about causality.  ... 
doi:10.1007/978-3-642-33636-2_1 fatcat:7xw7griu4vgi5kawnwwljlxpk4

Structural, functional and biological insights into the role of Mycobacterium tuberculosis VapBC11 toxin–antitoxin system: targeting a tRNase to tackle mycobacterial adaptation

Amar Deep, Prabhakar Tiwari, Sakshi Agarwal, Soni Kaundal, Saqib Kidwai, Ramandeep Singh, Krishan G Thakur
2018 Nucleic Acids Research  
Interestingly, overexpression of VapC11 resulted in the upregulation of chromosomal TA genes, suggesting the existence of highly coordinated crosstalk among TA systems.  ...  We used a combination of structural studies, molecular docking, mutational analysis and in vitro ribonuclease assays to enhance our understanding of the mode of substrate recognition by the VapC11 toxin  ...  The authors acknowledge the use of home-source X-ray and 3D facilities at CSIR-IMTECH.  ... 
doi:10.1093/nar/gky924 pmid:30329074 pmcid:PMC6265470 fatcat:5huzk742vnamdlje7yz6jnof4q

Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers

Robert Clarke, John J Tyson, Ming Tan, William T Baumann, Lu Jin, Jianhua Xuan, Yue Wang
2019 Endocrine-Related Cancer  
computational and mathematical models of the integrative, holistic functions of living systems.  ...  Endocrine-related cancers are well suited to study from a systems perspective because of the signaling complexities arising from the roles of growth factors, hormones, and their receptors as critical regulators  ...  is one of the central determinants of how signaling and function are related in biological systems.  ... 
doi:10.1530/erc-18-0309 pmid:30965282 pmcid:PMC7045974 fatcat:vamb4r65vbb5zobcov5ul52pjy

A network biology model of micronutrient related health

Ben van Ommen, Susan Fairweather-Tait, Andreas Freidig, Alwine Kardinaal, Augustin Scalbert, Suzan Wopereis
2008 British Journal of Nutrition  
New mechanistic insights have already been developed using biological network models, for example genes and protein-protein interactions in the aetiology of type 2 diabetes mellitus.  ...  The study of micronutrient-related health status requires a combination of data on markers of dietary exposure, markers of target function and biological response, health status metabolites, and disease  ...  The authors thank Dr John Newman (USDA Davis, USA), Dr Chris Evelo (Un Maastricht, Netherlands) and Prof John Hesketh (University of Newcastle, UK) for their discussions on parts of the selenium biological  ... 
doi:10.1017/s0007114508006922 pmid:18598592 fatcat:ctdidm2bmbf5roqnx57tashffm

Position Effects and Genetic Code in Relation to Epigenetic Systems

Seaward A. Sand
1961 American Naturalist  
We support Nanney in his re-emphasis of a distinction between genotype and phenotype and in the substantial insights of his contribution.  ...  Interactions among these heritable elements are of critical importance for biological control and integration.  ... 
doi:10.1086/282181 pmid:13746110 fatcat:75bjgwhsrnhsdh5bkqdzn5n7zy

Interaction relationships of osteoarthritis and rheumatoid arthritis related genes

Q Zhang, B Cheng, C-X Yang, H-A Ge
2014 European Review for Medical and Pharmacological Sciences  
We found most of those genes appear to play a key role in the anti-inflammatory and immunosuppressive effects. Our research would play a useful role in the diagnosis and treatment of OA and RA.  ...  Rheumatoid arthritis (RA) is a chronic, inflammatory type of arthritis. RA is also classified as a kind of autoimmune disease. To find the important genes in RA and OA.  ...  Materials and MethodS RA Related Genes An integrated analysis method was combined with the results of 3 studies that address a set of related research hypotheses.  ... 
pmid:24488905 fatcat:k5hxju3pgzettbsx4577loy3hi

PhysioSpace: Relating Gene Expression Experiments from Heterogeneous Sources Using Shared Physiological Processes

Michael Lenz, Bernhard M. Schuldt, Franz-Josef Müller, Andreas Schuppert, Enrique Hernandez-Lemus
2013 PLoS ONE  
The PhysioSpace is defined by a compendium of publicly available gene expression signatures representing a large set of biological phenotypes.  ...  Even though the time series data of cell line differentiation exhibited responses in larger clusters covering several biologically related patterns, top scoring patterns were highly consistent with a priory  ...  Schneckener for data preprocessing and helpful discussion.  ... 
doi:10.1371/journal.pone.0077627 pmid:24147039 pmcid:PMC3798402 fatcat:3yolk4ygdjga7nsfoohykhx6s4

Age-related epigenetic drift and phenotypic plasticity loss: implications in prevention of age-related human diseases

Yuanyuan Li, Trygve O Tollefsbol
2016 Epigenomics  
Acknowledgements The authors appreciate R Kala for proving insights for this manuscript. Financial & competing interests disclosure  ...  The plasticity of chromatin states and individual phenotype is a result of gene-environment interactions.  ...  A recent functional enrichment analysis revealed that the agingrelated methylation module is present in multiple genes that are involved in nervous system development, neuron differentiation and neurogenesis  ... 
doi:10.2217/epi-2016-0078 pmid:27882781 pmcid:PMC5618938 fatcat:xoob6u5c2rhtrip7byot52ido4

Dissecting spatio-temporal protein networks driving human heart development and related disorders

Kasper Lage, Kjeld Møllgård, Steven Greenway, Hiroko Wakimoto, Joshua M Gorham, Christopher T Workman, Eske Bendsen, Niclas T Hansen, Olga Rigina, Francisco S Roque, Cornelia Wiese, Vincent M Christoffels (+9 others)
2010 Molecular Systems Biology  
This design allows the formation of a complicated organ using simple building blocks, and suggests how mutations in the same genes can lead to diverse phenotypes.  ...  Aberrant organ development is associated with a wide spectrum of disorders, from schizophrenia to congenital heart disease, but systems-level insight into the underlying processes is very limited.  ...  KL is supported by a grant from 'Forskningsrådet for Sundhed og Sygdom'; and KL and PKD are supported by NICHD RO1 grant HD055150-03.  ... 
doi:10.1038/msb.2010.36 pmid:20571530 pmcid:PMC2913399 fatcat:xnf2baglmrbixld6dse4moy4we

DNA methylation in human lipid metabolism and related diseases

Kirstin Mittelstraß, Melanie Waldenberger
2018 Current Opinion in Lipidology  
Recent studies strongly support the importance of epigenetic modifications, such as DNA methylation, in lipid metabolism and related diseases for relevant biological insights, reliable biomarkers, and  ...  Summary The current review provides a literature overview of epigenetic modifications in lipid metabolism and other lipid-related phenotypes and diseases focusing on EWAS of DNA methylation from January  ...  Acknowledgements We would like to thank Rory Wilson and Sacha E. Horn for revision of the English text. Financial support and sponsorship  ... 
doi:10.1097/mol.0000000000000491 pmid:29517982 pmcid:PMC5882251 fatcat:gthfv6sf3ff3zmq5v5qnlnocfm

The Genetic Landscape of Parkinsonism-Related Dystonias and Atypical Parkinsonism-Related Syndromes

Monica Diez-Fairen, Pilar Alvarez Jerez, Joos Berghausen, Sara Bandres-Ciga
2021 International Journal of Molecular Sciences  
In recent decades, genetic research has nominated promising pathways and biological insights contributing to the etiological landscape of parkinsonism-related dystonias and atypical parkinsonism-related  ...  , often viewed as a precursor to Parkinson's disease.  ...  Democratization of data and resources is required. (3) A crucial step to gain biological insights underlying the clinical heterogeneity of these diseases is to generate deep clinical phenotypic data.  ... 
doi:10.3390/ijms22158100 pmid:34360863 pmcid:PMC8347917 fatcat:oqv7ocedobgdpebdt33rxueyai

CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

Tunca Doğan, Heval Atas, Vishal Joshi, Ahmet Atakan, Ahmet Sureyya Rifaioglu, Esra Nalbat, Andrew Nightingale, Rabie Saidi, Vladimir Volynkin, Hermann Zellner, Rengul Cetin-Atalay, Maria Martin (+1 others)
2021 Nucleic Acids Research  
CROssBAR is a comprehensive system that integrates large-scale biological/biomedical data from various resources and stores them in a NoSQL database.  ...  These intensely processed heterogeneous networks are expected to aid systems-level research, especially to infer biological mechanisms in relation to genes, proteins, their ligands, and diseases.  ...  We also thank Dr Ian Dunham (Director, Open Targets, UK) and Dr Andrew Leach (Team leader, ChEMBL, EMBL-EBI, UK) for insightful discussions.  ... 
doi:10.1093/nar/gkab543 pmid:34181736 fatcat:cdot5ur7qnen5fm25fmhlukqoq

Functional and physiological genomics of estrogen-related receptors (ERRs) in health and disease

Geneviève Deblois, Vincent Giguère
2011 Biochimica et Biophysica Acta - Molecular Basis of Disease  
We further show that although the three ERR isoforms control analogous gene networks, each isoform performs unique biological functions in a tissue-specific manner in response to a variety of physiological  ...  Indeed, we document that these approaches have allowed for the unambiguous identification of the estrogen-related receptors (ERRs) α, β, and γ (NR3B1, 2, and 3) as global regulators of cellular energy  ...  As discussed in the next sections, integration of gene expression profiles, location analyses data, and phenotypic analyses of ERR-perturbed biological systems have been used to uncover several functions  ... 
doi:10.1016/j.bbadis.2010.12.009 pmid:21172432 fatcat:pwqcnc6f2naxtjkntsubp6k72a

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

J. R. Karr, N. C. Phillips, M. W. Covert
2014 Database: The Journal of Biological Databases and Curation  
However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations.  ...  ., and Covert,M.W. WholeCellSimDB: a hybrid relational/HDF database for wholecell model predictions.  ...  Acknowledgements The authors thank Derek Macklin, Nicholas Ruggero, Neal Sidhwaney and Timothy O'Donnell for helpful discussions on data storage, annotation and efficient retrieval and Yingwei Wang for  ... 
doi:10.1093/database/bau095 pmid:25231498 pmcid:PMC4165886 fatcat:grkm6ptlq5duxkcvhcgzlj66cq

Coexpression and Transcriptome analyses identify active Apomixis-related genes in Paspalum notatum leaves

Fernanda A. de Oliveira, Bianca B. Z. Vigna, Carla C. da Silva, Alessandra P. Fávero, Frederico P. de Matta, Ana L. S. Azevedo, Anete P. de Souza
2020 BMC Genomics  
We identified genes exclusively expressed in each cytotype and genes differentially expressed between pairs of cytotypes.  ...  In this work, transcriptome sequencing was used to compare contrasting P. notatum cytotypes to identify differential expression patterns and candidate genes involved in the regulation of expression of  ...  Authors' contributions APS, BBZV and FAO conceived and designed the experiments; FAO performed the experiments and analyzed the data; FAO and CCS performed the qPCR analyses; APF prepared and provided  ... 
doi:10.1186/s12864-020-6518-z pmid:31992196 pmcid:PMC6986084 fatcat:hobwntcb3bf35l6zn64fcbuqdq
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