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Integrating Omics Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

Ravi Ramesh Pathak, Vrushank Davé
2014 Cellular Physiology and Biochemistry  
[ "systomics" approach would combine data obtained from Genomics & Epigenomics in Pulmonary Biology Genomics shifting approaches to understanding human diseases, including pulmonary disorders, as  ...  approach of systems biology a decade ago [1-6 technology provides omic scale data, while systems-level models and measurements predict and validate biological phenomena [3, 7 molecular diagnostics, genetic  ... 
doi:10.1159/000358693 pmid:24802001 pmcid:PMC4396816 fatcat:7gdra3kds5batnaimommlnx3pm

Intrinsically Disordered Proteins in Chronic Diseases

Kulkarni, Uversky
2019 Biomolecules  
t is now increasingly evident that a large fraction of the human proteome comprises proteins that, under physiological conditions, lack fixed, ordered 3D structures as a whole or have segments that are  ...  Using a combination of smFRET, NMR, and molecular dynamics (MD) simulation, the authors demonstrate that direct interactions between the two pairs of IDPs, 4.1G-CTD/NuMA and H1/ProTα, do form fuzzy complexes  ...  'Structure and functions of microtubule associated proteins tau and MAP2c: similarities and differences' [38] used a combination of NMR and cryo-electron microscopy to examine the propensities of MAPs  ... 
doi:10.3390/biom9040147 pmid:30979084 pmcid:PMC6523076 fatcat:5h4pecaei5f3zanndspziezi4m

Sleep and Big Data: harnessing data, technology and analytics for monitoring sleep and improving diagnostics, prediction, and interventions- an era for "Sleep-Omics?"

Susan Redline, Shaun M Purcell
2021 Sleep  
Together, these gaps point to a critical need to leverage larger sets of multilevel data more comprehensively and rigorously to better define the complex and dynamic processes underlying sleep and wake  ...  Advanced computational and analytical tools open the possibility to interrogate complex physiological and clinical problems at a scale Downloaded from https  ...  Acknowledgments Drs Redline and Purcell received grant support from the National Institutes of Health (contract 75N92019C00011 and HL R35 HL135818).  ... 
doi:10.1093/sleep/zsab107 pmid:33893509 pmcid:PMC8521745 fatcat:hfle2jcp4rbw3ipdimrk6qth5i

Synapse diversity and synaptome architecture in human genetic disorders

2019 Human Molecular Genetics  
The synaptome architecture is built from the hierarchical expression and assembly of proteins into complexes and supercomplexes which are distributed into different synapses.  ...  These include neurological and psychiatric disorders with early and late onset such as autism, schizophrenia and depression and many other rarer conditions.  ...  Considering that synapses are composed of combinations of complexes (and supercomplexes) and these in turn are composed of combinations of proteins, then the impact of a given mutation on a subset of synapses  ... 
doi:10.1093/hmg/ddz178 pmid:31348488 pmcid:PMC6872429 fatcat:4zv3lvc6l5g53jka74hnkozmra

Brain Microarray: Finding Needles in Molecular Haystacks

N. M. Lewandowski
2005 Journal of Neuroscience  
Editor's Note: Toolboxes are a new, occasional feature in the Journal designed to briefly highlight a new method or a resource of general use in neuroscience or to critically analyze existing approaches  ...  In contrast, the late-onset form, accounting for Ͼ95% of all cases, is a complex disorder, and its molecular causes remain elusive.  ...  Complex disorders emerge from an interplay between genes and the environment and constitute by far the vast majority of diseases.  ... 
doi:10.1523/jneurosci.4006-05.2005 pmid:16280569 fatcat:kx5w6crl4ndrji67kyfq6bfz4q

Taxonomy Meets Neurology, the Case of Amyotrophic Lateral Sclerosis

Giovanna Morello, Antonio Gianmaria Spampinato, Francesca Luisa Conforti, Sebastiano Cavallaro
2018 Frontiers in Neuroscience  
Rather than approaching ALS as a single entity, we advocate targeting therapies to distinct "clusters" of patients based on their specific genomic and molecular features.  ...  Our findings point to the existence of a molecular taxonomy for ALS, bringing us a step closer to the establishment of a precision medicine approach in neurology practice.  ...  Construction of a standardized model for the integrated analysis and interpretation of such multiple heterogeneous data types in the context of complex molecular pathways and networks is an imperative  ... 
doi:10.3389/fnins.2018.00673 pmid:30319346 pmcid:PMC6168652 fatcat:tvojawstmjde5ajdfqffgsuwui

Genetic bases for common polygenic diseases

S. M. Weissman
1995 Proceedings of the National Academy of Sciences of the United States of America  
Fundamentally, unlike single gene disorders where the data are essentially qualitative, the complex disorders require accurate and unbiased quantitative data and analysis.  ...  disorder, so that large samples are necessary and hidden small biases in selection of the patient and control groups could obscure positive data and make reproducibility difficult, as in the case of the  ... 
doi:10.1073/pnas.92.19.8543 pmid:7567972 pmcid:PMC41003 fatcat:m4ad6kkl7bcnxi44drm4z6fgh4

Integrating Genotypic Data with Transcriptomic and Proteomic Data

Denis C. Shields, Aisling M. O'Halloran
2002 Comparative and Functional Genomics  
Such studies may provide appreciable advances in our understanding of the genetic aetiology of complex disorders.  ...  The most powerful study designs may combine elements of both family and association studies applied to proteomic and transcriptomic analyses.  ...  Such integrated studies with well-measured molecular and clinical phenotypes in humans have the potential to transform our understanding of the genetic basis of complex disorders.  ... 
doi:10.1002/cfg.135 pmid:18628875 pmcid:PMC2447235 fatcat:sdvkicgwhndvzjjol3ul7gofmi

Molecular Recognition Features Facilitate the Binding Diversity of Hub Proteins

Wei-Lun Hsu
2011 Biophysical Journal  
Here we have combined single molecule and ensemble methods to characterize the solubility landscape and molecular details of polymer dynamics in different ionic compositions, phosphorylation states, and  ...  Our work explored hundreds of hub protein examples by analyzing the complexes deposited in Protein Data Bank that have same binding MoRFs or similar binding grooves.  ...  Here we have combined single molecule and ensemble methods to characterize the solubility landscape and molecular details of polymer dynamics in different ionic compositions, phosphorylation states, and  ... 
doi:10.1016/j.bpj.2010.12.530 fatcat:6kb3thh5mvan5hthgtdk7w7cny

Folding for binding or binding for folding?

Amedeo Caflisch
2003 Trends in Biotechnology  
A number of proteins are (partially) unstructured at physiological conditions and assume a well-defined three-dimensional structure only upon binding to another protein or macromolecular complex.  ...  Recent computer simulations by Verkhivker et al. have yielded an atomic detail picture of the folding of p27 and its concomitant binding to the phosphorylated cyclin A-cyclin dependent kinase 2 (Cdk2).  ...  The first uses either Monte Carlo or molecular dynamics (or a combination of both) to simply sample configuration space, e.g., to determine peptide or protein conformations with data obtained from NMR  ... 
doi:10.1016/s0167-7799(03)00208-7 pmid:14512226 fatcat:gxmduiqxmjgejngc4exwhfy6tq

Alanine Scan of a Small Molecule Interaction Site on the Disordered c-Myc Oncoprotein

Lisette M. Fred, Bethany L. Zablotsky, Kaitlyn P. Gerhart, Steven J. Metallo
2011 Biophysical Journal  
Here we have combined single molecule and ensemble methods to characterize the solubility landscape and molecular details of polymer dynamics in different ionic compositions, phosphorylation states, and  ...  Our work explored hundreds of hub protein examples by analyzing the complexes deposited in Protein Data Bank that have same binding MoRFs or similar binding grooves.  ...  Here we have combined single molecule and ensemble methods to characterize the solubility landscape and molecular details of polymer dynamics in different ionic compositions, phosphorylation states, and  ... 
doi:10.1016/j.bpj.2010.12.532 fatcat:wxo3dmg4x5gdxm6oiwc3wznpda

Native State Conformational Dynamics of Disordered Protein Respond to Chemical Environment

Ucheor B. Choi, Mark E. Bowen
2011 Biophysical Journal  
Here we have combined single molecule and ensemble methods to characterize the solubility landscape and molecular details of polymer dynamics in different ionic compositions, phosphorylation states, and  ...  Our work explored hundreds of hub protein examples by analyzing the complexes deposited in Protein Data Bank that have same binding MoRFs or similar binding grooves.  ...  Here we have combined single molecule and ensemble methods to characterize the solubility landscape and molecular details of polymer dynamics in different ionic compositions, phosphorylation states, and  ... 
doi:10.1016/j.bpj.2010.12.529 fatcat:prvxuh6yord3hfpylbxxnzo7ly

Elasticity of Intrinsically Disordered Nebulin Modules

Jeffrey G. Forbes, Richard J. Wittebort, Alexander Grishaev, Wanxia L. Tsai, Kuan Wang
2011 Biophysical Journal  
Here we have combined single molecule and ensemble methods to characterize the solubility landscape and molecular details of polymer dynamics in different ionic compositions, phosphorylation states, and  ...  Our work explored hundreds of hub protein examples by analyzing the complexes deposited in Protein Data Bank that have same binding MoRFs or similar binding grooves.  ...  Here we have combined single molecule and ensemble methods to characterize the solubility landscape and molecular details of polymer dynamics in different ionic compositions, phosphorylation states, and  ... 
doi:10.1016/j.bpj.2010.12.531 fatcat:lgkpair4indbbkfu3tgqj2ipc4

Metabolomic Analysis in Brain Research: Opportunities and Challenges

Catherine G. Vasilopoulou, Marigoula Margarity, Maria I. Klapa
2016 Frontiers in Physiology  
Metabolism being a fundamental part of molecular physiology, elucidating the structure and regulation of metabolic pathways is crucial for obtaining a comprehensive perspective of cellular function and  ...  Especially for CNS, metabolic network activity analysis can substantially enhance our knowledge about the complex structure of the mammalian brain and the mechanisms of neurological disorders, leading  ...  ACKNOWLEDGMENTS We gratefully acknowledge the Bodossakis Foundation and FORTH/ICE-HT through the TREAT-HEART research project, Action COOPERATION, Sub-Action II: "Large-Scale  ... 
doi:10.3389/fphys.2016.00183 pmid:27252656 pmcid:PMC4878281 fatcat:u2xn2pdcovab7musof3ybh5ume

Data integration in systems genetics and aging research [article]

Alexis Rapin, Maroun Bou Sleiman, Johan Auwerx
2022 arXiv   pre-print
They are rooted in complex physiological mechanisms impacted by heritable, environment and life-style factors that can be unique to each individual.  ...  We are using a large collection of omics and phenotype data derived from the BXD mouse genetic diversity panel to explore how good data management practices, as fostered by the FAIR principles, paired  ...  This is due to two main challenges: 1) the combination of heterogeneous and sparse data into coherent knowledge bases. And 2) deriving actionable insights out of complex patterns. V.  ... 
arXiv:2207.03540v1 fatcat:33qddw4isze5nafio6wc3a2nba
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