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A Data Fusion Approach to Enhance Association Study in Epilepsy

Simone Marini, Ivan Limongelli, Ettore Rizzo, Alberto Malovini, Edoardo Errichiello, Annalisa Vetro, Tan Da, Orsetta Zuffardi, Riccardo Bellazzi, Emilio Russo
2016 PLoS ONE  
Our method allows integrating association information from multiple genomic sources and aims at highlighting the set of common and rare variants that are capable to trigger the occurrence of a complex  ...  In this paper, we present a data fusion framework merging gene, domain, pathway and protein-protein interaction data related to a next generation sequencing epilepsy gene panel.  ...  Acknowledgments AV benefits of a research position granted by the University of Pavia in the context of the strategic plan: "Towards a governance model for the international migration: an interdisciplinary  ... 
doi:10.1371/journal.pone.0164940 pmid:27984588 pmcid:PMC5161322 fatcat:lvqs45uo2ba4nff34wdrxlb64m

Findings from the Section on Bioinformatics and Translational Informatics

H. Dauchel, T. Lecroq
2017 IMIA Yearbook of Medical Informatics  
integration of multi-omics data for cancer genomics and non-cancer complex diseases.  ...  Methods: We provide a synopsis of the articles selected for the IMIA Yearbook 2017, from which we attempt to derive a synthetic overview of current and future activities in the field.  ...  We also would like to greatly thank the IMIA Yearbook editors and managing editors Brigitte Séroussi, Lina Soualmia, and John Holmes.  ... 
doi:10.15265/iy-2016-050 pmid:27830252 pmcid:PMC5171571 fatcat:yf2ehgjj6bfwjm2ooniyr6a4pu

Findings from the Section on Bioinformatics and Translational Informatics

H. Dauchel, T. Lecroq
2017 IMIA Yearbook of Medical Informatics  
integration of multi-omics data for cancer genomics and non-cancer complex diseases.  ...  Methods: We provide a synopsis of the articles selected for the IMIA Yearbook 2017, from which we attempt to derive a synthetic overview of current and future activities in the field.  ...  We also would like to greatly thank the IMIA Yearbook editors and managing editors Brigitte Séroussi, Lina Soualmia, and John Holmes.  ... 
doi:10.1055/s-0037-1606501 fatcat:fdjdngr3jnhxvnf7pr6z4k73ay

Openness Weighted Association Studies: Leveraging Personal Genome Information to Prioritize Noncoding Variants

Shuang Song, Nayang Shan, Geng Wang, Xiting Yan, Jun S Liu, Lin Hou, Russell Schwartz
2021 Bioinformatics  
Results We develop a computational approach, Openness Weighted Association Studies (OWAS), to leverage and aggregate predictions of chromosome accessibility in personal genomes for prioritizing GWAS signals  ...  We use rheumatic arthritis (RA) and asthma (ATH) as examples to demonstrate how OWAS can be exploited to provide novel insights on complex diseases.  ...  Methods Method overview OWAS is a segment-based association approach, in which openness of a genomic segment is predicted for each personal genome, and subsequently tested for the association with the  ... 
doi:10.1093/bioinformatics/btab514 pmid:34260700 pmcid:PMC8665759 fatcat:52qt7pnd5nditb4wnri4hhgt3m

Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases

D. Smedley, S. Kohler, J. C. Czeschik, J. Amberger, C. Bocchini, A. Hamosh, J. Veldboer, T. Zemojtel, P. N. Robinson
2014 Bioinformatics  
to allow quick and effective searches for candidates that are likely to reward closer investigation.  ...  50% of cases, a figure which we confirmed using a prospective study of disease genes identified in 2012 and PPA data produced before that date.  ...  The eXtasy algorithm uses genomic data fusion to integrate variant impact prediction, haploinsufficiency prediction and phenotype-specific gene prioritization (Sifrim et al., 2013) .  ... 
doi:10.1093/bioinformatics/btu508 pmid:25078397 pmcid:PMC4221119 fatcat:x2xfpg5ierdkbdrzs6mpd5aqn4

Personalized medicine: hope or hype?

K. Salari, H. Watkins, E. A. Ashley
2012 European Heart Journal  
rare disease-causing genetic variants  ...  In this review, we will discuss the utility and limitations of personal genomic data in three domains: pharmacogenomics, assessment of genetic predispositions for common diseases, and identification of  ...  Rare genetic variant discovery The identification and characterization of rare genetic variants is a promising approach to elucidating the molecular underpinnings of rare and common genetic diseases.  ... 
doi:10.1093/eurheartj/ehs112 pmid:22659199 pmcid:PMC3388016 fatcat:2gzxra5ow5fgrcfccheg5wcoba

Big Biomedical data as the key resource for discovery science

Arthur W Toga, Ian Foster, Carl Kesselman, Ravi Madduri, Kyle Chard, Eric W Deutsch, Nathan D Price, Gustavo Glusman, Benjamin D Heavner, Ivo D Dinov, Joseph Ames, John Van Horn (+2 others)
2015 JAMIA Journal of the American Medical Informatics Association  
variant association 29 .  ...  We are developing application programming interfaces, a graphical user-focused knowledge discovery system, and interactive tools for data fusion, model-based metadata data integration, and searching across  ...  COMPETING INTERESTS The authors have no competing interests to declare.  ... 
doi:10.1093/jamia/ocv077 pmid:26198305 pmcid:PMC5009918 fatcat:mkyc2zhcsbahllwbj6yfo6jf2e

Genetic architecture of type 2 diabetes

Kazuo Hara, Nobuhiro Shojima, Jun Hosoe, Takashi Kadowaki
2014 Biochemical and Biophysical Research Communications - BBRC  
Analyses using a mixed--model framework to account for population structure and relatedness generated almost identical results.  ...  /rare and common variants both contribute substantially, and a 'neutral' model in which common variants explain 75% of T2D heritability.  ...  common, low--frequency, and rare variants.  ... 
doi:10.1016/j.bbrc.2014.08.012 pmid:25111817 fatcat:26ymoy3w4vadrpqh64lgxgop6q

Genetic Architecture of Type 2 Diabetes [chapter]

Rashmi B. Prasad, Leif Groop
2016 Textbook of Diabetes  
Analyses using a mixed--model framework to account for population structure and relatedness generated almost identical results.  ...  /rare and common variants both contribute substantially, and a 'neutral' model in which common variants explain 75% of T2D heritability.  ...  common, low--frequency, and rare variants.  ... 
doi:10.1002/9781118924853.ch14 fatcat:gwnby2yrz5hgrfhcd2l6bzy3t4

The genetic architecture of type 2 diabetes

Christian Fuchsberger, Jason Flannick, Tanya M. Teslovich, Anubha Mahajan, Vineeta Agarwala, Kyle J. Gaulton, Clement Ma, Pierre Fontanillas, Loukas Moutsianas, Davis J. McCarthy, Manuel A. Rivas, John R. B. Perry (+289 others)
2016 Nature  
Integration of biological insights gleaned from common and rare variant associations to T2D into a unified picture of disease pathophysiology will be required to fully understand the basis of this common  ...  /rare and common variants both contribute substantially, and a 'neutral' model in which common variants explain ~75% of T2D heritability.  ... 
doi:10.1038/nature18642 pmid:27398621 pmcid:PMC5034897 fatcat:6nhsfvilxne6tadwvu5ulpq26m

Whole-Genome Sequencing in Cancer

Eric Y. Zhao, Martin Jones, Steven J.M. Jones
2018 Cold Spring Harbor Perspectives in Medicine  
However, as sequencing costs reduce, and the tools to effectively analyze complex and large-scale data improve, the ability to effectively characterize whole genomes at scale in a clinically relevant time  ...  to exploit novel therapeutic rationales.  ...  see genomicsengland .co.uk), which is sequencing whole genomes for the purpose of better understanding rare and infectious diseases, and includes a common cancer component.  ... 
doi:10.1101/cshperspect.a034579 pmid:29844223 pmcid:PMC6396343 fatcat:liwpug46sjewfni3sgvyvm4jcq

Molecular-genetic profiling and high-throughput in vitro drug screening in NUT midline carcinoma—an aggressive and fatal disease

Anja Stirnweiss, Joyce Oommen, Rishi S. Kotecha, Ursula R. Kees, Alex H. Beesley
2017 OncoTarget  
NUT midline carcinoma (NMC) is a rare and aggressive cancer, with survival typically less than seven months, that can arise in people of any age.  ...  In conclusion, our data emphasize the heterogeneity of NMC and highlights genetic aberrations that could be explored to improve therapeutic strategies.  ...  Timothy Failes, Children's Cancer Institute Drug Discovery Centre, Sydney, Australia for performing the drug screening analysis, and the researchers and institutions that provided NMC cell lines.  ... 
doi:10.18632/oncotarget.22862 pmid:29348827 pmcid:PMC5762512 fatcat:bu7fxamnn5furpo7nid5alcd74

Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next-Generation Sequencing Era

Jiajia Chen, Daqing Zhang, Wenying Yan, Dongrong Yang, Bairong Shen
2013 BioMed Research International  
Nevertheless, many challenges still exist in exploiting the flood of sequence data and translating them into routine diagnostics and prognosis of prostate cancer.  ...  We highlight some fundamental issues of translational bioinformatics and the potential use of cloud computing in NGS data processing for the improvement of prostate cancer treatment.  ...  Authors' Contribution Jiajia Chen, Daqing Zhang, and Wenying Yan contributed equally to this work.  ... 
doi:10.1155/2013/901578 pmid:23957008 pmcid:PMC3727129 fatcat:wmsiqvou6vbqph5wox5sapgele

Multi-omics approaches in cancer research with applications in tumor subtyping, prognosis, and diagnosis

Otília Menyhárt, Balázs Győrffy
2021 Computational and Structural Biotechnology Journal  
We discuss algorithmic frameworks developed to reveal cancer subtypes, disease mechanisms, and methods for identifying driver genomic alterations and consider the significance of multi-omics in tumor classifications  ...  Progressive initiatives to enforce the standardization of sample processing and analytical pipelines, multidisciplinary training of experts for data analysis and interpretation are vital to facilitate  ...  Acknowledgements The authors wish to acknowledge the support of ELIXIR Hungary (www.elixir-hungary.org).  ... 
doi:10.1016/j.csbj.2021.01.009 pmid:33613862 pmcid:PMC7868685 fatcat:u7l3qybr5rhr5mcvj2o4q72zue

Evolving toward a human-cell based and multiscale approach to drug discovery for CNS disorders

Eric E. Schadt, Sean Buchanan, Kristen J. Brennand, Kalpana M. Merchant
2014 Frontiers in Pharmacology  
A disruptive approach to therapeutic discovery and development is required in order to significantly improve the success rate of drug discovery for central nervous system (CNS) disorders.  ...  The application of systems biology approaches to account for the multiscale nature of different data types, from genetic to molecular and cellular to clinical, can lead to new insights into human diseases  ...  The Brennand Laboratory is supported by a Brain and Behavior Young Investigator Grant, NIH grant R01 MH101454 (NIMH) and New York Stem Cell Foundation.  ... 
doi:10.3389/fphar.2014.00252 pmid:25520658 pmcid:PMC4251289 fatcat:ta7horidwbd5vfrnlhy4ldg6c4
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