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An integrative approach to ortholog prediction for disease-focused and other functional studies

Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E Mohr
2011 BMC Bioinformatics  
the functions of orthologs in other species.  ...  To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man  ...  Acknowledgements and Funding The authors would like to thank members of the Perrimon lab and Lizabeth Perkins for helpful suggestions and discussions.  ... 
doi:10.1186/1471-2105-12-357 pmid:21880147 pmcid:PMC3179972 fatcat:jtvaobinn5dzrgyl4omxu73spi

Gene2Function: An Integrated Online Resource for Gene Function Discovery

Yanhui Hu, Aram Comjean, Stephanie E. Mohr, Norbert Perrimon
2017 G3: Genes, Genomes, Genetics  
Model organism databases and other resources are rich with functional information but difficult to mine.  ...  One of the most powerful ways to develop hypotheses regarding the biological functions of conserved genes in a given species, such as humans, is to first look at what is known about their function in another  ...  ACKNOWLEDGMENTS The authors would like to thank Joseph Loscalzo, Richard Maas, and Calum MacRae of Brigham and Women's Hospital for critical guidance at an early stage.  ... 
doi:10.1534/g3.117.043885 pmid:28663344 pmcid:PMC5555488 fatcat:uv372vqaqzhtbm3uufom3symcm

Gene2Function: An Integrated Online Resource For Gene Function Discovery [article]

Yanhui Hu, Aram Comjean, Stephanie Mohr, Norbert Perrimon
2017 bioRxiv   pre-print
Model organism databases (MODs) and other resources are rich with functional information but difficult to mine.  ...  One of the most powerful ways to develop hypotheses regarding biological functions of conserved genes in a given species, such as in humans, is to first look at what is known about function in another  ...  A gene search at G2F connects users to ortholog information and an overview of functional information for orthologs.  ... 
doi:10.1101/133975 fatcat:k5767u2mhnawpmsmsiewuxrcju

Editorial: Orthology and applications

C. Dessimoz
2011 Briefings in Bioinformatics  
These observations underscore the need for differentiated and prudent approaches to propagating function annotations.  ...  ., in which they define and motivate new XML formats for protein sequences and orthology predictions.  ... 
doi:10.1093/bib/bbr057 pmid:21949264 fatcat:xlbn7of5ijej5czbvu7barsbee

FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update

Yanhui Hu, Aram Comjean, Charles Roesel, Arunachalam Vinayagam, Ian Flockhart, Jonathan Zirin, Lizabeth Perkins, Norbert Perrimon, Stephanie E. Mohr
2016 Nucleic Acids Research  
CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches.  ...  Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification  ...  The authors also extend our thanks to the members of the Perrimon lab and to the FlyBase consortium for helpful discussions regarding our online tools and website.  ... 
doi:10.1093/nar/gkw977 pmid:27924039 pmcid:PMC5210654 fatcat:zfht7ymfxrcydhtm7u4h646nse

Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle

Fabiana Perocchi, Lars J. Jensen, Julien Gagneur, Uwe Ahting, Christian von Mering, Peer Bork, Holger Prokisch, Lars M. Steinmetz
2006 PLoS Genetics  
We integrated genome-wide datasets to generate an accurate and inclusive mitochondrial parts list.  ...  Our network brings together annotated and predicted functions into a single framework.  ...  for network visualization software; and Curt Scharfe for providing annotated human mitochondrial disease genes.  ... 
doi:10.1371/journal.pgen.0020170 pmid:17054397 pmcid:PMC1617129 fatcat:evwyijuubzf75jntclidgqpgma

Pathway-Based Integrative Analysis of Metabolome and Microbiome Data from Hepatocellular Carcinoma and Liver Cirrhosis Patients

Boram Kim, Eun Ju Cho, Jung-Hwan Yoon, Soon Sun Kim, Jae Youn Cheong, Sung Won Cho, Taesung Park
2020 Cancers  
), for integrating microbiome and metabolomic data.  ...  To utilize both microbiome and metabolomic data sets, we propose an innovative, pathway-based analysis, Hierarchical structural Component Model for pathway analysis of Microbiome and Metabolome (HisCoM-MnM  ...  The author would like to thank Curt Balch, Bioscience Advising (https://bioscienceadvising.com/) for editing this manuscript for English language.  ... 
doi:10.3390/cancers12092705 pmid:32967314 fatcat:ivhabeofrbdfla7ryzfsijsd3y

A Genomewide Functional Network for the Laboratory Mouse

Yuanfang Guan, Chad L. Myers, Rong Lu, Ihor R. Lemischka, Carol J. Bult, Olga G. Troyanskaya, Andrey Rzhetsky
2008 PLoS Computational Biology  
In this study, we present a functional network for the laboratory mouse based on a Bayesian integration of diverse genetic and functional genomic data.  ...  We show that this network can accurately predict novel functional assignments and network components and present experimental evidence for predictions related to Nanog homeobox (Nanog), a critical gene  ...  Acknowledgments The authors would like to thank Dr. Judith Blake and her curatorial staff for manual review of a subset of our functional predictions.  ... 
doi:10.1371/journal.pcbi.1000165 pmid:18818725 pmcid:PMC2527685 fatcat:ibhjzy3ylrcutixfohknvv4chy

Optimizing translational research for exceptional health and life span: A systematic narrative of studies to identify translatable therapeutic target(s) for exceptional health span in humans

Nalini Raghavachari, Beth Wilmot, Chhanda Dutta
2022 The journals of gerontology. Series A, Biological sciences and medical sciences  
Other efforts related to translational longevity research include the 'Comprehensive Evaluation of Aging-Related Clinical Outcomes and Geroproteins study', which focuses on potential effects in humans  ...  The 'Predictive Human Mechanistic Markers Network' is devoted to the development of predictive markers of aging, for target engagement when testing novel interventions for healthy aging.  ...  The authors sincerely thank the principal investigators of the human longevity translational research studies, CARGO, and Predictive Markers Network for their careful review, input, and recommendations  ... 
doi:10.1093/gerona/glac065 pmid:35279027 fatcat:zqd23a3hyzahdhus2m7sw23oza

Quantitative and Systems Pharmacology 3. Network-Based Identification of New Targets for Natural Products Enables Potential Uses in Aging-Associated Disorders

Jiansong Fang, Li Gao, Huili Ma, Qihui Wu, Tian Wu, Jun Wu, Qi Wang, Feixiong Cheng
2017 Frontiers in Pharmacology  
In this study, we developed an integrated systems pharmacology infrastructure to uncover new indications for aging-associated disorders by natural products.  ...  In summary, this study offers a powerful systems pharmacology infrastructure to identify natural products for treatment of aging-associated disorders.  ...  In this study, we developed an integrated systems pharmacology infrastructure to identify new targets of natural products for treatment of aging-associated diseases.  ... 
doi:10.3389/fphar.2017.00747 pmid:29093681 pmcid:PMC5651538 fatcat:rv57vd54zzftrbjjhuh3x7xim4

Using Bioinformatics Tools for Identifying Disease-Causal Genetic Variants from Human Genomes

Youngmahn Han, Insung Ahn
2015 International Journal of Bio-Science and Bio-Technology  
Identification of the disease-causal genomic variants that alter human phenotypes, particularly those that lead to diseases, is the central goal of human genetics studies.  ...  In the past decade, genome-wide studies have identified several hundreds of common variants associated with complex human diseases and traits.  ...  Acknowledgment The author would like to acknowledge the Biomedical Prediction Technology Team: Insung Ahn, Thai Quang Tung, and Jinhwa Jang.  ... 
doi:10.14257/ijbsbt.2015.7.6.29 fatcat:pplv7uthsbdvdfc2pkccuk3ptq

Integrating Evolutionary Genetics to Medical Genomics: Evolutionary Approaches to Investigate Disease-Causing Variants [chapter]

Ugur Sezerman, Tugce Bozkurt, Fatma Sadife Isleyen
2020 Molecular Medicine [Working Title]  
Incorporating information from healthy population databases, other organisms' databases, and computational prediction tools are evolution-based strategies that give valuable insight to interpret the variant  ...  However, identifying the potential effects of the variations and their association with a particular disease phenotype is the main challenge in this field.  ...  The predicted orthologs serve as a valuable resource for the human disease gene variants prediction as FlyBase also indicates whether the human ortholog functionally complements the fly mutant upon transfer  ... 
doi:10.5772/intechopen.92738 fatcat:gy7xau3ulvcvvg3uvhvg6yc2we

WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data

Aman Chandra Kaushik, Aamir Mehmood, Xiaofeng Dai, Dong-Qing Wei
2020 Scientific Reports  
These types of known and predicted interactions, gained through multiple resources, are thought to be important for experimental data to satisfy comprehensive and quality needs.  ...  This database contains information concerning protein's functional partnerships and interactions along with their integration into a statistical model that can be computationally predicted for humans.  ...  Acknowledgements The simulations in this work were supported by the Center for  ... 
doi:10.1038/s41598-020-62508-8 pmid:32221380 pmcid:PMC7101429 fatcat:nvswk5pd5japzlkucdl3eentqi

Applications of comparative evolution to human disease genetics

Claire D McWhite, Benjamin J Liebeskind, Edward M Marcotte
2015 Current Opinion in Genetics and Development  
genes and phenotypes across species, and statistical methods for linking human diseases to model phenotypes.  ...  We review recent developments in comparative evolutionary approaches for finding models for genetic disease, including high-throughput generation of gene/phenotype relationship data, the linking of orthologous  ...  Network approaches Gene network-based approaches use networks to provide statistical frameworks for inferring new gene functions or disease associations.  ... 
doi:10.1016/j.gde.2015.08.004 pmid:26338499 pmcid:PMC4947381 fatcat:xcgt5oe6pvga5jemouyxho6pzq

Knowledge-based data analysis comes of age

M. F. Ochs
2009 Briefings in Bioinformatics  
Here we review the emergence of techniques that match mathematical structure to the biology, the use of integrated data and prior knowledge to guide statistical analysis, and the recent emergence of analysis  ...  First, analysis techniques need to be matched to the biological system, reflecting in their mathematical structure the underlying behavior being studied.  ...  This network integrated PPI including homologous interactions, phenotype and disease data from MGI and OMIM, phylogenetic profiles, functional relationship predictions, and tissue specific expression data  ... 
doi:10.1093/bib/bbp044 pmid:19854753 pmcid:PMC3700349 fatcat:takbpogtrnfmfbc6v2cazhfffy
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