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Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR

Sangeeta B. English, Shou-Ching Shih, Marco F. Ramoni, Lois E. Smith, Atul J. Butte
2009 Journal of Biomedical Informatics  
We use a Bayesian network to identify the most relevant sources of noise based on the successes and failures in validation for an initial set of selected genes, and then improve our subsequent selection  ...  of genes for validation based on eliminating these sources of noise.  ...  Harvard-MIT Division of Health Sciences and Technology, and the Lawson Wilkins Pediatric Endocrine Society.  ... 
doi:10.1016/j.jbi.2008.08.009 pmid:18790084 pmcid:PMC3962641 fatcat:hzud4lzapza7rpcrznsf7eqvni

Utilizing the Molecular Gateway: The Path to Personalized Cancer Management

J. B. Overdevest, D. Theodorescu, J. K. Lee
2009 Clinical Chemistry  
Role of Sponsor: The funding organizations played no role in the design of study, choice of enrolled patients, review and interpretation of data, or preparation or approval of manuscript.  ...  Although microarray technology remains the preeminent mode for biomarker discovery, qPCR analysis serves as a useful adjunct for validating microarray results, in addition to functioning as a targeted  ...  PHARMACOGENOMICS Pharmacogenomics is based on assessing a patient's genetic profile for known polymorphisms in specific networks of essential genes that encode either metabolic pathway effectors (enzymes  ... 
doi:10.1373/clinchem.2008.118554 pmid:19246616 pmcid:PMC4529063 fatcat:hxloa3cbtresjo4lnakr7oluaa

Advantages of Array-Based Technologies for Pre-Emptive Pharmacogenomics Testing

Al Shahandeh, Daniel Johnstone, Joshua Atkins, Jean-Marie Sontag, Moones Heidari, Nilofar Daneshi, Elvis Freeman-Acquah, Elizabeth Milward
2016 Microarrays  
While these methods can be valuable for screening a restricted set of genes for known or novel mutations, implementation of whole genome sequencing in clinical practice continues to present challenges.  ...  Microarrays presently remain the technology of choice in applications that require fast, cost-effective genome-wide screening of variants of known importance, particularly for large sample sizes.  ...  Author Contributions: All authors contributed to literature searching and to writing the review. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/microarrays5020012 pmid:27600079 pmcid:PMC5003488 fatcat:ecjkptdazvdpzjcfvm2skpdt5q

Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes

Christof Winter, Glen Kristiansen, Stephan Kersting, Janine Roy, Daniela Aust, Thomas Knösel, Petra Rümmele, Beatrix Jahnke, Vera Hentrich, Felix Rückert, Marco Niedergethmann, Wilko Weichert (+10 others)
2012 PLoS Computational Biology  
To address this problem, we developed a novel computational approach to identify genes prognostic for outcome that couples gene expression measurements from primary tumor samples with a network of known  ...  Predicting the clinical outcome of cancer patients based on the expression of marker genes in their tumors has received increasing interest in the past decade.  ...  Acknowledgments We thank our colleagues Nicholas Don-Doncow and Sainitin Donakonda for critical reading of the manuscript.  ... 
doi:10.1371/journal.pcbi.1002511 pmid:22615549 pmcid:PMC3355064 fatcat:pwviuxhmabbq5mjbuofspszqka

Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases

Xiaodan Wu, Luonan Chen, Xiangdong Wang
2014 Clinical and Translational Medicine  
Clinical bioinformatics should be a key approach to the identification and validation of disease-specific biomarkers.  ...  Identification and validation of interaction networks and network biomarkers have become more critical and important in the development of disease-specific biomarkers, which are functionally changed during  ...  Acknowledgements The work was supported by Shanghai Leading Academic Discipline Project  ... 
doi:10.1186/2001-1326-3-16 pmid:24995123 pmcid:PMC4072888 fatcat:qxjchyqltndxhdsyf3rihr5ce4

SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells

Huilei Xu, Ihor R Lemischka, Avi Ma'ayan
2010 BMC Systems Biology  
Our results reveal that an SVM approach can be useful for prioritizing genes for functional validation experiments and complement the analyses of high-throughput profiling experimental data in stem cell  ...  For example, the overlap among candidate self-renewal and pluripotency genes across different RNAi screens is surprisingly small.  ...  Mazloom and Ben Macarthur for helpful discussions.  ... 
doi:10.1186/1752-0509-4-173 pmid:21176149 pmcid:PMC3019180 fatcat:7dysnvjjbjfvzdzz7kygbcd7ky

High-Throughput Screening for the Identification of New Therapeutic Options for Metastatic Pheochromocytoma and Paraganglioma

Alessio Giubellino, Uma Shankavaram, Petra Bullova, Jan Schovanek, Yaqin Zhang, Min Shen, Nikita Patel, Abdel Elkahloun, Min-Jung Lee, Jane Trepel, Marc Ferrer, Karel Pacak (+1 others)
2014 PLoS ONE  
Using metaanalysis information from molecular targets of the top drugs identified by our screening with gene expression data from human and murine microarrays, we identified potential drugs to be used  ...  We applied this paradigm in a screening of a library of about 3,800 compounds (including FDA-approved drugs and pharmacologically active compounds) employing a model of metastatic pheochromocytoma, the  ...  Based on the list of genes compiled, we selected a subset of microarray data from a new murine MTT cell microarray and a published human SDHB microarray.  ... 
doi:10.1371/journal.pone.0090458 pmid:24699253 pmcid:PMC3974653 fatcat:2fnujlua3bgiznzbluvvo62ezq

Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells

Sarah Inwood, Michael Betenbaugh, Joseph Shiloach
2018 Genes  
A variety of screening methods were utilized for identifying specific microRNAs that can potentially improve the expression of proteins.  ...  MicroRNAs can target multiple genes in the same pathway, making them good targets of a specific cell process, such as reducing apoptosis, leading to improved protein production [22] .  ...  Acknowledgments: The authors thank D. Livnat for critical reading of the manuscript and editorial assistance.  ... 
doi:10.3390/genes9010025 pmid:29315258 pmcid:PMC5793178 fatcat:ccldkmim7jgn3i3cj7lfinl4j4

Discovery and validation of gene classifiers for endocrine-disrupting chemicals in zebrafish (danio rerio)

Rong-Lin Wang, David Bencic, Adam Biales, Robert Flick, Jim Lazorchak, Daniel Villeneuve, Gerald T Ankley
2012 BMC Genomics  
Development and application of transcriptomics-based gene classifiers for ecotoxicological applications lag far behind those of biomedical sciences.  ...  Candidate classifiers were evaluated by gene set enrichment analysis (GSEA) on both the original training data and a dedicated validation dataset.  ...  The authors wish to thank the two anonymous reviewers for their critiques of this manuscript.  ... 
doi:10.1186/1471-2164-13-358 pmid:22849515 pmcid:PMC3469349 fatcat:dfdnt7hqsjfrbiuzubdvbjgbzi

IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA

RACHEL KARCHIN, MICHAEL F. OCHS, JOSHUA M. STUART, JOEL S. BADER
2011 Biocomputing 2012  
There is also evidence that metabolic pathways rather than individual genes play the critical role in a number of metabolic diseases.  ...  The workshop focused on approaches to deduce changes in biological activity in cellular pathways and networks that drive phenotype from high-throughput data.  ...  Subsequent advances since the development of microarrays for gene expression have been very rapid.  ... 
doi:10.1142/9789814366496_0001 fatcat:4yzlyuv52zekhjrmtfsxcp47oa

IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA

Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader
2012 Biocomputing 2013  
There is also evidence that metabolic pathways rather than individual genes play the critical role in a number of metabolic diseases.  ...  The workshop focused on approaches to deduce changes in biological activity in cellular pathways and networks that drive phenotype from high-throughput data.  ...  Subsequent advances since the development of microarrays for gene expression have been very rapid.  ... 
doi:10.1142/9789814447973_0011 fatcat:x6d4foobrfanlgytjkhsega2fy

Clinical Applications of Artificial Intelligence on Accuracy of Cancer Prediction, Detection, and Diagnosis

William Huang, Chunli Zhao, Xiujun Fan
2020 International Journal of Innovative Research in Medical Science  
There are distinct aspects of medical procedures where artificial intelligence (AI) training can be applied; for example, the calculation of risk scores for patients based on mammographic screening, analysis  ...  In particular, the ability for deep learning machines to determine the risk, survivability, and prognosis of tumors based on medical cancer databases has intrigued healthcare researchers seeking to improve  ...  Conflicts of Interest The authors declare no conflict of interest.  ... 
doi:10.23958/ijirms/vol05-i10/978 fatcat:5o5qdykez5bondyrxpwlnd2qbe

Use of systems biology to decipher host–pathogen interaction networks and predict biomarkers

A. Dix, S. Vlaic, R. Guthke, J. Linde
2016 Clinical Microbiology and Infection  
After introducing general ideas of systems biology, we focus on (1) the detection of putative biomarkers for improved diagnosis and support of therapeutic decisions, (2) network modelling for the identification  ...  Pioneering work was done to predict molecular hostepathogen interactions networks based on dual RNA-seq data. However, currently this network modelling is restricted to a small number of genes.  ...  Frequently biomarker prediction is initiated by a genome-wide transcriptomic screening based on microarray or RNA-seq.  ... 
doi:10.1016/j.cmi.2016.04.014 pmid:27113568 fatcat:hg7z7udr4jhorpw4pfig2xxiqa

Disease proteomics

2008 Genomic Medicine  
A better understanding of the molecular pathways, regulatory networks and their dynamics, which determine their diverse differentiation fates, is needed for these therapeutic approaches to be successful  ...  This study indicates that quantitative proteomic profiling of tumor tissue versus non-cancerous tissue is a promising approach for the identification of potential biomarkers for HCC.  ...  A better understanding of the molecular pathways, regulatory networks and their dynamics, which determine their diverse differentiation fates, is needed for these therapeutic approaches to be successful  ... 
doi:10.1007/s11568-009-9091-8 pmid:19444648 pmcid:PMC2694876 fatcat:fqidbx6kjzcvtmbhqhy5n7mozq

Functional genomic approaches to improve crop plant heat stress tolerance

Baljeet Singh, Neha Salaria, Kajal Thakur, Sarvjeet Kukreja, Shristy Gautam, Umesh Goutam
2019 F1000Research  
This review discusses the potential of various functional genomic approaches, such as genome wide association studies, microarray, and suppression subtractive hybridization, in the process of discovering  ...  This review also discusses how these functionally validated genes can be used to improve heat stress tolerance through plant breeding, transgenics and genome editing approaches.  ...  All statements are correct and author can refer to others citations to make the paper more supported. The review is written with good English and it did not need any improvement.  ... 
doi:10.12688/f1000research.19840.1 pmid:31824669 pmcid:PMC6896246 fatcat:aqx4hfiqfnflvhqjpvcy6yiemi
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