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Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell types [article]

Jingqi Q. X. Gong, Eric A. Sobie
2017 bioRxiv   pre-print
These simulated measures were used to construct a cross-cell type regression model that predicts adult myocyte drug responses from iPSC-CM behaviors.  ...  We found that quantitatively accurate predictions of responses to selective or non-selective drugs could be generated based on iPSC-CM responses and that the method can be extended to predict drug responses  ...  In each case, filled symbols represent the direct estimate from alternative cell type responses, whereas open symbols represent the cross-cell type regression model predictions.  ... 
doi:10.1101/176321 fatcat:plg5wf5uazbs3eqigxkk2l33hq

Mining the Breast Cancer Proteome for Predictors of Drug Sensitivity

Leslie C Timpe Dian Li, Ten Yang Yen Judi Wong
2015 Journal of Proteomics & Bioinformatics  
Acknowledgements Support for this work was provided by grants from the National Institutes of Health, R15CA164929 and P20 MD000544, and the National Science Foundation, grant nos.  ...  Elastic net and lasso regression have been used previously for constructing regression models of the drug responses of cell lines using gene expression as predictor variables [3, 5, 11] , and the performance  ...  The drug response profiles and the protein data are both quantitative, hence predicting the sensitivities of cell lines to various drugs implies modeling quantitative drug response data as a function of  ... 
doi:10.4172/jpb.1000370 pmid:26516301 pmcid:PMC4621756 fatcat:ncifzuqfc5b45aue4v6vgs7lhu

Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell types

Jingqi Q. X. Gong, Eric A. Sobie
2018 npj Systems Biology and Applications  
The close match in Fig. 2C and 2D between the symbols (regression prediction) and the solid 92 lines (adult model simulation) indicates the accuracy of the model predictions (quantified in Table S3, 93  ...  to 77 quantitatively translate physiological responses across cell types. 78 A multivariable regression model can translate drug responses across cell types 79 We developed a statistical model, based  ...  In each case, filled symbols represent the direct estimate from alternative cell type responses, whereas open symbols represent the cross-cell type regression model predictions.  ... 
doi:10.1038/s41540-018-0047-2 pmid:29507757 pmcid:PMC5825396 fatcat:hludnopqu5fnrpbwauixfug4am

Population-Based Mechanistic Modeling Allows for Quantitative Predictions of Drug Responses across Cell Types

Jingqi Q.X. Gong, Eric A. Sobie
2018 Biophysical Journal  
The close match in Fig. 2C and 2D between the symbols (regression prediction) and the solid 92 lines (adult model simulation) indicates the accuracy of the model predictions (quantified in Table S3, 93  ...  to 77 quantitatively translate physiological responses across cell types. 78 A multivariable regression model can translate drug responses across cell types 79 We developed a statistical model, based  ...  In each case, filled symbols represent the direct estimate from alternative cell type responses, whereas open symbols represent the cross-cell type regression model predictions.  ... 
doi:10.1016/j.bpj.2017.11.2601 fatcat:t5iyb7wvgbef3m5cjcaed5acaq

Behavioral Effects of -Hydroxybutyrate, Its Precursor -Butyrolactone, and GABAB Receptor Agonists: Time Course and Differential Antagonism by the GABAB Receptor Antagonist 3-Aminopropyl(diethoxymethyl)phosphinic Acid (CGP35348)

W. Koek, S. L. Mercer, A. Coop, C. P. France
2009 Journal of Pharmacology and Experimental Therapeutics  
CGP35348 shifted the dose-response curve of each agonist to the right, but the magnitude of the shift differed among the agonists.  ...  Pigeons were trained to peck a key for access to food during response periods that started at different times after the beginning of the session.  ...  symbols, but not part of the linear portion of the dose-response curves, and not used in the regression calculations (see "Data Analysis")].  ... 
doi:10.1124/jpet.109.151845 pmid:19564487 pmcid:PMC2729800 fatcat:egigo6bignepti3sayrp76buo4

Prediction of doxorubicin sensitivity in gastric cancers based on a set of novel markers

Liu
1994 Oncology Reports  
of key drug sensitivity genes for doxorubicin could allow us to predict therapeutic response.  ...  The response prediction model will be of practical use to evaluate patient before chemotherapy.  ...  Acknowledgements This study was funded by the grants 30400016 and 30672369 from the National Natural Science Foundation of P.R. China.  ... 
doi:10.3892/or_00000097 fatcat:iauguy244neazopwed2s6z6zxe

Prediction of individual response to platinum/paclitaxel combination using novel marker genes in ovarian cancers

M. Komatsu
2006 Molecular Cancer Therapeutics  
patients based on the hypothesis that expression analysis of a set of the key drug sensitivity genes for platinum and paclitaxel could allow us to predict therapeutic response to the combination.  ...  Using expression data of genes quantified by real-time reverse transcription-PCR, we fixed the best linear model, which converted the quantified expres-sion data into an IC 50 of each drug.  ...  Our developed models may have some advantages in the prediction of drug response, and we believe that this developmental approach can contribute to a more accurate prediction model.  ... 
doi:10.1158/1535-7163.mct-05-0408 pmid:16546992 fatcat:avqnoq5pb5aypohagoi7yhuoy4

Genetic and environmental correlates of topiramate-induced cognitive impairment

Elizabeth T. Cirulli, Thomas J. Urban, Susan E. Marino, Kristen N. Linney, Angela K. Birnbaum, Chantal Depondt, Deborah K. Attix, Rodney A. Radtke, David B. Goldstein
2011 Epilepsia  
this drug to a patient.  ...  cognitive response.  ...  Dixon for testing of subjects, A. Husain, M. Mikati, W. Gallentine, S. Sinha, N. Walley, B. Legros, W. Van Paesschen and P. Tugendhaft for recruitment of subjects, and E.  ... 
doi:10.1111/j.1528-1167.2011.03322.x pmid:22091778 pmcid:PMC3253145 fatcat:6r6nzpp535hebipp5y4iklwll4

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines

Paul Geeleher, Nancy J Cox, R Huang
2014 Genome Biology  
First, we fitted models for whole-genome gene expression against drug sensitivity in a large panel of cell lines, using a method that allows every gene to influence the prediction.  ...  We demonstrate a method for the prediction of chemotherapeutic response in patients using only before-treatment baseline tumor gene expression data.  ...  The Cancer Genome Project funded by the Wellcome Trust Sanger Institute generated and made all CGP cell line drug sensitivity and baseline expression data publicly available.  ... 
doi:10.1186/gb-2014-15-3-r47 pmid:24580837 pmcid:PMC4054092 fatcat:psmf4vtmprdfbbcmzcpeiqvyuq

Combined effect of pH and concentration on the activities of gentamicin and oxacillin against Staphylococcus aureus in pharmacodynamic models of extracellular and intracellular infections

P. Baudoux, N. Bles, S. Lemaire, M.-P. Mingeot-Leclercq, P. M. Tulkens, F. Van Bambeke
2006 Journal of Antimicrobial Chemotherapy  
In broth, the EC 50 of gentamicin rose 316-fold and that of oxacillin decreased 15-fold with unchanged apparent E max [25 log (limit of detection)] between pH 7.4 and 5.  ...  Plots of log 10 colony-forming unit changes at 24 h versus log 10 of antibiotic concentration followed sigmoidal shapes, allowing calculation of EC 50 (relative potency) and apparent E max (relative efficacy  ...  the dose -response experiments were used to derive a pharmacological model based on the Hill equation (response versus log 10 of drug concentration, using a slope factor of 1), which allowed calculation  ... 
doi:10.1093/jac/dkl489 pmid:17220162 fatcat:pgmf2beu2ree7g3faj7y37op3e

Page 462 of Psychological Abstracts Vol. 85, Issue 2 [page]

1998 Psychological Abstracts  
of the regression model.  ...  (Royal Adelaide Hosp, Drug & Alcohol Resource Unit, Adelaide, SA, Australia) A new recruiting strategy to allow estimates of response rates in studies with people who inject drugs.  ... 

Quantifying glioblastoma drug penetrance from experimental data [article]

Susan Christine Massey, Javier Urcuyo, Bianca-Maria Marin, Jann Sarkaria, Kristin R. Swanson
2019 bioRxiv   pre-print
Mathematically modeling the dynamics of therapeutic response in patient-derived xenografts (PDX) and fitting the mathematical model to bioluminescence imaging flux data, we may be able to assess the degree  ...  to which both drug resistance and drug penetrance are driving varied responses to these therapies.  ...  Schematic of patient-derived xenograft response to therapy with ABT414 antibody drug conjugate, including key variables and parameters of the mathematical model. z=µr/µs to represent the degree to which  ... 
doi:10.1101/650184 fatcat:rhrra2axtbdi5hb2kfshrmvpxi

Machine learning-based prediction of response to PARP inhibition across cancer types [article]

Katherine E. Hill, Ahmed Rattani, Christopher E. Lietz, Cassandra Garbutt, Edwin Choy, Gregory M. Cote, Aedin Culhane, Andrew D. Kelly, Benjamin Haibe-Kains, Dimitrios Spentzos
2019 medRxiv   pre-print
Cross validated predictors generated with LASSO logistic regression using the PARPi signature genes accurately predicted PARPi response in a training set of olaparib treated cell lines (80-89%), an independent  ...  PARP inhibitors (PARPi) are FDA approved for the treatment of BRCA1/2 deficient breast and ovarian cancer, but a growing body of pre-clinical evidence suggests the drug class holds therapeutic potential  ...  Least angle regression (LARS) models significantly predicted each cell line's response to olaparib.  ... 
doi:10.1101/19007757 fatcat:2cx4r4t37zgnpchhmbz6dh3ed4

Impact of between-tissue differences on pan-cancer predictions of drug sensitivity

John P. Lloyd, Matthew B. Soellner, Sofia D. Merajver, Jun Z. Li, Ewa Szczurek
2021 PLoS Computational Biology  
Increased availability of drug response and genomics data for many tumor cell lines has accelerated the development of pan-cancer prediction models of drug response.  ...  Also unknown is whether the performance of pan-cancer models could vary by cancer type.  ...  models of pan-cancer drug response predictions for MEK inhibitors.  ... 
doi:10.1371/journal.pcbi.1008720 pmid:33630864 fatcat:rxedf4bo7rdgrggkninwsts5l4

A Drug Burden Index to Define the Functional Burden of Medications in Older People

Sarah N. Hilmer
2007 Archives of Internal Medicine  
Associations were strengthened when exposure was calculated by principles of dose response.  ...  An increase of 1 U in drug burden index was associated with a deficit of 0.15 point (PϽ.001) on the physical function scale and 1.5 points (P=.01) on the Digit Symbol Substitution Test.  ...  The model of drug burden described herein incorporates dose-response relationships and empirical data.  ... 
doi:10.1001/archinte.167.8.781 pmid:17452540 fatcat:mcds6ogmwjg3vhir7ftdqlrn4u
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