In the original version of this Article, Supplementary Table 10 contained incorrect primer sequences for the mobility shift assay for SNP rs4776984. These errors have now been fixed and the corrected version of the Su...
In the original version of this Article, Supplementary Table 10 contained incorrect primer sequences for the mobility shift assay for SNP rs4776984. These errors have now been fixed and the corrected version of the Supplementary Information PDF is available to download from the HTML version of the Article.
Flux Balance Analysis (FBA) is a widely used approach for studying biochemical networks, and in particular the genome-scale metabolic network reconstructions. It formulates the problem of predicting a cell's chemi...
详细信息
ISBN:
(纸本)9781479978878
Flux Balance Analysis (FBA) is a widely used approach for studying biochemical networks, and in particular the genome-scale metabolic network reconstructions. It formulates the problem of predicting a cell's chemical reaction fluxes as the linear optimization problem of maximizing a cellular objective (e.g., growth) subject to constraints capturing stoichiometry mass balances of the metabolic network and bounds that reflect the composition of the growth medium. In practice, however, reaction fluxes of the cells under specific growth conditions are available to be measured, but the primal FBA objective function is not necessarily known. Understanding its structure can elucidate the cellular metabolic control mechanisms and infer important information regarding an organism's evolution. To that end, we have developed an Inverse Flux Balance Analysis (InvFBA) method which is a novel inverse optimization-based framework for inferring metabolic objective functions. Within this framework, we present three different forms of objective functions: linear, quadratic, and non-parametric. We show that in all cases, the inverse problem is tractable and can be solved efficiently. We provide several numerical examples to show that the inference of the objective function is consistent with simulated flux data and actual measurements.
COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible...
详细信息
Donor selection for Hematopoietic Stem Cell Transplant often requires physicians to manually select 3 to 5 donors from a list of 100s of genetically compatible donors as identified by HLA-based matching algorithms. Th...
详细信息
ISBN:
(纸本)9781509002887
Donor selection for Hematopoietic Stem Cell Transplant often requires physicians to manually select 3 to 5 donors from a list of 100s of genetically compatible donors as identified by HLA-based matching algorithms. The decision process is complicated by a lack of strict guidelines governing a "secondary" selection process, which is based upon non-HLA donor attributes. Our research is aimed at modeling this "secondary" decision process which can help physicians choose the right donors, based on donor attributes and historical choice behavior. Proposed black box models will help in improving selection consistency.
A standard technique for understanding underlying dependency structures among a set of variables posits a shared conditional probability distribution for the variables measured on individ-uals within a group. This app...
详细信息
I1 Proceedings of the Fifteenth Annual UT- KBRIN bioinformatics Summit 2016 Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park P1 CC-PROMISE: Projection onto the Most Interesting Statistical Eviden...
详细信息
I1 Proceedings of the Fifteenth Annual UT- KBRIN bioinformatics Summit 2016 Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park P1 CC-PROMISE: Projection onto the Most Interesting Statistical Evidence (PROMISE) with Canonical Correlation to integrate gene expression and methylation data with multiple pharmacologic and clinical endpoints Xueyuan Cao, Stanley Pounds, Susana Raimondi, James Downing, Raul Ribeiro, Jeffery Rubnitz, Jatinder Lamba P2 Integration of microRNA-mRNA interaction networks with gene expression data to increase experimental power Bernie J Daigle, Jr. P3 Designing and writing software for in silico subtractive hybridization of large eukaryotic genomes Deborah Burgess, Stephanie Gehrlich, John C Carmen P4 Tracking the molecular evolution of Pax gene Nicholas Johnson; Chandrakanth Emani P5 Identifying genetic differences in thermally dimorphic and state specific fungi using in silico genomic comparison Stephanie Gehrlich, Deborah Burgess, John C Carmen P6 Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing Kalpani De Silva, Michael P Heaton, Theodore S Kalbfleisch P7 Mining physiological data to identify patients with similar medical events and phenotypes Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Şen, Eunice Y Huang P8 Smart brief for home health monitoring Mohammad Mohebbi, Luaire Florian, Douglas J Jackson, John F Naber P9 Side-effect term matching for computational adverse drug reaction predictions AKM Sabbir, Sally R Ellingson P10 Enrichment vs robustness: A comparison of transcriptomic data clustering metrics Yuping Lu, Charles A Phillips, Michael A Langston P11 Deep neural networks for transcriptome-based cancer classification Rahul K Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui P12 Motif discovery using K-means clustering Mohammed Sayed, Juw Won Park P13 Large scale discovery of active enhancers from nasce
暂无评论