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Probabilistic drug connectivity mapping

Juuso A Parkkinen, Samuel Kaski
2014 BMC Bioinformatics  
Results: We show that the probabilistic multi-source connectivity mapping method is superior to alternatives in finding functionally and chemically similar drugs from the Connectivity Map data set.  ...  We infer the relevance for retrieval by data-driven probabilistic modeling of the drug responses, resulting in probabilistic connectivity mapping, and further consider the available cell lines as different  ...  to probabilistic connectivity mapping.  ... 
doi:10.1186/1471-2105-15-113 pmid:24742351 pmcid:PMC4011783 fatcat:mbxzgdvc6jgx3l6i47jufpcvqi


2011 Biocomputing 2012  
We build sensitivity maps or truth tables for a cell line from experimentally generated tumor sensitivities to kinase inhibitor drugs and use them to predict the sensitivity of a new drug or drug combinations  ...  In this article, we present a novel approach to predict the tumor sensitivities of a drug based on the generation of deterministic and stochastic Kinase Inhibition Maps.  ...  Algorithm 5.1 Algorithm for constructing Probabilistic Kinase Inhibitor Map PKIM {Generate Kinase Inhibition Maps IM 1 and IM 0  ... 
doi:10.1142/9789814366496_0034 fatcat:r6axeyn5sbeohpxzjxyvmbihxi

Anatomical connection strength predicts dopaminergic drug effects on fronto-striatal function

Martine R. van Schouwenburg, Marcel P. Zwiers, Marieke E. van der Schaaf, Dirk E. M. Geurts, Arnt F. A. Schellekens, Jan K. Buitelaar, Robbert J. Verkes, Roshan Cools
2013 Psychopharmacology  
Anatomical frontostriatal connectivity also predicted drug effects on switchrelated functional connectivity between the basal ganglia and the prefrontal cortex.  ...  Human psychopharmacology and functional neuroimaging were combined with functional connectivity analyses and structural connectivity analyses to establish a link between dopaminergic drug effects on fronto-striatal  ...  are individual differences in drug effects on switchrelated BOLD signal from the basal ganglia, extracted from the cluster displayed in a Fig. 5 a 5 Group probability map of tracts generated by probabilistic  ... 
doi:10.1007/s00213-013-3000-5 pmid:23404064 pmcid:PMC3655213 fatcat:gpzmrbl5wjg6dhws7e5jeao7km

Longitudinal brain functional and structural connectivity changes after hemispherotomy in two pediatric patients with drug-resistant epilepsy

Yongxin Li, Ya Wang, Zhen Tan, Qian Chen, Wenhua Huang
2019 Epilepsy and Behavior Case Reports  
Two patients with different curative effects showed different trajectories of brain connectivity after surgery.  ...  Resting-state functional magnetic resonance imaging and diffusion tensor imaging were collected in two children with drug-resistnt epilepsy underwent hemispherotomy.  ...  For both patients, the thresholded and transformed probabilistic maps of each ROI represented the pattern of structural connections.  ... 
doi:10.1016/j.ebcr.2018.11.003 pmid:30723671 pmcid:PMC6350230 fatcat:lu6qlren45bhlgdqsffvixebji

Dopaminergic drug effects during reversal learning depend on anatomical connections between the orbitofrontal cortex and the amygdala

Marieke E. van der Schaaf, Marcel P. Zwiers, Martine R. van Schouwenburg, Dirk E. M. Geurts, Arnt F. A. Schellekens, Jan K. Buitelaar, Robbert Jan Verkes, Roshan Cools
2013 Frontiers in Neuroscience  
By using a fiber-based approach, we demonstrate that dopaminergic drug effects on striatal BOLD signal varied as a function of fractional anisotropy (FA) in a pathway connecting the OFC with the amygdala  ...  Here we assessed whether dopaminergic drug effects on human striatal BOLD signaling during reversal learning is associated with anatomical connectivity in an orbitofrontal-limbic-striatal network, as measured  ...  These individual maps were then binarized and summed across subjects to produce group probability maps.  ... 
doi:10.3389/fnins.2013.00142 pmid:23966907 pmcid:PMC3743215 fatcat:rwfdg2if7jdcdcxloekcffekea

A review of connectivity map and computational approaches in pharmacogenomics

Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina Galzko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
2017 Briefings in Bioinformatics  
and drug design.  ...  Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics  ...  [41] showed their proposed probabilistic connectivity mapping method is capable of identifying drug combinations.  ... 
doi:10.1093/bib/bbw112 pmid:28069634 pmcid:PMC5952941 fatcat:7dpcxwe2obbmnpl6geslg4gzp4

Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network

Jialiang Huang, Chaoqun Niu, Christopher D. Green, Lun Yang, Hongkang Mei, Jing-Dong J. Han, Robert B. Russell
2013 PLoS Computational Biology  
Here, we developed a metric "S-score" that measures the strength of network connection between drug targets to predict PD DDIs.  ...  Identifying drug-drug interactions (DDIs) is a major challenge in drug development.  ...  The expression connectivity score (C-score) of all possible drug pairs are locally calculated following the algorithms of Connectivity Map [12] , which uses gene-expression signatures to connect small  ... 
doi:10.1371/journal.pcbi.1002998 pmid:23555229 pmcid:PMC3605053 fatcat:ivzny2smiba2vcr64mpxj2csga

INGOT: Towards network-driven in silico combination therapy

Sourav S Bhowmick, Huey-Eng Chua, Jie Zheng
2014 2014 International Conference on Big Data and Smart Computing (BIGCOMP)  
Finally, optimal candidate drug combinations to modulate these targets are predicted by integrating and analyzing drug information (e.g., DrugBank) with the target nodes.  ...  Specifically, in ingot, a disease-related probabilistic signaling network (psn) is constructed by integrating publicly-available disease-specific signaling networks with expression data.  ...  An initial network analysis of the current drug targets of approved drugs indicated that drug targets are commonly highly connected but not essential nodes [25] , [36] .  ... 
doi:10.1109/bigcomp.2014.6741401 dblp:conf/bigcomp/BhowmickCZ14 fatcat:my6ou66ghrb2tf4tjj3cf3qgaa

Altered Fronto-Striatal Fiber Topography and Connectivity in Obsessive-Compulsive Disorder

Takashi Nakamae, Yuki Sakai, Yoshinari Abe, Seiji Nishida, Kenji Fukui, Kei Yamada, Manabu Kubota, Damiaan Denys, Jin Narumoto, Qiyong Gong
2014 PLoS ONE  
COG Z-component coordinates of connectivity maps for OFC ROI were located in the more dorsal part of the VS in OCD patients compared to HC.  ...  Obtained connectivity maps for each frontal region of interest (ROI) were normalized into standard space, and Z-component (dorsal-ventral) coordinate of center-of-gravity (COG) were compared between two  ...  Connectivity-based ROIs were created by thresholding connectivity maps at 25% and used as the target ROIs in following probabilistic tractography analysis.  ... 
doi:10.1371/journal.pone.0112075 pmid:25375933 pmcid:PMC4222976 fatcat:u63jwbc7zjha3gdmggst66q5wq


Maulik R. Kamdar, Mark A. Musen
2017 Proceedings of the 26th International Conference on World Wide Web - WWW '17  
Integrated approaches for pharmacology are required for the mechanism-based predictions of adverse drug reactions that manifest due to concomitant intake of multiple drugs.  ...  We calculate the underlying probability distributions in the drug-reaction HCRF using the datasets from the U.S. Food and Drug Administration's Adverse Event Reporting System.  ...  However, our method is able to generate a probabilistic score for associations that involve more than two drugs.  ... 
doi:10.1145/3038912.3052692 pmid:29479581 pmcid:PMC5824722 dblp:conf/www/KamdarM17 fatcat:y5ukjcapqvdtbdfbw52fscvs2a

Psilocybin induces spatially constrained alterations in thalamic functional organization and connectivity [article]

Andrew Gaddis, Daniel E. Lidstone, Mary Beth Nebel, Roland R. Griffiths, Stewart H. Mostofsky, Amanda Meija, Frederick S. Barrett
2022 bioRxiv   pre-print
Correlations with subjective reports of drug effect and comparisons with a previously reported analytic approach (treating the thalamus as a single functional unit) were conducted.  ...  These same components demonstrated alterations in thalamocortical connectivity, largely with visual and default mode networks.  ...  placebo and the psilocybin sessions (probabilistic effect map = placebo mean engagement map -psilocybin mean engagement map).  ... 
doi:10.1101/2022.02.28.482395 fatcat:cfpoi57u7jdvtotxn2rjsg5fj4

Finding melanoma drugs through a probabilistic knowledge graph

James P. McCusker, Michel Dumontier, Rui Yan, Sylvia He, Jonathan S. Dordick, Deborah L. McGuinness
2017 PeerJ Computer Science  
We show that probabilistic analysis of systems biology graphs increases drug candidate quality compared to non-probabilistic methods.  ...  Using drug, protein and disease interactions, we built an evidence-weighted knowledge graph of integrated interactions.  ...  Additionally, we aim to incorporate knowledge of the complementarity of drug and disease gene expression patterns as evidenced by the connectivity map (Lamb et al., 2006) , which could suggest therapeutic  ... 
doi:10.7717/peerj-cs.106 fatcat:qsbzdpslazeolaon75tzihrxiq

Nicotine remediates smoking withdrawal by modulating resting-state functional connectivity

D.M. Cole, C.F. Beckmann, C.J. Long, P.M. Matthews, M.J. Durcan, J.D. Beaver
2009 NeuroImage  
. • RSNs were identified with group probabilistic independent component analysis (ICA) as implemented in FSL MELODIC. • Individual subject maps were estimated for each session by entering group IC maps  ...  Dual regression and subsequent paired group comparison revealed several localised drug effects, with nicotine reducing withinRSN network functional connectivity (p<0.05, local FDR corrected).  ... 
doi:10.1016/s1053-8119(09)70367-2 fatcat:47wvl3hocbbq7ogrquhjeljgrq

Parcellation of the Hippocampus According to Its Connection Probability with Prefrontal Cortex Subdivisions in a Malaysian Malay Population: Preliminary Findings

Aimi Nadhiah Abdullah, Asma Hayati Ahmad, Rahimah Zakaria, Sofina Tamam, Jafri Malin Abdullah
2021 Malaysian Journal of Medical Sciences  
We performed diffusion magnetic resonance imaging with probabilistic tractography on four Malay males to parcellate the hippocampus according to its relative connection probability to the six subdivisions  ...  Our findings revealed that each hippocampus showed putative connectivity to all the subdivisions of PFC, with the highest connectivity to the orbitofrontal cortex (OFC).  ...  Probabilistic tractography maps were individually generated for the left and right halves of the masks.  ... 
doi:10.21315/mjms2021.28.3.6 pmid:34285645 pmcid:PMC8260070 fatcat:igbanye6wjadvb6wcokpd7fsoq

Reasoning about Knowledge from the Web [chapter]

Gjergji Kasneci
2012 Lecture Notes in Computer Science  
The latter feedback components are directly connected with the random variables representing the truth values of statements.  ...  this model, users and statements are represented by feature vector variables (e.g., user features are: id, gender, country, etc., and statement features: id, topic, relationship type, etc.), which are mapped  ... 
doi:10.1007/978-3-642-35623-0_19 fatcat:gzwxr2jkv5bebidbaup7mpawru
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