FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2887335093> ?p ?o ?g. }

• W2887335093 abstract "1 Abstract Background Many computational methods have been developed that leverage the results from biological experiments (such as Hi-C) to infer the 3D organization of the genome. Formally, this is referred to as the 3D genome reconstruction problem (3D-GRP). None of the existing methods for solving the 3D-GRP have utilized a non-procedural programming approach (such as constraint programming or integer programming) despite the established advantages and successful applications of such approaches for predicting the 3D structure of other biomolecules. Our objective was to develop a set of mathematical models and corresponding non-procedural implementations for solving the 3D-GRP to realize the same advantages. Results We present a set of non-procedural approaches for predicting 3D genome organization from Hi-C data (collectively referred to as SonHi-C and pronounced “sonic”). Specifically, this set is comprised of three mathematical models based on constraint programming ( CP ), graph matching ( GM ) and integer programming ( IP ). All of the mathematical models were implemented using non-procedural languages and tested with Hi-C data from Schizosaccharomyces pombe (fission yeast). The CP implementation could not optimally solve the problem posed by the fission yeast data after several days of execution time. The GM and IP implementations were able to predict a 3D model of the fission yeast genome in 1.088 and 294.44 seconds, respectively. These 3D models were then biologically validated through literature search which verified that the predictions were able to recapitulate key documented features of the yeast genome. Conclusions Overall, the mathematical models and programs developed here demonstrate the power of non-procedural programming and graph theoretic techniques for quickly and accurately modelling the 3D genome from Hi-C data. Additionally, they highlight the practical differences observed when differing non-procedural approaches are utilized to solve the 3D-GRP." @default.
• W2887335093 created "2018-08-22" @default.
• W2887335093 creator A5034538230 @default.
• W2887335093 creator A5050507388 @default.
• W2887335093 creator A5057648356 @default.
• W2887335093 date "2018-08-16" @default.
• W2887335093 modified "2023-09-27" @default.
• W2887335093 title "SonHi-C: a set of non-procedural approaches for predicting 3D genome organization from Hi-C data" @default.
• W2887335093 cites W1529984088 @default.
• W2887335093 cites W1845127254 @default.
• W2887335093 cites W1965863160 @default.
• W2887335093 cites W1974463674 @default.
• W2887335093 cites W1983439231 @default.
• W2887335093 cites W1985843769 @default.
• W2887335093 cites W1994536648 @default.
• W2887335093 cites W1995794660 @default.
• W2887335093 cites W2016370660 @default.
• W2887335093 cites W2020912279 @default.
• W2887335093 cites W2029222292 @default.
• W2887335093 cites W2029503535 @default.
• W2887335093 cites W2032131359 @default.
• W2887335093 cites W2039675632 @default.
• W2887335093 cites W2059764680 @default.
• W2887335093 cites W2063727779 @default.
• W2887335093 cites W2065294607 @default.
• W2887335093 cites W2070021921 @default.
• W2887335093 cites W2090037139 @default.
• W2887335093 cites W2097798909 @default.
• W2887335093 cites W2099357999 @default.
• W2887335093 cites W2101249563 @default.
• W2887335093 cites W2101497394 @default.
• W2887335093 cites W2101546138 @default.
• W2887335093 cites W2111526857 @default.
• W2887335093 cites W2124112771 @default.
• W2887335093 cites W2131973340 @default.
• W2887335093 cites W2145619687 @default.
• W2887335093 cites W2152971105 @default.
• W2887335093 cites W2154598603 @default.
• W2887335093 cites W2155142785 @default.
• W2887335093 cites W2159675211 @default.
• W2887335093 cites W2159875930 @default.
• W2887335093 cites W2164424155 @default.
• W2887335093 cites W2165780114 @default.
• W2887335093 cites W2277337138 @default.
• W2887335093 cites W2295297857 @default.
• W2887335093 cites W2404951087 @default.
• W2887335093 cites W2470258573 @default.
• W2887335093 cites W2509901086 @default.
• W2887335093 cites W2614469195 @default.
• W2887335093 cites W2796079887 @default.
• W2887335093 cites W2951074257 @default.
• W2887335093 cites W2951879533 @default.
• W2887335093 cites W2953340391 @default.
• W2887335093 cites W4233756358 @default.
• W2887335093 doi "https://doi.org/10.1101/392407" @default.
• W2887335093 hasPublicationYear "2018" @default.
• W2887335093 type Work @default.
• W2887335093 sameAs 2887335093 @default.
• W2887335093 citedByCount "0" @default.
• W2887335093 crossrefType "posted-content" @default.
• W2887335093 hasAuthorship W2887335093A5034538230 @default.
• W2887335093 hasAuthorship W2887335093A5050507388 @default.
• W2887335093 hasAuthorship W2887335093A5057648356 @default.
• W2887335093 hasBestOaLocation W28873350931 @default.
• W2887335093 hasConcept C104317684 @default.
• W2887335093 hasConcept C105795698 @default.
• W2887335093 hasConcept C11413529 @default.
• W2887335093 hasConcept C126255220 @default.
• W2887335093 hasConcept C137631369 @default.
• W2887335093 hasConcept C141231307 @default.
• W2887335093 hasConcept C153083717 @default.
• W2887335093 hasConcept C154945302 @default.
• W2887335093 hasConcept C165064840 @default.
• W2887335093 hasConcept C173404611 @default.
• W2887335093 hasConcept C177264268 @default.
• W2887335093 hasConcept C199360897 @default.
• W2887335093 hasConcept C201797286 @default.
• W2887335093 hasConcept C2524010 @default.
• W2887335093 hasConcept C26713055 @default.
• W2887335093 hasConcept C2776036281 @default.
• W2887335093 hasConcept C2777576037 @default.
• W2887335093 hasConcept C2779222958 @default.
• W2887335093 hasConcept C2779429346 @default.
• W2887335093 hasConcept C33923547 @default.
• W2887335093 hasConcept C41008148 @default.
• W2887335093 hasConcept C54355233 @default.
• W2887335093 hasConcept C55493867 @default.
• W2887335093 hasConcept C56086750 @default.
• W2887335093 hasConcept C58489278 @default.
• W2887335093 hasConcept C60644358 @default.
• W2887335093 hasConcept C80444323 @default.
• W2887335093 hasConcept C86803240 @default.
• W2887335093 hasConceptScore W2887335093C104317684 @default.
• W2887335093 hasConceptScore W2887335093C105795698 @default.
• W2887335093 hasConceptScore W2887335093C11413529 @default.
• W2887335093 hasConceptScore W2887335093C126255220 @default.
• W2887335093 hasConceptScore W2887335093C137631369 @default.
• W2887335093 hasConceptScore W2887335093C141231307 @default.
• W2887335093 hasConceptScore W2887335093C153083717 @default.
• W2887335093 hasConceptScore W2887335093C154945302 @default.

• next