[PDF] Top 20 Algorithms and Models for Genome Biology

... The models used in this section include: (1) an uncorrected analysis that adjusts only for standard covariates such as age, gender and batch, but does not correct for cell-type composition, (2) a reference-based ... See full document

... The KWIK framework was designed to address model-free reinforcement learning in large- state finite-action MDPs (see Li and Littman (2010) in particular). Li, Littman, Walsh, and Strehl (2011) suggest that other machine ... See full document

... The past decade has witnessed a significant progress in the computational inference of biological networks. A variety of approaches in the form of network models and algorithms have been proposed to ... See full document

... distributed algorithms, AD-LDA and AD-HDP, converged to good solutions in every single experiment (of the more than one hun- dred) we conducted using multiple real-world data ...LDA algorithms with ... See full document

... distribution-system models is formulated as an optimisation problem consisting of two normalised objective ...distribution models, the use of genetic algorithms proved very efficient with extremely ... See full document

... of genome rearrangement, a variant where edges have multiple colors, and a bi-directional sorting variant where edges are weighted on both genomes according to the chromatin conformation on ...each. Models ... See full document

... We complement our analytical results with experiments on simulated and real cancer sequencing data. For the first D>P model, we compare the number of patients required to identify driver genes using the single gene ... See full document

... mining algorithms and it is a subject of ongoing research, One important technique of data mining and of the concern of this paper is ...classification models that achieve higher accuracy rate and better ... See full document

... the genome sequencing project and less for any intrinsic value in furthering the understanding of ion ...these genome projects are spread widely through the animal kingdom, it has facilitated the work on ... See full document

... whole genome of a reference HCMV strain digested at unique restriction sites and a transfer vector containing the mutated gene digested with the same restric- tion enzyme ... See full document

... In this review, we explore the development of modified Cas9-based CRISPR systems for genome editing tasks, and the main approaches used to engineer these functionalities. This includes the mutagenesis of Cas9 ... See full document

... The first step to predict the behavior of a biological process is to create a model that closely mimics the real system. Prior information about the interaction mechanisms governing the sys- tem is often limited. This ... See full document

... tems Biology), that I realized how grievously I had been misled. Biology has some of the finest examples of how quantitative modeling and measurement have been used to unravel the world around us ... See full document

... In an effort to develop a model for the etiology of heart valve defects, Florian Wuennemann (Gregor Andelfinger ’ s group, CHU Sainte-Justine Research Centre, Universite de Montreal, Canada) described the identification ... See full document

... for genome engi- neering in human cell cultures, proving that it also works in eukaryotic systems [19, ...for genome engineering due to its ease in cloning new sequence-specific nucleases and the fact that ... See full document

... Results: In our case, this analysis brings both qualitative and quantitative information on the models, in the form of conservation laws, consistency checking, etc. thanks to finite domain constraint programming. ... See full document

... Hydra genome assembly are genes encoding two previously characterized proteins that have been reported to play roles in regeneration and ...Hydra genome that is not included in the assembled ... See full document

... in biology but are intrinsically complex to study; (i) they are not templated, so genome data does not enable prediction of glycosylation; (ii) glycans on cell surfaces are always changing due to the action ... See full document

... The models discussed above describe the spatial and temporal changes of certain quan- tities that are of interest in various biological systems. In particular, the differential equa- tions described above give ... See full document

... The process in Xenopus laevis has remained obscure till re- cently. Three papers report on different results. It was thought, for example, that the smaller nucleus in the myotube arose as a result of unequal, amitotic ... See full document