Methylation-Dependent Transition Rates Are Dependent on Local Sequence Lengths and Genomic Regions

Sequence-Dependent Persistence Lengths of DNA.

A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-stranded DNA is used to predict a sequence-averaged persistence length of lF = 53.5 nm in the sense of Flory, and of lp = 160 bp or 53.5 nm in the sense of apparent tangent-tangent correlation decay. These estimates are slightly higher than the consensus experimental values of 150 bp or 50 nm, but we believe ...

Central and Local Limit Theories in Markov Dependent Random Variables

Part-level Sequence Dependent Setup Time Reduction in CMS

This paper presents the idea of creating cells while reducing part-level sequence-dependent setup time in general cellular manufacturing systems (CMS). Setup time reduction in CMS has gained modest attention in the literature. This could be attributed to the fact that the fundamental problem in cell formation in CMS has been mainly related to material handling and machine utilization while setu...

Single-machine scheduling considering carryover sequence-dependent setup time, and earliness and tardiness penalties of production

Production scheduling is one of the very important problems that industry and production are confronted with it. Production scheduling is often planned in the industrial environments while productivity in production can improve significantly the expansion of simultaneous optimization of the scheduling plan. Production scheduling and production are two areas that have attracted much attention in...

Genomic Analysis of Sequence-Dependent DNA Curvature in Leishmania

Leishmania major is a flagellated protozoan parasite of medical importance. Like other members of the Trypanosomatidae family, it possesses unique mechanisms of gene expression such as constitutive polycistronic transcription of directional gene clusters, gene amplification, mRNA trans-splicing, and extensive editing of mitochondrial transcripts. The molecular signals underlying most of these p...