Reconstructing DNA copy number by joint segmentation of multiple sequences

The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations of cancerous cell, as well identify genomic variations responsible for disease phenotypes. A number of different high throughput technologies can be used to identify copy number variable sites, and the literature documents multiple effective algorithms. We focus here on the specific problem of detecting regions where variation in copy number is relatively common in the sample at hand: this encompasses the cases of copy number polymorphisms, related samples, technical replicates, and cancerous sub-populations from the same individual. We present an algorithm based on regularization approaches with significant computational advantages and competitive accuracy. We illustrate its applicability with simulated and real data sets.Comment: 54 pages, 5 figure

The Two-Spectra Inverse Problem for Semi-Infinite Jacobi Matrices in The Limit-Circle Case

We present a technique for reconstructing a semi-infinite Jacobi operator in the limit circle case from the spectra of two different self-adjoint extensions. Moreover, we give necessary and sufficient conditions for two real sequences to be the spectra of two different self-adjoint extensions of a Jacobi operator in the limit circle case.Comment: 26 pages. Changes in the presentation of some result

Inverse spectral problems for energy-dependent Sturm-Liouville equations

We study the inverse spectral problem of reconstructing energy-dependent Sturm-Liouville equations from their Dirichlet spectra and sequences of the norming constants. For the class of problems under consideration, we give a complete description of the corresponding spectral data, suggest a reconstruction algorithm, and establish uniqueness of reconstruction. The approach is based on connection between spectral problems for energy-dependent Sturm-Liouville equations and for Dirac operators of special form.Comment: AMS-LaTeX, 28 page

Reliability analysis of reconstructing phylogenies under long branch attraction conditions

Master's Project (M.S.) University of Alaska Fairbanks, 2018.In this simulation study we examined the reliability of three phylogenetic reconstruction techniques in a long branch attraction (LBA) situation: Maximum Parsimony (M P), Neighbor Joining (NJ), and Maximum Likelihood. Data were simulated under five DNA substitution models-JC, K2P, F81, HKY, and G T R-from four different taxa. Two branch length parameters of four taxon trees ranging from 0.05 to 0.75 with an increment of 0.02 were used to simulate DNA data under each model. For each model we simulated DNA sequences with 100, 250, 500 and 1000 sites with 100 replicates. When we have enough data the maximum likelihood technique is the most reliable of the three methods examined in this study for reconstructing phylogenies under LBA conditions. We also find that MP is the most sensitive to LBA conditions and that Neighbor Joining performs well under LBA conditions compared to MP