Andrew H. Chan

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Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most(More)
Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. In this paper, a new computational method is developed to address this challenge. Through an extensive simulation study, it is demonstrated that the method allows more accurate(More)
The role of pigments in generating the colour and maculation of birds' eggs is well characterized, whereas the effects of the eggshell's nanostructure on the visual appearance of eggs are little studied. Here, we examined the nanostructural basis of glossiness of tinamou eggs. Tinamou eggs are well known for their glossy appearance, but the underlying(More)
Text S1 Two-locus recursion relation Suppose we sample n haplotypes, observing their alleles at each of two loci and obtaining configuration n = (a, b, c). Here c = (cij) is a matrix of the counts of haplotypes for which both alleles were observed; cij is the number of haplotypes with allele i at the first locus and allele j at the second locus. We also(More)
MOTIVATION With advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo assemblies from short-reads remains challenging, primarily because of the complex repeat structures found(More)
This paper proposes a novel approach to check the authenticity of hardware based on the inevitable performance gap between real hardware and simulations or emulations that impersonate it. More specifically, we demonstrate that each processor design can be authenticated by requiring a checksum incorporating internals of complex micro-architectural mechanisms(More)
Corticosteroids such as dexamethasone are first line ophthalmic treatment for non-infectious posterior uveitis. Corticosteroids are often administered via intravitreal injection to treat this condition with frequent injections associated with poor treatment adherence and complications such as endophthalmitis. Current ocular implants provide sustained(More)
We report a new methodology for producing monometallic or bimetallic nanoparticles confined within hollow nitrogen-doped porous carbon capsules. The capsules are derived from metal-organic framework (MOF) crystals that are coated with a shell of a secondary material comprising either a metal-tannic acid coordination polymer or a resorcinol-formaldehyde(More)
Scalable Statistical Methods for Ancestral Inference from Genomic Variation Data by Andrew Hans Chan Doctor of Philosophy in Computer Science University of California, Berkeley Professor Yun S. Song, Chair Developments in DNA sequencing technology over the last few years have yielded unprecedented volumes of genetic data. The resulting datasets are(More)