Leonard McMillan - Academia.edu (original) (raw)

Papers by Leonard McMillan

In this paper we present a novel algorithm for reconstructing 3D scenes from a set of images. The... more In this paper we present a novel algorithm for reconstructing 3D scenes from a set of images. The user defines a set of polygonal regions with corresponding labels in each image using familiar 2D photo-editing tools. Our reconstruction algorithm computes the 3D model with maximum volume that is consistent with the set of regions in the input images. The algorithm is fast, uses only 2D intersection operations, and directly computes a polygonal model. We implemented a user-assisted system for 3D scene reconstruction and show results on scenes that are difficult or impossible to reconstruct with other methods.

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Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware, 2004

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Genetics, Jun 1, 2017

The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains deri... more The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here we present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. Our study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection. A distinct advantage of inbred panels is that genotyping only needs to be performed on the panel, not on each individual mouse. The initial CC genome data were haplotype reconstructions based on dense genotyping of the most recent common ancestors (MRCAs) of each strain followed by imputation from th...

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G3 (Bethesda, Md.), Dec 7, 2016

Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, ... more Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format) and alignments (BAM format) are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be use...

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ABSTRACTGene duplication and loss are major sources of genetic polymorphism in populations, and a... more ABSTRACTGene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127 kbp segmental duplication,R2d, in the house mouse (Mus musculus). R2dcontains a single protein-coding gene,Cwc22. De novoassembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to non-allelic gene conversion events spanning tens of kilobases.R2d2is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to more than 80 in wild mice sampled from around the globe. Hemizgyosity for high-copy-number alleles ofR2d2is associated inciswith meiotic drive, suppression of meiotic crossovers, and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in laboratory populations. We identify an additional 57 loci covering 0.8% of the mouse ge...

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G3 (Bethesda, Md.), Jan 18, 2015

Genotyping microarrays are an important resource for genetic mapping, population genetics and mon... more Genotyping microarrays are an important resource for genetic mapping, population genetics and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations and for substrain-level identification of laboratory mice. In addition to 141,090 SNP probes, GigaMUGA contains 2,006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically-diverse samples, from laboratory substrains to other Mus speci...

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G3 (Bethesda, Md.), Jan 19, 2015

Surveys of inbred strains of mice are standard approaches to determine the heritability and range... more Surveys of inbred strains of mice are standard approaches to determine the heritability and range of phenotypic variation for biomedical traits. In addition, they may lead to the identification of novel phenotypes and models of human disease. Surprisingly, male reproductive phenotypes are among the least represented traits in the Mouse Phenome Database. Here we report the results of a broad survey of the eight founder inbred strains of both the Collaborative Cross (CC) and the Diversity Outbred populations, two new mouse resources that are being used as platforms for systems genetics and sources of mouse models of human diseases. Our survey includes representatives of the three main subspecies of the house mice and a mix of classical and wild-derived inbred strains. In addition to standard staples of male reproductive phenotyping such as reproductive organ weights, sperm counts and sperm morphology, our survey includes sperm motility and the first survey of testis histology. As expe...

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PLoS genetics, 2015

New systems genetics approaches are needed to rapidly identify host genes and genetic networks th... more New systems genetics approaches are needed to rapidly identify host genes and genetic networks that regulate complex disease outcomes. Using genetically diverse animals from incipient lines of the Collaborative Cross mouse panel, we demonstrate a greatly expanded range of phenotypes relative to classical mouse models of SARS-CoV infection including lung pathology, weight loss and viral titer. Genetic mapping revealed several loci contributing to differential disease responses, including an 8.5Mb locus associated with vascular cuffing on chromosome 3 that contained 23 genes and 13 noncoding RNAs. Integrating phenotypic and genetic data narrowed this region to a single gene, Trim55, an E3 ubiquitin ligase with a role in muscle fiber maintenance. Lung pathology and transcriptomic data from mice genetically deficient in Trim55 were used to validate its role in SARS-CoV-induced vascular cuffing and inflammation. These data establish the Collaborative Cross platform as a powerful genetic ...

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A selective sweep is the result of strong positive selection rapidly driving newly occurring or s... more A selective sweep is the result of strong positive selection rapidly driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population or species. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little empirical evidence addresses whether "selfish" genes are capable of fixation -- thereby leaving signatures identical to classical selective sweeps -- despite being neutral or deleterious to organismal fitness. We previously reported the discovery of R2d2, a large copy-number variant that causes non-random segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a "selfish" sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations of mice. We replicate this f...

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Journal of the American Statistical Association, 2015

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Lecture Notes in Computer Science, 2014

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ACM SIGGRAPH ASIA 2008 courses, 2008

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In the real-time 3D graphics pipeline framework, rendering quality greatly depends on illuminatio... more In the real-time 3D graphics pipeline framework, rendering quality greatly depends on illumination and shading models. The highest-quality shading method in this framework is Phong shading. However, due to the computational complexity of Phong shading, current graphics hardware implementations use a simpler Gouraud shading. Today, programmable hardware shaders are becoming available, and, although real-time Phong shading is still not possible, there is no reason not to improve on Gouraud shading.

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