Publications by authors named "Simon Cawley"

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Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.
Ira W Deveson, Binsheng Gong, Kevin Lai, Jennifer S LoCoco, Todd A Richmond, Simon Cawley

Nat Biotechnol· September 2021

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Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.
Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Simon Cawley

Genome Biol· April 2021

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A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.
Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Simon Cawley

Genome Biol· April 2021

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Alternative base calling method for resequencing microarrays.
Xiaojun Di, Simon Cawley

Conf Proc IEEE Eng Med Biol Soc· October 2012

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Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array.
Thomas J Hoffmann, Mark N Kvale, Stephanie E Hesselson, Yiping Zhan, Christine Aquino, Simon Cawley

Genomics· August 2011

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An integrated semiconductor device enabling non-optical genome sequencing.
Jonathan M Rothberg, Wolfgang Hinz, Todd M Rearick, Jonathan Schultz, William Mileski, Simon E Cawley

Nature· July 2011

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Integrated detection and population-genetic analysis of SNPs and copy number variation.
Steven A McCarroll, Finny G Kuruvilla, Joshua M Korn, Simon Cawley, James Nemesh

Nat Genet· October 2008

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Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.
Joshua M Korn, Finny G Kuruvilla, Steven A McCarroll, Alec Wysoker, James Nemesh, Simon Cawley

Nat Genet· October 2008

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Differential dropout among SNP genotypes and impacts on association tests.
Ke Hao, Simon Cawley

Hum Hered· June 2007

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Multiple testing methods for ChIP-Chip high density oligonucleotide array data.
Sündüz Keleş, Mark J van der Laan, Sandrine Dudoit, Simon E Cawley

J Comput Biol· April 2006

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A genome-wide linkage analysis of alcoholism on microsatellite and single-nucleotide polymorphism data, using alcohol dependence phenotypes and electroencephalogram measures.
Chun Zhang, Simon Cawley, Guoying Liu, Manqiu Cao, Harley Gorrell

BMC Genet· December 2005

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Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14.
Howard J Edenberg, Laura J Bierut, Paul Boyce, Manqiu Cao, Simon Cawley

BMC Genet· December 2005

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ANOSVA: a statistical method for detecting splice variation from expression data.
Melissa S Cline, John Blume, Simon Cawley, Tyson A Clark, Jing-Shan Hu

Bioinformatics· June 2005

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Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays.
Xiaojun Di, Hajime Matsuzaki, Teresa A Webster, Earl Hubbell, Guoying Liu, Simon Cawley

Bioinformatics· May 2005

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Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.
Hajime Matsuzaki, Shoulian Dong, Halina Loi, Xiaojun Di, Guoying Liu, Simon Cawley

Nat Methods· November 2004

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Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Richard A Gibbs, George M Weinstock, Michael L Metzker, Donna M Muzny, Erica J Sodergren, Simon Cawley

Nature· April 2004

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Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.
Colin Dewey, Jia Qian Wu, Simon Cawley, Marina Alexandersson, Richard Gibbs

Genome Res· April 2004

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Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.
Dione Kampa, Jill Cheng, Philipp Kapranov, Mark Yamanaka, Shane Brubaker, Simon Cawley

Genome Res· March 2004

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Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.
Simon Cawley, Stefan Bekiranov, Huck H Ng, Philipp Kapranov, Edward A Sekinger

Cell· February 2004

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HMM sampling and applications to gene finding and alternative splicing.
Simon L Cawley, Lior Pachter

Bioinformatics· October 2003

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SLAM web server for comparative gene finding and alignment.
Simon Cawley, Lior Pachter, Marina Alexandersson

Nucleic Acids Res· July 2003

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SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.
Marina Alexandersson, Simon Cawley, Lior Pachter

Genome Res· March 2003

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Initial sequencing and comparative analysis of the mouse genome.

Nature· December 2002

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Applications of generalized pair hidden Markov models to alignment and gene finding problems.
Lior Pachter, Marina Alexandersson, Simon Cawley

J Comput Biol· October 2002

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Large-scale transcriptional activity in chromosomes 21 and 22.
Philipp Kapranov, Simon E Cawley, Jorg Drenkow, Stefan Bekiranov, Robert L Strausberg

Science· May 2002

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