Search Results - "Chen, Gary K"

Fast and flexible simulation of DNA sequence data by Chen, Gary K, Marjoram, Paul, Wall, Jeffrey D

“…Simulation of genomic sequences under the coalescent with recombination has conventionally been impractical for regions beyond tens of megabases. This work…”
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Determining reaction pathways at low temperatures by isotopic substitution: the case of BeD + + H2O by Yang, Tiangang, Zhao, Bin, Chen, Gary K, Guo, Hua, Campbell, Wesley C, Hudson, Eric R

“…Trapped Be+ ions are a leading platform for quantum information science (Gaebler et al 2016 Phys. Rev. Lett. 117 060505), but reactions with background gas…”
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Convex clustering: an attractive alternative to hierarchical clustering by Chen, Gary K, Chi, Eric C, Ranola, John Michael O, Lange, Kenneth

“…The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make…”
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Enriching the Analysis of Genomewide Association Studies with Hierarchical Modeling by Chen, Gary K., Witte, John S.

“…Genomewide association studies (GWAs) initially investigate hundreds of thousands of single-nucleotide polymorphisms (SNPs), and the most promising SNPs are…”
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Isomer-specific kinetics of the C+ + H2O reaction at the temperature of interstellar clouds by Yang, Tiangang, Li, Anyang, Chen, Gary K, Yao, Qian, Suits, Arthur G, Guo, Hua, Hudson, Eric R, Campbell, Wesley C

“…An important interstellar hydrocarbon chemical reaction has been measured in a laboratory. The reaction C + + H 2 O → HCO + /HOC + + H is one of the most…”
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Reproducibility, performance, and clinical utility of a genetic risk prediction model for prostate cancer in Japanese by Akamatsu, Shusuke, Takahashi, Atsushi, Takata, Ryo, Kubo, Michiaki, Inoue, Takahiro, Morizono, Takashi, Tsunoda, Tatsuhiko, Kamatani, Naoyuki, Haiman, Christopher A, Wan, Peggy, Chen, Gary K, Le Marchand, Loic, Kolonel, Laurence N, Henderson, Brian E, Fujioka, Tomoaki, Habuchi, Tomonori, Nakamura, Yusuke, Ogawa, Osamu, Nakagawa, Hidewaki

“…Prostate specific antigen (PSA) is widely used as a diagnostic biomarker for prostate cancer (PC). However, due to its low predictive performance, many…”
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Discovering epistasis in large scale genetic association studies by exploiting graphics cards by Chen, Gary K, Guo, Yunfei

“…Despite the enormous investments made in collecting DNA samples and generating germline variation data across thousands of individuals in modern genome-wide…”
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Population genetic structure and origins of Native Hawaiians in the multiethnic cohort study by Kim, Sung K, Gignoux, Christopher R, Wall, Jeffrey D, Lum-Jones, Annette, Wang, Hansong, Haiman, Christopher A, Chen, Gary K, Henderson, Brian E, Kolonel, Laurence N, Le Marchand, Loic, Stram, Daniel O, Saxena, Richa, Cheng, Iona

“…The population genetic structure of Native Hawaiians has yet to be comprehensively studied, and the ancestral origins of Polynesians remain in question. In…”
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cit: hypothesis testing software for mediation analysis in genomic applications by Millstein, Joshua, Chen, Gary K, Breton, Carrie V

“…The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data/models accommodated…”
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Optical Control of Reactions between Water and Laser-Cooled Be+ Ions by Yang, Tiangang, Li, Anyang, Chen, Gary K, Xie, Changjian, Suits, Arthur G, Campbell, Wesley C, Guo, Hua, Hudson, Eric R

“…We investigate reactions between laser-cooled Be+ ions and room-temperature water molecules using an integrated ion trap and high-resolution time-of-flight…”
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Iterative hard thresholding for model selection in genome‐wide association studies by Keys, Kevin L., Chen, Gary K., Lange, Kenneth

“…ABSTRACT A genome‐wide association study (GWAS) correlates marker and trait variation in a study sample. Each subject is genotyped at a multitude of SNPs…”
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The potential for enhancing the power of genetic association studies in African Americans through the reuse of existing genotype data by Chen, Gary K, Millikan, Robert C, John, Esther M, Ambrosone, Christine B, Bernstein, Leslie, Zheng, Wei, Hu, Jennifer J, Chanock, Stephen J, Ziegler, Regina G, Bandera, Elisa V, Henderson, Brian E, Haiman, Christopher A, Stram, Daniel O

“…We consider the feasibility of reusing existing control data obtained in genetic association studies in order to reduce costs for new studies. We discuss…”
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A scalable and portable framework for massively parallel variable selection in genetic association studies by CHEN, Gary K

“…The deluge of data emerging from high-throughput sequencing technologies poses large analytical challenges when testing for association to disease. We…”
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Genotype imputation via matrix completion by Chi, Eric C, Zhou, Hua, Chen, Gary K, Del Vecchyo, Diego Ortega, Lange, Kenneth

“…Most current genotype imputation methods are model-based and computationally intensive, taking days to impute one chromosome pair on 1000 people. We describe…”
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al3c: high-performance software for parameter inference using Approximate Bayesian Computation by Stram, Alexander H, Marjoram, Paul, Chen, Gary K

“…The development of Approximate Bayesian Computation (ABC) algorithms for parameter inference which are both computationally efficient and scalable in parallel…”
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Precise inference of copy number alterations in tumor samples from SNP arrays by Chen, Gary K, Chang, Xiao, Curtis, Christina, Wang, Kai

“…The accurate detection of copy number alterations (CNAs) in human genomes is important for understanding susceptibility to cancer and mechanisms of tumor…”
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Common variants at 11q12, 10q26 and 3p11.2 are associated with prostate cancer susceptibility in Japanese by Akamatsu, Shusuke, Takata, Ryo, Haiman, Christopher A, Takahashi, Atsushi, Inoue, Takahiro, Kubo, Michiaki, Furihata, Mutsuo, Kamatani, Naoyuki, Inazawa, Johji, Chen, Gary K, Le Marchand, Loïc, Kolonel, Laurence N, Katoh, Takahiko, Yamano, Yuko, Yamakado, Minoru, Takahashi, Hiroyuki, Yamada, Hiroki, Egawa, Shin, Fujioka, Tomoaki, Henderson, Brian E, Habuchi, Tomonori, Ogawa, Osamu, Nakamura, Yusuke, Nakagawa, Hidewaki

“…Hidewaki Nakagawa and colleagues identify three new genetic loci associated with prostate cancer in Japanese. We have previously reported multiple loci…”
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Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity by Sajuthi, Satria P., Sharma, Neeraj K., Chou, Jeff W., Palmer, Nicholette D., McWilliams, David R., Beal, John, Comeau, Mary E., Ma, Lijun, Calles-Escandon, Jorge, Demons, Jamehl, Rogers, Samantha, Cherry, Kristina, Menon, Lata, Kouba, Ethel, Davis, Donna, Burris, Marcie, Byerly, Sara J., Ng, Maggie C. Y., Maruthur, Nisa M., Patel, Sanjay R., Bielak, Lawrence F., Lange, Leslie A., Guo, Xiuqing, Sale, Michèle M., Chan, Kei Hang K., Monda, Keri L., Chen, Gary K., Taylor, Kira, Palmer, Cameron, Edwards, Todd L., North, Kari E., Haiman, Christopher A., Bowden, Donald W., Freedman, Barry I., Langefeld, Carl D., Das, Swapan K.

“…Relative to European Americans, type 2 diabetes (T2D) is more prevalent in African Americans (AAs). Genetic variation may modulate transcript abundance in…”
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Stochastic Epigenetic Mutations Influence Parkinson's Disease Risk, Progression, and Mortality by Chen, Gary K, Yan, Qi, Paul, Kimberly C, Kusters, Cynthia D J, Folle, Aline Duarte, Furlong, Melissa, Keener, Adrienne, Bronstein, Jeff, Horvath, Steve, Ritz, Beate

“…Stochastic epigenetic mutations (SEM) reflect a deviation from normal site-specific methylation patterns. Epigenetic mutation load (EML) captures the…”
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Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation by Pasaniuc, Bogdan, Sankararaman, Sriram, Torgerson, Dara G, Gignoux, Christopher, Zaitlen, Noah, Eng, Celeste, Rodriguez-Cintron, William, Chapela, Rocio, Ford, Jean G, Avila, Pedro C, Rodriguez-Santana, Jose, Chen, Gary K, Le Marchand, Loic, Henderson, Brian, Reich, David, Haiman, Christopher A, Gonzàlez Burchard, Esteban, Halperin, Eran

“…Local ancestry analysis of genotype data from recently admixed populations (e.g. Latinos, African Americans) provides key insights into population history and…”
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