Browsing by Author "Lin, Xihong"

Now showing items 1-20 of 30

    • Association Test Based on SNP Set: Logistic Kernel Machine Based Test vs. Principal Component Analysis 

      Zhao, Yang; Chen, Feng; Zhai, Rihong; Lin, Xihong; Diao, Nancy; Christiani, David C. (Public Library of Science, 2012)
      GWAS has facilitated greatly the discovery of risk SNPs associated with complex diseases. Traditional methods analyze SNP individually and are limited by low power and reproducibility since correction for multiple comparisons ...

    • Birth weight-for-gestational age is associated with DNA methylation at birth and in childhood 

      Agha, Golareh; Hajj, Hanine; Rifas-Shiman, Sheryl L.; Just, Allan C.; Hivert, Marie-France; Burris, Heather H.; Lin, Xihong; Litonjua, Augusto A.; Oken, Emily; DeMeo, Dawn L.; Gillman, Matthew W.; Baccarelli, Andrea A. (BioMed Central, 2016)
      Background: Both higher and lower fetal growth are associated with cardio-metabolic health later in life, suggesting that prenatal developmental programming determines long-term cardiovascular disease risk. Epigenetic ...

    • Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer 

      Byun, Jinyoung; Han, Younghun; Li, Yafang; Xia, Jun; Long, Erping; Choi, Jiyeon; Xiao, Xiangjun; Zhu, Meng; Zhou, Wen; Sun, Ryan; Bossé, Yohan; Song, Zhuoyi; Schwartz, Ann; Lusk, Christine; Rafnar, Thorunn; Stefansson, Kari; Zhang, Tongwu; Zhao, Wei; Pettit, Rowland W.; Liu, Yanhong; Li, Xihao; Zhou, Hufeng; Walsh, Kyle M.; Gorlov, Ivan; Gorlova, Olga; Zhu, Dakai; Rosenberg, Susan M.; Pinney, Susan; Bailey-Wilson, Joan E.; Mandal, Diptasri; de Andrade, Mariza; Gaba, Colette; Willey, James C.; You, Ming; Anderson, Marshall; Wiencke, John K.; Albanes, Demetrius; Lam, Stephan; Tardon, Adonina; Chen, Chu; Goodman, Gary; Bojeson, Stig; Brenner, Hermann; Landi, Maria Teresa; Chanock, Stephen J.; Johansson, Mattias; Muley, Thomas; Risch, Angela; Wichmann, H.-Erich; Bickeböller, Heike; Christiani, David C.; Rennert, Gad; Arnold, Susanne; Field, John K.; Shete, Sanjay; Le Marchand, Loic; Melander, Olle; Brunnstrom, Hans; Liu, Geoffrey; Andrew, Angeline S.; Kiemeney, Lambertus A.; Shen, Hongbing; Zienolddiny, Shanbeh; Grankvist, Kjell; Johansson, Mikael; Caporaso, Neil; Cox, Angela; Hong, Yun-Chul; Yuan, Jian-Min; Lazarus, Philip; Schabath, Matthew B.; Aldrich, Melinda C.; Patel, Alpa; Lan, Qing; Rothman, Nathaniel; Taylor, Fiona; Kachuri, Linda; Witte, John S.; Sakoda, Lori C.; Spitz, Margaret; Brennan, Paul; Lin, Xihong; McKay, James; Hung, Rayjean J.; Amos, Christopher I. (Springer Science and Business Media LLC, 2022-08)
      To identify novel genetic associations to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, Asian, and African populations and discovered five novel loci that ...

    • Dynamic Scan Procedure for Detecting Rare-Variant Association Regions in Whole-Genome Sequencing Studies 

      Li, Zilin; Li, Xihao; Liu, Yaowu; Shen, Jincheng; Chen, Han; Zhou, Hufeng; Morrison, Alanna C.; Boerwinkle, Eric; Lin, Xihong (Elsevier BV, 2019-05)
      Large-scale whole genome sequencing (WGS) studies have enabled the analysis of rare variants (RVs) associated with complex phenotypes. Commonly used RV association tests (RVATs) have limited scope to leverage variant ...

    • Estimation and Testing for the Effect of a Genetic Pathway on a Disease Outcome Using Logistic Kernel Machine Regression via Logistic Mixed Models 

      Liu, Dawei; Ghosh, Debashis; Lin, Xihong (BioMed Central, 2008)
      Background: Growing interest on biological pathways has called for new statistical methods for modeling and testing a genetic pathway effect on a health outcome. The fact that genes within a pathway tend to interact with ...

    • Federated Learning for Predicting Clinical Outcomes in COVID-19 Patients 

      Dayan, Ittai; Roth, Holger; Zhong, Aoxiao; Harouni, Ahmed; Gentili, Amilcare; Abidin, Anas; Liu, Andrew; Costa, Anthony Beardsworth; Wood, Bradford J.; Tsai, Chien-Sung; Wang, Chih-Hung; Hsu, Chun-Nan; Lee, CK; Ruan, Peiying; Xu, Daguang; Wu, Dufan; Huang, Eddie; Kitamura, Felipe Campos; Lacey, Griffin; Corradi, Gustavo César de Antônio; Nino Furnieles, Gustavo; Shin, Hao-Hsin; Obinata, Hirofumi; Ren, Hui; Crane, Jason C.; Tetreault, Jesse; Guan, Jiahui; Garrett, John W.; Kaggie, Josh D; Park, Jung Gil; Dreyer, Keith; Juluru, Krishna; Kersten, Kristopher; Rockenbach, Marcio Aloisio Bezerra Cavalcanti; Linguraru, Marius George; Haider, Masoom A.; AbdelMaseeh, Meena; Rieke, Nicola; Damasceno, Pablo F.; Silva, Pedro Mario Cruz e; Wang, Pochuan; Xu, Sheng; Kawano, Shuichi; Sriswasdi, Sira; Park, Soo-Young; Grist, Thomas M; Buch, Varun; Jantarabenjakul, Watsamon; Wang, Weichung; Tak, Won Young; Li, Xiang; Lin, Xihong; Kwon, Young Joon; Quraini, Abood; Feng, Andrew; Priest, Andrew N; Turkbey, Baris; Glicksberg, Benjamin; Canedo Bizzo, Bernardo; Kim, Byung Seok; Tor-Díez, Carlos; Lee, Chia-Cheng; Hsu, Chia-Jung; Lin, Chin; Lai, Chiu-Ling; Hess, Christopher P.; Compas, Colin; Bhatia, Deepeksha; Oermann, Eric K; Leibovitz, Evan; Sasaki, Hisashi; Mori, Hitoshi; Yang, Isaac; Sohn, Jae Ho; Murthy, Krishna Nand Keshava; Fu, Li-Chen; Mendonça, Matheus Ribeiro Furtado de; Fralick, Mike; Kang, Min Kyu; Adil, Mohammad; Gangai, Natalie; Vateekul, Peerapon; Elnajjar, Pierre; Hickman, Sarah; Majumdar, Sharmila; McLeod, Shelley L.; Reed, Sheridan; Graf, Stefan; Harmon, Stephanie; Kodama, Tatsuya; Puthanakit, Thanyawee; Mazzulli, Tony; Lavor, Vitor de Lima; Rakvongthai, Yothin; Lee, Yu Rim; Wen, Yuhong; Gilbert, Fiona J; Flores, Mona G.; Li, Quanzheng (2021-09-15)
      Federated learning (FL) is a method for training artificial intelligence (AI) models with data from multiple sources while maintaining the anonymity of the data, thus removing many barriers to data sharing. Here we use ...

    • Federated learning for predicting clinical outcomes in patients with COVID-19 

      Dayan, Ittai; Roth, Holger R.; Zhong, Aoxiao; Harouni, Ahmed; Gentili, Amilcare; Abidin, Anas Z.; Liu, Andrew; Costa, Anthony Beardsworth; Wood, Bradford J.; Tsai, Chien-Sung; Wang, Chih-Hung; Hsu, Chun-Nan; Lee, C. K.; Ruan, Peiying; Xu, Daguang; Wu, Dufan; Huang, Eddie; Kitamura, Felipe Campos; Lacey, Griffin; de Antônio Corradi, Gustavo César; Nino, Gustavo; Shin, Hao-Hsin; Obinata, Hirofumi; Ren, Hui; Crane, Jason C.; Tetreault, Jesse; Guan, Jiahui; Garrett, John W.; Kaggie, Joshua D.; Park, Jung Gil; Dreyer, Keith; Juluru, Krishna; Kersten, Kristopher; Rockenbach, Marcio Aloisio Bezerra Cavalcanti; Linguraru, Marius George; Haider, Masoom A.; AbdelMaseeh, Meena; Rieke, Nicola; Damasceno, Pablo F.; e Silva, Pedro Mario Cruz; Wang, Pochuan; Xu, Sheng; Kawano, Shuichi; Sriswasdi, Sira; Park, Soo Young; Grist, Thomas M.; Buch, Varun; Jantarabenjakul, Watsamon; Wang, Weichung; Tak, Won Young; Li, Xiang; Lin, Xihong; Kwon, Young Joon; Quraini, Abood; Feng, Andrew; Priest, Andrew N.; Turkbey, Baris; Glicksberg, Benjamin; Bizzo, Bernardo; Kim, Byung Seok; Tor-Díez, Carlos; Lee, Chia-Cheng; Hsu, Chia-Jung; Lin, Chin; Lai, Chiu-Ling; Hess, Christopher P.; Compas, Colin; Bhatia, Deepeksha; Oermann, Eric K.; Leibovitz, Evan; Sasaki, Hisashi; Mori, Hitoshi; Yang, Isaac; Sohn, Jae Ho; Murthy, Krishna Nand Keshava; Fu, Li-Chen; de Mendonça, Matheus Ribeiro Furtado; Fralick, Mike; Kang, Min Kyu; Adil, Mohammad; Gangai, Natalie; Vateekul, Peerapon; Elnajjar, Pierre; Hickman, Sarah; Majumdar, Sharmila; McLeod, Shelley L.; Reed, Sheridan; Gräf, Stefan; Harmon, Stephanie; Kodama, Tatsuya; Puthanakit, Thanyawee; Mazzulli, Tony; de Lavor, Vitor Lima; Rakvongthai, Yothin; Lee, Yu Rim; Wen, Yuhong; Gilbert, Fiona J.; Flores, Mona G.; Li, Quanzheng (Springer Science and Business Media LLC, 2021-09-15)

    • Fetal Window of Vulnerability to Airborne Polycyclic Aromatic Hydrocarbons on Proportional Intrauterine Growth Restriction 

      Choi, Hyunok; Wang, Lu; Lin, Xihong; Spengler, John D.; Perera, Frederica P. (Public Library of Science, 2012)
      Background: Although the entire duration of fetal development is generally considered a highly susceptible period, it is of public health interest to determine a narrower window of heightened vulnerability to polycyclic ...

    • Gene set analysis using variance component tests 

      Huang, Yen-Tsung; Lin, Xihong (BioMed Central, 2013)
      Background: Gene set analyses have become increasingly important in genomic research, as many complex diseases are contributed jointly by alterations of numerous genes. Genes often coordinate together as a functional ...

    • Gene-environment interaction effects on lung function- a genome-wide association study within the Framingham heart study 

      Liao, Shu-Yi; Lin, Xihong; Christiani, David C (BioMed Central, 2013)
      Background: Previous studies in occupational exposure and lung function have focused only on the main effect of occupational exposure or genetics on lung function. Some disease-susceptible genes may be missed due to their ...

    • Genetic Susceptible Locus in NOTCH2 Interacts with Arsenic in Drinking Water on Risk of Type 2 Diabetes 

      Pan, Wen-Chi; Kile, Molly L.; Seow, Wei Jie; Lin, Xihong; Quamruzzaman, Quazi; Rahman, Mahmuder; Mahiuddin, Golam; Mostofa, Golam; Lu, Quan; Christiani, David C. (Public Library of Science, 2013)
      Background: Chronic exposure to arsenic in drinking water is associated with increased risk of type 2 diabetes mellitus (T2DM) but the underlying molecular mechanism remains unclear. Objectives: This study evaluated the ...

    • Genome sequencing analysis identifies Epstein–Barr virus subtypes associated with high risk of nasopharyngeal carcinoma 

      Xu, Miao; Yao, Youyuan; Chen, Hui; Zhang, Shanshan; Cao, Su-Mei; Zhang, Zhe; Luo, Bing; Liu, Zhiwei; Li, Zilin; Xiang, Tong; He, Guiping; Feng, Qi-Sheng; Chen, Li-Zhen; Guo, Xiang; Jia, Wei-Hua; Chen, Ming-Yuan; Zhang, Xiao; Xie, Shang-Hang; Peng, Roujun; Chang, Ellen T.; Pedergnana, Vincent; Feng, Lin; Bei, Jin-Xin; Xu, Rui-Hua; Zeng, Mu-Sheng; Ye, Weimin; Adami, Hans-Olov; Lin, Xihong; Zhai, Weiwei; Zeng, Yi-Xin; Liu, Jianjun (Springer Science and Business Media LLC, 2019-06-17)
      Epstein-Barr virus (EBV) infection is ubiquitous worldwide and associated with multiple cancers including nasopharyngeal carcinoma (NPC). The role of EBV viral genomic variation in NPC development and its striking endemicity ...

    • Genome-Wide Analysis of Survival in Early-Stage Non–Small-Cell Lung Cancer 

      Huang, Yen-Tsung; Suk Heist, Rebecca; Chirieac, Lucian; Lin, Xihong; Skaug, Vidar; Zienolddiny, Shanbeh; Haugen, Aage; Wu, Michael C.; Wang, Zhaoxi; Su, Li; Asomaning, Kofi; Christiani, David (American Society of Clinical Oncology (ASCO), 2009-06-01)
      Purpose Lung cancer, of which 85% is non–small-cell (NSCLC), is the leading cause of cancer-related death in the United States. We used genome-wide analysis of tumor tissue to investigate whether single nucleotide ...

    • Metabolomics in Obesity and Methods for Analyzing Multiple Phenotypes 

      Liu, Zhonghua (2015-04-23)
      In this dissertation, we first assess the associations between circulating metabolites and body mass index in two U.S. prospective cohorts. Then, we propose several methods to analyze multiple phenotypes in genetic association ...

    • Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival 

      Wang, Zhaoxi; Choi, Sojung; Lee, Jinseon; Huang, Yen-Tsung; Chen, Feng; Zhao, Yang; Lin, Xihong; Neuberg, Donna; Kim, Jhingook; Christiani, David C (Libertas Academica, 2015)
      Mutations in the mtDNA genome have long been suspected to play an important role in cancer. Although most cancer cells harbor mtDNA mutations, the question of whether such mutations are associated with clinical prognosis ...

    • Novel structural co-expression analysis linking the NPM1-associated ribosomal biogenesis network to chronic myelogenous leukemia 

      Chan, Lawrence WC; Lin, Xihong; Yung, Godwin; Lui, Thomas; Chiu, Ya Ming; Wang, Fengfeng; Tsui, Nancy BY; Cho, William CS; Yip, SP; Siu, Parco M.; Wong, SC Cesar; Yung, Benjamin YM (Nature Publishing Group, 2015)
      Co-expression analysis reveals useful dysregulation patterns of gene cooperativeness for understanding cancer biology and identifying new targets for treatment. We developed a structural strategy to identify co-expressed ...

    • Ordinal Outcome Prediction and Treatment Selection in Personalized Medicine 

      Shen, Yuanyuan (2015-05-06)
      In personalized medicine, two important tasks are predicting disease risk and selecting appropriate treatments for individuals based on their baseline information. The dissertation focuses on providing improved risk ...

    • Population Differences in Transcript-Regulator Expression Quantitative Trait Loci 

      Bushel, Pierre R.; McGovern, Ray; Liu, Liwen; Hofmann, Oliver Marc; Huda, Ahsan; Lu, Jun; Hide, Winston; Lin, Xihong (Public Library of Science, 2012)
      Gene expression quantitative trait loci (eQTL) are useful for identifying single nucleotide polymorphisms (SNPs) associated with diseases. At times, a genetic variant may be associated with a master regulator involved in ...

    • Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behaviour, and Testing 

      Allen, William E.; Altae-Tran, Han; Briggs, James; Jin, Xin; McGee, Glen; Shi, Andy; Raghavan, Rumya; Kamariza, Mireille; Nova, Nicole; Pereta, Albert; Danford, Chris; Kamel, Amine; Gothe, Patrik; Milam, Evrhet; Aurambault, Jean; Primke, Thorben; Li, Weijie; Inkenbrandt, Josh; Huynh, Tuan; Chen, Evan; Lee, Christina; Croatto, Michael; Bentley, Helen; Lu, Wendy; Murray, Robert; Travassos, Mark; Coull, Brent; Openshaw, John; Greene, Casey S.; Shalem, Ophir; King, Gary; Probasco, Ryan; Cheng, David R.; Silbermann, Ben; Zhang, Feng; Lin, Xihong (Nature Human Behaviour, 2020-08-26)
      Despite the widespread implementation of public health measures, COVID-19 continues to spread in the United States. To facilitate an agile response to the pandemic, we developed How We Feel, a web and mobile application ...

    • Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing 

      Allen, William; Altae-Tran, Han; Briggs, James; Jin, Xin; McGee, Glen; Shi, Andy; Raghavan, Rumya; Kamariza, Mireille; Nova, Nicole; Pereta, Albert; Danford, Chris; Kamel, Amine; Gothe, Patrik; Milam, Evrhet; Aurambault, Jean; Primke, Thorben; Li, Weijie; Inkenbrandt, Josh; Huynh, Tuan; Chen, Evan; Lee, Christina; Croatto, Michael; Bentley, Helen; Lu, Wendy; Murray, Robert; Travassos, Mark; Coull, Brent; Openshaw, John; Greene, Casey S.; Shalem, Ophir; King, Gary; Probasco, Ryan; Cheng, David R.; Silbermann, Ben; Zhang, Feng; Lin, Xihong (Springer Science and Business Media LLC, 2020-08-26)
      Despite the widespread implementation of public health measures, COVID-19 continues to spread in the United States. To facilitate an agile response to the pandemic, we developed How We Feel, a web and mobile application ...