Now showing items 1-20 of 74

    • Coalescence computations for large samples drawn from populations of time-varying sizes 

      Polanski, Andrzej; Szczesna, Agnieszka; Garbulowski, Mateusz; Kimmel, Marek (2017)
      We present new results concerning probability distributions of times in the coalescence tree and expected allele frequencies for coalescent with large sample size. The obtained results are based on computational methodologies, ...
    • A genome-wide trans-ethnic interaction study links theᅠPIGR-FCAMRᅠlocus to coronary atherosclerosis via interactions between genetic variants and residential exposure to traffic 

      Ward-Caviness, Cavin K.; Neas, Lucas M.; Blach, Colette; Haynes, Carol S.; LaRocque-Abramson, Karen; Grass, Elizabeth; Dowdy, Z. Elaine; Devlin, Robert B.; Diaz-Sanchez, David; Cascio, Wayne E.; Miranda, Marie Lynn; Gregory, Simon G.; Shah, Svati H.; Kraus, William E.; Hauser, Elizabeth R. (2017)
      Air pollution is a worldwide contributor to cardiovascular disease mortality and morbidity. Traffic-related air pollution is a widespread environmental exposure and is associated with multiple cardiovascular outcomes such ...
    • Exercising control when confronted by a (Brownian) spider 

      Ernst, Philip (2016)
      We consider the Brownian “spider,” a construct introduced in Dubins and Schwarz (1988) and in Barlow and Pitman (1989). In this note, the author proves the “spider” bounds by using the dynamic programming strategy of ...
    • Mixed Effects Models for Resampled Network Statistics Improves Statistical Power to Find Differences in Multi-Subject Functional Connectivity 

      Narayan, Manjari; Allen, Genevera I. (2016)
      Many complex brain disorders, such as autism spectrum disorders, exhibit a wide range of symptoms and disability. To understand how brain communication is impaired in such conditions, functional connectivity studies seek ...
    • XMRF: an R package to fit Markov Networks to high-throughput genetics data 

      Wan, Ying-Wooi; Allen, Genevera I; Baker, Yulia; Yang, Eunho; Ravikumar, Pradeep; Anderson, Matthew; Liu, Zhandong (2016)
      Abstract Background Technological advances in medicine have led to a rapid proliferation of high-throughput “omics” data. Tools to mine this data and discover disrupted ...
    • ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data 

      Rustagi, Navin; Hampton, Oliver A; Li, Jie; Xi, Liu; Gibbs, Richard A; Plon, Sharon E; Kimmel, Marek; Wheeler, David A (2016)
      Abstract Background Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in ...
    • Implications of construction method and spatial scale on measures of the built environment 

      Strominger, Julie; Anthopolos, Rebecca; Miranda, Marie L (2016)
      Abstract Background Research surrounding the built environment (BE) and health has resulted in inconsistent findings. Experts have identified the need to examine methodological ...
    • Joint Bayesian variable and graph selection for regression models with network-structured predictors 

      Peterson, C.B.; Stingo, F.C.; Vannucci, M. (2016)
      In this work, we develop a Bayesian approach to perform selection of predictors that are linked within a network. We achieve this by combining a sparse regression model relating the predictors to a response variable with ...
    • On the time for Brownian motion to visit every point on a circle 

      Ernst, Philip; Shepp, Larry (2016)
      Consider a Wiener process W on a circle of circumference L. We prove the rather surprising result that the Laplace transform of the distribution of the first time, θL, when the Wiener process has visited every point of the ...
    • Concentrations of polybrominated diphenyl ethers (PBDEs) and 2,4,6-tribromophenol in human placental tissues 

      Leonetti, Christopher; Butt, Craig M.; Hoffman, Kate; Miranda, Marie Lynn; Stapleton, Heather M. (2016)
      Legacy environmental contaminants such as polybrominated diphenyl ethers (PBDEs) are widely detected in human tissues. However, few studies have measured PBDEs in placental tissues, and there are no reported measurements ...
    • A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells 

      Trevino, Victor; Cassese, Alberto; Nagy, Zsuzsanna; Zhuang, Xiaodong; Herbert, John; Antzack, Philipp; Clarke, Kim; Davies, Nicholas; Rahman, Ayesha; Campbell, Moray J.; Guindani, Michele; Bicknell, Roy; Vannucci, Marina; Falciani, Francesco (2016)
      The advent of functional genomics has enabled the genome-wide characterization of the molecular state of cells and tissues, virtually at every level of biological organization. The difficulty in organizing and mining this ...
    • A spatiotemporal nonparametric Bayesian model of multi-subject fMRI data 

      Zhang, Linlin; Guindani, Michele; Versace, Francesco; Engelmann, Jeffrey M.; Vannucci, Marina (2016)
      In this paper we propose a unified, probabilistically coherent framework for the analysis of task-related brain activity in multi-subject fMRI experiments. This is distinct from two-stage “group analysis” approaches ...
    • Chronic Infection Depletes Hematopoietic Stem Cells through Stress-Induced Terminal Differentiation 

      Matatall, Katie A.; Jeong, Mira; Chen, Siyi; Sun, Deqiang; Chen, Fengju; Mo, Qianxing; Kimmel, Marek; King, Katherine Y. (2016)
      Chronic infections affect a third of the world’s population and can cause bone marrow suppression, a severe condition that increases mortality from infection. To uncover the basis for infection-associated bone marrow ...
    • Development of an analytical method to quantify PBDEs, OH-BDEs, HBCDs, 2,4,6-TBP, EH-TBB, and BEH-TEBP in human serum 

      Butt, Craig M.; Miranda, Marie Lynn; Stapleton, Heather M. (2016)
      Polybrominated diphenyl ethers (PBDEs) flame retardants (FRs) were phased-out in the mid-2000s (penta- and octaBDE) and 2013 (decaBDE); however, their hydroxylated metabolites (OH-BDEs) are still commonly detected in human ...
    • Smoothing and Mean–Covariance Estimation of Functional Data with a Bayesian Hierarchical Model 

      Yang, Jingjing; Zhu, Hongxiao; Choi, Taeryon; Cox, Dennis D. (2016)
      Functional data, with basic observational units being functions (e.g., curves, surfaces) varying over a continuum, are frequently encountered in various applications. While many statistical tools have been developed for ...
    • Cross-Disciplinary Consultancy to Enhance Predictions of Asthma Exacerbation Risk in Boston 

      Reid, Margaret; Gunn, Julia; Shah, Snehal; Donovan, Michael; Eggo, Rosalind; Babin, Steven; Stajner, Ivanka; Rogers, Eric; Ensor, Katherine B.; Raun, Loren; Levy, Jonathan I.; Painter, Ian; Phipatanakul, Wanda; Yip, Fuyuen; Nath, Anjali; Streichert, Laura; Tong, Catherine; Burkom, Howard (2016)
      This paper continues an initiative conducted by the International Society for Disease Surveillance with funding from the Defense Threat Reduction Agency to connect near-term analytical needs of public health practice with ...
    • A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics 

      James, Regis A.; Campbell, Ian M.; Chen, Edward S.; Boone, Philip M.; Rao, Mitchell A.; Bainbridge, Matthew N.; Lupski, James R.; Yang, Yaping; Eng, Christine M.; Posey, Jennifer E.; Shaw, Chad A. (2016)
      Background: Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic ...
    • Time-dependence of graph theory metrics in functional connectivity analysis 

      Chiang, Sharon; Cassese, Alberto; Guindani, Michele; Vannucci, Marina; Yeh, Hsiang J.; Haneef, Zulfi; Stern, John M. (2016)
      Brain graphs provide a useful way to computationally model the network structure of the connectome, and this has led to increasing interest in the use ofᅠgraph theoryᅠto quantitate and investigate the topological characteristics ...
    • Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease 

      Allen, Genevera I.; Amoroso, Nicola; Anghel, Catalina; Balagurusamy, Venkat; Bare, Christopher J.; Beaton, Derek; Bellotti, Roberto; Bennett, David A.; Boehme, Kevin L.; Boutros, Paul C.; Caberlotto, Laura; Caloian, Cristian; Campbell, Frederick; Neto, Elias Chaibub; Chang, Yu-Chuan; Chen, Beibei; Chen, Chien-Yu; Chien, Ting-Ying; Clark, Tim; Das, Sudeshna; Davatzikos, Christos; Deng, Jieyao; Dillenberger, Donna; Dobson, Richard J.B.; Dong, Qilin; Doshi, Jimit; Duma, Denise; Errico, Rosangela; Erus, Guray; Everett, Evan; Fardo, David W.; Friend, Stephen H.; Frӧhlich, Holger; Gan, Jessica; St George-Hyslop, Peter; Ghosh, Satrajit S.; Glaab, Enrico; Green, Robert C.; Guan, Yuanfang; Hong, Ming-Yi; Huang, Chao; Hwang, Jinseub; Ibrahim, Joseph; Inglese, Paolo; Iyappan, Anandhi; Jiang, Qijia; Katsumata, Yuriko; Kauwe, John S.K.; Klein, Arno; Kong, Dehan; Krause, Roland; Lalonde, Emilie; Lauria, Mario; Lee, Eunjee; Lin, Xihui; Liu, Zhandong; Livingstone, Julie; Logsdon, Benjamin A.; Lovestone, Simon; Ma, Tsung-wei; Malhotra, Ashutosh; Mangravite, Lara M.; Maxwell, Taylor J.; Merrill, Emily; Nagorski, John; Namasivayam, Aishwarya; Narayan, Manjari; Naz, Mufassra; Newhouse, Stephen J.; Norman, Thea C.; Nurtdinov, Ramil N.; Oyang, Yen-Jen; Pawitan, Yudi; Peng, Shengwen; Peters, Mette A.; Piccolo, Stephen R.; Praveen, Paurush; Priami, Corrado; Sabelnykova, Veronica Y.; Senger, Philipp; Shen, Xia; Simmons, Andrew; Sotiras, Aristeidis; Stolovitzky, Gustavo; Tangaro, Sabina; Tateo, Andrea; Tung, Yi-An; Tustison, Nicholas J.; Varol, Erdem; Vradenburg, George; Weiner, Michael W.; Xiao, Guanghua; Xie, Lei; Xie, Yang; Xu, Jia; Yang, Hojin; Zhan, Xiaowei; Zhou, Yunyun; Zhu, Fan; Zhu, Hongtu; Zhu, Shanfeng; Alzheimer’s Disease Neuroimaging Initiative (2016)
      Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational ...
    • Wee-1 Kinase Inhibition Overcomes Cisplatin Resistance Associated with High-RiskTP53ᅠMutations in Head and Neck Cancer through Mitotic Arrest Followed by Senescence 

      Osman, Abdullah A.; Monroe, Marcus M.; Alves, Marcus V. Ortega; Patel, Ameeta A.; Katsonis, Panagiotis; Fitzgerald, Alison L.; Neskey, David M.; Frederick, Mitchell J.; Woo, Sang Hyeok; Caulin, Carlos; Hsu, Teng-Kuei; McDonald, Thomas O.; Kimmel, Marek; Meyn, Raymond E.; Lichtarge, Olivier; Myers, Jeffrey N. (2015)
      Although cisplatin has played a role in "standard-of-care" multimodality therapy for patients with advanced squamous cell carcinoma of the head and neck (HNSCC), the rate of treatment failure remains particularly high for ...