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  • 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 ...
  • 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 ...
  • Variant interpretation through Bayesian fusion of frequency and genomic knowledge 

    Shaw, Chad A.; Campbell, Ian M. (2015)
    Variant interpretation is a central challenge in genomic medicine. A recent study demonstrates the power of Bayesian statistical approaches to improve interpretation of variants in the context of specific genes and syndromes. ...
  • Bayesian Inference of Multiple Gaussian Graphical Models 

    Peterson, Christine B.; Stingo, Francesco C.; Vannucci, Marina (2015)
    In this article, we propose a Bayesian approach to inference on multiple Gaussian graphical models. Specifically, we address the problem of inferring multiple undirected networks in situations where some of the networks ...
  • 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 ...
  • Evolutionary Action Score of TP53 Coding Variants Is Predictive of Platinum Response in Head and Neck Cancer Patients 

    Osman, Abdullah A.; Neskey, David M.; Katsonis, Panagiotis; Patel, Ameeta A.; Ward, Alexandra M.; Hsu, Teng-Kuei; Hicks, Stephanie C.; McDonald, Thomas O.; Ow, Thomas J.; Alves, Marcus Ortega; Pickering, Curtis R.; Skinner, Heath D.; Zhao, Mei; Sturgis, Eric M.; Kies, Merrill S.; El-Naggar, Adel; Perrone, Federica; Licitra, Lisa; Bossi, Paolo; Kimmel, Marek; Frederick, Mitchell J.; Lichtarge, Olivier; Myers, Jeffrey N. (2015)
    TP53 is the most frequently altered gene in head and neck squamous cell carcinoma (HNSCC), with mutations occurring in over two thirds of cases; however, the predictive response of these mutations to cisplatin-based therapy ...
  • Evolutionary Action Score of TP53 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer 

    Neskey, David M.; Osman, Abdullah A.; Ow, Thomas J.; Katsonis, Panagiotis; McDonald, Thomas; Hicks, Stephanie C.; Hsu, Teng-Kuei; Pickering, Curtis R.; Ward, Alexandra; Patel, Ameeta; Yordy, John S.; Skinner, Heath D.; Giri, Uma; Sano, Daisuke; Story, Michael D.; Beadle, Beth M.; El-Naggar, Adel K.; Kies, Merrill S.; William, William N.; Caulin, Carlos; Frederick, Mitchell; Kimmel, Marek; Myers, Jeffrey N.; Lichtarge, Olivier (2015)
    TP53 is the most frequently altered gene in head and neck squamous cell carcinoma, with mutations occurring in over two-thirds of cases, but the prognostic significance of these mutations remains elusive. In the current ...
  • A Bayesian model for the identification of differentially expressed genes in Daphnia magna exposed to munition pollutants 

    Cassese, Alberto; Guindani, Michele; Antczak, Philipp; Falciani, Francesco; Vannucci, Marina (2015)
    In this article we propose a Bayesian hierarchical model for the identification of differentially expressed genes in Daphnia magna organisms exposed to chemical compounds, specifically munition pollutants in water. The ...
  • Resting state functional MRI reveals abnormal network connectivity in neurofibromatosis 1 

    Tomson, Steffie N.; Schreiner, Matthew J.; Narayan, Manjari; Rosser, Tena; Enrique, Nicole; Silva, Alcino J.; Allen, Genevera I.; Bookheimer, Susan Y.; Bearden, Carrie E. (2015)
    Neurofibromatosis type I (NF1) is a genetic disorder caused by mutations in the neurofibromin 1 gene at locus 17q11.2. Individuals with NF1 have an increased incidence of learning disabilities, attention deficits, and ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Model-based clustering of large networks 

    Vu, Duy Q.; Hunter, David R.; Schweinberger, Michael (2013)
    We describe a network clustering framework, based on finite mixture models, that can be applied to discrete-valued networks with hundreds of thousands of nodes and billions of edge variables. Relative to other recent ...
  • 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, ...
  • 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 ...

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