Now showing items 1-20 of 66

    • A Bayesian Integrative Model for Genetical Genomics with Spatially Informed Variable Selection 

      Cassese, Alberto; Guindani, Michele; Vannucci, Marina (2014)
      We consider a Bayesian hierarchical model for the integration of gene expression levels with comparative genomic hybridization (CGH) array measurements collected on the same subjects. The approach defines a measurement ...
    • A Hierarchical Bayesian Model for the Identification of PET Markers Associated to the Prediction of Surgical Outcome after Anterior Temporal Lobe Resection 

      Chiang, Sharon; Guindani, Michele; Yeh, Hsiang J.; Dewar, Sandra; Haneef, Zulfi; Stern, John M.; Vannucci, Marina (2017)
      We develop an integrative Bayesian predictive modeling framework that identifies individual pathological brain states based on the selection of fluoro-deoxyglucose positron emission tomography (PET) imaging biomarkers and ...
    • A systems biology approach reveals common metastatic pathways in osteosarcoma 

      Flores, Ricardo J.; Li, Yiting; Yu, Alexander; Shen, Jianhe; Rao, Pulivarthi H.; Lau, Serrine S.; Vannucci, Marina; Lau, Ching C.; Man, Tsz-Kwong (2012)
      Background: Osteosarcoma (OS) is the most common malignant bone tumor in children and adolescents. The survival rate of patients with metastatic disease remains very dismal. Nevertheless, metastasis is a complex process ...
    • Accuracy of optical spectroscopy for the detection of cervical intraepithelial neoplasia without colposcopic tissue information; a step toward automation for low resource settings 

      Yamal, Jose-Miguel; Zewdie, Getie A.; Cox, Dennis D.; Atkinson, E. Neely; Cantor, Scott B.; MacAulay, Calum; Davies, Kalatu; Adewole, Isaac; Buys, Timon P. H.; Follen, Michele (2012-04)
      Optical spectroscopy has been proposed as an accurate and low-cost alternative for detection of cervical intraepithelial neoplasia. We previously published an algorithm using optical spectroscopy as an adjunct to colposcopy and ...
    • An Alternative Approach for Estimating the Accuracy of Colposcopy in Detecting Cervical Precancer 

      Davies, Kalatu R.; Cantor, Scott B.; Cox, Dennis D.; Follen, Michele (2015)
      Introduction: Since colposcopy helps to detect cervical cancer in its precancerous stages, as new strategies and technologies are developed for the clinical management of cervical neoplasia, precisely determining the ...
    • An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data 

      Wadsworth, W. Duncan; Argiento, Raffaele; Guindani, Michele; Galloway-Pena, Jessica; Shelbourne, Samuel A.; Vannucci, Marina (2017)
      Abstract Background The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious ...
    • BayesBD: An R Package for Bayesian Inference on Image Boundaries 

      Syring, Nicholas; Li, Meng (2017)
      We present the BayesBD package providing Bayesian inference for boundaries of noisy images. The BayesBD package implements flexible Gaussian process priors indexed by the circle to recover the boundary in a binary or ...
    • Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction 

      Li, Qiwei; Dahl, David B.; Vannucci, Marina; Joo, Hyun; Tsai, Jerry W. (2014)
      Determining the primary structure (i.e., amino acid sequence) of a protein has become cheaper, faster, and more accurate. Higher order protein structure provides insight into a protein's function in the cell. Understanding ...
    • A Bayesian Nonparametric Approach for Functional Data Classification with Application to Hepatic Tissue Characterization 

      Fronczyk, Kassandra M.; Guindani, Michele; Hobbs, Brian P.; Ng, Chaan S.; Vannucci, Marina (2015)
      Computed tomography perfusion (CTp) is an emerging functional imaging technology that provides a quantitative assessment of the passage of fluid through blood vessels. Tissue perfusion plays a critical role in oncology due ...
    • Brominated flame retardants in placental tissues: associations with infant sex and thyroid hormone endpoints 

      Leonetti, Christopher; Butt, Craig M; Hoffman, Kate; Hammel, Stephanie C; Miranda, Marie L; Stapleton, Heather M (2016)
      Abstract Background Brominated flame retardants (BFRs) are endocrine disruptors that bioaccumulate in the placenta, but it remains unclear if they disrupt tissue thyroid ...
    • Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways 

      Czerkies, Maciej; Korwek, Zbigniew; Prus, Wiktor; Kochańczyk, Marek; Jaruszewicz-Błońska, Joanna; Tudelska, Karolina; Błoński, Sławomir; Kimmel, Marek; Brasier, Allan R.; Lipniacki, Tomasz (2018)
      The innate immune system processes pathogen-induced signals into cell fate decisions. How information is turned to decision remains unknown. By combining stochastic mathematical modelling and experimentation, we demonstrate ...
    • 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 ...
    • Classification of hyperspectral imagery with neural networks: comparison to conventional tools 

      Merényi, Erzsébet; Farrand, William H.; Taranik, James V.; Minor, Timothy B. (2014)
      Efficient exploitation of hyperspectral imagery is of great importance in remote sensing. Artificial intelligence approaches have been receiving favorable reviews for classification of hyperspectral data because the ...
    • 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, ...
    • Computational finance: correlation, volatility, and markets 

      Ensor, Katherine Bennett; Koev, Ginger M. (2014)
      Financial data by nature are inter-related and should be analyzed using multivariate methods. Many models exist for the joint analysis of multiple financial instruments. Early models often assumed some type of constant ...
    • Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κ B-dependent genes regulated by TNFα and heat shock 

      Janus, Patryk; Stokowy, Tomasz; Jaksik, Roman; Szoltysek, Katarzyna; Handschuh, Luiza; Podkowinski, Jan; Widlak, Wieslawa; Kimmel, Marek; Widlak, Piotr (2015)
      Heat shock inhibits NF-κB signaling, yet the knowledge about its influence on the regulation of NF-κB-dependent genes is limited. Using genomic approaches, i.e., expression microarrays and ChIP-Seq, we aimed to establish ...
    • 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 ...
    • 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 ...
    • Dynamic Cross Talk Model of the Epithelial Innate Immune Response to Double-Stranded RNA Stimulation: Coordinated Dynamics Emerging from Cell-Level Noise 

      Bertolusso, Roberto; Tian, Bing; Zhao, Yingxin; Vergara, Leoncio; Sabree, Aqeeb; Iwanaszko, Marta; Lipniacki, Tomasz; Brasier, Allan R.; Kimmel, Marek (2014)
      We present an integrated dynamical cross-talk model of the epithelial innate immune reponse (IIR) incorporating RIG-I and TLR3 as the two major pattern recognition receptors (PRR) converging on the RelA and IRF3 transcriptional ...
    • Evolutionary action and structural basis of the allosteric switch controlling β2AR functional selectivity 

      Schönegge, Anne-Marie; Gallion, Jonathan; Picard, Louis-Philippe; Wilkins, Angela D.; Le Gouill, Christian; Audet, Martin; Stallaert, Wayne; Lohse, Martin J.; Kimmel, Marek; Lichtarge, Olivier; Bouvier, Michel (2017)
      Functional selectivity of G-protein-coupled receptors is believed to originate from ligand-specific conformations that activate only subsets of signaling effectors. In this study, to identify molecular motifs playing ...