Now showing items 10-29 of 63

    • 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 ...
    • 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, ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 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 ...
    • Factors affecting ambulance utilization for asthma attack treatment: understanding where to target interventions 

      Raun, L.H.; Ensor, K.B.; Campos, L.A.; Persse, D. (2015)
      Objectives: Asthma is a serious, sometimes fatal condition, in which attacks vary in severity, potentially requiring emergency medical services (EMS) ambulance treatment. A portion of asthma attacks requiring EMS ambulance ...
    • 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 ...
    • Graphical Models via Univariate Exponential Family Distributions 

      Yang, Eunho; Ravikumar, Pradeep; Allen, Genevera I.; Liu, Zhandong (2015)
      Undirected graphical models, or Markov networks, are a popular class of statistical models, used in a wide variety of applications. Popular instances of this class include Gaussian graphical models and Ising models. In ...
    • Heavy-tailed densities 

      Rojo, Javier (2013)
      The concept of heavy- or long-tailed densities (or distributions) has attracted much well-deserved attention in the literature. A quick search in Google using the keywords long-tailed statistics retrieves almost 12 million ...
    • A hierarchical Bayesian model for inference of copy number variants and their association to gene expression 

      Cassese, Alberto; Guindani, Michele; Tadesse, Mahlet G.; Falciani, Francesco; Vannucci, Marina (2014)
      A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on ...
    • Hyaluronan turnover and hypoxic brown adipocytic differentiation are co-localized with ossification in calcified human aortic valves 

      Stephens, Elizabeth H.; Saltarrelli, Jerome G. Jr.; Balaoing, Liezl R.; Baggett, L. Scott; Nandi, Indrajit; Anderson, Kristin M.; Morrisett, Joel D.; Reardon, Michael J.; Simpson, Melanie A.; Weigel, Paul H.; Olmsted-Davis, Elizabeth A.; Davis, Alan R.; Grande-Allen, K. Jane (2012)
      The calcification process in aortic stenosis has garnered considerable interest but only limited investigation into selected signaling pathways. This study investigated mechanisms related to hypoxia, hyaluronan homeostasis, ...
    • Imaging genetics via sparse canonical correlation analysis 

      Chi, Eric C.; Allen, Genevera I.; Zhou, Hua; Kohannim, Omid; Lange, Kenneth; Thompson, Paul M. (2013)
      The collection of brain images from populations of subjects who have been genotyped with genome-wide scans makes it feasible to search for genetic effects on the brain. Even so, multivariate methods are sorely needed that ...
    • 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 ...
    • Inferring metabolic networks using the Bayesian adaptive graphical lasso with informative priors 

      Peterson, Christine; Vannucci, Marina; Karakas, Cemal; Choi, William; Ma, Lihua; Maletic-Savatic, Mirjana (2013)
      Metabolic processes are essential for cellular function and survival. We are interested in inferring a metabolic network in activated microglia, a major neuroimmune cell in the brain responsible for the neuroinflammation ...
    • An Integrative Bayesian Modeling Approach to Imaging Genetics 

      Stingo, Francesco C.; Guindani, Michele; Vannucci, Marina; Calhoun, Vince D. (2013)