Search Results - "Heckerman, David"

Epigenome-wide association studies without the need for cell-type composition by Zou, James, Lippert, Christoph, Heckerman, David, Aryee, Martin, Listgarten, Jennifer

“…A statistical approach using a linear mixed model and principal-component analysis discovers phenotype-specific changes in epigenomes without requiring…”
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Beyond Atopy: Multiple Patterns of Sensitization in Relation to Asthma in a Birth Cohort Study by SIMPSON, Angela, TAN, Vincent Y. F, WINN, John, SVENSEN, Markus, BISHOP, Christopher M, HECKERMAN, David E, BUCHAN, Lain, CUSTOVIC, Adnan

“…The pattern of IgE response (over time or to specific allergens) may reflect different atopic vulnerabilities which are related to the presence of asthma in a…”
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Ranking of non-coding pathogenic variants and putative essential regions of the human genome by Wells, Alex, Heckerman, David, Torkamani, Ali, Yin, Li, Sebat, Jonathan, Ren, Bing, Telenti, Amalio, di Iulio, Julia

“…A gene is considered essential if loss of function results in loss of viability, fitness or in disease. This concept is well established for coding genes;…”
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Efficient Control of Population Structure in Model Organism Association Mapping by Kang, Hyun Min, Zaitlen, Noah A, Wade, Claire M, Kirby, Andrew, Heckerman, David, Daly, Mark J, Eskin, Eleazar

“…Genomewide association mapping in model organisms such as inbred mouse strains is a promising approach for the identification of risk factors related to human…”
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Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes by Tang, Haibao, Kirkness, Ewen F., Lippert, Christoph, Biggs, William H., Fabani, Martin, Guzman, Ernesto, Ramakrishnan, Smriti, Lavrenko, Victor, Kakaradov, Boyko, Hou, Claire, Hicks, Barry, Heckerman, David, Och, Franz J., Caskey, C. Thomas, Venter, J. Craig, Telenti, Amalio

“…Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the…”
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Chromosome 9p21 in amyotrophic lateral sclerosis in Finland: a genome-wide association study by Laaksovirta, Hannu, MD, Peuralinna, Terhi, MSc, Schymick, Jennifer C, PhD, Scholz, Sonja W, MD, Lai, Shaoi-Lin, MD, Myllykangas, Liisa, MD, Sulkava, Raimo, MD, Jansson, Lilja, Hernandez, Dena G, MSc, Gibbs, J Raphael, BS, Nalls, Michael A, PhD, Heckerman, David, MD, Tienari, Pentti J, MD, Traynor, Bryan J, Dr

“…Summary Background The genetic cause of amyotrophic lateral sclerosis (ALS) is not well understood. Finland is a well suited location for a genome-wide…”
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Correction for hidden confounders in the genetic analysis of gene expression by Listgarten, Jennifer, Kadie, Carl, Schadt, Eric E., Heckerman, David

“…Understanding the genetic underpinnings of disease is important for screening, treatment, drug development, and basic biological insight. One way of getting at…”
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Selection bias at the heterosexual HIV-1 transmission bottleneck by Carlson, Jonathan M., Schaefer, Malinda, Monaco, Daniela C., Batorsky, Rebecca, Claiborne, Daniel T., Prince, Jessica, Deymier, Martin J., Ende, Zachary S., Klatt, Nichole R., DeZiel, Charles E., Lin, Tien-Ho, Peng, Jian, Seese, Aaron M., Shapiro, Roger, Frater, John, Ndung'u, Thumbi, Tang, Jianming, Goepfert, Paul, Gilmour, Jill, Price, Matt A., Kilembe, William, Heckerman, David, Goulder, Philip J.R., Allen, Todd M., Allen, Susan, Hunter, Eric

“…HIV needs to be fit to transmit Although you might not think it, it's hard to catch HIV. Less than 1% of unprotected sexual exposures result in infection. What…”
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Widespread Impact of HLA Restriction on Immune Control and Escape Pathways of HIV-1 by Carlson, Jonathan M, Listgarten, Jennifer, Pfeifer, Nico, Tan, Vincent, Kadie, Carl, Walker, Bruce D, Ndung'u, Thumbi, Shapiro, Roger, Frater, John, Brumme, Zabrina L, Goulder, Philip J R, Heckerman, David

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Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection by LESLIE, Alasdair, MATTHEWS, Philippa C, GOULDER, Philip J. R, LISTGARTEN, Jennifer, CARLSON, Jonathan M, KADIE, Carl, NDUNG'U, Thumbi, BRANDER, Christian, COOVADIA, Hoosen, WALKER, Bruce D, HECKERMAN, David

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HIV-Specific CD4 T Cell Responses to Different Viral Proteins Have Discordant Associations with Viral Load and Clinical Outcome by RANASINGHE, Srinika, FLANDERS, Michael, STREECK, Hendrik, CUTLER, Sam, SOGHOIAN, Damien Z, GHEBREMICHAEL, Musie, DAVIS, Isaiah, LINDQVIST, Madelene, PEREYRA, Florencia, WALKER, Bruce D, HECKERMAN, David

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Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop by Souza, Glaucia Mendes, Van Sluys, Marie-Anne, Lembke, Carolina Gimiliani, Lee, Hayan, Margarido, Gabriel Rodrigues Alves, Hotta, Carlos Takeshi, Gaiarsa, Jonas Weissmann, Diniz, Augusto Lima, Oliveira, Mauro de Medeiros, Ferreira, Sávio de Siqueira, Nishiyama, Milton Yutaka, ten-Caten, Felipe, Ragagnin, Geovani Tolfo, Andrade, Pablo de Morais, de Souza, Robson Francisco, Nicastro, Gianlucca Gonçalves, Pandya, Ravi, Kim, Changsoo, Guo, Hui, Durham, Alan Mitchell, Carneiro, Monalisa Sampaio, Zhang, Jisen, Zhang, Xingtan, Zhang, Qing, Ming, Ray, Schatz, Michael C, Davidson, Bob, Paterson, Andrew H, Heckerman, David

“…ABSTRACT Background Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets of chromosomes from 2 Saccharum…”
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CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control by Mothe, Beatriz, Llano, Anuska, Ibarrondo, Javier, Zamarreño, Jennifer, Schiaulini, Mattia, Miranda, Cristina, Ruiz-Riol, Marta, Berger, Christoph T, Herrero, M José, Palou, Eduard, Plana, Montse, Rolland, Morgane, Khatri, Ashok, Heckerman, David, Pereyra, Florencia, Walker, Bruce D, Weiner, David, Paredes, Roger, Clotet, Bonaventura, Felber, Barbara K, Pavlakis, George N, Mullins, James I, Brander, Christian

“…Cytotoxic T lymphocyte (CTL) responses targeting specific HIV proteins, in particular Gag, have been associated with relative control of viral replication in…”
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ConPADE: genome assembly ploidy estimation from next-generation sequencing data by Margarido, Gabriel R A, Heckerman, David

“…As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft…”
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Quantifying the uncertainty in heritability by Furlotte, Nicholas A, Heckerman, David, Lippert, Christoph

“…The use of mixed models to determine narrow-sense heritability and related quantities such as SNP heritability has received much recent attention. Less…”
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HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: Immune Escape and Viral Load by ROUSSEAU, Christine M, DANIELS, Marcus G, MAUST, Brandon S, LEARN, Gerald H, NICKLE, David C, COOVADIA, Hoosen, NDUNG'U, Thumbi, FRAHM, Nicole, BRANDER, Christian, WALKER, Bruce D, GOULDER, Philip J. R, BHATTACHARYA, Tanmoy, CARLSON, Jonathan M, HECKERMAN, David E, KORBER, Bette T, MULLINS, James, KADIE, Carl, CRAWFORD, Hayley, PRENDERGAST, Andrew, MATTHEWS, Philippa, PAYNE, Rebecca, ROLLAND, Morgane, RAUGI, Dana N

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Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations by Bhattacharya, Tanmoy, Daniels, Marcus, Heckerman, David, Foley, Brian, Frahm, Nicole, Kadie, Carl, Carlson, Jonathan, Yusim, Karina, McMahon, Ben, Gaschen, Brian, Mallal, Simon, Mullins, James I, Nickle, David C, Herbeck, Joshua, Rousseau, Christine, Learn, Gerald H, Miura, Toshiyuki, Brander, Christian, Walker, Bruce, Korber, Bette

“…Escape from T cell-mediated immune responses affects the ongoing evolution of rapidly evolving viruses such as HIV. By applying statistical approaches that…”
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Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection by BRUMME, Zabrina L, BRUMME, Chanson J, JESSEN, Heiko, KELLEHER, Anthony D, ROSENBERG, Eric, KALDOR, John, YUKI, Yuko, CARRINGTON, Mary, ALLEN, Todd M, MALLAL, Simon, ALTFELD, Marcus, HECKERMAN, David, CARLSON, Jonathan, WALKER, Bruce D, STREECK, Hendrik, JOHN, Mina, EICHBAUM, Quentin, BLOCK, Brian L, BAKER, Brett, KADIE, Carl, MARKOWITZ, Martin

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Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1 by CARLSON, Jonathan M, BRUMME, Chanson J, HAUBRICH, Richard, NELSON, George, PFEIFER, Nico, DEZIEL, Charles E, HECKERMAN, David, APPS, Richard, CARRINGTON, Mary, MALLAL, Simon, RICHARD HARRIGAN, P, JOHN, Mina, MARTIN, Eric, BRUMME, Zabrina L, LISTGARTEN, Jennifer, BROCKMAN, Mark A, LE, Anh Q, CHUI, Celia K. S, COTTON, Laura A, KNAPP, David J. H. F, RIDDLER, Sharon A

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Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis by Prince, Jessica L, Claiborne, Daniel T, Carlson, Jonathan M, Schaefer, Malinda, Yu, Tianwei, Lahki, Shabir, Prentice, Heather A, Yue, Ling, Vishwanathan, Sundaram A, Kilembe, William, Goepfert, Paul, Price, Matthew A, Gilmour, Jill, Mulenga, Joseph, Farmer, Paul, Derdeyn, Cynthia A, Tang, Jiaming, Heckerman, David, Kaslow, Richard A, Allen, Susan A, Hunter, Eric

“…Initial studies of 88 transmission pairs in the Zambia Emory HIV Research Project cohort demonstrated that the number of transmitted HLA-B associated…”
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