User profiles for C. M. Kadie
Carl KadieMicrosoft Research (retired) Verified email at benkadie.com Cited by 22642 |
FaST linear mixed models for genome-wide association studies
We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm
for genome-wide association studies (GWAS) that scales linearly with cohort size in both run …
for genome-wide association studies (GWAS) that scales linearly with cohort size in both run …
HIV-1 adaptation to NK-cell-mediated immune pressure
…, D Heckerman, A Schneidewind, L Fadda, CM Kadie… - Nature, 2011 - nature.com
Natural killer (NK) cells have an important role in the control of viral infections, recognizing
virally infected cells through a variety of activating and inhibitory receptors 1 , 2 , 3 . …
virally infected cells through a variety of activating and inhibitory receptors 1 , 2 , 3 . …
Improved linear mixed models for genome-wide association studies
Methods) that includes family members and non-Caucasians, FaST-LMM-Select yielded
slightly less inflation, fewer false positives and fewer false negatives (due to lack of dilution) …
slightly less inflation, fewer false positives and fewer false negatives (due to lack of dilution) …
[HTML][HTML] HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins
Background Despite the extensive genetic diversity of HIV-1, viral evolution in response to
immune selective pressures follows broadly predictable mutational patterns. Sites and …
immune selective pressures follows broadly predictable mutational patterns. Sites and …
Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection
Mutations that allow escape from CD8 T-cell responses are common in HIV-1 and may attenuate
pathogenesis by reducing viral fitness. While this has been demonstrated for individual …
pathogenesis by reducing viral fitness. While this has been demonstrated for individual …
Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters
The mechanisms underlying HIV-1 control by protective HLA class I alleles are not fully
understood and could involve selection of escape mutations in functionally important Gag …
understood and could involve selection of escape mutations in functionally important Gag …
A powerful and efficient set test for genetic markers that handles confounders
Motivation: Approaches for testing sets of variants, such as a set of rare or common variants
within a gene or pathway, for association with complex traits are important. In particular, set …
within a gene or pathway, for association with complex traits are important. In particular, set …
[HTML][HTML] An exhaustive epistatic SNP association analysis on expanded Wellcome Trust data
We present an approach for genome-wide association analysis with improved power on the
Wellcome Trust data consisting of seven common phenotypes and shared controls. We …
Wellcome Trust data consisting of seven common phenotypes and shared controls. We …
Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans
A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed
HIV-1 controllers, suppress viral replication to very low levels in the absence of therapy. …
HIV-1 controllers, suppress viral replication to very low levels in the absence of therapy. …
Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase–integrase sequences from HIV-1 elite controllers
…, E Martin, BL Block, A Trocha, CM Kadie… - JAIDS Journal of …, 2011 - journals.lww.com
… After transfection, cells were rested for 45 minutes at room temperature, transferred to 25
cm 2 flasks in 5 mL of R10+ medium, and fed with 5 mL R10+ medium on day 5. GFP …
cm 2 flasks in 5 mL of R10+ medium, and fed with 5 mL R10+ medium on day 5. GFP …