Jennifer Listgarten

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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 time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algorithms. Our algorithm can analyze data(More)
Multiple realizations of continuous-valued time series from a stochastic process often contain systematic variations in rate and amplitude. To leverage the information contained in such noisy replicate sets, we need to align them in an appropriate way (for example, to allow the data to be properly combined by adaptive averaging). We present the Continuous(More)
CRISPR-Cas9-based genetic screens are a powerful new tool in biology. By simply altering the sequence of the single-guide RNA (sgRNA), one can reprogram Cas9 to target different sites in the genome with relative ease, but the on-target activity and off-target effects of individual sgRNAs can vary widely. Here, we use recently devised sgRNA design rules to(More)
Supplementary File Title Supplementary Figure 1 A comparison of P values for the algorithms described in Table 1 Supplementary Table 1 SNPs found to be significant by at least one of the algorithms in Table 1 Supplementary Methods Supplementary methods Supplementary Note 1 Experiments with synthetic data Supplementary Note 2 An efficient algorithm for(More)
Understanding the genetic underpinnings of disease is important for screening, treatment, drug development, and basic biological insight. One way of getting at such an understanding is to find out which parts of our DNA, such as single-nucleotide polymorphisms, affect particular intermediary processes such as gene expression. Naively, such associations can(More)
Previous studies have identified a central role for HLA-B alleles in influencing control of HIV infection. An alternative possibility is that a small number of HLA-B alleles may have a very strong impact on HIV disease outcome, dominating the contribution of other HLA alleles. Here, we find that even following the exclusion of subjects expressing any of the(More)
Hereditary predisposition and causative environmental exposures have long been recognized in human malignancies. In most instances, cancer cases occur sporadically, suggesting that environmental influences are critical in determining cancer risk. To test the influence of genetic polymorphisms on breast cancer risk, we have measured 98 single nucleotide(More)
Promiscuous binding of T helper epitopes to MHC class II molecules has been well established, but few examples of promiscuous class I-restricted epitopes exist. To address the extent of promiscuity of HLA class I peptides, responses to 242 well-defined viral epitopes were tested in 100 subjects regardless of the individuals' HLA type. Surprisingly, half of(More)
In epigenome-wide association studies, cell-type composition often differs between cases and controls, yielding associations that simply tag cell type rather than reveal fundamental biology. Current solutions require actual or estimated cell-type composition--information not easily obtainable for many samples of interest. We propose a method,(More)
MOTIVATION There is a pressing need for improved proteomic screening methods allowing for earlier diagnosis of disease, systematic monitoring of physiological responses and the uncovering of fundamental mechanisms of drug action. The combined platform of LC-MS (Liquid-Chromatography-Mass-Spectrometry) has shown promise in moving toward a solution in these(More)