Statistical Genetics journal club

Next meeting

2pm, 24 Sep 2019
Room 115, Level 1, Building 184, Parkville Campus, University of Melbourne

Fortes-Lima CA, Laurent R, Thouzeau V, Toupance B, Verdu P (2019). Complex genetic admixture histories reconstructed with Approximate Bayesian Computations, bioRxiv.

About the club

This journal club is hosted by Melbourne Integrative Genomics (MIG) at the University of Melbourne. It is currently managed by Damjan Vukcevic.

Mailing list

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Proposed papers

Please send suggestions to Damjan Vukcevic. Papers must be related to genetics or genomics and must have substantial statistical content.

Liu X, Li YI, Pritchard JK (2019). Trans effects on gene expression can drive omnigenic inheritance, Cell. (pubmed, biorxiv)

Wainschtein P, …, Weir BS, Laurie CC, Yang J, Visscher PM (2019). Recovery of trait heritability from whole genome sequence data, bioRxiv.

Gigante S, van Dijk D, Moon K, Strzalkowski A, Wolf G, Krishnaswamy S (2019). Modeling Global Dynamics from Local Snapshots with Deep Generative Neural Networks, arXiv.

Wald NJ, Old R (2019). The illusion of polygenic disease risk prediction, Genetics in Medicine. (pubmed)

Martin AR, Kanai M, Kamatani Y, Okada Y, Neale BM, Daly MJ (2019). Clinical use of current polygenic risk scores may exacerbate health disparities, Nature genetics. (pubmed)

Speidel L, Forest M, Shi S, Myers S (2019). A method for genome-wide genealogy estimation for thousands of samples, bioRxiv. (software)

Hou K, Burch KS, Majumdar A, Shi H, N Mancuso N, Wu Y, Sankararaman S, Pasaniuc B (2019). Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture, bioRxiv.

Zhu X, Stephens M (2018). Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes, Nature Communications. (pubmed, pmc)

Zhang Y, Qi G, Park JH, Chatterjee N (2018). Estimation of complex effect-size distributions using summary-level statistics from genome-wide association studies across 32 complex traits, Nature Genetics. (pubmed, biorxiv)

Márquez-Luna C, Gazal S, Loh P-R, Kim SS, Furlotte N, Auton A, 23andMe, Price AL (2018). Modeling functional enrichment improves polygenic prediction accuracy in UK Biobank and 23andMe data sets, bioRxiv.

Zhu Z, …, Visscher PM, Wray NR, Yang J (2018). Causal associations between risk factors and common diseases inferred from GWAS summary data, Nature Communications. (pubmed, pmc, biorxiv)

Brown BC, AGEN-T2G, Ye CJ, Price AL, Zaitlen N (2016). Transethnic Genetic-Correlation Estimates from Summary Statistics, AJHG. (pubmed, pmc, biorxiv)

Previous papers

13 Sep 2019. Almarri MA, Bergström A, Prado-Martinez J, Dunham AS, Chen Y, Tyler-Smith C, Xue Y (2019). Population Structure, Stratification and Introgression of Human Structural Variation in the HGDP, bioRxiv.

27 Aug 2019. Veturi Y, de Los Campos G, Yi N, Huang W, Vazquez AI, Kühnel B (2019). Modeling Heterogeneity in the Genetic Architecture of Ethnically Diverse Groups Using Random Effect Interaction Models, Genetics. (pubmed, pmc)

22 Jul 2019. Urbut SM, Wang G, Carbonetto P, Stephens M (2019). Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions, Nature Genetics. (pubmed, biorxiv)

27 May 2019. Ge T, Chen CY, Ni Y, Feng, YA, Smoller JW (2019). Polygenic prediction via Bayesian regression and continuous shrinkage priors, Nature Communications. (biorxiv)

2 May 2019. Karczewski KJ, …, Neale BM, Daly MJ, MacArthur DG (2019). Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes, bioRxiv. (blog)

11 Apr 2019. Albers PK, McVean G (2018). Dating genomic variants and shared ancestry in population-scale sequencing data, bioRxiv.

11 Mar 2019. Zhang C, Matsen IV FA (2018). Generalizing Tree Probability Estimation via Bayesian Networks, NIPS 2018. (pdf, blog)

10 Dec 2018. Khera AV, Chaffin M, Aragam KG, Haas ME, Roselli C, Choi SH, Natarajan P, Lander ES, Lubitz SA, Ellinor PT, Kathiresan S (2018). Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations, Nature Genetics. (pubmed)

19 Nov 2018. Kelleher J, Wong Y, Albers P, Wohns AW, McVean G (2018). Inferring the ancestry of everyone, bioRxiv.

5 Nov 2018. Bradburd GS, Coop GM, Ralph PL (2018). Inferring Continuous and Discrete Population Genetic Structure Across Space, Genetics. (pubmed, pmc, biorxiv)

8 Oct 2018. Shi H, Kichaev G, Pasaniuc B (2016). Contrasting the Genetic Architecture of 30 Complex Traits from Summary Association Data, AJHG. (pubmed, pmc, biorxiv)

10 Sep 2018. Tran D, Blei DM (2017). Implicit Causal Models for Genome-wide Association Studies, arXiv. (openreview)

13 Aug 2018. Mak TSH, Porsch RM, Choi SW, Zhou X, Sham PC (2017). Polygenic scores via penalized regression on summary statistics, Genetic Epidemiology.

18 Jul 2018. He Q, Pilosof S, Tiedje KE, Ruybal-Pesántez S, Artzy-Randrup Y, Baskerville EB, Day KP, Pascual M (2018). Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum, Nature Communications. (pubmed, ‘behind the paper’)

27 Jun 2018. Durvasula A, Sankararaman S (2018). Recovering signals of ghost archaic admixture in the genomes of present-day Africans, bioRxiv.

28 May 2018. Kelleher J, Thornton K, Ashander J, Ralph P (2018). Efficient pedigree recording for fast population genetics simulation, bioRxiv.

9 May 2018. Cabreros I, Storey JD (2017). A nonparametric estimator of population structure unifying admixture models and principal components analysis, bioRxiv.

18 Apr 2018. Chan J, Perrone V, Spence JP, Jenkins PA, Mathieson S, Song YS (2018). A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks, bioRxiv. (arxiv)

28 Mar 2018. Li YI, Knowles DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK (2018). Annotation-free quantification of RNA splicing using LeafCutter, Nature Genetics. (biorxiv)