Journal Club

What: Complex Trait Genomics Journal Club for researchers in and around Brisbane

When: Every Tuesday lunch time at 11:30am-1pm

Where: Multi media room 3.141, Institute for Molecular Bioscience, St Lucia campus (building #80)

Instructions: Presenters create some slides and bring some cakes (sorry, it’s tradition).

Volunteer: Click the following link here to sign up on the doodle poll.

Mailing list: To subscribe to the mailing list, get in touch with Luke Lloyd-Jones.

Archive

2016

 
29/11/2016 presented by Kartik Chundru
 
Scaling probabilistic models of genetic variation to millions of humans. Prem Gopalan, Wei Hao, David M Blei, and John D Storey. Nature genetics, 48(11):1587--1590, 2016.
 
22/11/2016 presented by Restu Restuadi
 
The effect of host genetics on the gut microbiome. Marc Jan Bonder, Alexander Kurilshikov, Ettje F Tigchelaar, Zlatan Mujagic, Floris Imhann, Arnau Vich Vila, Patrick Deelen, Tommi Vatanen, Melanie Schirmer, Sanne P Smeekens, et al. Nature genetics, 48(11):1407--1412, 2016.
 
15/11/2016 presented by Yang Wu
 
Genetic and epigenetic fine mapping of causal autoimmune disease variants. Kyle Kai-How Farh, Alexander Marson, Jiang Zhu, Markus Kleinewietfeld, William J Housley, Samantha Beik, Noam Shoresh, Holly Whitton, Russell JH Ryan, Alexander A Shishkin, et al. Nature, 518(7539):337--343, 2015.
 
08/11/2016 presented by Jian Yang
 
The contribution of rare variation to prostate cancer heritability. Nicholas Mancuso, Nadin Rohland, Kristin A Rand, Arti Tandon, Alexander Allen, Dominique Quinque, Swapan Mallick, Heng Li, Alex Stram, Xin Sheng, et al. Nature genetics, 2015.
 
01/11/2016 presented by Irfahan Kassam
 
Sex-Specific Selection and Sex-Biased Gene Expression in Humans and Flies. Changde Cheng and Mark Kirkpatrick. PLoS Genet, 12(9):e1006170, 2016.
 
25/10/2016 presented by Lachlan Strike
 
A comprehensive transcriptional map of primate brain development. Trygve E Bakken, Jeremy A Miller, Song-Lin Ding, Susan M Sunkin, Kimberly A Smith, Lydia Ng, Aaron Szafer, Rachel A Dalley, Joshua J Royall, Tracy Lemon, et al. Nature, 535(7612):367--375, 2016.
 
18/10/2016 presented by Costanza Vallerga
 
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Steve Horvath, Michael Gurven, Morgan E Levine, Benjamin C Trumble, Hillard Kaplan, Hooman Allayee, Beate R Ritz, Brian Chen, Ake T Lu, Tammy M Rickabaugh, et al. Genome biology, 17(1):171, 2016.
 
11/10/2016 presented by Adriaan van der Graaf
 
Analysis of protein-coding genetic variation in 60,706 humans. Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O?Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings, et al. Nature, 536(7616):285--291, 2016.
 
04/10/2016 presented by Zhihong Zhu
 
Defining the consequences of genetic variation on a proteome-wide scale. Joel M Chick, Steven C Munger, Petr Simecek, Edward L Huttlin, Kwangbom Choi, Daniel M Gatti, Narayanan Raghupathy, Karen L Svenson, Gary A Churchill, and Steven P Gygi. Nature, 534(7608):500--505, 2016.
 
13/09/2016 presented by Fleur Garton
 
Inferring expressed genes by whole-genome sequencing of plasma DNA. Peter Ulz, Gerhard G Thallinger, Martina Auer, Ricarda Graf, Karl Kashofer, Stephan W Jahn, Luca Abete, Gunda Pristauz, Edgar Petru, Jochen B Geigl, et al. Nature Genetics, 48(10):1273--1278, 2016.
 
06/09/2016 presented by Beben Benyamin
 
The genetic architecture of type 2 diabetes. Christian Fuchsberger, Jason Flannick, Tanya M Teslovich, Anubha Mahajan, Vineeta Agarwala, Kyle J Gaulton, Clement Ma, Pierre Fontanillas, Loukas Moutsianas, Davis J McCarthy, et al. Nature, 2016.
 
30/08/2016 presented by Zhijun Liu
 
Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Roddy Walsh, Kate Thomson, James S Ware, Birgit H Funke, Jessica Woodley, Karen J McGuire, Francesco Mazzarotto, Edward Blair, Anneke Seller, Jenny C Taylor, et al. bioRxiv, page 041111, 2016.
 
23/08/2016 presented by Matthew Robinson
 
Tensor decomposition for multiple-tissue gene expression experiments. Victoria Hore, Ana Viñuela, Alfonso Buil, Julian Knight, Mark I McCarthy, Kerrin Small, and Jonathan Marchini. Nature Genetics, 48(9):1094--1100, 2016.
 
16/08/2016 presented by Qian Zhang
 
Blood DNA methylation biomarkers predict clinical reactivity in food-sensitized infants. David Martino, Thanh Dang, Alexandra Sexton-Oates, Susan Prescott, Mimi LK Tang, Shyamali Dharmage, Lyle Gurrin, Jennifer Koplin, Anne-Louise Ponsonby, Katrina J Allen, et al. Journal of Allergy and Clinical Immunology, 135(5):1319--1328, 2015. [ DOI ]
 
08/08/2016 presented by Jenny Pavlides
 
Gene expression in human brain implicates sexually dimorphic pathways in autism spectrum disorders. Donna M Werling, Neelroop N Parikshak, and Daniel H Geschwind. Nature communications, 7, 2016. [ DOI ]
 
26/07/2016 presented by Qiongyi Zhao
 
TT-seq maps the human transient transcriptome. Björn Schwalb, Margaux Michel, Benedikt Zacher, Katja Frühauf, Carina Demel, Achim Tresch, Julien Gagneur, and Patrick Cramer. Science, 352(6290):1225--1228, 2016. [ DOI ]
 
22/07/2016 presented by Jian Zeng
 
RiVIERA-MT: A Bayesian model to infer risk variants in related traits using summary statistics and functional genomic annotations. Yue Li and Manolis Kellis. bioRxiv, page 059345, 2016. [ DOI ]
 
12/07/2016 presented by Jing Guo
 
The phenotypic legacy of admixture between modern humans and Neandertals. Corinne N Simonti, Benjamin Vernot, Lisa Bastarache, Erwin Bottinger, David S Carrell, Rex L Chisholm, David R Crosslin, Scott J Hebbring, Gail P Jarvik, Iftikhar J Kullo, et al. Science, 351(6274):737--741, 2016. [ DOI ]
 
21/06/2016 presented by Joseph Powell
 
FTO obesity variant circuitry and adipocyte browning in humans. Melina Claussnitzer, Simon N Dankel, Kyoung-Han Kim, Gerald Quon, Wouter Meuleman, Christine Haugen, Viktoria Glunk, Isabel S Sousa, Jacqueline L Beaudry, Vijitha Puviindran, et al. N Engl J Med, 2015(373):895--907, 2015. [ DOI ]
 
14/06/2016 presented by Stuart MacGregor
 
Physical and neurobehavioral determinants of reproductive onset and success. Felix R Day, Hannes Helgason, Daniel I Chasman, Lynda M Rose, Po-Ru Loh, Robert A Scott, Agnar Helgason, Augustine Kong, Gisli Masson, Olafur Th Magnusson, et al. Nature genetics, 2016. [ DOI ]
 
07/06/2016 presented by Allan McRae
 
RNA splicing is a primary link between genetic variation and disease. Yang I Li, Bryce van de Geijn, Anil Raj, David A Knowles, Allegra A Petti, David Golan, Yoav Gilad, and Jonathan K Pritchard. Science, 352(6285):600--604, 2016. [ DOI ]
 
31/05/2016 presented by Jake Gratten
 
Timing, rates and spectra of human germline mutation. Raheleh Rahbari, Arthur Wuster, Sarah J Lindsay, Robert J Hardwick, Ludmil B Alexandrov, Saeed Al Turki, Anna Dominiczak, Andrew Morris, David Porteous, Blair Smith, et al. Nature genetics, 2015. [ DOI ]
 
24/05/2016 presented by Margaret Wright
 
Association of child poverty, brain development, and academic achievement. Nicole L Hair, Jamie L Hanson, Barbara L Wolfe, and Seth D Pollak. JAMA pediatrics, 169(9):822--829, 2015. [ DOI ]
 
17/05/2016 presented by Niamh Mullins
 
A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases. Buhm Han, Jennie G Pouget, Kamil Slowikowski, Eli Stahl, Cue Hyunkyu Lee, Dorothee Diogo, Xinli Hu, Yu Rang Park, Eunji Kim, Peter K Gregersen, et al. Nature genetics, 2016. [ DOI ]
 
10/05/2016 presented by Baptiste CouvyDuchesne
 
Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Eli A Stahl, Daniel Wegmann, Gosia Trynka, Javier Gutierrez-Achury, Ron Do, Benjamin F Voight, Peter Kraft, Robert Chen, Henrik J Kallberg, Fina AS Kurreeman, et al. Nature genetics, 44(5):483--489, 2012. [ DOI ]
 
03/05/2016 presented by Futao Zhang
 
Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies. Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban G Burchard, Eleazar Eskin, James Zou, et al. Nature Methods, 13(5):443--445, 2016. [ DOI ]
 
26/04/2016 presented by Peter Visscher
 
The complex genetic and molecular basis of a model quantitative trait. Robert A Linder, Fabian Seidl, Kimberly Ha, and Ian M Ehrenreich. Molecular biology of the cell, 27(1):209--218, 2016. [ DOI ]
 
19/04/2016 presented by Narelle Hansell
 
Canonical genetic signatures of the adult human brain. Michael Hawrylycz, Jeremy A Miller, Vilas Menon, David Feng, Tim Dolbeare, Angela L Guillozet-Bongaarts, Anil G Jegga, Bruce J Aronow, Chang-Kyu Lee, Amy Bernard, et al. Nature neuroscience, 18(12):1832--1844, 2015. [ DOI ]
 
12/04/2016 presented by Janette Edson
 
Medical implications of technical accuracy in genome sequencing. Rachel L Goldfeder, James R Priest, Justin M Zook, Megan E Grove, Daryl Waggott, Matthew T Wheeler, Marc Salit, and Euan A Ashley. Genome medicine, 8(1):1, 2016. [ DOI ]
 
15/03/2016 presented by Anna Vinkhuyzen
 
Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease. Michael R Johnson, Kirill Shkura, Sarah R Langley, Andree Delahaye-Duriez, Prashant Srivastava, W David Hill, Owen JL Rackham, Gail Davies, Sarah E Harris, Aida Moreno-Moral, et al. Nature neuroscience, 2015. [ DOI ]
 
08/03/2016 presented by Loic Yengo
 
Why significant variables aren’t automatically good predictors. Adeline Lo, Herman Chernoff, Tian Zheng, and Shaw-Hwa Lo. Proceedings of the National Academy of Sciences, 112(45):13892--13897, 2015. [ DOI ]
 
01/03/2016 presented by Robert Maier
 
Winners curse correction and variable thresholding improve performance of polygenic risk modeling based on summary-level data from genome-wide association studies. Jianxin Shi, JuHyun Park, Jubao Duan, Sonja Berndt, Winton Moy, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, et al. bioRxiv, page 034082, 2016. [ DOI ]
 
16/02/2016 presented by Maciej Trzaskowski
 
Transethnic genetic correlation estimates from summary statistics support widespread non-additive effects. Brielin C Brown, Asian Genetic Epidemiology Network-Type, Chun Jimmie Ye, Alkes L Price, Noah Zaitlen, et al. bioRxiv, page 036657, 2016. [ DOI ]
 
09/02/2016 presented by Naomi Wray
 
An Ancestry Based Approach for Detecting Interactions. Danny Park, Itamar Eskin, Eun Yong Kang, Eric R Gamazon, Celeste Eng, Christopher R Gignoux, Joshua M Galanter, Esteban Burchard, J Ye Chun, Hugues Aschard, et al. bioRxiv, page 036640, 2016. [ DOI ]
 
02/02/2016 presented by Luke Lloyd-Jones
 
Abundant contribution of short tandem repeats to gene expression variation in humans. Melissa Gymrek, Thomas Willems, Audrey Guilmatre, Haoyang Zeng, Barak Markus, Stoyan Georgiev, Mark J Daly, Alkes L Price, Jonathan K Pritchard, Andrew J Sharp, et al. Nature genetics, 2015. [ DOI ]

2015

 
24/11/2015 presented by Matthew Robinson
 
Recent mitochondrial DNA mutations increase the risk of developing common late-onset human diseases. Gavin Hudson, Aurora Gomez-Duran, Ian J Wilson, and Patrick F Chinnery. 2014. [ DOI ]
 
17/11/2015 presented by Irfahan Kassam
 
Runs of homozygosity: association with coronary artery disease and gene expression in monocytes and macrophages. Paraskevi Christofidou, Christopher P Nelson, Majid Nikpay, Liming Qu, Mingyao Li, Christina Loley, Radoslaw Debiec, Peter S Braund, Matthew Denniff, Fadi J Charchar, et al. The American Journal of Human Genetics, 97(2):228--237, 2015. [ DOI ]
 
03/11/2015 presented by Costanza Vallerga
 
Diagnosis of Parkinson's disease on the basis of clinical and genetic classification: a population-based modelling study. Mike A Nalls, Cory Y McLean, Jacqueline Rick, Shirley Eberly, Samantha J Hutten, Katrina Gwinn, Margaret Sutherland, Maria Martinez, Peter Heutink, Nigel M Williams, et al. The Lancet Neurology, 14(10):1002--1009, 2015. [ DOI ]
 
20/10/2015 presented by Zhihong Zhu
 
Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Suna Onengut-Gumuscu, Wei-Min Chen, Oliver Burren, Nick J Cooper, Aaron R Quinlan, Josyf C Mychaleckyj, Emily Farber, Jessica K Bonnie, Michal Szpak, Ellen Schofield, et al. Nature genetics, 2015. [ DOI ]
 
13/10/2015 presented by Restu Restuadi
 
Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Norihiro Kato, Marie Loh, Fumihiko Takeuchi, Niek Verweij, Xu Wang, Weihua Zhang, Tanika N Kelly, Danish Saleheen, Benjamin Lehne, Irene Mateo Leach, et al. Nature genetics, 2015. [ DOI ]
 
06/10/2015 presented by Zong-Hong Zhang
 
Haploinsufficiency of TBK1 causes familial ALS and fronto-temporal dementia. Axel Freischmidt, Thomas Wieland, Benjamin Richter, Wolfgang Ruf, Veronique Schaeffer, Kathrin Müller, Nicolai Marroquin, Frida Nordin, Annemarie Hübers, Patrick Weydt, et al. Nature neuroscience, 18(5):631--636, 2015. [ DOI ]
 
29/09/2015 presented by Jian Yang
 
A gene-based association method for mapping traits using reference transcriptome data. Eric R Gamazon, Heather E Wheeler, Kaanan P Shah, Sahar V Mozaffari, Keston Aquino-Michaels, Robert J Carroll, Anne E Eyler, Joshua C Denny, Dan L Nicolae, Nancy J Cox, et al. Nature genetics, 47(9):1091--1098, 2015. [ DOI ]
 
22/09/2015 presented by Maciej Trzaskowski
 
Application of high-dimensional feature selection: evaluation for genomic prediction in man. ML Bermingham, R Pong-Wong, A Spiliopoulou, C Hayward, I Rudan, H Campbell, AF Wright, JF Wilson, F Agakov, P Navarro, et al. Scientific reports, 5, 2015. [ DOI ]
 
08/09/2015 presented by Luke Lloyd-Jones
 
Wavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assays. Heejung Shim and Matthew Stephens. arXiv preprint arXiv:1307.7203, 2013.
 
01/09/2015 presented by Jake Gratten
 
Recombination affects accumulation of damaging and disease-associated mutations in human populations. Julie G Hussin, Alan Hodgkinson, Youssef Idaghdour, Jean-Christophe Grenier, Jean-Philippe Goulet, Elias Gbeha, Elodie Hip-Ki, and Philip Awadalla. Nature genetics, 47(4):400--404, 2015. [ DOI ]
 
26/08/2015 presented by Alex Holloway
 
Eight thousand years of natural selection in Europe. Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Bastien Llamas, Joseph Pickrell, Harald Meller, Manuel A Rojo Guerra, Johannes Krause, David Anthony, et al. bioRxiv, page 016477, 2015. [ DOI ]
 
18/08/2015 presented by Dave Evans
 
Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression. Jack Bowden, George Davey Smith, Stephen Burgess, and MRC Integrative Epidemiology Unit. 2015. [ DOI ]
 
11/08/2015 presented by Qiongyi Zhao
 
Assembly and diploid architecture of an individual human genome via single-molecule technologies. Matthew Pendleton, Robert Sebra, Andy Wing Chun Pang, Ajay Ummat, Oscar Franzen, Tobias Rausch, Adrian M Stütz, William Stedman, Thomas Anantharaman, Alex Hastie, et al. Nature methods, 2015. [ DOI ]
 
04/08/2015 presented by Beben Benyamin
 
Self-control forecasts better psychosocial outcomes but faster epigenetic aging in low-SES youth. Gregory E Miller, Tianyi Yu, Edith Chen, and Gene H Brody. Proceedings of the National Academy of Sciences, 112(33):10325--10330, 2015. [ DOI ]
 
14/07/2015 presented by Allan McRae
 
A unique gene regulatory network resets the human germline epigenome for development. Walfred WC Tang, Sabine Dietmann, Naoko Irie, Harry G Leitch, Vasileios I Floros, Charles R Bradshaw, Jamie A Hackett, Patrick F Chinnery, and M Azim Surani. Cell, 161(6):1453--1467, 2015. [ DOI ]
 
30/06/2015 presented by Peter Visscher
 
The architecture of parent-of-origin effects in mice. Richard Mott, Wei Yuan, Pamela Kaisaki, Xiangchao Gan, James Cleak, Andrew Edwards, Amelie Baud, and Jonathan Flint. Cell, 156(1):332--342, 2014. [ DOI ]
 
23/06/2015 presented by Divya Mehta
 
Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Amy R Vandiver, Rafael A Irizarry, Kasper D Hansen, Luis A Garza, Arni Runarsson, Xin Li, Anna L Chien, Timothy S Wang, Sherry G Leung, Sewon Kang, et al. Genome biology, 16(1):80, 2015. [ DOI ]
 
16/06/2015 presented by Anita Goldinger
 
Genome-wide patterns and properties of de novo mutations in humans. Laurent C Francioli, Paz P Polak, Amnon Koren, Androniki Menelaou, Sung Chun, Ivo Renkens, Cornelia M van Duijn, Morris Swertz, Cisca Wijmenga, Gertjan van Ommen, et al. Nature genetics, 2015. [ DOI ]
 
02/06/2015 presented by Naomi Wray
 
Integrative analysis of 111 reference human epigenomes. Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller, et al. Nature, 518:317--330, 2015. [ DOI ]
 
19/05/2015 presented by Andrew Bakshi
 
JEPEG: a summary statistics based tool for gene-level joint testing of functional variants. Donghyung Lee, Vernell S Williamson, T Bernard Bigdeli, Brien P Riley, Ayman H Fanous, Vladimir I Vladimirov, and Silviu-Alin Bacanu. Bioinformatics, 2014. [ DOI ]
 
12/05/2015 presented by Patrick Turley
 
Testing for genetic associations in arbitrarily structured populations. Minsun Song, Wei Hao, and John D Storey. bioRxiv, 2014. [ DOI ]
 
05/05/2015 presented by Jake Carroll
 
State of the Union – QBI’s HPC resources in the context of high-throughput biocomputing.
 
21/04/2015 presented by Peter Smartt
 
A bio-inspired computing model for ovarian carcinoma classification and oncogene detection. Meng-Hsiun Tsai, Mu-Yen Chen, Steve G Huang, Yao-Ching Hung, and Hsin-Chieh Wang. Bioinformatics, 2014. [ DOI ]
 
14/04/2015 presented by Anna Vinkhuyzen
 
Adjusting for heritable covariates can bias effect estimates in genome-wide association studies. Hugues Aschard, Bjarni J Vilhjálmsson, Amit D Joshi, Alkes L Price, and Peter Kraft. The American Journal of Human Genetics, 96(2):329--339, 2015. [ DOI ]
 
07/04/2015 presented by Guo-Bo Chen
 
The fine-scale genetic structure of the British population. Stephen Leslie, Bruce Winney, Garrett Hellenthal, Dan Davison, Abdelhamid Boumertit, Tammy Day, Katarzyna Hutnik, Ellen C Royrvik, Barry Cunliffe, Daniel J Lawson, et al. Nature, 519(7543):309--314, 2015. [ DOI ]
 
17/03/2015 presented by Robert Maier
 
An Atlas of Genetic Correlations across Human Diseases and Traits. Brendan Bulik-Sullivan, Hilary K Finucane, Verneri Anttila, Alexander Gusev, Felix R Day, John RB Perry, Nick Patterson, Elise Robinson, Mark J Daly, Alkes L Price, et al. bioRxiv, 2015. [ DOI ]
 
10/03/2015 presented by Joseph Powell
 
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. Alfonso Buil, Andrew Anand Brown, Tuuli Lappalainen, Ana Viñuela, Matthew N Davies, Hou-Feng Zheng, J Brent Richards, Daniel Glass, Kerrin S Small, Richard Durbin, et al. Nature Genetics, 47(1):88--91, 2015. [ DOI ]
 
03/03/2015 presented by Gerhard Moser
 
Efficient Bayesian mixed model analysis increases association power in large cohorts. Po-Ru Loh, George Tucker, Brendan K Bulik-Sullivan, Bjarni J Vilhjalmsson, Hilary K Finucane, Daniel I Chasman, Paul M Ridker, Benjamin M Neale, Bonnie Berger, Nick Patterson, et al. bioRxiv, 2014. [ DOI ]