Organisers: Jonathan Marchini, University of Oxford, UK; Simon Myers, University of Oxford, UK; Jotun Hein, University of Oxford, UK; Peter Ralph, University of South California, USA
The 2nd Probabilistic Modeling in Genomics Conference (ProbGen16), was held at the Department of Statistics, University of Oxford, UK.
The conference covered probabilistic models, algorithms, and statistical methods across a broad range of applications in genetics and genomics. We invited abstract submissions on a range of topics including Population Genetics, Functional Genomics, Systems and Structural Biology, Methods for Genome-wide Association Studies, Causal inference in genetic studies, Assembly and Variant identification, Phylogenetics, Natural Selection and Quantitative Genetics.
Alongside invited speakers, oral presentations were selected from submitted abstracts. We particularly encouraged abstract submissions for oral and/or poster presentations from junior investigators, including postdoctoral fellows and graduate students.
This is an annual meeting, held at Cold Spring Harbor in 2015, and which evolved from the success of previous similarly-themed workshops held at the HHMI Janelia Farm Research Campus (2013) and Merton College, Oxford (2014).
The conference talks were held in the new Department of Statistics building in central Oxford, with conference accommodation across the road at Somerville College.
Keynote Speaker: Simon Tavare, Cancer Research UK Cambridge Institute, UK
Invited session chairs: Chiara Sabatti, Stanford, USA; Lior Pachter, Berkeley, USA; Maria De Iorio, UCL, UK; John Marioni, EMBL-EBI, Hinxton, UK; Ida Moltke, Copenhagen, Denmark.
CONFERENCE SCHEDULE
MONDAY, September 12 – SESSION 1: DEMOGRAPHY AND ADMIXTURE I
Chairpersons : Maria De Iorio, Department of Statistical Science, UCL; Simon Myers, University of Oxford
Ancestry-specific recent effective population size
Sharon R. Browning, Brian L. Browning
Presenter affiliation: University of Washington, Seattle, USA
SMC2: Using particle filters to infer historic population sizes and migration rates from whole genomes and multiple samples
Donna Henderson, Joe Zhu, Gerton Lunter
Presenter affiliation: University of Oxford, UK
Inferring migration and population-size surfaces across time periods
Hussein Al-Asadi, Desislava Petkova, John Novembre, Matthew Stephens
Presenter affiliation: University of Chicago, Chicago IL
Invited Talk : Tree bridging Markov chain Monte Carlo for ancestral inference
Maria De Iorio, Kari Heine, Alexandros Beskos, Ajay Jasra, David Balding
Presenter affiliation: Department of Statistical Science, UCL
A hidden Markov model approach to the analysis of archaic introgression into modern human genomes
Richard Durbin, Laurits Skov
Presenter affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Modeling recent Siberian ancestry in Native Americans using rare mutations
Stephan Schiffels, Pavel Flegontov
Presenter affiliation: Max Planck Institute for the Science of Human History, Germany
A discriminative model for inferring genome-wide maps of Neanderthal and Denisovan ancestry
Sriram Sankararaman, Swapan Mallick, Nick Patterson, David Reich
Presenter affiliation: Department of Computer Science, UCLA
MONDAY, September 12 – SESSION 2: METHODS FOR SEQUENCE ANALYSIS
Chairpersons : Lior Pachter, University of Berkeley; Jotun Hein, University of Oxford
Bayesian Identification of Bacterial Strains from Sequencing Data
Aravind Sankar, Tommi Mäklin, Brandon Malone, Sion C. Bayliss, Ben Pascoe, Guillaume Méric, Matthew D. Hitchings, Samuel K. Sheppard, Edward J. Feil, Jukka Corander, Antti Honkela
Presenter affiliation: University of Helsinki, Finland
SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
Nicola De Maio, Chieh-Hsi Wu, Daniel J Wilson
Presenter affiliation: University of Oxford, UK
A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference
Sorina Maciuca, Carlos del Ojo Elias, Gil McVean, Zamin Iqbal
Presenter affiliation: University of Oxford, UK
Invited Talk : Response error linear modeling of sequence counts
Harold Pimentel, Nicolas Bray, Suzette Puente, Páll Melsted and Lior Pachter
Presenter affiliation: University of Berkeley, USA
Fast, Scalable Prediction of Deleterious Noncoding Variants from Genomic Data
Siepel, Adam, Huang, Yi-fei, Gulko, Brad
Presenter affiliation: Simons Center for Quantitative Biology and CSHL
Using probabilistic models to incorporate ALL the NGS data
Susan Holmes, Ben Callahan
Presenter affiliation: Statistics Department, Stanford, USA
Processing variant data for millions of samples
Jerome Kelleher, Gil McVean
Presenter affiliation: University of Oxford, UK
MONDAY, September 12 – 6.00PM-6.45PM
KEYNOTE SPEAKER : Professor Simon Tavaré FRS, FMedSci
Director, Cancer Research UK Cambridge Institute
Department of Applied Mathematics and Theoretical Physics, Cambridge
Title : “Is stochastic modeling useful in cancer research?”
TUESDAY, September 13 – SESSION 3: FUNCTIONAL GENOMICS
Chairpersons : John Marioni, EMBL-European Bioinformatics Institute; Jonathan Marchini, University of Oxford.
Bayesian latent variable models for single-cell trajectory learning
Kieran Campbell, Christopher Yau
Presenter affiliation: University of Oxford, UK
Latent factor models for single-cell RNA-seq data: adapting to violated assumptions
Barbara E Engelhardt, Mehmet Basbug
Presenter affiliation: Princeton University, USA
Trans-factors underlying cell-type dependent allele-specific expression inferred from brain organoid single-cell RNA-Seq data
Cornelis A. Albers
Presenter affiliation: Radboud University Medical Centre, Nijmegen, the Netherlands
Invited Talk : Computational challenges in single-cell genomics
John Marioni
Presenter affiliation: EMBL-European Bioinformatics Institute, Hinxton, UK
Scalable latent-factor models for scRNA-seq separate biological drivers from confounding factors
Florian Buettner, Naruemon Pratanwanich, John C. Marioni and Oliver Stegle
Presenter affiliation: EMBL-European Bioinformatics Institute, Hinxton, UK
Identifying vaccine-specific B-cells from repertoire sequencing data
Anna Fowler, Jacob Galson, Dominic Kelly, Gerton Lunter
Presenter affiliation: University of Oxford, UK
Causal profile subgraph embeddings of metabolic and immune response mediated gene regulation from time series gene expression
Jonathan Lu, Bianca Dumitrascu, Ian C McDowell, Soledad Villar, Tim Redd , Barbara Engelhardt
Presenter affiliation: Princeton University, USA
TUESDAY, September 13 – SESSION 4: QUANTITATIVE GENETICS
Chairpersons : Chiara Sabatti, Stanford University, USA; Jonathan Marchini, University of Oxford, UK
Quantifying selection and demographic effects on quantitative genetic variation: an application to anthropomorphic traits
Yuval Simons and Guy Sella
Presenter affiliation: Columbia University, USA
Pedigree reconstruction in the era of many thousands of samples
Amy L. Williams, Ryan O’Hern, John Blangero
Presenter affiliation: Cornell University, USA
EXSIM: Detecting deviation from polygenic modes of inheritance in the extreme tails of human complex traits
Andrew R Wood, Robin Beaumont, Katherine S Ruth, Jessica Tyrrell, Samuel E Jones, Hanieh Yaghootkar, Marcus A Tuke, Rachel M Freathy, Anna Murray, Zoltán Kutalik, Michael N Weedon, Timothy M Frayling
Presenter affiliation: University of Exeter, UK
Estimation of heritability without environmental bias through relatedness disequilibrium
Alexander I. Young, Mike Frigge, Kari Sefansson, Augustine Kong
Presenter affiliation: University of Oxford, UK
Invited Talk : Selective inference for gene mapping
Chiara Sabatti
Presenter affiliation: Stanford University, USA
Modelling GWAS summary statistics as mixtures of latent heritable effects
Lloyd T. Elliott, Kevin Sharp, Steve Smith, Jonathan Marchini
Presenter affiliation: University of Oxford, UK
Using genomic predictions for detection of pleiotropy, and to enable
multivariate association studies
Joel Mefford, Noah Zaitlen, John Witte
Presenter affiliation: University of California, San Francisco, USA
Bayesian multivariate analysis of large genetic studies identifies novel associations
Michael C. Turchin, Matthew Stephens
Presenter affiliation: University of Chicago, USA
WEDNESDAY, September 14 – SESSION 5: DEMOGRAPHY AND ADMIXTURE II
Chairpersons : Ida Moltke , University of Copenhagen; Peter Ralph, University of Oregon
Multiway Admixture Event Modelling without Specifying Groups
Michael Salter-Townshend, Simon Myers
Presenter affiliation: University of Oxford, UK
Inferring recent demography via isolation by distance of long shared genome blocks
Harald Ringbauer, Graham Coop, Nick Barton
Presenter affiliation: Institute of Science and Technology Austria
Variation in mutation rates among human populations
Iain Mathieson, David Reich
Presenter affiliation: Harvard Medical School, USA
Invited Talk : Ancestry specific association mapping in admixed populations
Line Skotte, Thorfinn S Korneliussen, Ida Moltke,Anders Albrechtsen
Presenter affiliation: University of Copenhagen, Denmark
Using chromosome painting to uncover an ancient exodus from Africa surviving in Papua New Guinea
Daniel John Lawson
Presenter affiliation: University of Bristol, UK
Coalescence times at two loci under Markovian coalescent approximations and pedigree models
Shai Carmi, Léandra King, Peter Wilton, Asger Hobolth, John Wakeley
Presenter affiliation: The Hebrew University of Jerusalem, Israel
Extended haplotype sharing in a bottlenecked Finnish population provides insights into founder and rare disease risk alleles
Alicia R. Martin, Sini Kerminen, Antti-Pekka Sarin, Aarno Palotie, Samuli Ripatti, Matti Pirinen, Mark J. Daly
Presenter affiliation: Massachusetts General Hospital, Boston, USA
Fast decoding of pairwise coalescent times in large SNP array data sets
Pier Francesco Palamara, Jonathan Terhorst, Yun S. Song, Alkes L. Price
Presenter affiliation: Harvard School of Public Health, Boston, USA