Monday 12th September - Wednesday 14th September 2016

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. 



MONDAY, September 12 - 9.00AM-12.00PM




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 - 3.00PM-5.50PM




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 - 9.00AM-12.00PM




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 - 3.00PM-6.10PM




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 - 9.00AM-12.10PM




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