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, 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, University of Oxford, UK

Inferring migration and population-size surfaces across time periods, Hussein Al-Asadi, Desislava Petkova, John Novembre, Matthew Stephens, 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, Department of Statistical Science, UCL

A hidden Markov model approach to the analysis of archaic introgression into modern human genome, Richard Durbin, Laurits Skov, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

Modeling recent Siberian ancestry in Native Americans using rare mutations, Stephan Schiffels, Pavel Flegontov, 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, 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, University of Helsinki, Finland

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent, Nicola De Maio, Chieh-Hsi Wu, Daniel J Wilson, 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, University of Oxford, UK

Invited Talk : Response error linear modeling of sequence counts, Harold Pimentel, Nicolas Bray, Suzette Puente, Páll Melsted and Lior Pachter, University of Berkeley, USA

Fast, Scalable Prediction of Deleterious Noncoding Variants from Genomic Data, Adam Siepel, Yi-fei Huang, Brad Gulko, Simons Center for Quantitative Biology and CSHL

Using probabilistic models to incorporate ALL the NGS data, Susan Holmes, Ben Callahan, Statistics Department, Stanford, USA

Processing variant data for millions of samples, Jerome Kelleher, Gil McVean, 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, University of Oxford, UK

Latent factor models for single-cell RNA-seq data: adapting to violated assumptions, Barbara E Engelhardt, Mehmet Basbug, Princeton University, USA

Trans-factors underlying cell-type dependent allele-specific expression inferred from brain organoid single-cell RNA-Seq data, Cornelis A. Albers, Radboud University Medical Centre, Nijmegen, the Netherlands

Invited Talk: Computational challenges in single-cell genomics, John Marioni, 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, EMBL-European Bioinformatics Institute, Hinxton, UK

Identifying vaccine-specific B-cells from repertoire sequencing data, Anna Fowler, Jacob Galson, Dominic Kelly, Gerton Lunter, 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, 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, Columbia University, USA

Pedigree reconstruction in the era of many thousands of samples, Amy L. Williams, Ryan O’Hern, John Blangero, 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 , University of Exeter, UK

Estimation of heritability without environmental bias through relatedness disequilibrium, Alexander I. Young, Mike Frigge, Kari Sefansson, Augustine Kong, University of Oxford, UK

Invited Talk: Selective inference for gene mapping, Chiara Sabatti, Stanford University, USA

Modelling GWAS summary statistics as mixtures of latent heritable effects, Lloyd T. Elliott, Kevin Sharp, Steve Smith, Jonathan Marchini, University of Oxford, UK

Using genomic predictions for detection of pleiotropy, and to enable multivariate association studies, Joel Mefford, Noah Zaitlen, John Witte, University of California, San Francisco, USA

Bayesian multivariate analysis of large genetic studies identifies novel associations, Michael C. Turchin, Matthew Stephens, 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, University of Oxford, UK

Inferring recent demography via isolation by distance of long shared genome blocks, Harald Ringbauer, Graham Coop, Nick Barton, Institute of Science and Technology Austria

Variation in mutation rates among human populations, Iain Mathieson, David Reich, Harvard Medical School, USA

Invited Talk: Ancestry specific association mapping in admixed populations, Line Skotte, Thorfinn S Korneliussen, Ida Moltke, Anders Albrechtsen, University of Copenhagen, Denmark

Using chromosome painting to uncover an ancient exodus from Africa surviving in Papua New Guinea, Daniel John Lawson, 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, 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, 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, Harvard School of Public Health, Boston, USA