Publications

※ and † indicate equal contribution or joint supervision

Genetics

Genome-wide classification of epigenetic activity reveals regions of enriched heritability in immune-related traits. M. Stricker, W. Zhang, W. Cheng, S. Gazal, C. Dendrou, S. Nahkuri†, P. F. Palamara†. Cell Genomics. January 2024. [paper] [software]

Haplotype-based inference of recent effective population size in modern and ancient DNA samples. R. Fournier, Z. Tsangalidou, D. Reich†, P. F. Palamara†. Nature Communications. December 2023. [paper] [software]

Inference of coalescence times and variant ages using convolutional neural networks. J. Nait Saada※, Z. Tsangalidou※, M. Stricker, P. F. Palamara. Molecular Biology and Evolution. September 2023. Preliminary version presented at NeurIPS 2021 Workshop on Learning Meaningful Representations of Life (LMRL). [paper] [software]

HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes. S. Wharrie, Z. Yang, V. Raj, R. Monti, R. Gupta, Y. Wang, A. Martin, L. O’Connor, S. Kaski, P. Marttinen, P. F. Palamara, C. Lippert, A. Ganna. Bioinformatics. September 2023. Preliminary version presented at NeurIPS 2022 Workshop on Synthetic Data for Empowering ML Research. [paper] [software]

Social and genetic diversity among the first farmers of Central Europe. P. Gelabert, et al. bioRxiv. July 2023. [preprint]

Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. B. C. Zhang, A. Biddanda, Á. F. Gunnarsson, F. Cooper, P. F. Palamara. Nature Genetics. May 2023. [paper]

Cell-free DNA TAPS provides multimodal information for early cancer detection. P. Siejka-Zielińska, J. Cheng, F. Jackson, Y. Liu, Z. Soonawalla, S. Reddy, M. Silva, L. Puta, M. Vanette McCain, E. L. Culver, N. Bekkali, B. Schuster-Böckler, P. F. Palamara, D. Mann, H. Reeves, E. Barnes, S. Sivakumar, C. Song. Science advances. September 2021. [paper]

Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations. J. Nait Saada, G. Kalantzis, D. Shyr, F. Cooper, M. Robinson, A. Gusev†, P. F. Palamara†. Nature Communications. November 2020. [paper] [software] [data]

Genome-wide natural selection signatures are linked to genetic risk of modern phenotypes in the Japanese population. Y. Yasumizu※, S. Sakaue※, T. Konuma, K. Suzuki, K. Matsuda, Y. Murakami, M. Kubo, P. Palamara, Y. Kamatani, Y. Okada. Molecular Biology and Evolution. January 2020. [paper]

Quantification of frequency-dependent genetic architectures in 25 UK Biobank traits reveals action of negative selection. A. Schoech, D. Jordan, P. Loh, S. Gazal, L. O’Connor, D. Balick, P. Palamara, H. Finucane, S. Sunyaev, A. Price. Nature Communications. February 2019. [paper] [preprint]

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. Y. Reshef, H. Finucane, D. Kelley, A. Gusev, D. Kotliar, J. Ulirsch, F. Hormozdiari, L. O’Connor, B. van de Geijn, P. Loh, S. Grossman, G. Bhatia, S. Gazal, P. Palamara, L. Pinello, N. Patterson, R. Adams, A. Price. Nature Genetics. September 2018. [paper] [preprint]

High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. P. Palamara, J. Terhorst, Y. Song, A. Price. Nature Genetics. August 2018. [paper] [preprint] [full-text]

Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations. P. Loh※, G. Genovese※, R. Handsaker, H. Finucane, Y. Reshef, P. Palamara, B. Birmann, S. Bakhoum, S. McCarroll†, A. Price†. Nature. July 2018. [paper] [full-text]

Linkage disequilibrium dependent architecture of human complex traits reveals action of negative selection. S. Gazal, H. Finucane, N. Furlotte, P. Loh, P. Palamara, X. Liu, A. Schoech, B. Bulik-Sullivan, B. Neale, A. Gusev, A. Price. Nature Genetics. October 2017. [paper] [preprint]

Reference-based phasing using the Haplotype Reference Consortium panel. P. Loh, P. Danecek, P. Palamara, C. Fuchsberger, Y. Reshef, H. Finucane, S. Schoenherr, L. Forer, S. McCarthy, G. Abecasis, R. Durbin, A. Price. Nature Genetics. October 2016. [paper] [preprint]

ARGON: fast, whole-genome simulation of the discrete time Wright-Fisher process. P. Palamara. Bioinformatics. June 2016. [paper] [preprint]

Fast and accurate long-range phasing in a UK Biobank cohort. P. Loh, P. Palamara, A. Price. Nature Genetics. June 2016. [paper] [preprint]

Leveraging distant relatedness to quantify human mutation and gene conversion rates. P. Palamara, L. Francioli, P. Wilton, G. Genovese, A. Gusev, H. Finucane, S. Sankararaman, The Genome of the Netherlands Consortium, S. Sunyaev, P. de Bakker, J. Wakeley, I. Pe’er, A. Price. The American Journal of Human Genetics. November 2015. [paper] [preprint]

Whole-genome sequence variation, population structure and demographic history of the Dutch population. The Genome of the Netherlands Consortium. Nature Genetics. June 2014. [paper]

Inference of historical migration rates via haplotype sharing. P. Palamara and I. Pe’er. Bioinformatics. July 2013. [paper]

The variance of identity-by-descent sharing in the Wright-Fisher model. S. Carmi, P. Palamara, V. Vacic, T. Lencz, A. Darvasi, I. Pe’er. Genetics. March 2013. [paper]

Length distributions of identity by descent reveal fine-scale demographic history. P. Palamara, T. Lencz, A. Darvasi, I. Pe’er. The American Journal of Human Genetics. November 2012. [paper]
C. W. Cotterman Award ("one of two articles published in the AJHG that best represent outstanding scientific contributions to the field of human genetics by pre/post-doctoral trainees").

North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. C. Campbell※, P. Palamara※, M. Dubrovsky※, L. Botigue, M. Fellous, G. Atzmon, C. Oddoux, A. Pearlman, L. Hao, B. Henn, E. Burns, C. Bustamante, D. Comas, E. Friedman, I. Pe’er, H. Ostrer. Proceedings of the National Academy of Sciences. August 2012. [paper]

The Impact of Converso Jews on the Genomes of Modern Latin Americans. C. Velez※, P. Palamara※, J. Guevara-Aguirre※, L. Hao, T. Karafet, M. Guevara-Aguirre, A. Pearlman, C. Oddoux, M. Hammer, E. Burns, I. Pe’er, G. Atzmon, H. Ostrer. Human Genetics. February 2012. [paper]

The Architecture of long-range haplotypes shared across populations. A. Gusev※, P. Palamara※, G. Aponte, Z. Zhuang, A. Darvasi, P. Gregersen, I. Pe’er. Molecular Biology and Evolution. October 2011. [paper]

A Minimal Descriptor of an Ancestral Recombination Graph. L. Parida, P. Palamara, A. Javed. BMC Bioinformatics. February 2011. [paper]

Abraham's Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry. G. Atzmon※, L. Hao※, I. Pe’er※, C. Velez, A. Pearlman, P. Palamara, B. Morrow, E. Friedman, C. Oddoux, E. Burns, H. Ostrer. The American Journal of Human Genetics. June 2010. [paper]

Consortium publications

WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene. L. Nersisyan, et al. (Genome of Netherlands consortium). Scientific Reports. December 2019. [paper]

Skewed X-inactivation is common in the general female population. E. Shvetsova, et al. (Genome of Netherlands consortium). European Journal of Human Genetics. March 2019. [paper]

Negative selection in humans and fruit flies involves synergistic epistasis. M. Sohail, et al. (Genome of Netherlands consortium). Science. May 2017. [paper] [preprint]

A framework for the detection of de novo mutations in family-based sequencing data. L. Francioli, et al. (Genome of Netherlands consortium). European Journal of Human Genetics. February 2017. [paper]

Genome-wide patterns and properties of de novo mutations in humans. L. Francioli, et al. (Genome of Netherlands consortium). Nature Genetics. July 2016. [paper]

Uncompromised 10-year survival of oldest old carrying somatic mutations in DNMT3A and TET2. E. van den Akker, et al. (Genome of Netherlands consortium). Blood. March 2016. [paper]

Population-specific genotype imputations using minimac or IMPUTE2. E. van Leeuwen, et al. (Genome of Netherlands consortium). Nature Protocols. September 2015. [paper]

Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. E. Van Leeuwen, et al. (Genome of Netherlands consortium). Nature Communications. March 2015. [paper]

Improved imputation quality of low-frequency and rare variants in European samples using the Genome of The Netherlands. P. Deelen, et al. (Genome of Netherlands consortium). European Journal of Human Genetics. November 2014. [paper]

Artificial intelligence and cognitive robotics

Petri Net Plans: A Framework for Cooperation and Coordination in Multi-Robot Systems. V. Ziparo, L. Iocchi, P. Lima, D. Nardi, P. Palamara. JAAMAS - Autonomous Agents and Multi-Agent Systems. July 2010. [paper]

Policy Gradient Learning for Quadruped Soccer Robots. A. Cherubini, F. Giannone, L. Iocchi, D. Nardi and P. Palamara. RAS - Robotics and Autonomous Systems. July, 2010. [paper]

Teamwork Design Based on Petri Net Plans. P. Palamara, V. Ziparo, L. Iocchi, D. Nardi, P. Lima. RoboCup 2008: Robot Soccer World Cup XII, Suzhou, China. July 2008. [paper]

A robotic soccer passing task using petri net plans. P. Palamara, V. Ziparo, L. locchi, D. Nardi, P. Lima, H. Costelha. International joint conference on Autonomous agents and multiagent systems (AAMAS 2008), Estoril, Portugal. May 2008. [paper]
Best Robotic Demo Award.

Petri net plans: a formal model for representation and execution of multi-robot plans. V. Ziparo, L. Iocchi, D. Nardi, P. Palamara, H. Costelha. International joint conference on Autonomous agents and multiagent systems (AAMAS 2008), Estoril, Portugal. May 2008. [paper]

An extended policy gradient algorithm for robot task learning. A. Cherubini, F. Giannone, L. Iocchi, P. F. Palamara. International Conference on Intelligent Robots and Systems (IROS 2007), San Diego (CA), USA. October 2007. [paper]

Presentations and posters

Inference and analysis of biobank-scale genome-wide genealogies.

• (Presented by Pier Palamara) Institut Pasteur, Talk. November 2023, Paris, France.

Improved imputation and association of rare variants using ultra-fast inference of ancestral recombination graphs.

• (Presented by Árni Freyr Gunnarsson) American Society of Human Genetics (ASHG), Talk. November 2023, Washington (DC), USA.

Scalable methods for the analysis of human evolutionary history and heritable traits.

• (Presented by Romain Fournier, Hrushikesh Loya, Pier Palamara) BDI/WHG (gen)omics seminar, Talk. March 2023, Oxford, UK.
• Centre for Human Genetics Lunchtime Lab Talks, Talk. November 2023, Oxford, UK.

Inference of coalescence times and allele ages using deep neural networks identifies signatures of natural selection.

• (Presented by Zoi Tsangalidou) American Society of Human Genetics (ASHG), Talk. October 2022, Los Angeles (CA), USA.
  • C. J. Epstein Trainee Award for Excellence in Human Genetics Research - Finalist (top 2.6% of scored abstracts)

Biobank-scale inference of ancestral recombination graphs enables genealogy-based mixed model association of complex traits.

• (Presented by Pier Palamara) Probabilistic Modeling in Genomics, Talk. April 2022, Oxford, UK.
• Computational Genomics Summer Institute, UCLA. July 2022, Los Angeles (CA), USA.
• Oxford Statistical Genomics Summer School, Talk. June 2022 and June 2023, Oxford, UK.

Biobank-scale inference of ancestral recombination graphs reveals association to rare and common variants in complex traits.

• (Presented by Brian Zhang) American Society of Human Genetics (ASHG), Talk. October 2021, Online.
  • C. J. Epstein Trainee Award for Excellence in Human Genetics Research - Semifinalist

Machine learning in genomics.

• (Presented by Pier Palamara) Talk, Oxford Machine Learning Summer School. August 2020, Online.

Leveraging identity-by-descent across 500,000 UK Biobank samples to detect association to ultra-rare variants.

• (Presented by Yiorgos Kalantzis) American Society of Human Genetics (ASHG), Talk, Session 028. October 2020, Online.
  • C. J. Epstein Trainee Award for Excellence in Human Genetics Research - Semifinalist

Biobank-scale detection of hidden relatedness reveals fine-scale evolutionary history and enriched disease heritability.

• (Presented by Pier Palamara) American Society of Human Genetics (ASHG), Talk, Invited Session 037. October 2020, Online.

Identity-by-descent detection across 487,409 British samples reveals fine-scale population structure, evolutionary history, and trait associations.

• (Presented by Juba Nait Saada) European Society of Human Genetics (ESHG), Talk, June 2020, Online.
  • One of 5 abstracts (out of ~2800 submissions) selected for the “What’s New?” Highlight Session
  • Recipient of one of 5 ESHG Fellowships of Excellence for Young Investigators.

Fast identity by descent detection across 500,000 UK Biobank samples reveals recent evolutionary history and population structure.

• (Presented by Juba Nait Saada) American Society of Human Genetics (ASHG), Talk. October 2019, Houston (TX), USA.
  • C. J. Epstein Trainee Award for Excellence in Human Genetics Research - Semifinalist

Hidden relatedness, natural selection and disease heritability in the human genome.

• Institute for Molecular Medicine Finland (FIMM), Talk, December 2019, Helsinki, Finland.
• Max Planck IMPRS for Evolutionary Biology Retreat, Talk, September 2018, Breklum, Germany.
• Amazon, Talk. April 2018, Berlin, Germany.
• SABS DTC, Talk. Oxford University, March 2018, Oxford, UK.
• OxWaSP DTC workshop, Talk. October 2017, Warwick, UK.

High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability.

• American Society of Human Genetics (ASHG), Talk. Oct 2017, Orlando (FL), USA.
  • C. J. Epstein Trainee Award for Excellence in Human Genetics Research - Semifinalist
• Probabilistic Modeling in Genomics (ProbGen), Talk. Sept 2017, Aarhus, Denmark.
• Broad Institute Medical and Population Genetics (MPG) Meeting, Talk. June 2017, Boston (MA), USA.
• University of Pennsylvania Mathematical Biology seminar, Talk, May 2017, Philadelphia (PA), USA.
• Harvard Chan School of Public Health Program in Genetic Epidemiology and Statistical Genetics, Talk. May 2017, Boston (MA), USA.

Leveraging deep genealogical structure to estimate the phenotypic contribution of rare variants.

• American Society of Human Genetics (ASHG), Poster. Oct 2016, Vancouver, Canada.
  • Reviewers’ Choice Abstract
• Harvard School of Public Health Program in Genetic Epidemiology and Statistical Genetics, Talk. May 2016, Boston, USA.

Fast decoding of pairwise coalescent times in large SNP array data sets.

• Probabilistic Modeling in Genomics (ProbGen), Talk. Sept 2016, Oxford, UK.

Leveraging distant relatedness to quantify human mutation and gene conversion rates.

• American Society of Human Genetics (ASHG), Talk. Oct 2015, Baltimore (MD), USA.
  • C. J. Epstein Trainee Award for Excellence in Human Genetics Research - Semifinalist.
• Probabilistic Modeling in Genomics, Poster. Oct 2015, Cold Spring Harbor (NY), USA.
• Harvard School of Public Health Program in Genetic Epidemiology and Statistical Genetics, Talk. April 2015, Boston, USA.

Population genetics of identity by descent.

• Genome of the Netherlands Symposium, Talk. Apr 2015, Utrecht, Netherlands.

Inference of human mutation rates using cryptic relatedness in a European population.

• The human mutation rate meeting (THMR), Talk. Feb 2015, Max Planck Institute Leipzig, Germany. Nice caricature by Alex Cagan.

Inference of mutation rates using hidden relatedness.

• American Society of Human Genetics (ASHG), Poster. Oct 2014, Sand Diego (CA), USA.

Regional-Scale Demographic Inference: The Population Structure of the Netherlands.

• 14th international Meeting on Human Genome Variation and Complex Genome Analysis (HGV), Talk. Oct 2013, Seoul, Korea.

Inference of historical migration rates via haplotype sharing.

• 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB), Talk. July 2013, Berlin, Germany.

Haplotype sharing reveals fine-scale demographic history.

• European Society of Human Genetics, Talk. June 2013, Paris, France.
  • Lodewijk Sandkuijl Young Investigator Award Award for outstanding talk in complex genetics and statistical genetics.

Haplotype sharing distributions for fine-scale demographic inference.

• Evolutionary Genomics Seminar, Stanford, Talk. April 2013.
• Harvard Schoold of Public Health, Talk. March 2013.
• Department of Genetics, University of Pennsylvania, Talk. July 2012.

Length distributions of identity by descent reveal fine-scale demographic history.

• American Society of Human Genetics (ASHG), Poster. Nov 2012, SF, CA, USA.
• 13th international Meeting on Human Genome Variation and Complex Genome Analysis (HGV), Poster. Sept 2012, Shanghai, China.
  • Best Poster award.
• International Congress of Human Genetics, Poster. Oct 2011, Montreal, Canada.

Inference of Recent Demographic Events Based On Haplotype Sharing.

• American Society of Human Genetics (ASHG), Poster. Nov 2010, Washington, DC, USA.

Inference of Long-Range Haplotypes in Large Cohorts of Unrelated Individuals.

• American Society of Human Genetics (ASHG), Poster. Oct 2009, Honolulu, HI, USA.

The Architecture of Long Range Haplotypes Shared Across Populations.

• Int. Meeting on Genetics of Complex Diseases and Isolated Populations, Poster. June 2009, Trieste, Italy.

A robotic soccer passing task using petri net plans.

• AAMAS 2008, Demonstration. Estoril, Portugal.
  • Best Robotic Demo award.