and indicate equal contribution

Genetics

  • 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. In press. [preprint]

  • An atlas of 8,342 mosaic structural variants reveals genetic drivers of clonal hematopoiesis. P. Loh, G. Genovese, R. Handsaker, H. Finucane, Y. Reshef, P. Palamara, B. Birmann, S. Bakhoum, S. McCarroll, A. Price. Nature. In press.

  • 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. Under Review. [preprint]

  • Quantification of frequency-dependent genetic architectures and action of negative selection in 25 UK Biobank traits. A. Schoech, D. Jordan, P. Loh, S. Gazal, L. O’Connor, D. Balick, P. Palamara, H. Finucane, S. Sunyaev, A. Price. Under Review. [preprint]

  • 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

  • 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]

Theses and technical reports

  • Population Genetics of Identity By Descent. P. Palamara. Ph.D. Thesis, Columbia University. May 2014. [paper]

Presentations and posters

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