Robert J. Prill  Robert J. Prill photo         

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Senior Scientist, Computational Biology & Bioinformatics
Research Staff Member - San Jose, CA



Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
McIntyre, Alexa BR and Ounit, Rachid and Afshinnekoo, Ebrahim and Prill, Robert J and H{\'e}naff, Elizabeth and Alexander, Noah and Minot, Samuel S and Danko, David and Foox, Jonathan and Ahsanuddin, Sofia and others
Genome biology 18(1), 182, BioMed Central, 2017

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City
Maritz, Julia M and Sullivan, Steven A and Prill, Robert J and Aksoy, Emre and Scheid, Paul and Carlton, Jane M
PloS one 12(4), e0175527, Public Library of Science, 2017

A communal catalogue reveals Earth’s multiscale microbial diversity
Thompson, Luke R and Sanders, Jon G and McDonald, Daniel and Amir, Amnon and Ladau, Joshua and Locey, Kenneth J and Prill, Robert J and Tripathi, Anupriya and Gibbons, Sean M and Ackermann, Gail and others
Nature 551(7681), Nature Publishing Group, 2017


Microbiome changes through ontogeny of a tick pathogen vector
Zolnik, Christine P and Prill, Robert J and Falco, Richard C and Daniels, Thomas J and Kolokotronis, Sergios-Orestis
Molecular ecology 25(19), 4963--4977, Wiley Online Library, 2016


Noise-driven causal inference in biomolecular networks.
Robert J Prill, Robert Vogel, Guillermo A Cecchi, Gregoire Altan-Bonnet, Gustavo Stolovitzky
PLoS One 10(6), e0125777, 2015

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.
Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M Maritz, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Amber Simmons, Timothy Nessel, Bharathi Sundaresh, Elizabeth Pereira, Ellen
Cell Syst 1(1), 72--87, 2015


BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters.
Hailiang Huang, Sandeep Tata, Robert J Prill
Bioinformatics 29(1), 135--136, 2013


Wisdom of crowds for robust gene network inference.
Daniel Marbach, James C Costello, Robert Kuffner, Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, Manolis Kellis, James J Collins, Gustavo Stolovitzky
Nat Methods 9(8), 796--804, 2012


Crowdsourcing network inference: the DREAM predictive signaling network challenge.
Robert J Prill, Julio Saez-Rodriguez, Leonidas G Alexopoulos, Peter K Sorger, Gustavo Stolovitzky
Sci Signal 4(189), mr7, 2011


Revealing strengths and weaknesses of methods for gene network inference.
Daniel Marbach, Robert J Prill, Thomas Schaffter, Claudio Mattiussi, Dario Floreano, Gustavo Stolovitzky
Proc Natl Acad Sci U S A 107(14), 6286--6291, 2010

Towards a rigorous assessment of systems biology models: the DREAM3 challenges.
Robert J Prill, Daniel Marbach, Julio Saez-Rodriguez, Peter K Sorger, Leonidas G Alexopoulos, Xiaowei Xue, Neil D Clarke, Gregoire Altan-Bonnet, Gustavo Stolovitzky
PLoS One 5(2), e9202, 2010


Lessons from the DREAM2 Challenges.
Gustavo Stolovitzky, Robert J Prill, Andrea Califano
Ann N Y Acad Sci1158, 159--195, 2009


Dynamic properties of network motifs contribute to biological network organization.
Robert J Prill, Pablo A Iglesias, Andre Levchenko
PLoS Biol 3(11), e343, 2005