Raphael Gottardo

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 6

Top Topics

Varying Degrees

Statistical Analyses

Gene Expression

Top Venues

PLoS Comput. Biol.

Publications

Oliver Y. Chén, Duy Thanh Vu, Gilbert Greub, Hengyi Cao, Xingru He, Yannick Muller, Constantinos Petrovas, Haochang Shou, Viet-Dung Nguyen, Bangdong Zhi, Laurent Perez, Jean Louis Raisaro, Guy Nagels, Maarten De Vos, Wei He, Raphael Gottardo, Palie Smart, Marcus Munafò, Giuseppe Pantaleo
The Statistical Analysis of the Varying Brain. SSP (2023)
Bryan T. Mayer, Allan C. deCamp, Yunda Huang, Joshua T. Schiffer, Raphael Gottardo, Peter B. Gilbert, Daniel B. Reeves
Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention. PLoS Comput. Biol. 18 (4) (2022)
Evan Greene, Greg Finak, Leonard A. D'Amico, Nina Bhardwaj, Candice D. Church, Chihiro Morishima, Nirasha Ramchurren, Janis M. Taube, Paul T. Nghiem, Martin A. Cheever, Steven P. Fling, Raphael Gottardo
New interpretable machine-learning method for single-cell data reveals correlates of clinical response to cancer immunotherapy. Patterns 2 (12) (2021)
William Chad Young, Lindsay N. Carpp, Sidhartha Chaudhury, Jason A. Regules, Elke S. Bergmann-Leitner, Christian Ockenhouse, Ulrike Wille-Reece, Allan C. deCamp, Ellis Hughes, Celia Mahoney, Suresh Pallikkuth, Savita Pahwa, S. Moses Dennison, Sarah V. Mudrak, S. Munir Alam, Kelly E. Seaton, Rachel L. Spreng, Jon Fallon, Ashlin Michell, Fernando Ulloa-Montoya, Margherita Coccia, Erik Jongert, Galit Alter, Georgia D. Tomaras, Raphael Gottardo
Comprehensive Data Integration Approach to Assess Immune Responses and Correlates of RTS, S/AS01-Mediated Protection From Malaria Infection in Controlled Human Malaria Infection Trials. Frontiers Big Data 4 (2021)
Evan Greene, Greg Finak, Raphael Gottardo
Selective Clustering Annotated using Modes of Projections. CoRR (2018)
Phu Van, Wenxin Jiang, Raphael Gottardo, Greg Finak
ggCyto: next generation open-source visualization software for cytometry. Bioinform. 34 (22) (2018)
Paul Thatcher Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J. Gartland, Allan C. deCamp, Craig A. Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B. Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Meera Bose, Miguel A. Arroyo, Robert J. O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L. Robb, Tatsiana Kirys, Ivelin Georgiev, Peter D. Kwong, Konrad Scheffler, Sergei L. Kosakovsky Pond, Jonathan M. Carlson, Nelson Michael, William R. Schief, James I. Mullins, Jerome H. Kim, Peter B. Gilbert
: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. PLoS Comput. Biol. 11 (2) (2015)
Mehrnoush Malek, Mohammad Jafar Taghiyar, Lauren Chong, Greg Finak, Raphael Gottardo, Ryan Remy Brinkman
flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification. Bioinform. 31 (4) (2015)
Mélanie Courtot, Justin Meskas, Alexander D. Diehl, Radina Droumeva, Raphael Gottardo, Adrin Jalali, Mohammad Jafar Taghiyar, Holden T. Maecker, J. Philip McCoy, Alan Ruttenberg, Richard H. Scheuermann, Ryan Remy Brinkman
flowCL: ontology-based cell population labelling in flow cytometry. Bioinform. 31 (8) (2015)
Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphael Gottardo
OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis. PLoS Comput. Biol. 10 (8) (2014)
Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem, Raphael Gottardo
Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells. PLoS Comput. Biol. 10 (7) (2014)
Yunda Huang, Raphael Gottardo
Comparability and reproducibility of biomedical data. Briefings Bioinform. 14 (4) (2013)
Andrew McDavid, Greg Finak, Pratip K. Chattopadhyay, Maria Dominguez, Laurie Lamoreaux, Steven S. Ma, Mario Roederer, Raphael Gottardo
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinform. 29 (4) (2013)
Sangsoon Woo, Xuekui Zhang, Renan Sauteraud, François Robert, Raphael Gottardo
PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. Bioinform. 29 (16) (2013)
Greg C. Imholte, Marie-Pier Scott-Boyer, Aurélie Labbe, Christian F. Deschepper, Raphael Gottardo
iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data. Bioinform. 29 (21) (2013)
Kenneth Lo, Raphael Gottardo
Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution. Stat. Comput. 22 (1) (2012)
Francois Caron, Arnaud Doucet, Raphael Gottardo
On-line changepoint detection and parameter estimation with application to genomic data. Stat. Comput. 22 (2) (2012)
Greg Finak, Wenxin Jiang, Jorge Pardo, Adam Asare, Raphael Gottardo
QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data. BMC Bioinform. 13 (2012)
Arnaud Droit, Charles Cheung, Raphael Gottardo
rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments. Bioinform. 26 (5) (2010)
Greg Finak, Juan-Manuel Perez, Andrew Weng, Raphael Gottardo
Optimizing Transformations for Automated, High Throughput Analysis of Flow Cytometry Data. BMC Bioinform. 11 (2010)
Greg Finak, Ali Bashashati, Ryan Remy Brinkman, Raphael Gottardo
Merging Mixture Components for Cell Population Identification in Flow Cytometry. Adv. Bioinformatics 2009 (2009)
Raphael Gottardo, Ryan Remy Brinkman, George Luta, Matthew P. Wand
Recent Bioinformatics Advances in the Analysis of High Throughput Flow Cytometry Data. Adv. Bioinformatics 2009 (2009)
Kenneth Lo, Florian Hahne, Ryan Remy Brinkman, Raphael Gottardo
flowClust: a Bioconductor package for automated gating of flow cytometry data. BMC Bioinform. 10 (2009)
Kenneth Lo, Raphael Gottardo
Flexible empirical Bayes models for differential gene expression. Bioinform. 23 (3) (2007)