Raphael Gottardo

According to our database, Raphael Gottardo authored at least 24 papers between 2007 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

The Statistical Analysis of the Varying Brain.

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

Proceedings of the IEEE Statistical Signal Processing Workshop, 2023

2022

Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention.

Bryan T. Mayer, Allan C. deCamp, Yunda Huang, Joshua T. Schiffer, Raphael Gottardo, Peter B. Gilbert, Daniel B. Reeves

PLoS Comput. Biol., 2022

2021

New interpretable machine-learning method for single-cell data reveals correlates of clinical response to cancer immunotherapy.

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

Patterns, 2021

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.

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

Frontiers Big Data, 2021

2018

Selective Clustering Annotated using Modes of Projections.

Evan Greene, Greg Finak, Raphael Gottardo

CoRR, 2018

ggCyto: next generation open-source visualization software for cytometry.

Phu Van, Wenxin Jiang, Raphael Gottardo, Greg Finak

Bioinform., 2018

2015

: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.

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

PLoS Comput. Biol., 2015

flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.

Mehrnoush Malek, Mohammad Jafar Taghiyar, Lauren Chong, Greg Finak, Raphael Gottardo, Ryan Remy Brinkman

Bioinform., 2015

flowCL: ontology-based cell population labelling in flow cytometry.

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

Bioinform., 2015

2014

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells.

Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem, Raphael Gottardo

PLoS Comput. Biol., 2014

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis.

Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphael Gottardo

PLoS Comput. Biol., 2014

2013

PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.

Sangsoon Woo, Xuekui Zhang, Renan Sauteraud, François Robert, Raphael Gottardo

Bioinform., 2013

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.

Andrew McDavid, Greg Finak, Pratip K. Chattopadhyay, Maria Dominguez, Laurie Lamoreaux, Steven S. Ma, Mario Roederer, Raphael Gottardo

Bioinform., 2013

iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.

Greg C. Imholte, Marie-Pier Scott-Boyer, Aurélie Labbe, Christian F. Deschepper, Raphael Gottardo

Bioinform., 2013

Comparability and reproducibility of biomedical data.

Yunda Huang, Raphael Gottardo

Briefings Bioinform., 2013

2012

Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution.

Kenneth Lo, Raphael Gottardo

Stat. Comput., 2012

On-line changepoint detection and parameter estimation with application to genomic data.

Francois Caron, Arnaud Doucet, Raphael Gottardo

Stat. Comput., 2012

QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data.

Greg Finak, Wenxin Jiang, Jorge Pardo, Adam Asare, Raphael Gottardo

BMC Bioinform., 2012

2010

Optimizing Transformations for Automated, High Throughput Analysis of Flow Cytometry Data.

Greg Finak, Juan-Manuel Perez, Andrew Weng, Raphael Gottardo

BMC Bioinform., 2010

rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments.

Arnaud Droit, Charles Cheung, Raphael Gottardo

Bioinform., 2010

2009

flowClust: a Bioconductor package for automated gating of flow cytometry data.

Kenneth Lo, Florian Hahne, Ryan Remy Brinkman, Raphael Gottardo

BMC Bioinform., 2009

Recent Bioinformatics Advances in the Analysis of High Throughput Flow Cytometry Data.

Raphael Gottardo, Ryan Remy Brinkman, George Luta, Matthew P. Wand

Adv. Bioinformatics, 2009

Merging Mixture Components for Cell Population Identification in Flow Cytometry.

Greg Finak, Ali Bashashati, Ryan Remy Brinkman, Raphael Gottardo

Adv. Bioinformatics, 2009

2007

Flexible empirical Bayes models for differential gene expression.

Kenneth Lo, Raphael Gottardo

Bioinform., 2007