Raphael Gottardo

26 papers Journal 25Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
<tt>tagtango</tt>: an application to compare single-cell annotations.
Bioinform.
Bernat Bramon Mora, Helen Lindsay, Antonin Thiébaut, Kenneth D. Stuart, Raphael Gottardo
2025 J jnl
ProteinPNet: Prototypical Part Networks for Concept Learning in Spatial Proteomics.
CoRR
Louis McConnell, Jieran Sun, Theo Maffei, Raphael Gottardo, Marianna Rapsomaniki
2023 — conf
The Statistical Analysis of the Varying Brain.
SSP
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
2022 J jnl
Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention.
PLoS Comput. Biol.
Bryan T. Mayer, Allan C. deCamp, Yunda Huang, Joshua T. Schiffer, Raphael Gottardo, Peter B. Gilbert, Daniel B. Reeves
2021 J jnl
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
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
2021 J jnl
New interpretable machine-learning method for single-cell data reveals correlates of clinical response to cancer immunotherapy.
Patterns
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
2018 J jnl
Selective Clustering Annotated using Modes of Projections.
CoRR
Evan Greene, Greg Finak, Raphael Gottardo
2018 J jnl
ggCyto: next generation open-source visualization software for cytometry.
Bioinform.
Phu Van, Wenxin Jiang, Raphael Gottardo, Greg Finak
2015 J jnl
: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.
PLoS Comput. Biol.
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
2015 J jnl
flowCL: ontology-based cell population labelling in flow cytometry.
Bioinform.
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
2015 J jnl
flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.
Bioinform.
Mehrnoush Malek, Mohammad Jafar Taghiyar, Lauren Chong, Greg Finak, Raphael Gottardo, Ryan Remy Brinkman
2014 J jnl
Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells.
PLoS Comput. Biol.
Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem, Raphael Gottardo
2014 J jnl
OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis.
PLoS Comput. Biol.
Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphael Gottardo
2013 J jnl
Comparability and reproducibility of biomedical data.
Briefings Bioinform.
Yunda Huang, Raphael Gottardo
2013 J jnl
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.
Bioinform.
Andrew McDavid, Greg Finak, Pratip K. Chattopadhyay, Maria Dominguez, Laurie Lamoreaux, Steven S. Ma, Mario Roederer, Raphael Gottardo
2013 J jnl
PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.
Bioinform.
Sangsoon Woo, Xuekui Zhang, Renan Sauteraud, François Robert, Raphael Gottardo
2013 J jnl
iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.
Bioinform.
Greg C. Imholte, Marie-Pier Scott-Boyer, Aurélie Labbe, Christian F. Deschepper, Raphael Gottardo
2012 J jnl
Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution.
Stat. Comput.
Kenneth Lo, Raphael Gottardo
2012 J jnl
On-line changepoint detection and parameter estimation with application to genomic data.
Stat. Comput.
Francois Caron, Arnaud Doucet, Raphael Gottardo
2012 J jnl
QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data.
BMC Bioinform.
Greg Finak, Wenxin Jiang, Jorge Pardo, Adam Asare, Raphael Gottardo
2010 J jnl
Optimizing Transformations for Automated, High Throughput Analysis of Flow Cytometry Data.
BMC Bioinform.
Greg Finak, Juan-Manuel Perez, Andrew Weng, Raphael Gottardo
2010 J jnl
rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments.
Bioinform.
Arnaud Droit, Charles Cheung, Raphael Gottardo
2009 J jnl
Merging Mixture Components for Cell Population Identification in Flow Cytometry.
Adv. Bioinformatics
Greg Finak, Ali Bashashati, Ryan Remy Brinkman, Raphael Gottardo
2009 J jnl
Recent Bioinformatics Advances in the Analysis of High Throughput Flow Cytometry Data.
Adv. Bioinformatics
Raphael Gottardo, Ryan Remy Brinkman, George Luta, Matthew P. Wand
2009 J jnl
flowClust: a Bioconductor package for automated gating of flow cytometry data.
BMC Bioinform.
Kenneth Lo, Florian Hahne, Ryan Remy Brinkman, Raphael Gottardo
2007 J jnl
Flexible empirical Bayes models for differential gene expression.
Bioinform.
Kenneth Lo, Raphael Gottardo