Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data.

by Xuekui Zhang, Gordon Robertson, Sangsoon Woo, Brad G Hoffman, Raphael Gottardo
Published 2012-01-01

An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.

by Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphael Gottardo
Published 2011-02-01

Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells.

by Diane L Bolton, Kathleen McGinnis, Greg Finak, Pratip Chattopadhyay, Raphael Gottardo, Mario Roederer
Published 2017-06-01

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis [version 2; referees: 2 approved, 1 approved with re...

by Greg Finak, Bryan Mayer, William Fulp, Paul Obrecht, Alicia Sato, Eva Chung, Drienna Holman, Raphael Gottardo
Published 2018-07-01

Modeling bi-modality improves characterization of cell cycle on gene expression in single cells.

by Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem, Raphael Gottardo
Published 2014-07-01

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.

by Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W Newell, John Ramey, Mark M Davis, Spyros A Kalams, Stephen C De Rosa, Raphael Gottardo
Published 2014-08-01

A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level

by Florian Mair, Jami R. Erickson, Valentin Voillet, Yannick Simoni, Timothy Bi, Aaron J. Tyznik, Jody Martin, Raphael Gottardo, Evan W. Newell, Martin Prlic
Published 2020-04-01

The inner foreskin of healthy males at risk of HIV infection harbors epithelial CD4+ CCR5+ cells and has features of an inflamed epidermal barrier.

by Maria P Lemos, Javier R Lama, Shelly T Karuna, Youyi Fong, Silvia M Montano, Carmela Ganoza, Raphael Gottardo, Jorge Sanchez, M Juliana McElrath
Published 2014-01-01

Characterization of two in vivo challenge models to measure functional activity of monoclonal antibodies to Plasmodium falciparum circumsporozoite protein

by Rama Raghunandan, Bryan T. Mayer, Yevel Flores-Garcia, Monica W. Gerber, Raphael Gottardo, Hugo Jhun, Sonia M. Herrera, Daniel W. Perez-Ramos, Emily Locke, C. Richter King, Fidel Zavala
Published 2020-03-01

Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period.

by Julian Rothen, Carl Murie, Jason Carnes, Atashi Anupama, Salim Abdulla, Mwajuma Chemba, Maxmillian Mpina, Marcel Tanner, B Kim Lee Sim, Stephen L Hoffman, Raphael Gottardo, Claudia Daubenberger, Ken Stuart
Published 2018-01-01

PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy

by Nathalie Labarrière, Sylvain Simon, Virginie Vignard, Tiffany Beauvais, Valentin Voillet, Camille Dabrowski, Nicolas Jouand, Amir Khammari, Cécile Braudeau, Régis Josien, Caroline Laheurte, François Aubin, Charles Nardin, Samuel Rulli, Raphael Gottardo, Candice D Church
Published 2020-07-01

Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy

by Alyssa Sheih, Valentin Voillet, Laïla-Aïcha Hanafi, Hannah A. DeBerg, Masanao Yajima, Reed Hawkins, Vivian Gersuk, Stanley R. Riddell, David G. Maloney, Martin E. Wohlfahrt, Dnyanada Pande, Mark R. Enstrom, Hans-Peter Kiem, Jennifer E. Adair, Raphaël Gottardo, Peter S. Linsley, Cameron J. Turtle
Published 2020-01-01

Integrated systems approach defines the antiviral pathways conferring protection by the RV144 HIV vaccine

by Slim Fourati, Susan Pereira Ribeiro, Filipa Blasco Tavares Pereira Lopes, Aarthi Talla, Francois Lefebvre, Mark Cameron, J. Kaewkungwal, P. Pitisuttithum, S. Nitayaphan, S. Rerks-Ngarm, Jerome H. Kim, Rasmi Thomas, Peter B. Gilbert, Georgia D. Tomaras, Richard A. Koup, Nelson L. Michael, M. Juliana McElrath, Raphael Gottardo, Rafick-Pierre Sékaly
Published 2019-02-01

Correction: Mucosal effects for tenofovir 1% gel

by Florian Hladik, Adam Burgener, Lamar Ballweber, Raphael Gottardo, Lucia Vojtech, Slim Fourati, James Y Dai, Mark J Cameron, Johanna Strobl, Sean M Hughes, Craig Hoesley, Philip Andrew, Sherri Johnson, Jeanna Piper, David R Friend, T Blake Ball, Ross D Cranston, Kenneth H Mayer, M Juliana McElrath, Ian McGowan
Published 2015-03-01

Mucosal effects of tenofovir 1% gel

by Florian Hladik, Adam Burgener, Lamar Ballweber, Raphael Gottardo, Lucia Vojtech, Slim Fourati, James Y Dai, Mark J Cameron, Johanna Strobl, Sean M Hughes, Craig Hoesley, Philip Andrew, Sherri Johnson, Jeanna Piper, David R Friend, T Blake Ball, Ross D Cranston, Kenneth H Mayer, M Juliana McElrath, Ian McGowan
Published 2015-02-01

Vaccine-induced Human Antibodies Specific for the Third Variable Region of HIV-1 gp120 Impose Immune Pressure on Infecting Viruses

by Susan Zolla-Pazner, Paul T. Edlefsen, Morgane Rolland, Xiang-Peng Kong, Allan deCamp, Raphael Gottardo, Constance Williams, Sodsai Tovanabutra, Sandra Sharpe-Cohen, James I. Mullins, Mark S. deSouza, Nicos Karasavvas, Sorachai Nitayaphan, Supachai Rerks-Ngarm, Punnee Pitisuttihum, Jaranit Kaewkungwal, Robert J. O'Connell, Merlin L. Robb, Nelson L. Michael, Jerome H. Kim, Peter Gilbert
Published 2014-11-01

Optimal priming of poxvirus vector (NYVAC)-based HIV vaccine regimens for T cell responses requires three DNA injections. Results of the randomized multicentre EV03/ANRS VAC20 Phas...

by Yves Lévy, Christine Lacabaratz, Kim Ellefsen-Lavoie, Wolfgang Stöhr, Jean-Daniel Lelièvre, Pierre-Alexandre Bart, Odile Launay, Jonathan Weber, Bernd Salzberger, Aurélie Wiedemann, Mathieu Surenaud, David M Koelle, Hans Wolf, Ralf Wagner, Véronique Rieux, David C Montefiori, Nicole L Yates, Georgia D Tomaras, Raphael Gottardo, Bryan Mayer, Song Ding, Rodolphe Thiébaut, Sheena McCormack, Geneviève Chêne, Giuseppe Pantaleo
Published 2020-06-01

Targeting HIV-1 Env gp140 to LOX-1 Elicits Immune Responses in Rhesus Macaques.

by Gerard Zurawski, Sandra Zurawski, Anne-Laure Flamar, Laura Richert, Ralf Wagner, Georgia D Tomaras, David C Montefiori, Mario Roederer, Guido Ferrari, Christine Lacabaratz, Henri Bonnabau, Peter Klucar, Zhiqing Wang, Kathryn E Foulds, Shing-Fen Kao, Nicole L Yates, Celia LaBranche, Bertram L Jacobs, Karen Kibler, Benedikt Asbach, Alexander Kliche, Andres Salazar, Steve Reed, Steve Self, Raphael Gottardo, Lindsey Galmin, Deborah Weiss, Anthony Cristillo, Rodolphe Thiebaut, Giuseppe Pantaleo, Yves Levy
Published 2016-01-01

Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial.

by Susan Zolla-Pazner, Allan C deCamp, Timothy Cardozo, Nicos Karasavvas, Raphael Gottardo, Constance Williams, Daryl E Morris, Georgia Tomaras, Mangala Rao, Erik Billings, Phillip Berman, Xiaoying Shen, Charla Andrews, Robert J O'Connell, Viseth Ngauy, Sorachai Nitayaphan, Mark de Souza, Bette Korber, Richard Koup, Robert T Bailer, John R Mascola, Abraham Pinter, David Montefiori, Barton F Haynes, Merlin L Robb, Supachai Rerks-Ngarm, Nelson L Michael, Peter B Gilbert, Jerome H Kim
Published 2013-01-01

Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial.

by Raphael Gottardo, Robert T Bailer, Bette T Korber, S Gnanakaran, Joshua Phillips, Xiaoying Shen, Georgia D Tomaras, Ellen Turk, Gregory Imholte, Larry Eckler, Holger Wenschuh, Johannes Zerweck, Kelli Greene, Hongmei Gao, Phillip W Berman, Donald Francis, Faruk Sinangil, Carter Lee, Sorachai Nitayaphan, Supachai Rerks-Ngarm, Jaranit Kaewkungwal, Punnee Pitisuttithum, James Tartaglia, Merlin L Robb, Nelson L Michael, Jerome H Kim, Susan Zolla-Pazner, Barton F Haynes, John R Mascola, Steve Self, Peter Gilbert, David C Montefiori
Published 2013-01-01