Bibliotecas PUC-SP - Busca Integrada

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

Bằng Xuekui Zhang, Gordon Robertson, Sangsoon Woo, Brad G Hoffman, Raphael Gottardo
Xuất bản năm PLoS ONE (2012-01-01)

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

Bằng Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphael Gottardo
Xuất bản năm PLoS ONE (2011-02-01)

IDEAS: individual level differential expression analysis for single-cell RNA-seq data

Bằng Mengqi Zhang, Si Liu, Zhen Miao, Fang Han, Raphael Gottardo, Wei Sun
Xuất bản năm Genome Biology (2022-01-01)

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

Bằng Diane L Bolton, Kathleen McGinnis, Greg Finak, Pratip Chattopadhyay, Raphael Gottardo, Mario Roederer
Xuất bản năm PLoS Pathogens (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...

Bằng Greg Finak, Bryan Mayer, William Fulp, Paul Obrecht, Alicia Sato, Eva Chung, Drienna Holman, Raphael Gottardo
Xuất bản năm Gates Open Research (2018-07-01)

Unsupervised Clustering of Cell Populations in Germinal Centers Using Multiplexed Immunofluorescence

Bằng Simon Burgermeister, Michail Orfanakis, Spiros Georgakis, Cloe Brenna, Helen Lindsay, Craig Fenwick, Giuseppe Pantaleo, Raphael Gottardo, Constantinos Petrovas
Xuất bản năm Biology (2025-05-01)

The Human Exersome Initiative (HEI): Rationale, study design, and protocol.

Bằng Daria Neyroud, Julia Primavesi, Guia Tagliapietra, Chantal Daucourt, Hector Gallart-Ayala, Raphael Gottardo, Julijana Ivanisevic, Aaron L Baggish
Xuất bản năm PLoS ONE (2025-01-01)

Cellular and molecular determinants mediating the dysregulated germinal center immune dynamics in systemic lupus erythematosus

Bằng Spiros Georgakis, Kalliopi Ioannidou, Bernat Bramon Mora, Michail Orfanakis, Cloe Brenna, Yannick D. Muller, Perla M. Del Rio Estrada, Perla M. Del Rio Estrada, Ashish A. Sharma, Giuseppe Pantaleo, Laurence de Leval, Denis Comte, Raphael Gottardo, Raphael Gottardo, Constantinos Petrovas
Xuất bản năm Frontiers in Immunology (2025-02-01)

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

Bằng Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem, Raphael Gottardo
Xuất bản năm PLoS Computational Biology (2014-07-01)

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

Bằng Bryan T Mayer, Allan C deCamp, Yunda Huang, Joshua T Schiffer, Raphael Gottardo, Peter B Gilbert, Daniel B Reeves
Xuất bản năm PLoS Computational Biology (2022-04-01)

Early and Long-Term HIV-1 Immunogenicity Induced in Macaques by the Combined Administration of DNA, NYVAC and Env Protein-Based Vaccine Candidates: The AUP512 Study

Bằng Beatriz Perdiguero, Beatriz Perdiguero, Benedikt Asbach, Carmen E. Gómez, Carmen E. Gómez, Josef Köstler, Josef Köstler, Susan W. Barnett, Marguerite Koutsoukos, Deborah E. Weiss, Anthony D. Cristillo, Kathryn E. Foulds, Mario Roederer, David C. Montefiori, Nicole L. Yates, Guido Ferrari, Xiaoying Shen, Sheetal Sawant, Georgia D. Tomaras, Alicia Sato, William J. Fulp, Raphael Gottardo, Raphael Gottardo, Raphael Gottardo, Song Ding, Jonathan L. Heeney, Giuseppe Pantaleo, Mariano Esteban, Mariano Esteban, Ralf Wagner, Ralf Wagner
Xuất bản năm Frontiers in Immunology (2022-07-01)

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

Bằng Florian Mair, Jami R. Erickson, Valentin Voillet, Yannick Simoni, Timothy Bi, Aaron J. Tyznik, Jody Martin, Raphael Gottardo, Evan W. Newell, Martin Prlic
Xuất bản năm Cell Reports (2020-04-01)

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

Bằng Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W Newell, John Ramey, Mark M Davis, Spyros A Kalams, Stephen C De Rosa, Raphael Gottardo
Xuất bản năm PLoS Computational Biology (2014-08-01)

ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets

Bằng Ye Zheng, Daniel P. Caron, Ju Yeong Kim, Seong-Hwan Jun, Yuan Tian, Florian Mair, Kenneth D. Stuart, Peter A. Sims, Raphael Gottardo
Xuất bản năm Nature Communications (2025-07-01)

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

Bằng Maria P Lemos, Javier R Lama, Shelly T Karuna, Youyi Fong, Silvia M Montano, Carmela Ganoza, Raphael Gottardo, Jorge Sanchez, M Juliana McElrath
Xuất bản năm PLoS ONE (2014-01-01)

803 Triple checkpoint blockade, but not anti-PD1 alone, enhances the efficacy of engineered adoptive T cell therapy in advanced ovarian cancer

Bằng Philip D Greenberg, Valentin Voillet, Raphael Gottardo, Kristin G Anderson, Breanna M Bates, Madison G Burnett, Susan L Ruskin, Yapeng Su, Magdalia L Suarez Gutierrez
Xuất bản năm Journal for ImmunoTherapy of Cancer (2023-11-01)

Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations

Bằng H Nayanga Thirimanne, Feinan Wu, Derek H Janssens, Jherek Swanger, Ahmed Diab, Heather M Feldman, Robert A Amezquita, Raphael Gottardo, Patrick J Paddison, Steven Henikoff, Bruce E Clurman
Xuất bản năm eLife (2022-02-01)

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

Bằng 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
Xuất bản năm PLoS ONE (2018-01-01)

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

Bằng 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
Xuất bản năm Malaria Journal (2020-03-01)

661 Neoantigen-specific CD4+ T cells in human melanoma have diverse differentiation states and correlate with CD8+ T cell, macrophage, and B cell function

Bằng Evan Hall, Stanley Riddell, Sylvia Lee, David Byrd, Shailender Bhatia, Scott Tykodi, Raphael Gottardo, Naina Singhi, Ata Moshiri, Evan Newell, Carolyn Shasha, Julia Szeto, Teresa Kim, Venu Pillarisetty, Kimberly Smythe, Joshua Veatch
Xuất bản năm Journal for ImmunoTherapy of Cancer (2021-11-01)