Julia Ponomarenko
Julia Ponomarenko
Centre for Genomic Regulation (CRG), Barcelona, Spain
Verified email at
Cited by
Cited by
ElliPro: a new structure-based tool for the prediction of antibody epitopes
J Ponomarenko, HH Bui, W Li, N Fusseder, PE Bourne, A Sette, B Peters
BMC bioinformatics 9, 1-8, 2008
The immune epitope database (IEDB) 3.0
R Vita, JA Overton, JA Greenbaum, J Ponomarenko, JD Clark, JR Cantrell, ...
Nucleic acids research 43 (D1), D405-D412, 2015
Immune epitope database analysis resource
Y Kim, J Ponomarenko, Z Zhu, D Tamang, P Wang, J Greenbaum, ...
Nucleic acids research 40 (W1), W525-W530, 2012
The immune epitope database and analysis resource: from vision to blueprint
B Peters, J Sidney, P Bourne, HH Bui, S Buus, G Doh, W Fleri, ...
PLoS biology 3 (3), e91, 2005
Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population
JA Greenbaum, MF Kotturi, Y Kim, C Oseroff, K Vaughan, N Salimi, R Vita, ...
Proceedings of the National Academy of Sciences 106 (48), 20365-20370, 2009
Immune epitope database analysis resource (IEDB-AR)
Q Zhang, P Wang, Y Kim, P Haste-Andersen, J Beaver, PE Bourne, ...
Nucleic acids research 36 (suppl_2), W513-W518, 2008
An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms
J Tapial, KCH Ha, T Sterne-Weiler, A Gohr, U Braunschweig, ...
Genome research 27 (10), 1759-1768, 2017
Towards a consensus on datasets and evaluation metrics for developing B‐cell epitope prediction tools
JA Greenbaum, PH Andersen, M Blythe, HH Bui, RE Cachau, J Crowe, ...
Journal of Molecular Recognition: An Interdisciplinary Journal 20 (2), 75-82, 2007
Antibody-protein interactions: benchmark datasets and prediction tools evaluation
JV Ponomarenko, PE Bourne
BMC structural biology 7 (1), 1-19, 2007
The microbiome in respiratory medicine: current challenges and future perspectives
R Faner, O Sibila, A Agustí, E Bernasconi, JD Chalmers, GB Huffnagle, ...
European Respiratory Journal 49 (4), 2017
Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways
VFS Shih, J Davis-Turak, M Macal, JQ Huang, J Ponomarenko, JD Kearns, ...
Nature immunology 13 (12), 1162-1170, 2012
The design and implementation of the immune epitope database and analysis resource
B Peters, J Sidney, P Bourne, HH Bui, S Buus, G Doh, W Fleri, ...
Immunogenetics 57, 326-336, 2005
Conformational and physicochemical DNA features specific for transcription factor binding sites.
JV Ponomarenko, MP Ponomarenko, AS Frolov, DG Vorobyev, ...
Bioinformatics (Oxford, England) 15 (7), 654-668, 1999
B cell epitope prediction
JV Ponomarenko, MHV Van Regenmortel
Structural bioinformatics 2, 849-879, 2009
The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50
CS Cheng, KE Feldman, J Lee, S Verma, DB Huang, K Huynh, M Chang, ...
Science signaling 4 (161), ra11-ra11, 2011
Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition
JR Willis, P González-Torres, AA Pittis, LA Bejarano, L Cozzuto, ...
Microbiome 6, 1-17, 2018
Scalable design of paired CRISPR guide RNAs for genomic deletion
C Pulido-Quetglas, E Aparicio-Prat, C Arnan, T Polidori, T Hermoso, ...
PLoS computational biology 13 (3), e1005341, 2017
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.
MP Ponomarenko, JV Ponomarenko, AS Frolov, NL Podkolodny, ...
Bioinformatics (Oxford, England) 15 (7), 687-703, 1999
rSNP_Guide: An integrated database‐tools system for studying SNPs and site‐directed mutations in transcription factor binding sites
JV Ponomarenko, GV Orlova, TI Merkulova, EV Gorshkova, ON Fokin, ...
Human mutation 20 (4), 239-248, 2002
IEDB-3D: structural data within the immune epitope database
J Ponomarenko, N Papangelopoulos, DM Zajonc, B Peters, A Sette, ...
Nucleic acids research 39 (suppl_1), D1164-D1170, 2010
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