User profiles for J. Ponomarenko

Julia Ponomarenko

Centre for Genomic Regulation (CRG), Barcelona, Spain
Verified email at crg.eu
Cited by 7660

Towards a consensus on datasets and evaluation metrics for developing B‐cell epitope prediction tools

…, C Pinilla, JV Ponomarenko… - Journal of Molecular …, 2007 - Wiley Online Library
… Non-redundant datasets of representative threedimensional structures of protein antigens
and antigen–antibody complexes from the PDB were assembled by Dr Julia Ponomarenko. …

The microbiome in respiratory medicine: current challenges and future perspectives

…, J Ponomarenko, S Sethi, J Dorca… - European …, 2017 - Eur Respiratory Soc
The healthy lung has previously been considered to be a sterile organ because standard
microbiological culture techniques consistently yield negative results. However, culture-…

The immune epitope database (IEDB) 3.0

…, JA Greenbaum, J Ponomarenko… - Nucleic acids …, 2015 - academic.oup.com
The IEDB, www.iedb.org , contains information on immune epitopes—the molecular targets
of adaptive immune responses—curated from the published literature and submitted by …

[HTML][HTML] ElliPro: a new structure-based tool for the prediction of antibody epitopes

J Ponomarenko, HH Bui, W Li, N Fusseder… - BMC …, 2008 - Springer
Background Reliable prediction of antibody, or B-cell, epitopes remains challenging yet
highly desirable for the design of vaccines and immunodiagnostics. A correlation between …

Immune epitope database analysis resource

Y Kim, J Ponomarenko, Z Zhu, D Tamang… - Nucleic acids …, 2012 - academic.oup.com
The immune epitope database analysis resource (IEDB-AR: http://tools.iedb.org ) is a
collection of tools for prediction and analysis of molecular targets of T- and B-cell immune …

Immune epitope database analysis resource (IEDB-AR)

…, C Lundegaard, M Nielsen, J Ponomarenko… - Nucleic acids …, 2008 - academic.oup.com
We present a new release of the immune epitope database analysis resource (IEDB-AR,
http://tools.immuneepitope.org ), a repository of web-based tools for the prediction and analysis …

[HTML][HTML] The immune epitope database and analysis resource: from vision to blueprint

…, R Kubo, O Lund, D Nemazee, JV Ponomarenko… - PLoS …, 2005 - journals.plos.org
J Exp Med 168: 559–570. … Moult J, Fidelis K, Zemla A, Hubbard T (2003) Critical
assessment of methods of protein structure prediction (CASP)-round V. Proteins 53: Suppl …

Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population

…, N Salimi, R Vita, J Ponomarenko… - Proceedings of the …, 2009 - National Acad Sciences
A major concern about the ongoing swine-origin H1N1 influenza virus (S-OIV) outbreak is that
the virus may be so different from seasonal H1N1 that little immune protection exists in the …

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

…, T Rayon, M Manzanares, J Ponomarenko… - Genome …, 2017 - genome.cshlp.org
Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in
metazoans. However, the functions of most AS events are not known, and programs of regulated …

[HTML][HTML] Antibody-protein interactions: benchmark datasets and prediction tools evaluation

JV Ponomarenko, PE Bourne - BMC structural biology, 2007 - Springer
Background The ability to predict antibody binding sites (aka antigenic determinants or B-cell
epitopes) for a given protein is a precursor to new vaccine design and diagnostics. Among …