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List of works by Julia Ponomarenko

An integrative approach to inferring gene regulatory module networks

scientific article

Analysis of Human RSV Immunity at the Molecular Level: Learning from the Past and Present

scientific article

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

scientific article

Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology

scientific article

BiologicalNetworks 2.0--an integrative view of genome biology data

scientific article

BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies

scientific article

Building an automated classification of DNA-binding protein domains.

scientific article

Conservancy of mAb Epitopes in Ebolavirus Glycoproteins of Previous and 2014 Outbreaks

scientific article published on 3 November 2014

Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways

scientific journal article

Curation of complex, context-dependent immunological data

scientific article

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

scientific article

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB)

scientific article

IEDB-3D: structural data within the immune epitope database

scientific article

Immune epitope database analysis resource

scientific article

Immune epitope database analysis resource (IEDB-AR).

scientific article published on 31 May 2008

IntegromeDB: an integrated system and biological search engine

scientific article (publication date: 19 January 2012)

IκBε is a key regulator of B cell expansion by providing negative feedback on cRel and RelA in a stimulus-specific manner

scientific article published on 03 March 2014

Limitations of Ab initio predictions of peptide binding to MHC class II molecules

scientific article

Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools

scholarly article published 26 October 2018

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

scientific article

SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data ⬇️

scientific article

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

scientific article

Semantic integration of data on transcriptional regulation

scientific article

Ten Simple Rules on How to Organize a Scientific Retreat

scientific article (publication date: February 2017)

The design and implementation of the immune epitope database and analysis resource

scientific article published on 14 May 2005

The immune epitope database (IEDB) 3.0.

scientific article

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

scientific article

The microbiome in respiratory medicine: current challenges and future perspectives

scientific article

The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50

scientific article published on 22 February 2011

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

scientific article

rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation

scientific article published on January 2003

rSNP_Guide: an integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites

scientific article

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