Julia V. Ponomarenko

According to our database, Julia V. Ponomarenko authored at least 28 papers between 1997 and 2019.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2019

Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards.

Jose Espinosa-Carrasco, Antonio Hermoso Pulido, Ionas Erb, Mara Dierssen, Julia V. Ponomarenko, Cédric Notredame

Nucleic Acids Res., 2019

2017

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

Carlos Pulido-Quetglas, Estel Aparicio-Prat, Carme Arnan, Taisia Polidori, Toni Hermoso, Emilio Palumbo, Julia V. Ponomarenko, Roderic Guigó, Rory Johnson

PLoS Comput. Biol., 2017

Ten Simple Rules on How to Organize a Scientific Retreat.

Julia V. Ponomarenko, Romina Garrido, Roderic Guigó

PLoS Comput. Biol., 2017

2015

The immune epitope database (IEDB) 3.0.

Randi Vita, James A. Overton, Jason A. Greenbaum, Julia V. Ponomarenko, Jason D. Clark, Jason R. Cantrell, Daniel K. Wheeler, Joseph L. Gabbard, Deborah Hix, Alessandro Sette, Bjoern Peters

Nucleic Acids Res., 2015

2012

Immune epitope database analysis resource.

Yohan Kim, Julia V. Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E. Bourne, Morten Nielsen, Bjoern Peters

Nucleic Acids Res., 2012

2011

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

Julia V. Ponomarenko, Nikitas Papangelopoulos, Dirk M. Zajonc, Björn Peters, Alessandro Sette, Philip E. Bourne

Nucleic Acids Res., 2011

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

Sergey Kozhenkov, Mayya Sedova, Yulia Dubinina, Amarnath Gupta, Animesh Ray, Julia V. Ponomarenko, Michael Baitaluk

BMC Syst. Biol., 2011

2010

BiologicalNetworks 2.0 - an integrative view of genome biology data.

Sergey Kozhenkov, Yulia Dubinina, Mayya Sedova, Amarnath Gupta, Julia V. Ponomarenko, Michael Baitaluk

BMC Bioinform., 2010

Semantic integration of data on transcriptional regulation.

Michael Baitaluk, Julia V. Ponomarenko

Bioinform., 2010

2008

Immune epitope database analysis resource (IEDB-AR).

Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia V. Ponomarenko, Alessandro Sette, Zhanyang Zhu, Björn Peters

Nucleic Acids Res., 2008

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

Julia V. Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E. Bourne, Alessandro Sette, Björn Peters

BMC Bioinform., 2008

2006

Curation of complex, context-dependent immunological data.

Randi Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, Muthu Sathiamurthy, John Mokili, Huynh-Hoa Bui, Philip E. Bourne, Julia V. Ponomarenko, Romulo de Castro Jr., Russell K. Chan, John Sidney, Stephen S. Wilson, Scott Stewart, Scott Way, Björn Peters, Alessandro Sette

BMC Bioinform., 2006

The Immune Epitope Database and Analysis Resource.

Alessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Søren Buus, Ward Fleri, R. Kubo, Ole Lund, D. Nemazee, Julia V. Ponomarenko, Muthu Sathiamurthy, Scott Stewart, Scott Way, Stephen S. Wilson, Björn Peters

Proceedings of the Pattern Recognition in Bioinformatics, International Workshop, 2006

2005

Mining Genome Variation to Associate Genetic Disease with Mutation Alterations and Ortho/Paralogous Polimorphysms in Transcription Factor Binding Site.

Julia V. Ponomarenko, Galina Orlova, Tatyana I. Merkulova, Gennady V. Vasiliev, Mikhail P. Ponomarenko

Int. J. Artif. Intell. Tools, 2005

2003

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

Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Anatoly S. Frolov, Vadim P. Valuev, Mikhail P. Ponomarenko

Nucleic Acids Res., 2003

2002

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

Julia V. Ponomarenko, Galina Orlova, Anatoly S. Frolov, Mikhail S. Gelfand, Mikhail P. Ponomarenko

Nucleic Acids Res., 2002

Mining DNA sequences to predict sites which mutations cause genetic diseases.

Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Mikhail P. Ponomarenko

Knowl. Based Syst., 2002

Building an automated classification of DNA-binding protein domains.

Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov

Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations.

Julia V. Ponomarenko, Tatyana I. Merkulova, Gennady V. Vasiliev, Zoya B. Levashova, Galina Orlova, Sergey V. Lavryushev, Oleg N. Fokin, Mikhail P. Ponomarenko, Anatoly S. Frolov, Akinori Sarai

Nucleic Acids Res., 2001

ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another.

Julia V. Ponomarenko, Dagmara P. Furman, Anatoly S. Frolov, Nikolay L. Podkolodny, Galina Orlova, Mikhail P. Ponomarenko, Nikolay A. Kolchanov, Akinori Sarai

Nucleic Acids Res., 2001

Mining SNPs for Associating Disease Penetration with Transcription Factor Binding Site Alterations.

Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Mikhail P. Ponomarenko

Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

Mining Genome Variation to Associate Disease with Transcription Factor Binding Site Alteration.

Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Elena Gorshkova, Oleg N. Fokin, Mikhail P. Ponomarenko

Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering, 2001

2000

SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation.

Julia V. Ponomarenko, Galina Orlova, Mikhail P. Ponomarenko, Sergey V. Lavryushev, Anatoly S. Frolov, Svetlana V. Zybova, Nikolay A. Kolchanov

Nucleic Acids Res., 2000

1999

Conformational and physicochemical DNA features specific for transcription factor binding sites.

Julia V. Ponomarenko, Mikhail P. Ponomarenko, Anatoly S. Frolov, Denis G. Vorobiev, G. Christian Overton, Nikolay A. Kolchanov

Bioinform., 1999

Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.

Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Olga A. Podkolodnaya, Denis G. Vorobiev, Nikolay A. Kolchanov, G. Christian Overton

Bioinform., 1999

Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.

Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay L. Podkolodny, Ludmila K. Savinkova, Nikolay A. Kolchanov, G. Christian Overton

Bioinform., 1999

Nucleosomal DNA property database.

Victor G. Levitsky, Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay A. Kolchanov

Bioinform., 1999

1997

Identification of the significant conformational features of functional sites in B-DNA.

Mikhail P. Ponomarenko, Julia V. Ponomarenko, Alexander E. Kel, Nikolay A. Kolchanov, N. Karas, Edgar Wingender, Heinz Sklenar

Proceedings of the German Conference on Bioinformatics, 1997