Julia V. Ponomarenko

Publication Activity (10 Years)

Years Active: 1997-2019
Publications (10 Years): 3

Top Topics

Production Rules

Web Usage Mining

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Jose Espinosa-Carrasco, Antonio Hermoso Pulido, Ionas Erb, Mara Dierssen, Julia V. Ponomarenko, Cédric Notredame
Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Carlos Pulido-Quetglas, Estel Aparicio-Prat, Carme Arnan, Taisia Polidori, Toni Hermoso, Emilio Palumbo, Julia V. Ponomarenko, Roderic Guigó, Rory Johnson
Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PLoS Comput. Biol. 13 (3) (2017)
Julia V. Ponomarenko, Romina Garrido, Roderic Guigó
Ten Simple Rules on How to Organize a Scientific Retreat. PLoS Comput. Biol. 13 (2) (2017)
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
The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 43 (Database-Issue) (2015)
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
Immune epitope database analysis resource. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Sergey Kozhenkov, Mayya Sedova, Yulia Dubinina, Amarnath Gupta, Animesh Ray, Julia V. Ponomarenko, Michael Baitaluk
BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies. BMC Syst. Biol. 5 (2011)
Julia V. Ponomarenko, Nikitas Papangelopoulos, Dirk M. Zajonc, Björn Peters, Alessandro Sette, Philip E. Bourne
IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res. 39 (Database-Issue) (2011)
Sergey Kozhenkov, Yulia Dubinina, Mayya Sedova, Amarnath Gupta, Julia V. Ponomarenko, Michael Baitaluk
BiologicalNetworks 2.0 - an integrative view of genome biology data. BMC Bioinform. 11 (2010)
Michael Baitaluk, Julia V. Ponomarenko
Semantic integration of data on transcriptional regulation. Bioinform. 26 (13) (2010)
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
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Julia V. Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E. Bourne, Alessandro Sette, Björn Peters
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinform. 9 (2008)
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
Curation of complex, context-dependent immunological data. BMC Bioinform. 7 (2006)
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
The Immune Epitope Database and Analysis Resource. PRIB (2006)
Julia V. Ponomarenko, Galina Orlova, Tatyana I. Merkulova, Gennady V. Vasiliev, Mikhail P. Ponomarenko
Mining Genome Variation to Associate Genetic Disease with Mutation Alterations and Ortho/Paralogous Polimorphysms in Transcription Factor Binding Site. Int. J. Artif. Intell. Tools 14 (4) (2005)
Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Anatoly S. Frolov, Vadim P. Valuev, Mikhail P. Ponomarenko
rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. Nucleic Acids Res. 31 (1) (2003)
Julia V. Ponomarenko, Galina Orlova, Anatoly S. Frolov, Mikhail S. Gelfand, Mikhail P. Ponomarenko
SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data. Nucleic Acids Res. 30 (1) (2002)
Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov
Building an automated classification of DNA-binding protein domains. ECCB (2002)
Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Mikhail P. Ponomarenko
Mining DNA sequences to predict sites which mutations cause genetic diseases. Knowl. Based Syst. 15 (4) (2002)
Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Mikhail P. Ponomarenko
Mining SNPs for Associating Disease Penetration with Transcription Factor Binding Site Alterations. German Conference on Bioinformatics (2001)
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
rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Res. 29 (1) (2001)
Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Elena Gorshkova, Oleg N. Fokin, Mikhail P. Ponomarenko
Mining Genome Variation to Associate Disease with Transcription Factor Binding Site Alteration. BIBE (2001)
Julia V. Ponomarenko, Dagmara P. Furman, Anatoly S. Frolov, Nikolay L. Podkolodny, Galina Orlova, Mikhail P. Ponomarenko, Nikolay A. Kolchanov, Akinori Sarai
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Res. 29 (1) (2001)
Julia V. Ponomarenko, Galina Orlova, Mikhail P. Ponomarenko, Sergey V. Lavryushev, Anatoly S. Frolov, Svetlana V. Zybova, Nikolay A. Kolchanov
SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucleic Acids Res. 28 (1) (2000)
Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Olga A. Podkolodnaya, Denis G. Vorobiev, Nikolay A. Kolchanov, G. Christian Overton
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. Bioinform. 15 (7) (1999)
Julia V. Ponomarenko, Mikhail P. Ponomarenko, Anatoly S. Frolov, Denis G. Vorobiev, G. Christian Overton, Nikolay A. Kolchanov
Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinform. 15 (7) (1999)
Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay L. Podkolodny, Ludmila K. Savinkova, Nikolay A. Kolchanov, G. Christian Overton
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinform. 15 (7) (1999)
Victor G. Levitsky, Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay A. Kolchanov
Nucleosomal DNA property database. Bioinform. 15 (7) (1999)
Mikhail P. Ponomarenko, Julia V. Ponomarenko, Alexander E. Kel, Nikolay A. Kolchanov, N. Karas, Edgar Wingender, Heinz Sklenar
Identification of the significant conformational features of functional sites in B-DNA. German Conference on Bioinformatics (1997)