Julia V. Ponomarenko

28 papers C 2Journal 23Unranked 3

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