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Julia V. Ponomarenko
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2010 – 2019
- 2019
- [j23]Jose Espinosa-Carrasco
, Antonio Hermoso Pulido
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): W600-W604 (2019) - 2017
- [j22]Julia V. Ponomarenko
Ten Simple Rules on How to Organize a Scientific Retreat. PLoS Comput. Biol. 13(2) (2017) - [j21]Carlos Pulido-Quetglas, Estel Aparicio-Prat, Carme Arnan
Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PLoS Comput. Biol. 13(3) (2017) - 2015
- [j20]Randi Vita
The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 43(Database-Issue): 405-412 (2015) - 2012
- [j19]Yohan Kim, Julia V. Ponomarenko
Immune epitope database analysis resource. Nucleic Acids Res. 40(Web-Server-Issue): 525-530 (2012) - 2011
- [j18]Sergey Kozhenkov, Mayya Sedova
BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies. BMC Syst. Biol. 5: 7 (2011) - [j17]Julia V. Ponomarenko
IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res. 39(Database-Issue): 1164-1170 (2011) - 2010
- [j16]Michael Baitaluk, Julia V. Ponomarenko
Semantic integration of data on transcriptional regulation. Bioinform. 26(13): 1651-1661 (2010) - [j15]Sergey Kozhenkov, Yulia Dubinina, Mayya Sedova
BiologicalNetworks 2.0 - an integrative view of genome biology data. BMC Bioinform. 11: 610 (2010)
2000 – 2009
- 2008
- [j14]Julia V. Ponomarenko
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinform. 9 (2008) - [j13]Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 36(Web-Server-Issue): 513-518 (2008) - 2006
- [j12]Randi Vita
Curation of complex, context-dependent immunological data. BMC Bioinform. 7: 341 (2006) - [c5]Alessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Søren Buus, Ward Fleri, R. Kubo, Ole Lund
The Immune Epitope Database and Analysis Resource. PRIB 2006: 126-132 - 2005
- [j11]Julia V. Ponomarenko, Galina Orlova
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): 599-620 (2005) - 2003
- [j10]Julia V. 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): 118-121 (2003) - 2002
- [j9]Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova
Mining DNA sequences to predict sites which mutations cause genetic diseases. Knowl. Based Syst. 15(4): 225-233 (2002) - [j8]Julia V. 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): 195-199 (2002) - [c4]Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov:
Building an automated classification of DNA-binding protein domains. ECCB 2002: 192-201 - 2001
- [j7]Julia V. Ponomarenko
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Res. 29(1): 284-287 (2001) - [j6]Julia V. Ponomarenko
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): 312-316 (2001) - [c3]Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova
Mining Genome Variation to Associate Disease with Transcription Factor Binding Site Alteration. BIBE 2001: 153-160 - [c2]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: 112-117 - 2000
- [j5]Julia V. Ponomarenko
SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucleic Acids Res. 28(1): 205-208 (2000)
1990 – 1999
- 1999
- [j4]Victor G. Levitsky
Nucleosomal DNA property database. Bioinform. 15(7): 582-592 (1999) - [j3]Mikhail P. Ponomarenko, Julia V. Ponomarenko
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. Bioinform. 15(7): 631-643 (1999) - [j2]Julia V. Ponomarenko
Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinform. 15(7): 654-668 (1999) - [j1]Mikhail P. Ponomarenko, Julia V. Ponomarenko
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinform. 15(7): 687-703 (1999) - 1997
- [c1]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: 171
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