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 (German Conference on Bioinformatics, 1997)

Nucleosomal DNA property database. - Victor G. Levitsky; Mikhail P. Ponomarenko; Julia V. Ponomarenko; Anatoly S. Frolov; Nikolay A. Kolchanov (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)

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)

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)

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)

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 (BIBE, 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 (German Conference on Bioinformatics, 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)

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)

Building an automated classification of DNA-binding protein domains. - Julia V. Ponomarenko; Philip E. Bourne; Ilya N. Shindyalov (ECCB, 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)

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)

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)

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)

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; et al. (PRIB, 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.; et al. (BMC Bioinform., 2006)

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)

Immune epitope database analysis resource (IEDB-AR). - Qing Zhang; Peng Wang 014; Yohan Kim; Pernille Haste-Andersen; John E. Beaver; Philip E. Bourne; Huynh-Hoa Bui; Søren Buus; Sune Frankild; Jason Greenbaum; Ole Lund; Claus Lundegaard; et al. (Nucleic Acids Res., 2008)

Semantic integration of data on transcriptional regulation. - Michael Baitaluk; Julia V. Ponomarenko (Bioinform., 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)

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)

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)

Immune epitope database analysis resource. - Yohan Kim; Julia V. Ponomarenko; Zhanyang Zhu; Dorjee Tamang; Peng Wang 014; Jason Greenbaum; Claus Lundegaard; Alessandro Sette; Ole Lund; Philip E. Bourne; Morten Nielsen 001; Bjoern Peters (Nucleic Acids Res., 2012)

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)

Ten Simple Rules on How to Organize a Scientific Retreat. - Julia V. Ponomarenko; Romina Garrido; Roderic Guigó (PLoS Comput. Biol., 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)

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)