• case-insensitive prefix search: default
  e.g., sig matches "SIGIR" as well as "signal"
• exact word search: append dollar sign ($) to word
  e.g., graph$ matches "graph", but not "graphics"
• boolean and: separate words by space
  e.g., codd model
• boolean or: connect words by pipe symbol (|)
  e.g., graph|network

Update May 7, 2017: Please note that we had to disable the phrase search operator (.) and the boolean not operator (-) due to technical problems. For the time being, phrase search queries will yield regular prefix search result, and search terms preceded by a minus will be interpreted as regular (positive) search terms.

found 28 matches

• 2019
• 
  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): W600-W604 (2019)
• 2017
• 
  Julia V. Ponomarenko, Romina Garrido, Roderic Guigó:
  Ten Simple Rules on How to Organize a Scientific Retreat. PLoS Comput. Biol. 13(2) (2017)
• 
  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)
• 2015
• 
  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): 405-412 (2015)
• 2012
• 
  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): 525-530 (2012)
• 2011
• 
  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: 7 (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): 1164-1170 (2011)
• 2010
• 
  Michael Baitaluk, Julia V. Ponomarenko:
  Semantic integration of data on transcriptional regulation. Bioinform. 26(13): 1651-1661 (2010)
• 
  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: 610 (2010)
• 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)
• 
  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): 513-518 (2008)
• 2006
• 
  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: 341 (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: 126-132
• 2005
• 
  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): 599-620 (2005)
• 2003
• 
  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): 118-121 (2003)
• 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): 225-233 (2002)
• 
  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): 195-199 (2002)
• 
  Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov:
  Building an automated classification of DNA-binding protein domains. ECCB 2002: 192-201
• 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): 284-287 (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): 312-316 (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: 153-160
• 
  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
• 
  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): 205-208 (2000)
• 1999
• 
  Victor G. Levitsky, Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay A. Kolchanov:
  Nucleosomal DNA property database. Bioinform. 15(7): 582-592 (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): 687-703 (1999)
• 
  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): 631-643 (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): 654-668 (1999)
• 1997
• 
  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