Julia V. Ponomarenko

	2008
19		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 Bioinformatics 9: (2008)
18		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 Research 36(Web-Server-Issue): 513-518 (2008)
	2006
17		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
16		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 Bioinformatics 7: 341 (2006)
	2005
15		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. International Journal on Artificial Intelligence Tools 14(4): 599-620 (2005)
	2003
14		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 Research 31(1): 118-121 (2003)
	2002
13		Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov: Building an automated classification of DNA-binding protein domains. ECCB 2002: 192-201
12		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)
11		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 Research 30(1): 195-199 (2002)
	2001
10		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
9		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
8		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 Research 29(1): 284-287 (2001)
7		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 Research 29(1): 312-316 (2001)
	2000
6		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 Research 28(1): 205-208 (2000)
	1999
5		Victor G. Levitsky, Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay A. Kolchanov: Nucleosomal DNA property database. Bioinformatics 15(7): 582-592 (1999)
4		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. Bioinformatics 15(7): 631-643 (1999)
3		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. Bioinformatics 15(7): 654-668 (1999)
2		Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay L. Podkolodny, L. K. Savinkova, Nikolay A. Kolchanov, G. Christian Overton: Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinformatics 15(7): 687-703 (1999)
	1997
1		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

Coauthor Index

1	John E. Beaver	[18]
2	Philip E. Bourne	[13] [16] [17] [18] [19]
3	Huynh-Hoa Bui	[16] [17] [18] [19]
4	Søren Buus	[17] [18]
5	Romulo de Castro Jr.	[16]
6	Russell K. Chan	[16]
7	Ward Fleri	[16] [17]
8	Oleg N. Fokin	[7] [9] [10] [12] [14]
9	Sune Frankild	[18]
10	Anatoly S. Frolov	[2] [3] [4] [5] [6] [7] [8] [11] [14]
11	Dagmara P. Furman	[8]
12	Nicholas Fusseder	[19]
13	Mikhail S. Gelfand	[11]
14	Elena Gorshkova	[9] [10] [12] [14]
15	Jason Greenbaum	[18]
16	Howard Grey	[16]
17	Pernille Haste-Andersen	[18]
18	N. Karas	[1]
19	Alexander E. Kel	[1]
20	Yohan Kim	[18]
21	Nikolay A. Kolchanov	[1] [2] [3] [4] [5] [6] [8]
22	R. Kubo	[17]
23	Sergey V. Lavryushev	[6] [7]
24	Zoya B. Levashova	[7]
25	Victor G. Levitsky	[5]
26	Wei Li	[19]
27	Ole Lund	[17] [18]
28	Claus Lundegaard	[18]
29	Tatyana I. Merkulova	[7] [9] [10] [12] [14] [15]
30	John Mokili	[16]
31	D. Nemazee	[17]
32	Morten Nielsen	[18]
33	Galina Orlova	[6] [7] [8] [9] [10] [11] [12] [14] [15]
34	G. Christian Overton	[2] [3] [4]
35	Björn Peters	[16] [17] [18] [19]
36	Olga A. Podkolodnaya	[4]
37	Nikolay L. Podkolodny	[2] [8]
38	Mikhail P. Ponomarenko	[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [14] [15]
39	Nima Salimi	[16]
40	Akinori Sarai	[7] [8]
41	Muthu Sathiamurthy	[16] [17]
42	L. K. Savinkova	[2]
43	Alessandro Sette	[16] [17] [18] [19]
44	Ilya N. Shindyalov	[13]
45	John Sidney	[16] [17]
46	Heinz Sklenar	[1]
47	Scott Stewart	[16] [17]
48	Vadim P. Valuev	[14]
49	Gennady V. Vasiliev	[7] [15]
50	Kerrie Vaughan	[16]
51	Randi Vita	[16]
52	Denis G. Vorobiev	[3] [4]
53	Peng Wang	[18]
54	Scott Way	[16] [17]
55	Stephen S. Wilson	[16] [17]
56	Edgar Wingender	[1]
57	Laura Zarebski	[16]
58	Qing Zhang	[18]
59	Zhanyang Zhu	[18]
60	Svetlana V. Zybova	[6]