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Items: 43

1.

Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools.

Espinosa-Carrasco J, Erb I, Hermoso Pulido T, Ponomarenko J, Dierssen M, Notredame C.

iScience. 2018 Oct 26;9:244-257. doi: 10.1016/j.isci.2018.10.023. [Epub ahead of print]

2.

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.

Tapial J, Ha KCH, Sterne-Weiler T, Gohr A, Braunschweig U, Hermoso-Pulido A, Quesnel-Vallières M, Permanyer J, Sodaei R, Marquez Y, Cozzuto L, Wang X, Gómez-Velázquez M, Rayon T, Manzanares M, Ponomarenko J, Blencowe BJ, Irimia M.

Genome Res. 2017 Oct;27(10):1759-1768. doi: 10.1101/gr.220962.117. Epub 2017 Aug 30.

3.

The microbiome in respiratory medicine: current challenges and future perspectives.

Faner R, Sibila O, Agustí A, Bernasconi E, Chalmers JD, Huffnagle GB, Manichanh C, Molyneaux PL, Paredes R, Pérez Brocal V, Ponomarenko J, Sethi S, Dorca J, Monsó E.

Eur Respir J. 2017 Apr 12;49(4). pii: 1602086. doi: 10.1183/13993003.02086-2016. Print 2017 Apr. Review.

4.

A De Novo Nonsense Mutation in MAGEL2 in a Patient Initially Diagnosed as Opitz-C: Similarities Between Schaaf-Yang and Opitz-C Syndromes.

Urreizti R, Cueto-Gonzalez AM, Franco-Valls H, Mort-Farre S, Roca-Ayats N, Ponomarenko J, Cozzuto L, Company C, Bosio M, Ossowski S, Montfort M, Hecht J, Tizzano EF, Cormand B, Vilageliu L, Opitz JM, Neri G, Grinberg D, Balcells S.

Sci Rep. 2017 Mar 10;7:44138. doi: 10.1038/srep44138.

5.

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, Ponomarenko J, Guigo R, Johnson R.

PLoS Comput Biol. 2017 Mar 2;13(3):e1005341. doi: 10.1371/journal.pcbi.1005341. eCollection 2017 Mar.

6.

Ten Simple Rules on How to Organize a Scientific Retreat.

Ponomarenko J, Garrido R, Guigó R.

PLoS Comput Biol. 2017 Feb 2;13(2):e1005344. doi: 10.1371/journal.pcbi.1005344. eCollection 2017 Feb. No abstract available.

7.

Analysis of Human RSV Immunity at the Molecular Level: Learning from the Past and Present.

Vaughan K, Ponomarenko J, Peters B, Sette A.

PLoS One. 2015 May 22;10(5):e0127108. doi: 10.1371/journal.pone.0127108. eCollection 2015. Review.

8.

Conservancy of mAb Epitopes in Ebolavirus Glycoproteins of Previous and 2014 Outbreaks.

Ponomarenko J, Vaughan K, Sette A, Maurer-Stroh S.

PLoS Curr. 2014 Nov 3;6. pii: ecurrents.outbreaks.f1a7028a13ce1c5f0bdbb4b0cc0b919b. doi: 10.1371/currents.outbreaks.f1a7028a13ce1c5f0bdbb4b0cc0b919b.

9.

The immune epitope database (IEDB) 3.0.

Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B.

Nucleic Acids Res. 2015 Jan;43(Database issue):D405-12. doi: 10.1093/nar/gku938. Epub 2014 Oct 9.

10.

Elucidation of antioxidant properties of wood bark derived saturated diarylheptanoids: a comprehensive (DFT-supported) understanding.

Ponomarenko J, Trouillas P, Martin N, Dizhbite T, Krasilnikova J, Telysheva G.

Phytochemistry. 2014 Jul;103:178-187. doi: 10.1016/j.phytochem.2014.03.010. Epub 2014 Apr 3.

PMID:
24703933
11.

IκBε is a key regulator of B cell expansion by providing negative feedback on cRel and RelA in a stimulus-specific manner.

Alves BN, Tsui R, Almaden J, Shokhirev MN, Davis-Turak J, Fujimoto J, Birnbaum H, Ponomarenko J, Hoffmann A.

J Immunol. 2014 Apr 1;192(7):3121-32. doi: 10.4049/jimmunol.1302351. Epub 2014 Mar 3.

12.

An integrative approach to inferring gene regulatory module networks.

Baitaluk M, Kozhenkov S, Ponomarenko J.

PLoS One. 2012;7(12):e52836. doi: 10.1371/journal.pone.0052836. Epub 2012 Dec 20.

13.

Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways.

Shih VF, Davis-Turak J, Macal M, Huang JQ, Ponomarenko J, Kearns JD, Yu T, Fagerlund R, Asagiri M, Zuniga EI, Hoffmann A.

Nat Immunol. 2012 Dec;13(12):1162-70. doi: 10.1038/ni.2446. Epub 2012 Oct 21.

14.

Immune epitope database analysis resource.

Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W525-30. doi: 10.1093/nar/gks438. Epub 2012 May 18.

15.

IntegromeDB: an integrated system and biological search engine.

Baitaluk M, Kozhenkov S, Dubinina Y, Ponomarenko J.

BMC Genomics. 2012 Jan 19;13:35. doi: 10.1186/1471-2164-13-35.

16.

The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50.

Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A.

Sci Signal. 2011 Feb 22;4(161):ra11. doi: 10.1126/scisignal.2001501.

17.

BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies.

Kozhenkov S, Sedova M, Dubinina Y, Gupta A, Ray A, Ponomarenko J, Baitaluk M.

BMC Syst Biol. 2011 Jan 14;5:7. doi: 10.1186/1752-0509-5-7.

18.

BiologicalNetworks 2.0--an integrative view of genome biology data.

Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M.

BMC Bioinformatics. 2010 Dec 29;11:610. doi: 10.1186/1471-2105-11-610.

19.

IEDB-3D: structural data within the immune epitope database.

Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1164-70. doi: 10.1093/nar/gkq888. Epub 2010 Oct 28.

20.

Semantic integration of data on transcriptional regulation.

Baitaluk M, Ponomarenko J.

Bioinformatics. 2010 Jul 1;26(13):1651-61. doi: 10.1093/bioinformatics/btq231. Epub 2010 Apr 28.

21.

Limitations of Ab initio predictions of peptide binding to MHC class II molecules.

Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B.

PLoS One. 2010 Feb 17;5(2):e9272. doi: 10.1371/journal.pone.0009272.

22.

Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population.

Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B.

Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20365-70. doi: 10.1073/pnas.0911580106. Epub 2009 Nov 16.

23.

ElliPro: a new structure-based tool for the prediction of antibody epitopes.

Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B.

BMC Bioinformatics. 2008 Dec 2;9:514. doi: 10.1186/1471-2105-9-514.

24.

Immune epitope database analysis resource (IEDB-AR).

Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W513-8. doi: 10.1093/nar/gkn254. Epub 2008 May 31.

25.
27.

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools.

Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B.

J Mol Recognit. 2007 Mar-Apr;20(2):75-82. Review.

PMID:
17205610
28.

Curation of complex, context-dependent immunological data.

Vita R, Vaughan K, Zarebski L, Salimi N, Fleri W, Grey H, Sathiamurthy M, Mokili J, Bui HH, Bourne PE, Ponomarenko J, de Castro R Jr, Chan RK, Sidney J, Wilson SS, Stewart S, Way S, Peters B, Sette A.

BMC Bioinformatics. 2006 Jul 12;7:341.

29.

The design and implementation of the immune epitope database and analysis resource.

Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger SP, Stewart S, Surko P, Way S, Wilson S, Sette A.

Immunogenetics. 2005 Jun;57(5):326-36. Epub 2005 May 14.

30.

The immune epitope database and analysis resource: from vision to blueprint.

Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A.

PLoS Biol. 2005 Mar;3(3):e91. No abstract available.

31.

Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.

Ponomarenko JV, Bourne PE, Shindyalov IN.

Proteins. 2005 Mar 1;58(4):855-65.

PMID:
15645518
32.

rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation.

Ponomarenko JV, Merkulova TI, Orlova GV, Fokin ON, Gorshkova EV, Frolov AS, Valuev VP, Ponomarenko MP.

Nucleic Acids Res. 2003 Jan 1;31(1):118-21.

33.

Building an automated classification of DNA-binding protein domains.

Ponomarenko JV, Bourne PE, Shindyalov IN.

Bioinformatics. 2002;18 Suppl 2:S192-201.

PMID:
12386003
34.

rSNP_Guide: an integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites.

Ponomarenko JV, Orlova GV, Merkulova TI, Gorshkova EV, Fokin ON, Vasiliev GV, Frolov AS, Ponomarenko MP.

Hum Mutat. 2002 Oct;20(4):239-48. Review.

PMID:
12325018
35.
36.

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations.

Ponomarenko JV, Merkulova TI, Vasiliev GV, Levashova ZB, Orlova GV, Lavryushev SV, Fokin ON, Ponomarenko MP, Frolov AS, Sarai A.

Nucleic Acids Res. 2001 Jan 1;29(1):312-6.

37.

ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another.

Ponomarenko JV, Furman DP, Frolov AS, Podkolodny NL, Orlova GV, Ponomarenko MP, Kolchanov NA, Sarai A.

Nucleic Acids Res. 2001 Jan 1;29(1):284-7.

38.

SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation.

Ponomarenko JV, Orlova GV, Ponomarenko MP, Lavryushev SV, Frolov AS, Zybova SV, Kolchanov NA.

Nucleic Acids Res. 2000 Jan 1;28(1):205-8.

39.

Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.

Ponomarenko MP, Ponomarenko JV, Frolov AS, Podkolodny NL, Savinkova LK, Kolchanov NA, Overton GC.

Bioinformatics. 1999 Jul-Aug;15(7-8):687-703.

PMID:
10487875
40.

Conformational and physicochemical DNA features specific for transcription factor binding sites.

Ponomarenko JV, Ponomarenko MP, Frolov AS, Vorobyev DG, Overton GC, Kolchanov NA.

Bioinformatics. 1999 Jul-Aug;15(7-8):654-68.

PMID:
10487873
41.

Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.

Ponomarenko MP, Ponomarenko JV, Frolov AS, Podkolodnaya OA, Vorobyev DG, Kolchanov NA, Overton GC.

Bioinformatics. 1999 Jul-Aug;15(7-8):631-43.

PMID:
10487871
42.

Nucleosomal DNA property database.

Levitsky VG, Ponomarenko MP, Ponomarenko JV, Frolov AS, Kolchanov NA.

Bioinformatics. 1999 Jul-Aug;15(7-8):582-92.

PMID:
10487866
43.

Search for DNA conformational features for functional sites. Investigation of the TATA box.

Ponomarenko MP, Ponomarenko JV, Kel AE, Kolchanov NA.

Pac Symp Biocomput. 1997:340-51.

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