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Results: 1 to 20 of 39

References for PMC Articles for PubMed (Select 21693021)

1.

Towards a knowledge-based Human Protein Atlas.

Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Björling L, Ponten F.

Nat Biotechnol. 2010 Dec;28(12):1248-50. doi: 10.1038/nbt1210-1248. No abstract available.

PMID:
21139605
2.

Recent advances in B-cell epitope prediction methods.

El-Manzalawy Y, Honavar V.

Immunome Res. 2010 Nov 3;6 Suppl 2:S2. doi: 10.1186/1745-7580-6-S2-S2.

3.

The immune epitope database 2.0.

Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B.

Nucleic Acids Res. 2010 Jan;38(Database issue):D854-62. doi: 10.1093/nar/gkp1004. Epub 2009 Nov 11.

4.

Unlocking the secrets of the genome.

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium.

Nature. 2009 Jun 18;459(7249):927-30. doi: 10.1038/459927a. No abstract available.

5.

COBEpro: a novel system for predicting continuous B-cell epitopes.

Sweredoski MJ, Baldi P.

Protein Eng Des Sel. 2009 Mar;22(3):113-20. doi: 10.1093/protein/gzn075. Epub 2008 Dec 10.

6.

Predicting linear B-cell epitopes using string kernels.

El-Manzalawy Y, Dobbs D, Honavar V.

J Mol Recognit. 2008 Jul-Aug;21(4):243-55. doi: 10.1002/jmr.893.

7.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

8.

Prediction of linear B-cell epitopes using amino acid pair antigenicity scale.

Chen J, Liu H, Yang J, Chou KC.

Amino Acids. 2007 Sep;33(3):423-8. Epub 2007 Jan 26.

PMID:
17252308
9.

New developments in the InterPro database.

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8.

10.
11.

Prediction of residues in discontinuous B-cell epitopes using protein 3D structures.

Haste Andersen P, Nielsen M, Lund O.

Protein Sci. 2006 Nov;15(11):2558-67. Epub 2006 Sep 25.

12.
13.

Improved method for predicting linear B-cell epitopes.

Larsen JE, Lund O, Nielsen M.

Immunome Res. 2006 Apr 24;2:2.

14.

Machine learning approaches for prediction of linear B-cell epitopes on proteins.

Söllner J, Mayer B.

J Mol Recognit. 2006 May-Jun;19(3):200-8.

PMID:
16598694
15.

SCRATCH: a protein structure and structural feature prediction server.

Cheng J, Randall AZ, Sweredoski MJ, Baldi P.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W72-6.

16.

CEP: a conformational epitope prediction server.

Kulkarni-Kale U, Bhosle S, Kolaskar AS.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W168-71.

17.

Bcipep: a database of B-cell epitopes.

Saha S, Bhasin M, Raghava GP.

BMC Genomics. 2005 May 29;6:79.

18.

Benchmarking B cell epitope prediction: underperformance of existing methods.

Blythe MJ, Flower DR.

Protein Sci. 2005 Jan;14(1):246-8. Epub 2004 Dec 2.

19.

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Edgar RC.

Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. Print 2004.

20.

Modeller: generation and refinement of homology-based protein structure models.

Fiser A, Sali A.

Methods Enzymol. 2003;374:461-91. No abstract available.

PMID:
14696385
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