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Items: 1 to 20 of 54

1.

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW.

Science. 2008 Sep 26;321(5897):1801-6. doi: 10.1126/science.1164368. Epub 2008 Sep 4.

2.

An integrated genomic analysis of human glioblastoma multiforme.

Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW.

Science. 2008 Sep 26;321(5897):1807-12. doi: 10.1126/science.1164382. Epub 2008 Sep 4.

3.

Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA.

Cell. 2008 Sep 5;134(5):866-76. doi: 10.1016/j.cell.2008.08.012. Epub 2008 Aug 21.

4.

Raster3D: photorealistic molecular graphics.

Merritt EA, Bacon DJ.

Methods Enzymol. 1997;277:505-24. No abstract available.

PMID:
18488322
5.

Comparative protein structure modeling using MODELLER.

Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A.

Curr Protoc Protein Sci. 2007 Nov;Chapter 2:Unit 2.9. doi: 10.1002/0471140864.ps0209s50.

PMID:
18429317
6.

Comparative protein structure modeling using Modeller.

Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A.

Curr Protoc Bioinformatics. 2006 Oct;Chapter 5:Unit-5.6. doi: 10.1002/0471250953.bi0506s15.

7.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.

Nucleic Acids Res. 2008 Jan;36(Database issue):D25-30. Epub 2007 Dec 11.

8.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21. Epub 2007 Nov 27.

9.

ToxoDB: an integrated Toxoplasma gondii database resource.

Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ Jr, Wang H, Brunk BP.

Nucleic Acids Res. 2008 Jan;36(Database issue):D553-6. Epub 2007 Nov 14.

10.

Ensembl 2008.

Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.

Nucleic Acids Res. 2008 Jan;36(Database issue):D707-14. Epub 2007 Nov 13.

11.

Host pathogen protein interactions predicted by comparative modeling.

Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A.

Protein Sci. 2007 Dec;16(12):2585-96. Epub 2007 Oct 26.

12.

Draft genome of the filarial nematode parasite Brugia malayi.

Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL.

Science. 2007 Sep 21;317(5845):1756-60.

13.

Structure-based activity prediction for an enzyme of unknown function.

Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM.

Nature. 2007 Aug 16;448(7155):775-9. Epub 2007 Jul 1.

14.

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.

Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S4.

15.

DBAli tools: mining the protein structure space.

Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W393-7. Epub 2007 May 3.

16.
17.

A composite score for predicting errors in protein structure models.

Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA.

Protein Sci. 2006 Jul;15(7):1653-66. Epub 2006 Jun 2.

18.

Protein complex compositions predicted by structural similarity.

Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS.

Nucleic Acids Res. 2006 May 31;34(10):2943-52. Print 2006.

19.

The UCSC Known Genes.

Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D.

Bioinformatics. 2006 May 1;22(9):1036-46. Epub 2006 Feb 24.

PMID:
16500937
20.

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.

Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC.

Biochemistry. 2006 Feb 28;45(8):2545-55.

PMID:
16489747

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