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Results: 1 to 20 of 35

1.

Defining functional DNA elements in the human genome.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review.

PMID:
24753594
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities.

Risk BA, Edwards NJ, Giddings MC.

J Proteome Res. 2013 Sep 6;12(9):4240-7. doi: 10.1021/pr400286p. Epub 2013 Aug 8.

PMID:
23875887
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Comparative genome analysis of ciprofloxacin-resistant Pseudomonas aeruginosa reveals genes within newly identified high variability regions associated with drug resistance development.

Su HC, Khatun J, Kanavy DM, Giddings MC.

Microb Drug Resist. 2013 Dec;19(6):428-36. doi: 10.1089/mdr.2012.0258. Epub 2013 Jun 29.

PMID:
23808957
[PubMed - indexed for MEDLINE]
4.

Peppy: proteogenomic search software.

Risk BA, Spitzer WJ, Giddings MC.

J Proteome Res. 2013 Jun 7;12(6):3019-25. doi: 10.1021/pr400208w. Epub 2013 May 6.

PMID:
23614390
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Agent-based modeling of competence phenotype switching in Bacillus subtilis.

Stiegelmeyer SM, Giddings MC.

Theor Biol Med Model. 2013 Apr 3;10:23. doi: 10.1186/1742-4682-10-23.

PMID:
23551850
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions.

Khatun J, Yu Y, Wrobel JA, Risk BA, Gunawardena HP, Secrest A, Spitzer WJ, Xie L, Wang L, Chen X, Giddings MC.

BMC Genomics. 2013 Feb 28;14:141. doi: 10.1186/1471-2164-14-141.

PMID:
23448259
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

GOFAST: an integrated approach for efficient and comprehensive membrane proteome analysis.

Yu Y, Xie L, Gunawardena HP, Khatun J, Maier C, Spitzer W, Leerkes M, Giddings MC, Chen X.

Anal Chem. 2012 Nov 6;84(21):9008-14. doi: 10.1021/ac300134e. Epub 2012 Oct 25.

PMID:
23030679
[PubMed - indexed for MEDLINE]
8.

Long noncoding RNAs are rarely translated in two human cell lines.

Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE Jr, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, Lipovich L.

Genome Res. 2012 Sep;22(9):1646-57. doi: 10.1101/gr.134767.111.

PMID:
22955977
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

PMID:
22955620
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data.

Jefferys SR, Giddings MC.

Bioinformatics. 2011 Mar 15;27(6):844-52. doi: 10.1093/bioinformatics/btr027.

PMID:
21389073
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Automated data integration and determination of posttranslational modifications with the protein inference engine.

Jefferys SR, Giddings MC.

Methods Mol Biol. 2011;694:255-90. doi: 10.1007/978-1-60761-977-2_17.

PMID:
21082440
[PubMed - indexed for MEDLINE]
12.

The development of ciprofloxacin resistance in Pseudomonas aeruginosa involves multiple response stages and multiple proteins.

Su HC, Ramkissoon K, Doolittle J, Clark M, Khatun J, Secrest A, Wolfgang MC, Giddings MC.

Antimicrob Agents Chemother. 2010 Nov;54(11):4626-35. doi: 10.1128/AAC.00762-10. Epub 2010 Aug 9.

PMID:
20696867
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

An agent-based model of signal transduction in bacterial chemotaxis.

Miller J, Parker M, Bourret RB, Giddings MC.

PLoS One. 2010 May 13;5(5):e9454. doi: 10.1371/journal.pone.0009454.

PMID:
20485527
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Ultra-Structure database design methodology for managing systems biology data and analyses.

Maier CW, Long JG, Hemminger BM, Giddings MC.

BMC Bioinformatics. 2009 Aug 19;10:254. doi: 10.1186/1471-2105-10-254.

PMID:
19691849
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA.

Wilkinson KA, Vasa SM, Deigan KE, Mortimer SA, Giddings MC, Weeks KM.

RNA. 2009 Jul;15(7):1314-21. doi: 10.1261/rna.1536209. Epub 2009 May 20.

PMID:
19458034
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis.

Vasa SM, Guex N, Wilkinson KA, Weeks KM, Giddings MC.

RNA. 2008 Oct;14(10):1979-90. doi: 10.1261/rna.1166808. Epub 2008 Sep 4.

PMID:
18772246
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

Wilkinson KA, Gorelick RJ, Vasa SM, Guex N, Rein A, Mathews DH, Giddings MC, Weeks KM.

PLoS Biol. 2008 Apr 29;6(4):e96. doi: 10.1371/journal.pbio.0060096.

PMID:
18447581
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Using GFS to identify encoding genomic loci from protein mass spectral data.

Holmes MR, Giddings MC.

Curr Protoc Bioinformatics. 2008 Mar;Chapter 13:Unit 13.9. doi: 10.1002/0471250953.bi1309s21.

PMID:
18428684
[PubMed - indexed for MEDLINE]
19.

On the process of becoming a great scientist.

Giddings MC.

PLoS Comput Biol. 2008 Feb;4(2):e33. doi: 10.1371/journal.pcbi.0040033. No abstract available.

PMID:
18282088
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification.

Khatun J, Hamlett E, Giddings MC.

Bioinformatics. 2008 Mar 1;24(5):674-81. doi: 10.1093/bioinformatics/btn011. Epub 2008 Jan 10.

PMID:
18187442
[PubMed - indexed for MEDLINE]
Free PMC Article

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