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Results: 1 to 20 of 32

1.

A quantitative atlas of polyadenylation in five mammals.

Derti A, Garrett-Engele P, Macisaac KD, Stevens RC, Sriram S, Chen R, Rohl CA, Johnson JM, Babak T.

Genome Res. 2012 Jun;22(6):1173-83. doi: 10.1101/gr.132563.111. Epub 2012 Mar 27.

PMID:
22454233
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.

Babak T, Garrett-Engele P, Armour CD, Raymond CK, Keller MP, Chen R, Rohl CA, Johnson JM, Attie AD, Fraser HB, Schadt EE.

BMC Genomics. 2010 Aug 13;11:473. doi: 10.1186/1471-2164-11-473.

PMID:
20707912
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification.

Castle JC, Armour CD, Löwer M, Haynor D, Biery M, Bouzek H, Chen R, Jackson S, Johnson JM, Rohl CA, Raymond CK.

PLoS One. 2010 Jul 26;5(7):e11779. doi: 10.1371/journal.pone.0011779.

PMID:
20668672
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.

Castle JC, Biery M, Bouzek H, Xie T, Chen R, Misura K, Jackson S, Armour CD, Johnson JM, Rohl CA, Raymond CK.

BMC Genomics. 2010 Apr 16;11:244. doi: 10.1186/1471-2164-11-244.

PMID:
20398377
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis.

Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, Rohl CA, Johnson JM, Raymond CK.

Nat Methods. 2009 Sep;6(9):647-9. doi: 10.1038/nmeth.1360. Epub 2009 Aug 9.

PMID:
19668204
[PubMed - indexed for MEDLINE]
6.

Definition, conservation and epigenetics of housekeeping and tissue-enriched genes.

She X, Rohl CA, Castle JC, Kulkarni AV, Johnson JM, Chen R.

BMC Genomics. 2009 Jun 17;10:269. doi: 10.1186/1471-2164-10-269.

PMID:
19534766
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Pokefind: a novel topological filter for use with protein structure prediction.

Khatib F, Rohl CA, Karplus K.

Bioinformatics. 2009 Jun 15;25(12):i281-8. doi: 10.1093/bioinformatics/btp198.

PMID:
19478000
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Mapping the genetic architecture of gene expression in human liver.

Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R.

PLoS Biol. 2008 May 6;6(5):e107. doi: 10.1371/journal.pbio.0060107.

PMID:
18462017
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Rapid knot detection and application to protein structure prediction.

Khatib F, Weirauch MT, Rohl CA.

Bioinformatics. 2006 Jul 15;22(14):e252-9.

PMID:
16873480
[PubMed - indexed for MEDLINE]
Free Article
10.

Physically realistic homology models built with ROSETTA can be more accurate than their templates.

Misura KM, Chivian D, Rohl CA, Kim DE, Baker D.

Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5361-6. Epub 2006 Mar 27.

PMID:
16567638
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Prediction of CASP6 structures using automated Robetta protocols.

Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D.

Proteins. 2005;61 Suppl 7:157-66.

PMID:
16187358
[PubMed - indexed for MEDLINE]
12.

Protein structure estimation from minimal restraints using Rosetta.

Rohl CA.

Methods Enzymol. 2005;394:244-60.

PMID:
15808223
[PubMed - indexed for MEDLINE]
13.

Modeling structurally variable regions in homologous proteins with rosetta.

Rohl CA, Strauss CE, Chivian D, Baker D.

Proteins. 2004 May 15;55(3):656-77.

PMID:
15103629
[PubMed - indexed for MEDLINE]
14.

Protein structure prediction using Rosetta.

Rohl CA, Strauss CE, Misura KM, Baker D.

Methods Enzymol. 2004;383:66-93. No abstract available.

PMID:
15063647
[PubMed]
15.

Automated prediction of CASP-5 structures using the Robetta server.

Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D.

Proteins. 2003;53 Suppl 6:524-33.

PMID:
14579342
[PubMed - indexed for MEDLINE]
16.

Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.

Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss CE, Baker D.

Proteins. 2003;53 Suppl 6:457-68.

PMID:
14579334
[PubMed - indexed for MEDLINE]
17.

An improved protein decoy set for testing energy functions for protein structure prediction.

Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D.

Proteins. 2003 Oct 1;53(1):76-87.

PMID:
12945051
[PubMed - indexed for MEDLINE]
18.

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.

Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D.

J Mol Biol. 2003 Aug 1;331(1):281-99.

PMID:
12875852
[PubMed - indexed for MEDLINE]
19.

Circular dichroism spectra of short, fixed-nucleus alanine helices.

Chin DH, Woody RW, Rohl CA, Baldwin RL.

Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15416-21. Epub 2002 Nov 11.

PMID:
12427967
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

De novo prediction of three-dimensional structures for major protein families.

Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D.

J Mol Biol. 2002 Sep 6;322(1):65-78.

PMID:
12215415
[PubMed - indexed for MEDLINE]

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