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Items: 1 to 50 of 133

1.

Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.

Lin L, McKerrow WH, Richards B, Phonsom C, Lawrence CE.

BMC Bioinformatics. 2018 Mar 5;19(1):82. doi: 10.1186/s12859-018-2078-5.

2.

Predicting RNA hyper-editing with a novel tool when unambiguous alignment is impossible.

McKerrow WH, Savva YA, Rezaei A, Reenan RA, Lawrence CE.

BMC Genomics. 2017 Jul 10;18(1):522. doi: 10.1186/s12864-017-3898-9.

3.

The response of muscle protein synthesis following whole-body resistance exercise is greater following 40 g than 20 g of ingested whey protein.

Macnaughton LS, Wardle SL, Witard OC, McGlory C, Hamilton DL, Jeromson S, Lawrence CE, Wallis GA, Tipton KD.

Physiol Rep. 2016 Aug;4(15). pii: e12893. doi: 10.14814/phy2.12893.

4.

An Integrated Perspective on Phylogenetic Workflows.

Guang A, Zapata F, Howison M, Lawrence CE, Dunn CW.

Trends Ecol Evol. 2016 Feb;31(2):116-126. doi: 10.1016/j.tree.2015.12.007. Epub 2016 Jan 5. Review.

PMID:
26775796
5.

Detecting non-allelic homologous recombination from high-throughput sequencing data.

Parks MM, Lawrence CE, Raphael BJ.

Genome Biol. 2015 Apr 8;16:72. doi: 10.1186/s13059-015-0633-1.

6.

Mast cells promote blood brain barrier breakdown and neutrophil infiltration in a mouse model of focal cerebral ischemia.

McKittrick CM, Lawrence CE, Carswell HV.

J Cereb Blood Flow Metab. 2015 Mar 31;35(4):638-47. doi: 10.1038/jcbfm.2014.239.

7.

Human Hematopoietic Signal peptide-containing Secreted 1 (hHSS1) modulates genes and pathways in glioma: implications for the regulation of tumorigenicity and angiogenesis.

Junes-Gill KS, Lawrence CE, Wheeler CJ, Cordner R, Gill TG, Mar V, Shiri L, Basile LA.

BMC Cancer. 2014 Dec 6;14:920. doi: 10.1186/1471-2407-14-920.

8.

Single low-dose rHuIL-12 safely triggers multilineage hematopoietic and immune-mediated effects.

Gokhale MS, Vainstein V, Tom J, Thomas S, Lawrence CE, Gluzman-Poltorak Z, Siebers N, Basile LA.

Exp Hematol Oncol. 2014 Apr 11;3(1):11. doi: 10.1186/2162-3619-3-11.

9.

Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila.

St Laurent G, Tackett MR, Nechkin S, Shtokalo D, Antonets D, Savva YA, Maloney R, Kapranov P, Lawrence CE, Reenan RA.

Nat Struct Mol Biol. 2013 Nov;20(11):1333-9. doi: 10.1038/nsmb.2675. Epub 2013 Sep 29.

PMID:
24077224
10.

Assessing the validity and reproducibility of genome-scale predictions.

Sugden LA, Tackett MR, Savva YA, Thompson WA, Lawrence CE.

Bioinformatics. 2013 Nov 15;29(22):2844-51. doi: 10.1093/bioinformatics/btt508. Epub 2013 Sep 17.

11.

A cyclic peptide inhibitor of HIF-1 heterodimerization that inhibits hypoxia signaling in cancer cells.

Miranda E, Nordgren IK, Male AL, Lawrence CE, Hoakwie F, Cuda F, Court W, Fox KR, Townsend PA, Packham GK, Eccles SA, Tavassoli A.

J Am Chem Soc. 2013 Jul 17;135(28):10418-25. doi: 10.1021/ja402993u. Epub 2013 Jul 9.

12.

Mast cells and vascular diseases.

Kennedy S, Wu J, Wadsworth RM, Lawrence CE, Maffia P.

Pharmacol Ther. 2013 Apr;138(1):53-65. doi: 10.1016/j.pharmthera.2013.01.001. Epub 2013 Jan 16. Review.

PMID:
23333349
13.

RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences.

Wei D, Alpert LV, Lawrence CE.

Bioinformatics. 2011 Sep 15;27(18):2486-93. doi: 10.1093/bioinformatics/btr421. Epub 2011 Jul 24.

14.

Discovery of tetrahydroisoquinoline (THIQ) derivatives as potent and orally bioavailable LFA-1/ICAM-1 antagonists.

Zhong M, Shen W, Barr KJ, Arbitrario JP, Arkin MR, Bui M, Chen T, Cunningham BC, Evanchik MJ, Hanan EJ, Hoch U, Huen K, Hyde J, Kumer JL, Lac T, Lawrence CE, Martell JR, Oslob JD, Paulvannan K, Prabhu S, Silverman JA, Wright J, Yu CH, Zhu J, Flanagan WM.

Bioorg Med Chem Lett. 2010 Sep 1;20(17):5269-73. doi: 10.1016/j.bmcl.2010.06.145. Epub 2010 Jul 23.

PMID:
20655213
15.

Transmembrane tumor necrosis factor alpha is required for enteropathy and is sufficient to promote parasite expulsion in gastrointestinal helminth infection.

Ierna MX, Scales HE, Mueller C, Lawrence CE.

Infect Immun. 2009 Sep;77(9):3879-85. doi: 10.1128/IAI.01461-08. Epub 2009 Jun 29.

16.

Neither interleukin-4 receptor alpha expression on CD4+ T cells, or macrophages and neutrophils is required for protective immunity to Trichinella spiralis.

Michels CE, Scales HE, Saunders KA, McGowan S, Brombracher F, Alexander J, Lawrence CE.

Immunology. 2009 Sep;128(1 Suppl):e385-94. doi: 10.1111/j.1365-2567.2008.02987.x. Epub 2008 Dec 16.

17.

Exact calculation of distributions on integers, with application to sequence alignment.

Newberg LA, Lawrence CE.

J Comput Biol. 2009 Jan;16(1):1-18. doi: 10.1089/cmb.2008.0137.

18.

The impact of Fc engineering on an anti-CD19 antibody: increased Fcgamma receptor affinity enhances B-cell clearing in nonhuman primates.

Zalevsky J, Leung IW, Karki S, Chu SY, Zhukovsky EA, Desjarlais JR, Carmichael DF, Lawrence CE.

Blood. 2009 Apr 16;113(16):3735-43. doi: 10.1182/blood-2008-10-182048. Epub 2008 Dec 24.

19.

Mast cell production of IL-4 and TNF may be required for protective and pathological responses in gastrointestinal helminth infection.

Ierna MX, Scales HE, Saunders KL, Lawrence CE.

Mucosal Immunol. 2008 Mar;1(2):147-55. doi: 10.1038/mi.2007.16. Epub 2008 Jan 23.

PMID:
19079172
20.

Radon-222 exhalation from open ground on and around a uranium mine in the wet-dry tropics.

Lawrence CE, Akber RA, Bollhöfer A, Martin P.

J Environ Radioact. 2009 Jan;100(1):1-8. doi: 10.1016/j.jenvrad.2008.09.003. Epub 2008 Nov 7.

PMID:
18995934
21.

Discovery of a potent and selective aurora kinase inhibitor.

Oslob JD, Romanowski MJ, Allen DA, Baskaran S, Bui M, Elling RA, Flanagan WM, Fung AD, Hanan EJ, Harris S, Heumann SA, Hoch U, Jacobs JW, Lam J, Lawrence CE, McDowell RS, Nannini MA, Shen W, Silverman JA, Sopko MM, Tangonan BT, Teague J, Yoburn JC, Yu CH, Zhong M, Zimmerman KM, O'Brien T, Lew W.

Bioorg Med Chem Lett. 2008 Sep 1;18(17):4880-4. doi: 10.1016/j.bmcl.2008.07.073. Epub 2008 Jul 24.

PMID:
18678489
22.

Automated mapping of large-scale chromatin structure in ENCODE.

Lian H, Thompson WA, Thurman R, Stamatoyannopoulos JA, Noble WS, Lawrence CE.

Bioinformatics. 2008 Sep 1;24(17):1911-6. doi: 10.1093/bioinformatics/btn335. Epub 2008 Jun 30.

23.

Measuring global credibility with application to local sequence alignment.

Webb-Robertson BJ, McCue LA, Lawrence CE.

PLoS Comput Biol. 2008 May 16;4(5):e1000077. doi: 10.1371/journal.pcbi.1000077.

24.

Using the Gibbs motif sampler to find conserved domains in DNA and protein sequences.

Thompson W, McCue LA, Lawrence CE.

Curr Protoc Bioinformatics. 2005 Jul;Chapter 2:Unit 2.8. doi: 10.1002/0471250953.bi0208s10.

PMID:
18428748
25.

Centroid estimation in discrete high-dimensional spaces with applications in biology.

Carvalho LE, Lawrence CE.

Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3209-14. doi: 10.1073/pnas.0712329105. Epub 2008 Feb 27.

26.

Using the Gibbs Motif Sampler for phylogenetic footprinting.

Thompson W, Conlan S, McCue LA, Lawrence CE.

Methods Mol Biol. 2007;395:403-24.

PMID:
17993688
27.

Effect of target secondary structure on RNAi efficiency.

Shao Y, Chan CY, Maliyekkel A, Lawrence CE, Roninson IB, Ding Y.

RNA. 2007 Oct;13(10):1631-40. Epub 2007 Aug 7.

28.

A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction.

Newberg LA, Thompson WA, Conlan S, Smith TM, McCue LA, Lawrence CE.

Bioinformatics. 2007 Jul 15;23(14):1718-27. Epub 2007 May 8.

29.

The Gibbs Centroid Sampler.

Thompson WA, Newberg LA, Conlan S, McCue LA, Lawrence CE.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W232-7. Epub 2007 May 5.

30.

PhyloScan: identification of transcription factor binding sites using cross-species evidence.

Carmack CS, McCue LA, Newberg LA, Lawrence CE.

Algorithms Mol Biol. 2007 Jan 23;2:1.

31.
32.

Inhibition of autoimmune type 1 diabetes by gastrointestinal helminth infection.

Saunders KA, Raine T, Cooke A, Lawrence CE.

Infect Immun. 2007 Jan;75(1):397-407. Epub 2006 Oct 16.

33.
34.

The relative inefficiency of sequence weights approaches in determining a nucleotide position weight matrix.

Newberg LA, McCue LA, Lawrence CE.

Stat Appl Genet Mol Biol. 2005;4:Article13. Epub 2005 Jun 1.

35.

Mammalian genomes ease location of human DNA functional segments but not their description.

Newberg LA, Lawrence CE.

Stat Appl Genet Mol Biol. 2004;3:Article23. Epub 2004 Sep 30.

36.

Clustering of RNA secondary structures with application to messenger RNAs.

Ding Y, Chan CY, Lawrence CE.

J Mol Biol. 2006 Jun 9;359(3):554-71. Epub 2006 Feb 2.

PMID:
16631786
37.

Contribution of the histone H3 and H4 amino termini to Gcn4p- and Gcn5p-mediated transcription in yeast.

Yu C, Palumbo MJ, Lawrence CE, Morse RH.

J Biol Chem. 2006 Apr 7;281(14):9755-64. Epub 2006 Feb 4.

38.

OX40 interactions in gastrointestinal nematode infection.

Ierna MX, Scales HE, Schwarz H, Bunce C, McIlgorm A, Garside P, Lawrence CE.

Immunology. 2006 Jan;117(1):108-16.

39.

Structure clustering features on the Sfold Web server.

Chan CY, Lawrence CE, Ding Y.

Bioinformatics. 2005 Oct 15;21(20):3926-8. Epub 2005 Aug 18.

PMID:
16109749
40.
41.

Contrasting effects of acute and chronic gastro-intestinal helminth infections on a heterologous immune response in a transgenic adoptive transfer model.

Boitelle A, Di Lorenzo C, Scales HE, Devaney E, Kennedy MW, Garside P, Lawrence CE.

Int J Parasitol. 2005 Jun;35(7):765-75. Epub 2005 Apr 18.

PMID:
15893319
42.

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2099-104. Epub 2005 Jan 31.

43.

Decoding human regulatory circuits.

Thompson W, Palumbo MJ, Wasserman WW, Liu JS, Lawrence CE.

Genome Res. 2004 Oct;14(10A):1967-74.

44.

Effect of inducible costimulator blockade on the pathological and protective immune responses induced by the gastrointestinal helminth Trichinella spiralis.

Scales HE, Ierna MX, Gutierrez-Ramos JC, Coyle AJ, Garside P, Lawrence CE.

Eur J Immunol. 2004 Oct;34(10):2854-62.

45.

Mouse mast cell protease-1 is required for the enteropathy induced by gastrointestinal helminth infection in the mouse.

Lawrence CE, Paterson YY, Wright SH, Knight PA, Miller HR.

Gastroenterology. 2004 Jul;127(1):155-65.

PMID:
15236182
46.

Sfold web server for statistical folding and rational design of nucleic acids.

Ding Y, Chan CY, Lawrence CE.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W135-41.

47.

A statistical sampling algorithm for RNA secondary structure prediction.

Ding Y, Lawrence CE.

Nucleic Acids Res. 2003 Dec 15;31(24):7280-301.

48.

Is there a common mechanism of gastrointestinal nematode expulsion?

Lawrence CE.

Parasite Immunol. 2003 May;25(5):271-81. Review.

49.

Comparative analyses of multi-species sequences from targeted genomic regions.

Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED.

Nature. 2003 Aug 14;424(6950):788-93.

PMID:
12917688
50.

Gibbs Recursive Sampler: finding transcription factor binding sites.

Thompson W, Rouchka EC, Lawrence CE.

Nucleic Acids Res. 2003 Jul 1;31(13):3580-5.

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