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Items: 1 to 50 of 69

1.

MiR-19b non-canonical binding is directed by HuR and confers chemosensitivity through regulation of P-glycoprotein in breast cancer.

Thorne JL, Battaglia S, Baxter DE, Hayes JL, Hutchinson SA, Jana S, Millican-Slater RA, Smith L, Teske MC, Wastall LM, Hughes TA.

Biochim Biophys Acta Gene Regul Mech. 2018 Nov;1861(11):996-1006. doi: 10.1016/j.bbagrm.2018.08.005. Epub 2018 Aug 31.

PMID:
30343695
2.

Exploring the biophysical properties of phytosterols in the plasma membrane for novel cancer prevention strategies.

Fakih O, Sanver D, Kane D, Thorne JL.

Biochimie. 2018 Oct;153:150-161. doi: 10.1016/j.biochi.2018.04.028. Epub 2018 May 3. Review.

PMID:
29730298
3.

Information Criteria for Comparing Partition Schemes.

Seo TK, Thorne JL.

Syst Biol. 2018 Jul 1;67(4):616-632. doi: 10.1093/sysbio/syx097.

PMID:
29309694
4.

Grouping substitution types into different relaxed molecular clocks.

Lee HJ, Kishino H, Rodrigue N, Thorne JL.

Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). pii: 20150141. doi: 10.1098/rstb.2015.0141.

5.

A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast.

Ji X, Griffing A, Thorne JL.

Mol Biol Evol. 2016 Sep;33(9):2469-76. doi: 10.1093/molbev/msw114. Epub 2016 Jun 13.

PMID:
27297467
6.

Chemotherapy induces Notch1-dependent MRP1 up-regulation, inhibition of which sensitizes breast cancer cells to chemotherapy.

Kim B, Stephen SL, Hanby AM, Horgan K, Perry SL, Richardson J, Roundhill EA, Valleley EM, Verghese ET, Williams BJ, Thorne JL, Hughes TA.

BMC Cancer. 2015 Sep 11;15:634. doi: 10.1186/s12885-015-1625-y.

7.

Roles of solvent accessibility and gene expression in modeling protein sequence evolution.

Wang K, Yu S, Ji X, Lakner C, Griffing A, Thorne JL.

Evol Bioinform Online. 2015 Apr 29;11:85-96. doi: 10.4137/EBO.S22911. eCollection 2015.

8.

Relaxing the Molecular Clock to Different Degrees for Different Substitution Types.

Lee HJ, Rodrigue N, Thorne JL.

Mol Biol Evol. 2015 Aug;32(8):1948-61. doi: 10.1093/molbev/msv099. Epub 2015 Apr 29.

9.

Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

Lassiter ES, Russ C, Nusbaum C, Zeng Q, Saville AC, Olarte RA, Carbone I, Hu CH, Seguin-Orlando A, Samaniego JA, Thorne JL, Ristaino JB.

Curr Genet. 2015 Nov;61(4):567-77. doi: 10.1007/s00294-015-0480-3. Epub 2015 Mar 10.

10.

Nuclear receptors and the Warburg effect in cancer.

Thorne JL, Campbell MJ.

Int J Cancer. 2015 Oct 1;137(7):1519-27. doi: 10.1002/ijc.29012. Epub 2014 Jun 16. Review.

11.

Cooperative behavior of the nuclear receptor superfamily and its deregulation in prostate cancer.

Long MD, Thorne JL, Russell J, Battaglia S, Singh PK, Sucheston-Campbell LE, Campbell MJ.

Carcinogenesis. 2014 Feb;35(2):262-71. doi: 10.1093/carcin/bgt334. Epub 2013 Oct 8.

12.

MiR-26b is down-regulated in carcinoma-associated fibroblasts from ER-positive breast cancers leading to enhanced cell migration and invasion.

Verghese ET, Drury R, Green CA, Holliday DL, Lu X, Nash C, Speirs V, Thorne JL, Thygesen HH, Zougman A, Hull MA, Hanby AM, Hughes TA.

J Pathol. 2013 Nov;231(3):388-99. doi: 10.1002/path.4248.

13.

Neoadjuvant chemotherapy induces expression levels of breast cancer resistance protein that predict disease-free survival in breast cancer.

Kim B, Fatayer H, Hanby AM, Horgan K, Perry SL, Valleley EM, Verghese ET, Williams BJ, Thorne JL, Hughes TA.

PLoS One. 2013 May 2;8(5):e62766. doi: 10.1371/journal.pone.0062766. Print 2013.

14.

Recruitment of NCOR1 to VDR target genes is enhanced in prostate cancer cells and associates with altered DNA methylation patterns.

Doig CL, Singh PK, Dhiman VK, Thorne JL, Battaglia S, Sobolewski M, Maguire O, O'Neill LP, Turner BM, McCabe CJ, Smiraglia DJ, Campbell MJ.

Carcinogenesis. 2013 Feb;34(2):248-56. doi: 10.1093/carcin/bgs331. Epub 2012 Oct 20.

15.

Heterochromatin protein 1 gamma and IκB kinase alpha interdependence during tumour necrosis factor gene transcription elongation in activated macrophages.

Thorne JL, Ouboussad L, Lefevre PF.

Nucleic Acids Res. 2012 Sep;40(16):7676-89. doi: 10.1093/nar/gks509. Epub 2012 May 30.

16.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

17.

History can matter: non-Markovian behavior of ancestral lineages.

Cartwright RA, Lartillot N, Thorne JL.

Syst Biol. 2011 May;60(3):276-90. doi: 10.1093/sysbio/syr012. Epub 2011 Mar 11.

18.

Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution.

Yokoyama KD, Thorne JL, Wray GA.

Genome Biol Evol. 2011;3:66-74. doi: 10.1093/gbe/evq078. Epub 2010 Nov 30.

19.

Epigenetic control of a VDR-governed feed-forward loop that regulates p21(waf1/cip1) expression and function in non-malignant prostate cells.

Thorne JL, Maguire O, Doig CL, Battaglia S, Fehr L, Sucheston LE, Heinaniemi M, O'Neill LP, McCabe CJ, Turner BM, Carlberg C, Campbell MJ.

Nucleic Acids Res. 2011 Mar;39(6):2045-56. doi: 10.1093/nar/gkq875. Epub 2010 Nov 17.

20.

Elevated NCOR1 disrupts PPARalpha/gamma signaling in prostate cancer and forms a targetable epigenetic lesion.

Battaglia S, Maguire O, Thorne JL, Hornung LB, Doig CL, Liu S, Sucheston LE, Bianchi A, Khanim FL, Gommersall LM, Coulter HS, Rakha S, Giddings I, O'Neill LP, Cooper CS, McCabe CJ, Bunce CM, Campbell MJ.

Carcinogenesis. 2010 Sep;31(9):1650-60. doi: 10.1093/carcin/bgq086. Epub 2010 May 13.

21.

Elevated NCOR1 disrupts a network of dietary-sensing nuclear receptors in bladder cancer cells.

Abedin SA, Thorne JL, Battaglia S, Maguire O, Hornung LB, Doherty AP, Mills IG, Campbell MJ.

Carcinogenesis. 2009 Mar;30(3):449-56. doi: 10.1093/carcin/bgp005. Epub 2009 Jan 6.

22.

Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences.

Choi SC, Redelings BD, Thorne JL.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3931-9. doi: 10.1098/rstb.2008.0167.

23.

Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates.

Kitazoe Y, Kishino H, Hasegawa M, Nakajima N, Thorne JL, Tanaka M.

PLoS One. 2008 Oct 6;3(10):e3343. doi: 10.1371/journal.pone.0003343.

24.

Transcription factors, chromatin and cancer.

Thorne JL, Campbell MJ, Turner BM.

Int J Biochem Cell Biol. 2009 Jan;41(1):164-75. doi: 10.1016/j.biocel.2008.08.029. Epub 2008 Sep 2. Review.

PMID:
18804550
25.

Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci.

Choi SC, Stone EA, Kishino H, Thorne JL.

Gene. 2009 Jul 15;441(1-2):45-52. doi: 10.1016/j.gene.2008.07.020. Epub 2008 Jul 29.

26.

Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors.

Xiang QY, Thorne JL, Seo TK, Zhang W, Thomas DT, Ricklefs RE.

Mol Phylogenet Evol. 2008 Oct;49(1):327-42. doi: 10.1016/j.ympev.2008.07.010. Epub 2008 Jul 19.

PMID:
18682295
27.

Protein evolution constraints and model-based techniques to study them.

Thorne JL.

Curr Opin Struct Biol. 2007 Jun;17(3):337-41. Epub 2007 Jun 14. Review.

PMID:
17572082
28.

Quantifying the impact of protein tertiary structure on molecular evolution.

Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL.

Mol Biol Evol. 2007 Aug;24(8):1769-82. Epub 2007 May 23.

PMID:
17522088
29.

Population genetics without intraspecific data.

Thorne JL, Choi SC, Yu J, Higgs PG, Kishino H.

Mol Biol Evol. 2007 Aug;24(8):1667-77. Epub 2007 Apr 29.

PMID:
17470435
30.

Testing for spatial clustering of amino acid replacements within protein tertiary structure.

Yu J, Thorne JL.

J Mol Evol. 2006 Jun;62(6):682-92. Epub 2006 Apr 25.

PMID:
16752209
31.

Dependence among sites in RNA evolution.

Yu J, Thorne JL.

Mol Biol Evol. 2006 Aug;23(8):1525-37. Epub 2006 May 23.

PMID:
16720696
32.

Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data.

Seo TK, Kishino H, Thorne JL.

Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4436-41. Epub 2005 Mar 11.

33.

Molecular evidence on plant divergence times.

Sanderson MJ, Thorne JL, Wikström N, Bremer K.

Am J Bot. 2004 Oct;91(10):1656-65. doi: 10.3732/ajb.91.10.1656.

34.
35.

Time flies, a new molecular time-scale for brachyceran fly evolution without a clock.

Wiegmann BM, Yeates DK, Thorne JL, Kishino H.

Syst Biol. 2003 Dec;52(6):745-56.

PMID:
14668115
36.

Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution.

Hasegawa M, Thorne JL, Kishino H.

Genes Genet Syst. 2003 Aug;78(4):267-83. Review.

37.

Protein evolution with dependence among codons due to tertiary structure.

Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL.

Mol Biol Evol. 2003 Oct;20(10):1692-704. Epub 2003 Jul 28.

PMID:
12885968
38.

Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach.

Scholl EH, Thorne JL, McCarter JP, Bird DM.

Genome Biol. 2003;4(6):R39. Epub 2003 May 19.

39.

Divergence time and evolutionary rate estimation with multilocus data.

Thorne JL, Kishino H.

Syst Biol. 2002 Oct;51(5):689-702.

PMID:
12396584
40.

Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach.

Seo TK, Thorne JL, Hasegawa M, Kishino H.

Genetics. 2002 Apr;160(4):1283-93.

41.

A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times.

Seo TK, Thorne JL, Hasegawa M, Kishino H.

Bioinformatics. 2002 Jan;18(1):115-23.

PMID:
11836219
42.

Performance of a divergence time estimation method under a probabilistic model of rate evolution.

Kishino H, Thorne JL, Bruno WJ.

Mol Biol Evol. 2001 Mar;18(3):352-61.

PMID:
11230536
43.

Models of protein sequence evolution and their applications.

Thorne JL.

Curr Opin Genet Dev. 2000 Dec;10(6):602-5. Review.

PMID:
11088008
44.

Estimating the rate of evolution of the rate of molecular evolution.

Thorne JL, Kishino H, Painter IS.

Mol Biol Evol. 1998 Dec;15(12):1647-57.

PMID:
9866200
45.

PASSML: combining evolutionary inference and protein secondary structure prediction.

Liò P, Goldman N, Thorne JL, Jones3 DT.

Bioinformatics. 1998;14(8):726-33.

PMID:
9789098
46.
47.

Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.

Goldman N, Thorne JL, Jones DT.

J Mol Biol. 1996 Oct 25;263(2):196-208.

PMID:
8913301
48.

Combining protein evolution and secondary structure.

Thorne JL, Goldman N, Jones DT.

Mol Biol Evol. 1996 May;13(5):666-73.

PMID:
8676741
49.

Estimation and reliability of molecular sequence alignments.

Thorne JL, Churchill GA.

Biometrics. 1995 Mar;51(1):100-13.

PMID:
7766767
50.

Freeing phylogenies from artifacts of alignment.

Thorne JL, Kishino H.

Mol Biol Evol. 1992 Nov;9(6):1148-62.

PMID:
1435239

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