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Items: 47

1.

Combining CDK4/6 inhibition with taxanes enhances anti-tumor efficacy by sustained impairment of pRB-E2F pathways in squamous cell lung cancer.

Cao J, Zhu Z, Wang H, Nichols TC, Lui GYL, Deng S, Rejto PA, VanArsdale T, Hardwick JS, Weinrich SL, Wei P.

Oncogene. 2019 Jan 30. doi: 10.1038/s41388-019-0708-7. [Epub ahead of print]

PMID:
30700828
2.

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA.

Deng S, Lira M, Huang D, Wang K, Valdez C, Kinong J, Rejto PA, Bienkowska J, Hardwick J, Xie T.

BMC Bioinformatics. 2018 Oct 20;19(1):387. doi: 10.1186/s12859-018-2428-3.

3.

Outlier analysis of functional genomic profiles enriches for oncology targets and enables precision medicine.

Zhu Z, Ihle NT, Rejto PA, Zarrinkar PP.

BMC Genomics. 2016 Jun 13;17:455. doi: 10.1186/s12864-016-2807-y.

4.

OASIS: web-based platform for exploring cancer multi-omics data.

Fernandez-Banet J, Esposito A, Coffin S, Horvath IB, Estrella H, Schefzick S, Deng S, Wang K, AChing K, Ding Y, Roberts P, Rejto PA, Kan Z.

Nat Methods. 2016 Jan;13(1):9-10. doi: 10.1038/nmeth.3692. No abstract available.

PMID:
26716558
5.

Whole Exome Sequencing of Rapid Autopsy Tumors and Xenograft Models Reveals Possible Driver Mutations Underlying Tumor Progression.

Xie T, Musteanu M, Lopez-Casas PP, Shields DJ, Olson P, Rejto PA, Hidalgo M.

PLoS One. 2015 Nov 10;10(11):e0142631. doi: 10.1371/journal.pone.0142631. eCollection 2015.

6.

Patterns of somatic alterations between matched primary and metastatic colorectal tumors characterized by whole-genome sequencing.

Xie T, Cho YB, Wang K, Huang D, Hong HK, Choi YL, Ko YH, Nam DH, Jin J, Yang H, Fernandez J, Deng S, Rejto PA, Lee WY, Mao M.

Genomics. 2014 Oct;104(4):234-41. doi: 10.1016/j.ygeno.2014.07.012. Epub 2014 Jul 25.

7.

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer.

Wang K, Yuen ST, Xu J, Lee SP, Yan HH, Shi ST, Siu HC, Deng S, Chu KM, Law S, Chan KH, Chan AS, Tsui WY, Ho SL, Chan AK, Man JL, Foglizzo V, Ng MK, Chan AS, Ching YP, Cheng GH, Xie T, Fernandez J, Li VS, Clevers H, Rejto PA, Mao M, Leung SY.

Nat Genet. 2014 Jun;46(6):573-82. doi: 10.1038/ng.2983. Epub 2014 May 11.

PMID:
24816253
8.

MTOR mutations in the crosshairs of targeted therapy.

Rejto PA, Abraham RT.

Cancer Discov. 2014 May;4(5):513-5. doi: 10.1158/2159-8290.CD-14-0332.

9.

Cross-species analysis of genetically engineered mouse models of MAPK-driven colorectal cancer identifies hallmarks of the human disease.

Belmont PJ, Budinska E, Jiang P, Sinnamon MJ, Coffee E, Roper J, Xie T, Rejto PA, Derkits S, Sansom OJ, Delorenzi M, Tejpar S, Hung KE, Martin ES.

Dis Model Mech. 2014 Jun;7(6):613-23. doi: 10.1242/dmm.013904. Epub 2014 Apr 17.

10.

Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma.

Fernandez-Banet J, Lee NP, Chan KT, Gao H, Liu X, Sung WK, Tan W, Fan ST, Poon RT, Li S, Ching K, Rejto PA, Mao M, Kan Z.

Genomics. 2014 Feb-Mar;103(2-3):189-203. doi: 10.1016/j.ygeno.2014.01.003. Epub 2014 Jan 21.

11.

Molecular predictors of sensitivity to the insulin-like growth factor 1 receptor inhibitor Figitumumab (CP-751,871).

Pavlicek A, Lira ME, Lee NV, Ching KA, Ye J, Cao J, Garza SJ, Hook KE, Ozeck M, Shi ST, Yuan J, Zheng X, Rejto PA, Kan JL, Christensen JG.

Mol Cancer Ther. 2013 Dec;12(12):2929-39. doi: 10.1158/1535-7163.MCT-13-0442-T. Epub 2013 Oct 9.

12.

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma.

Kan Z, Zheng H, Liu X, Li S, Barber TD, Gong Z, Gao H, Hao K, Willard MD, Xu J, Hauptschein R, Rejto PA, Fernandez J, Wang G, Zhang Q, Wang B, Chen R, Wang J, Lee NP, Zhou W, Lin Z, Peng Z, Yi K, Chen S, Li L, Fan X, Yang J, Ye R, Ju J, Wang K, Estrella H, Deng S, Wei P, Qiu M, Wulur IH, Liu J, Ehsani ME, Zhang C, Loboda A, Sung WK, Aggarwal A, Poon RT, Fan ST, Wang J, Hardwick J, Reinhard C, Dai H, Li Y, Luk JM, Mao M.

Genome Res. 2013 Sep;23(9):1422-33. doi: 10.1101/gr.154492.113. Epub 2013 Jun 20.

13.

Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma.

Wang K, Lim HY, Shi S, Lee J, Deng S, Xie T, Zhu Z, Wang Y, Pocalyko D, Yang WJ, Rejto PA, Mao M, Park CK, Xu J.

Hepatology. 2013 Aug;58(2):706-17. doi: 10.1002/hep.26402. Epub 2013 Jul 1.

PMID:
23505090
14.

A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations.

Xie T, D' Ario G, Lamb JR, Martin E, Wang K, Tejpar S, Delorenzi M, Bosman FT, Roth AD, Yan P, Bougel S, Di Narzo AF, Popovici V, Budinská E, Mao M, Weinrich SL, Rejto PA, Hodgson JG.

PLoS One. 2012;7(7):e42001. doi: 10.1371/journal.pone.0042001. Epub 2012 Jul 31.

15.

Dose-dependent effects of small-molecule antagonists on the genomic landscape of androgen receptor binding.

Zhu Z, Shi M, Hu W, Estrella H, Engebretsen J, Nichols T, Briere D, Hosea N, Los G, Rejto PA, Fanjul A.

BMC Genomics. 2012 Jul 31;13:355. doi: 10.1186/1471-2164-13-355.

16.

Biomarker and pharmacologic evaluation of the γ-secretase inhibitor PF-03084014 in breast cancer models.

Zhang CC, Pavlicek A, Zhang Q, Lira ME, Painter CL, Yan Z, Zheng X, Lee NV, Ozeck M, Qiu M, Zong Q, Lappin PB, Wong A, Rejto PA, Smeal T, Christensen JG.

Clin Cancer Res. 2012 Sep 15;18(18):5008-19. doi: 10.1158/1078-0432.CCR-12-1379. Epub 2012 Jul 17.

17.

A novel SND1-BRAF fusion confers resistance to c-Met inhibitor PF-04217903 in GTL16 cells through [corrected] MAPK activation.

Lee NV, Lira ME, Pavlicek A, Ye J, Buckman D, Bagrodia S, Srinivasa SP, Zhao Y, Aparicio S, Rejto PA, Christensen JG, Ching KA.

PLoS One. 2012;7(6):e39653. doi: 10.1371/journal.pone.0039653. Epub 2012 Jun 22. Erratum in: PLoS One. 2012;7(8). doi: 10.1371/annotation/d988dd75-bcd2-4859-b20b-487e1bf2513b.

18.

An integrated genomic approach to identify predictive biomarkers of response to the aurora kinase inhibitor PF-03814735.

Hook KE, Garza SJ, Lira ME, Ching KA, Lee NV, Cao J, Yuan J, Ye J, Ozeck M, Shi ST, Zheng X, Rejto PA, Kan JL, Christensen JG, Pavlicek A.

Mol Cancer Ther. 2012 Mar;11(3):710-9. doi: 10.1158/1535-7163.MCT-11-0184. Epub 2012 Jan 5.

19.

Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer.

Wang K, Kan J, Yuen ST, Shi ST, Chu KM, Law S, Chan TL, Kan Z, Chan AS, Tsui WY, Lee SP, Ho SL, Chan AK, Cheng GH, Roberts PC, Rejto PA, Gibson NW, Pocalyko DJ, Mao M, Xu J, Leung SY.

Nat Genet. 2011 Oct 30;43(12):1219-23. doi: 10.1038/ng.982.

PMID:
22037554
20.

Structure-based and property-compliant library design of 11β-HSD1 adamantyl amide inhibitors.

Paderes GD, Dress K, Huang B, Elleraas J, Rejto PA, Pauly T.

Methods Mol Biol. 2011;685:191-215. doi: 10.1007/978-1-60761-931-4_10.

PMID:
20981525
21.

P-cadherin expression as a prognostic biomarker in a 3992 case tissue microarray series of breast cancer.

Turashvili G, McKinney SE, Goktepe O, Leung SC, Huntsman DG, Gelmon KA, Los G, Rejto PA, Aparicio SA.

Mod Pathol. 2011 Jan;24(1):64-81. doi: 10.1038/modpathol.2010.189. Epub 2010 Sep 17.

22.

Statistical method on nonrandom clustering with application to somatic mutations in cancer.

Ye J, Pavlicek A, Lunney EA, Rejto PA, Teng CH.

BMC Bioinformatics. 2010 Jan 7;11:11. doi: 10.1186/1471-2105-11-11.

23.

A novel selective 11beta-hydroxysteroid dehydrogenase type 1 inhibitor prevents human adipogenesis.

Bujalska IJ, Gathercole LL, Tomlinson JW, Darimont C, Ermolieff J, Fanjul AN, Rejto PA, Stewart PM.

J Endocrinol. 2008 May;197(2):297-307. doi: 10.1677/JOE-08-0050.

24.

Antisense inhibition of 11betahydroxysteroid dehydrogenase type 1 improves diabetes in a novel cortisone-induced diabetic KK mouse model.

Bhat BG, Younis H, Herrera J, Palacio K, Pascual B, Hur G, Jessen B, Ogilvie KM, Rejto PA.

Biochem Biophys Res Commun. 2008 Jan 25;365(4):740-5. Epub 2007 Nov 20.

PMID:
18029262
25.
26.

Identification and characterization of a novel and functional murine Pin1 isoform.

Zhu JX, Dagostino E, Rejto PA, Mroczkowski B, Murray B.

Biochem Biophys Res Commun. 2007 Aug 3;359(3):529-35. Epub 2007 May 25.

PMID:
17548053
27.

Crystal structure of human ABAD/HSD10 with a bound inhibitor: implications for design of Alzheimer's disease therapeutics.

Kissinger CR, Rejto PA, Pelletier LA, Thomson JA, Showalter RE, Abreo MA, Agree CS, Margosiak S, Meng JJ, Aust RM, Vanderpool D, Li B, Tempczyk-Russell A, Villafranca JE.

J Mol Biol. 2004 Sep 17;342(3):943-52.

PMID:
15342248
28.

Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 8. Pharmacological optimization of orally bioavailable 2-pyridone-containing peptidomimetics.

Dragovich PS, Prins TJ, Zhou R, Johnson TO, Hua Y, Luu HT, Sakata SK, Brown EL, Maldonado FC, Tuntland T, Lee CA, Fuhrman SA, Zalman LS, Patick AK, Matthews DA, Wu EY, Guo M, Borer BC, Nayyar NK, Moran T, Chen L, Rejto PA, Rose PW, Guzman MC, Dovalsantos EZ, Lee S, McGee K, Mohajeri M, Liese A, Tao J, Kosa MB, Liu B, Batugo MR, Gleeson JP, Wu ZP, Liu J, Meador JW 3rd, Ferre RA.

J Med Chem. 2003 Oct 9;46(21):4572-85.

PMID:
14521419
29.

Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface.

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PW.

Proteins. 2003 Nov 1;53(2):201-19.

PMID:
14517972
30.

Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding.

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PW.

Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5148-53. Epub 2003 Apr 15.

32.

Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective.

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PW.

Curr Opin Struct Biol. 2002 Apr;12(2):197-203. Review.

PMID:
11959497
33.

Hierarchy of simulation models in predicting structure and energetics of the Src SH2 domain binding to tyrosyl phosphopeptides.

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Schaffer L, Arthurs S, Colson AB, Freer ST, Larson V, Luty BA, Marrone T, Rose PW.

J Med Chem. 2002 Jan 3;45(1):72-89.

PMID:
11754580
34.

Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Schaffer L, Arthurs S, Colson AB, Freer ST, Larson V, Luty BA, Marrone T, Rose PW.

Proteins. 2001 Dec 1;45(4):456-70.

PMID:
11746693
35.

Deciphering common failures in molecular docking of ligand-protein complexes.

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Arthurs S, Colson AB, Freer ST, Larson V, Luty BA, Marrone T, Rose PW.

J Comput Aided Mol Des. 2000 Nov;14(8):731-51.

PMID:
11131967
36.

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions.

Verkhivker GM, Rejto PA, Bouzida D, Arthurs S, Colson AB, Freer ST, Gehlhaar DK, Larson V, Luty BA, Marrone T, Rose PW.

J Mol Recognit. 1999 Nov-Dec;12(6):371-89. Review.

PMID:
10611647
37.

Thermodynamics and kinetics of ligand-protein binding studied with the weighted histogram analysis method and simulated annealing.

Bouzida D, Arthurs S, Colson AB, Freer ST, Gehlhaar DK, Larson V, Luty BA, Rejto PA, Rose PW, Verkhivker GM.

Pac Symp Biocomput. 1999:426-37.

38.

Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 4. Incorporation of P1 lactam moieties as L-glutamine replacements.

Dragovich PS, Prins TJ, Zhou R, Webber SE, Marakovits JT, Fuhrman SA, Patick AK, Matthews DA, Lee CA, Ford CE, Burke BJ, Rejto PA, Hendrickson TF, Tuntland T, Brown EL, Meador JW 3rd, Ferre RA, Harr JE, Kosa MB, Worland ST.

J Med Chem. 1999 Apr 8;42(7):1213-24.

PMID:
10197965
40.
42.

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

Rejto PA, Verkhivker GM.

Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):8945-50.

45.

Protein conformational substates from X-ray crystallography.

Rejto PA, Freer ST.

Prog Biophys Mol Biol. 1996;66(2):167-96. Review. No abstract available.

PMID:
9175428
46.

Visualization of fast energy flow and solvent caging in unimolecular dynamics.

Rejto PA, Bindewald E, Chandler D.

Nature. 1995 May 11;375(6527):129-31.

PMID:
7753167
47.

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming.

Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, Fogel LJ, Freer ST.

Chem Biol. 1995 May;2(5):317-24.

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