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Items: 1 to 50 of 81

1.

A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints.

Ebrahimi P, Kaur S, Baronti L, Petzold K, Chen AA.

Methods. 2019 Jun 1;162-163:96-107. doi: 10.1016/j.ymeth.2019.05.001. Epub 2019 May 3.

PMID:
31059830
2.

CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry.

Myers CA, D'Esposito RJ, Fabris D, Ranganathan SV, Chen AA.

J Phys Chem B. 2019 May 23;123(20):4347-4357. doi: 10.1021/acs.jpcb.9b01018. Epub 2019 May 10.

PMID:
31042389
3.

The pseudokinase MLKL activates PAD4-dependent NET formation in necroptotic neutrophils.

D'Cruz AA, Speir M, Bliss-Moreau M, Dietrich S, Wang S, Chen AA, Gavillet M, Al-Obeidi A, Lawlor KE, Vince JE, Kelliher MA, Hakem R, Pasparakis M, Williams DA, Ericsson M, Croker BA.

Sci Signal. 2018 Sep 4;11(546). pii: eaao1716. doi: 10.1126/scisignal.aao1716.

4.

Direct Measurement of the Key E_{c.m.}=456  keV Resonance in the Astrophysical ^{19}Ne(p,γ)^{20}Na Reaction and Its Relevance for Explosive Binary Systems.

Wilkinson R, Lotay G, Lennarz A, Ruiz C, Christian G, Akers C, Catford WN, Chen AA, Connolly D, Davids B, Hutcheon DA, Jedrejcic D, Laird AM, Martin L, McNeice E, Riley J, Williams M.

Phys Rev Lett. 2017 Dec 15;119(24):242701. doi: 10.1103/PhysRevLett.119.242701. Epub 2017 Dec 11.

PMID:
29286739
5.

Oncogenic DNA viruses found in salivary gland tumors.

Chen AA, Gheit T, Stellin M, Lupato V, Spinato G, Fuson R, Menegaldo A, Mckay-Chopin S, Dal Cin E, Tirelli G, Da Mosto MC, Tommasino M, Boscolo-Rizzo P.

Oral Oncol. 2017 Dec;75:106-110. doi: 10.1016/j.oraloncology.2017.11.005. Epub 2017 Nov 10.

PMID:
29224806
6.

Study of the ^{26}Al^{m}(d,p)^{27}Al Reaction and the Influence of the ^{26}Al 0^{+} Isomer on the Destruction of ^{26}Al in the Galaxy.

Almaraz-Calderon S, Rehm KE, Gerken N, Avila ML, Kay BP, Talwar R, Ayangeakaa AD, Bottoni S, Chen AA, Deibel CM, Dickerson C, Hanselman K, Hoffman CR, Jiang CL, Kuvin SA, Nusair O, Pardo RC, Santiago-Gonzalez D, Sethi J, Ugalde C.

Phys Rev Lett. 2017 Aug 18;119(7):072701. doi: 10.1103/PhysRevLett.119.072701. Epub 2017 Aug 17.

PMID:
28949677
7.

A motive for killing: effector functions of regulated lytic cell death.

Bliss-Moreau M, Chen AA, D'Cruz AA, Croker BA.

Immunol Cell Biol. 2017 Feb;95(2):146-151. doi: 10.1038/icb.2016.113. Epub 2016 Nov 9. Review.

8.

Advances in RNA molecular dynamics: a simulator's guide to RNA force fields.

Vangaveti S, Ranganathan SV, Chen AA.

Wiley Interdiscip Rev RNA. 2017 Mar;8(2). doi: 10.1002/wrna.1396. Epub 2016 Oct 4. Review.

PMID:
27704698
9.

Free-energy landscape of a hyperstable RNA tetraloop.

Miner JC, Chen AA, García AE.

Proc Natl Acad Sci U S A. 2016 Jun 14;113(24):6665-70. doi: 10.1073/pnas.1603154113. Epub 2016 May 27.

10.

Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces.

Ranganathan SV, Halvorsen K, Myers CA, Robertson NM, Yigit MV, Chen AA.

Langmuir. 2016 Jun 21;32(24):6028-34. doi: 10.1021/acs.langmuir.6b00456. Epub 2016 Jun 6.

PMID:
27219463
11.

Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators.

Takahashi MK, Watters KE, Gasper PM, Abbott TR, Carlson PD, Chen AA, Lucks JB.

RNA. 2016 Jun;22(6):920-33. doi: 10.1261/rna.054916.115. Epub 2016 Apr 21.

12.

Direct Measurement of the Astrophysical ^{38}K(p,γ)^{39}Ca Reaction and Its Influence on the Production of Nuclides toward the End Point of Nova Nucleosynthesis.

Lotay G, Christian G, Ruiz C, Akers C, Burke DS, Catford WN, Chen AA, Connolly D, Davids B, Fallis J, Hager U, Hutcheon DA, Mahl A, Rojas A, Sun X.

Phys Rev Lett. 2016 Apr 1;116(13):132701. doi: 10.1103/PhysRevLett.116.132701. Epub 2016 Apr 1.

PMID:
27081974
13.

Isospin Mixing Reveals ^{30}P(p,γ)^{31}S Resonance Influencing Nova Nucleosynthesis.

Bennett MB, Wrede C, Brown BA, Liddick SN, Pérez-Loureiro D, Bardayan DW, Chen AA, Chipps KA, Fry C, Glassman BE, Langer C, Larson NR, McNeice EI, Meisel Z, Ong W, O'Malley PD, Pain SD, Prokop CJ, Schatz H, Schwartz SB, Suchyta S, Thompson P, Walters M, Xu X.

Phys Rev Lett. 2016 Mar 11;116(10):102502. doi: 10.1103/PhysRevLett.116.102502. Epub 2016 Mar 8.

PMID:
27015475
14.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M.

Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029.

15.

Human Papillomavirus 18 Genetic Variation and Cervical Cancer Risk Worldwide.

Chen AA, Gheit T, Franceschi S, Tommasino M, Clifford GM; IARC HPV Variant Study Group.

J Virol. 2015 Oct;89(20):10680-7. doi: 10.1128/JVI.01747-15. Epub 2015 Aug 12.

16.

Evidence of soft dipole resonance in ^{11}li with isoscalar character.

Kanungo R, Sanetullaev A, Tanaka J, Ishimoto S, Hagen G, Myo T, Suzuki T, Andreoiu C, Bender P, Chen AA, Davids B, Fallis J, Fortin JP, Galinski N, Gallant AT, Garrett PE, Hackman G, Hadinia B, Jansen G, Keefe M, Krücken R, Lighthall J, McNeice E, Miller D, Otsuka T, Purcell J, Randhawa JS, Roger T, Rojas A, Savajols H, Shotter A, Tanihata I, Thompson IJ, Unsworth C, Voss P, Wang Z.

Phys Rev Lett. 2015 May 15;114(19):192502. Epub 2015 May 12.

PMID:
26024166
17.

Computer-automated time-lapse analysis results correlate with embryo implantation and clinical pregnancy: a blinded, multi-centre study.

VerMilyea MD, Tan L, Anthony JT, Conaghan J, Ivani K, Gvakharia M, Boostanfar R, Baker VL, Suraj V, Chen AA, Mainigi M, Coutifaris C, Shen S.

Reprod Biomed Online. 2014 Dec;29(6):729-36. doi: 10.1016/j.rbmo.2014.09.005. Epub 2014 Sep 21.

18.

Using the Eeva Test™ adjunctively to traditional day 3 morphology is informative for consistent embryo assessment within a panel of embryologists with diverse experience.

Diamond MP, Suraj V, Behnke EJ, Yang X, Angle MJ, Lambe-Steinmiller JC, Watterson R, Athayde Wirka K, Chen AA, Shen S.

J Assist Reprod Genet. 2015 Jan;32(1):61-8. doi: 10.1007/s10815-014-0366-1. Epub 2014 Oct 21.

19.

Prevalence of human papillomavirus in cancer of the oropharynx by gender.

Combes JD, Chen AA, Franceschi S.

Cancer Epidemiol Biomarkers Prev. 2014 Dec;23(12):2954-8. doi: 10.1158/1055-9965.EPI-14-0580. Epub 2014 Sep 9.

20.

Atypical embryo phenotypes identified by time-lapse microscopy: high prevalence and association with embryo development.

Athayde Wirka K, Chen AA, Conaghan J, Ivani K, Gvakharia M, Behr B, Suraj V, Tan L, Shen S.

Fertil Steril. 2014 Jun;101(6):1637-48.e1-5. doi: 10.1016/j.fertnstert.2014.02.050. Epub 2014 Apr 14.

PMID:
24726214
21.

Human papillomavirus 45 genetic variation and cervical cancer risk worldwide.

Chen AA, Heideman DA, Boon D, Gheit T, Snijders PJ, Tommasino M, Franceschi S, Clifford GM; IARC HPV Variant Study Group.

J Virol. 2014 Apr;88(8):4514-21. doi: 10.1128/JVI.03534-13. Epub 2014 Feb 5.

22.

Classical-NOVA CONTRIBUTION to the Milky Way's ²⁶Al abundance: exit channel of the key ²⁵Al(p,γ) ²⁶Si resonance.

Bennett MB, Wrede C, Chipps KA, José J, Liddick SN, Santia M, Bowe A, Chen AA, Cooper N, Irvine D, McNeice E, Montes F, Naqvi F, Ortez R, Pain SD, Pereira J, Prokop C, Quaglia J, Quinn SJ, Schwartz SB, Shanab S, Simon A, Spyrou A, Thiagalingam E.

Phys Rev Lett. 2013 Dec 6;111(23):232503. Epub 2013 Dec 4.

PMID:
24476263
23.

Human papillomavirus 33 worldwide genetic variation and associated risk of cervical cancer.

Chen AA, Heideman DA, Boon D, Chen Z, Burk RD, De Vuyst H, Gheit T, Snijders PJ, Tommasino M, Franceschi S, Clifford GM.

Virology. 2014 Jan 5;448:356-62. doi: 10.1016/j.virol.2013.10.033. Epub 2013 Nov 12.

24.

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations.

Chen AA, García AE.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16820-5. doi: 10.1073/pnas.1309392110. Epub 2013 Sep 16. Review.

25.

[Leaching kinetics of josephinite tailings with sulfuric acid].

Chen AA, Zhou SQ, Huang PF.

Huan Jing Ke Xue. 2013 Jul;34(7):2729-34. Chinese.

PMID:
24028005
26.

Improving embryo selection using a computer-automated time-lapse image analysis test plus day 3 morphology: results from a prospective multicenter trial.

Conaghan J, Chen AA, Willman SP, Ivani K, Chenette PE, Boostanfar R, Baker VL, Adamson GD, Abusief ME, Gvakharia M, Loewke KE, Shen S.

Fertil Steril. 2013 Aug;100(2):412-9.e5. doi: 10.1016/j.fertnstert.2013.04.021. Epub 2013 May 28.

PMID:
23721712
27.

The essential role of stacking adenines in a two-base-pair RNA kissing complex.

Stephenson W, Asare-Okai PN, Chen AA, Keller S, Santiago R, Tenenbaum SA, Garcia AE, Fabris D, Li PT.

J Am Chem Soc. 2013 Apr 17;135(15):5602-11. doi: 10.1021/ja310820h. Epub 2013 Apr 8.

28.

Biomarkers identified with time-lapse imaging: discovery, validation, and practical application.

Chen AA, Tan L, Suraj V, Reijo Pera R, Shen S.

Fertil Steril. 2013 Mar 15;99(4):1035-43. doi: 10.1016/j.fertnstert.2013.01.143. Review.

29.

Is γ-ray emission from novae affected by interference effects in the 18F(p,α)15O reaction?

Laird AM, Parikh A, Murphy AS, Wimmer K, Chen AA, Deibel CM, Faestermann T, Fox SP, Fulton BR, Hertenberger R, Irvine D, José J, Longland R, Mountford DJ, Sambrook B, Seiler D, Wirth HF.

Phys Rev Lett. 2013 Jan 18;110(3):032502. Epub 2013 Jan 15.

PMID:
23373915
30.

Time-lapse microscopy and image analysis in basic and clinical embryo development research.

Wong C, Chen AA, Behr B, Shen S.

Reprod Biomed Online. 2013 Feb;26(2):120-9. doi: 10.1016/j.rbmo.2012.11.003. Epub 2012 Nov 20. Review.

PMID:
23273754
31.

High-throughput quantitative real-time polymerase chain reaction array for absolute and relative quantification of rhesus macaque types I, II, and III interferon and their subtypes.

Schramm LM, Kirschman KD, Heuer M, Chen AA, Verthelyi D, Puig M, Rabin RL.

J Interferon Cytokine Res. 2012 Sep;32(9):407-15. doi: 10.1089/jir.2012.0015. Epub 2012 Jul 20.

32.

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.

Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M.

Nature. 2012 Jul 26;487(7408):491-5. doi: 10.1038/nature11288.

33.

Rapid casting of patterned vascular networks for perfusable engineered three-dimensional tissues.

Miller JS, Stevens KR, Yang MT, Baker BM, Nguyen DH, Cohen DM, Toro E, Chen AA, Galie PA, Yu X, Chaturvedi R, Bhatia SN, Chen CS.

Nat Mater. 2012 Sep;11(9):768-74. doi: 10.1038/nmat3357. Epub 2012 Jul 1.

34.
35.

Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations.

Chen AA, García AE.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):E1530-9. doi: 10.1073/pnas.1119552109. Epub 2012 May 23.

36.

Antitumor activity of a recombinant soluble ectodomain of mutant human fibroblast growth factor receptor-2 IIIc.

Wang J, Liu XT, Huang H, Xiao G, Zhou ZY, Chen Y, Yu ZH, He SL, Chen AA, Wang DD, He Y, Zhang ZC, Hong A.

Mol Cancer Ther. 2011 Sep;10(9):1656-66. doi: 10.1158/1535-7163.MCT-11-0163. Epub 2011 Jul 12.

37.

Humanized mice with ectopic artificial liver tissues.

Chen AA, Thomas DK, Ong LL, Schwartz RE, Golub TR, Bhatia SN.

Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11842-7. doi: 10.1073/pnas.1101791108. Epub 2011 Jul 11.

38.

Multiplexed, high-throughput analysis of 3D microtissue suspensions.

Chen AA, Underhill GH, Bhatia SN.

Integr Biol (Camb). 2010 Oct;2(10):517-27. doi: 10.1039/c0ib00054j. Epub 2010 Sep 1.

39.

Pharmacologic prophylaxis and risk factors for intraoperative floppy-iris syndrome in phacoemulsification performed by resident physicians.

Chen AA, Kelly JP, Bhandari A, Wu MC.

J Cataract Refract Surg. 2010 Jun;36(6):898-905. doi: 10.1016/j.jcrs.2009.12.039.

PMID:
20494759
40.

Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.

Chen AA, Draper DE, Pappu RV.

J Mol Biol. 2009 Jul 24;390(4):805-19. doi: 10.1016/j.jmb.2009.05.071. Epub 2009 May 29.

41.

Genetic variation in the vitamin C transporter, SLC23A2, modifies the risk of HPV16-associated head and neck cancer.

Chen AA, Marsit CJ, Christensen BC, Houseman EA, McClean MD, Smith JF, Bryan JT, Posner MR, Nelson HH, Kelsey KT.

Carcinogenesis. 2009 Jun;30(6):977-81. doi: 10.1093/carcin/bgp076. Epub 2009 Apr 3.

42.

Aedes aegypti in Jamaica, West Indies: container productivity profiles to inform control strategies.

Chadee DD, Huntley S, Focks DA, Chen AA.

Trop Med Int Health. 2009 Feb;14(2):220-7. doi: 10.1111/j.1365-3156.2008.02216.x.

43.

Simulations of RNA interactions with monovalent ions.

Chen AA, Marucho M, Baker NA, Pappu RV.

Methods Enzymol. 2009;469:411-32. doi: 10.1016/S0076-6879(09)69020-0. Epub 2009 Nov 17.

PMID:
20946801
44.

Modulation of hepatocyte phenotype in vitro via chemomechanical tuning of polyelectrolyte multilayers.

Chen AA, Khetani SR, Lee S, Bhatia SN, Van Vliet KJ.

Biomaterials. 2009 Feb;30(6):1113-20. doi: 10.1016/j.biomaterials.2008.10.055. Epub 2008 Nov 28.

45.

T-cadherin modulates hepatocyte functions in vitro.

Khetani SR, Chen AA, Ranscht B, Bhatia SN.

FASEB J. 2008 Nov;22(11):3768-75. doi: 10.1096/fj.07-105155. Epub 2008 Jul 17.

46.

Is there a role for FISH in the management and surveillance of patients with upper tract transitional-cell carcinoma?

Chen AA, Grasso M.

J Endourol. 2008 Jun;22(6):1371-4. doi: 10.1089/end.2008.0096.

PMID:
18578665
47.

A clinical and biochemical critical pathway for the evaluation of patients with suspected acute congestive heart failure: The ProBNP Investigation of Dyspnea in the Emergency Department (PRIDE) algorithm.

Baggish AL, Cameron R, Anwaruddin S, Chen AA, Krauser DG, Tung R, Januzzi JL Jr.

Crit Pathw Cardiol. 2004 Dec;3(4):171-6. doi: 10.1097/01.hpc.0000145817.68289.a2.

PMID:
18340169
48.

A clinical and biochemical score for mortality prediction in patients with acute dyspnoea: derivation, validation and incorporation into a bedside programme.

Baggish AL, Lloyd-Jones DM, Blatt J, Richards AM, Lainchbury J, O'Donoghue M, Sakhuja R, Chen AA, Januzzi JL.

Heart. 2008 Aug;94(8):1032-7. Epub 2007 Oct 18.

PMID:
17947362
49.

Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements.

Chen AA, Pappu RV.

J Phys Chem B. 2007 Oct 18;111(41):11884-7. Epub 2007 Sep 22.

PMID:
17887792
50.

Measurement of the interleukin family member ST2 in patients with acute dyspnea: results from the PRIDE (Pro-Brain Natriuretic Peptide Investigation of Dyspnea in the Emergency Department) study.

Januzzi JL Jr, Peacock WF, Maisel AS, Chae CU, Jesse RL, Baggish AL, O'Donoghue M, Sakhuja R, Chen AA, van Kimmenade RR, Lewandrowski KB, Lloyd-Jones DM, Wu AH.

J Am Coll Cardiol. 2007 Aug 14;50(7):607-13. Epub 2007 Jul 30.

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