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Items: 1 to 20 of 27

1.

Correction: Sequencing as a first-line methodology for cystic fibrosis carrier screening.

Beauchamp KA, Taber KAJ, Grauman PV, Spurka L, Lim-Harashima J, Svenson A, Goldberg JD, Muzzey D.

Genet Med. 2019 May 15. doi: 10.1038/s41436-019-0543-9. [Epub ahead of print]

PMID:
31089271
2.

The dynamic conformational landscape of the protein methyltransferase SETD8.

Chen S, Wiewiora RP, Meng F, Babault N, Ma A, Yu W, Qian K, Hu H, Zou H, Wang J, Fan S, Blum G, Pittella-Silva F, Beauchamp KA, Tempel W, Jiang H, Chen K, Skene RJ, Zheng YG, Brown PJ, Jin J, Luo C, Chodera JD, Luo M.

Elife. 2019 May 13;8. pii: e45403. doi: 10.7554/eLife.45403. [Epub ahead of print]

3.

Sequencing as a first-line methodology for cystic fibrosis carrier screening.

Beauchamp KA, Johansen Taber KA, Grauman PV, Spurka L, Lim-Harashima J, Svenson A, Goldberg JD, Muzzey D.

Genet Med. 2019 Apr 30. doi: 10.1038/s41436-019-0525-y. [Epub ahead of print] Erratum in: Genet Med. 2019 May 15;:.

PMID:
31036917
4.

Clinical impact and cost-effectiveness of a 176-condition expanded carrier screen.

Beauchamp KA, Johansen Taber KA, Muzzey D.

Genet Med. 2019 Feb 14. doi: 10.1038/s41436-019-0455-8. [Epub ahead of print]

PMID:
30760891
5.

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.

Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD.

Entropy (Basel). 2018 May;20(5). pii: 318. doi: 10.3390/e20050318. Epub 2018 Apr 26.

6.

Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK.

J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30.

PMID:
30351006
7.

Clinical utility of expanded carrier screening: results-guided actionability and outcomes.

Johansen Taber KA, Beauchamp KA, Lazarin GA, Muzzey D, Arjunan A, Goldberg JD.

Genet Med. 2019 May;21(5):1041-1048. doi: 10.1038/s41436-018-0321-0. Epub 2018 Oct 11.

PMID:
30310157
8.

Validation of an Expanded Carrier Screen that Optimizes Sensitivity via Full-Exon Sequencing and Panel-wide Copy Number Variant Identification.

Hogan GJ, Vysotskaia VS, Beauchamp KA, Seisenberger S, Grauman PV, Haas KR, Hong SH, Jeon D, Kash S, Lai HH, Melroy LM, Theilmann MR, Chu CS, Iori K, Maguire JR, Evans EA, Haque IS, Mar-Heyming R, Kang HP, Muzzey D.

Clin Chem. 2018 Jul;64(7):1063-1073. doi: 10.1373/clinchem.2018.286823. Epub 2018 May 14.

PMID:
29760218
9.

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS.

PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. eCollection 2017 Jul.

10.

Systematic design and comparison of expanded carrier screening panels.

Beauchamp KA, Muzzey D, Wong KK, Hogan GJ, Karimi K, Candille SI, Mehta N, Mar-Heyming R, Kaseniit KE, Kang HP, Evans EA, Goldberg JD, Lazarin GA, Haque IS.

Genet Med. 2018 Jan;20(1):55-63. doi: 10.1038/gim.2017.69. Epub 2017 Jun 22.

11.

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15.

Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS.

J Phys Chem B. 2017 Apr 27;121(16):4023-4039. doi: 10.1021/acs.jpcb.7b02320. Epub 2017 Apr 6.

PMID:
28306259
12.

MSMBuilder: Statistical Models for Biomolecular Dynamics.

Harrigan MP, Sultan MM, Hernández CX, Husic BE, Eastman P, Schwantes CR, Beauchamp KA, McGibbon RT, Pande VS.

Biophys J. 2017 Jan 10;112(1):10-15. doi: 10.1016/j.bpj.2016.10.042.

13.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

Parton DL, Grinaway PB, Hanson SM, Beauchamp KA, Chodera JD.

PLoS Comput Biol. 2016 Jun 23;12(6):e1004728. doi: 10.1371/journal.pcbi.1004728. eCollection 2016 Jun.

14.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, Pande VS.

Biophys J. 2015 Oct 20;109(8):1528-32. doi: 10.1016/j.bpj.2015.08.015.

15.

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

Beauchamp KA, Behr JM, Rustenburg AS, Bayly CI, Kroenlein K, Chodera JD.

J Phys Chem B. 2015 Oct 8;119(40):12912-20. doi: 10.1021/acs.jpcb.5b06703. Epub 2015 Sep 29.

16.

From a structural average to the conformational ensemble of a DNA bulge.

Shi X, Beauchamp KA, Harbury PB, Herschlag D.

Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):E1473-80. doi: 10.1073/pnas.1317032111. Epub 2014 Mar 31.

17.

Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

Beauchamp KA, Pande VS, Das R.

Biophys J. 2014 Mar 18;106(6):1381-90. doi: 10.1016/j.bpj.2014.02.009.

18.

A molecular interpretation of 2D IR protein folding experiments with Markov state models.

Baiz CR, Lin YS, Peng CS, Beauchamp KA, Voelz VA, Pande VS, Tokmakoff A.

Biophys J. 2014 Mar 18;106(6):1359-70. doi: 10.1016/j.bpj.2014.02.008.

19.

Probing the origins of two-state folding.

Lane TJ, Schwantes CR, Beauchamp KA, Pande VS.

J Chem Phys. 2013 Oct 14;139(14):145104. doi: 10.1063/1.4823502.

20.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, Pande VS.

J Chem Theory Comput. 2013 Jan 8;9(1):461-469. Epub 2012 Oct 18.

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