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Items: 39

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.

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.

9.

Differential Pressure Shunt for Simultaneous Diversion of Ventricular Fluid and Extracerebral Fluid.

Craig D, Winston KR, Folzenlogen Z, Beauchamp KA.

Pediatr Neurosurg. 2018;53(1):13-17. doi: 10.1159/000480020. Epub 2017 Sep 22.

PMID:
28934739
10.

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.

11.

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.

12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

To milliseconds and beyond: challenges in the simulation of protein folding.

Lane TJ, Shukla D, Beauchamp KA, Pande VS.

Curr Opin Struct Biol. 2013 Feb;23(1):58-65. doi: 10.1016/j.sbi.2012.11.002. Epub 2012 Dec 10. Review.

23.

Simple few-state models reveal hidden complexity in protein folding.

Beauchamp KA, McGibbon R, Lin YS, Pande VS.

Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17807-13. doi: 10.1073/pnas.1201810109. Epub 2012 Jul 9.

24.

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.

Beauchamp KA, Lin YS, Das R, Pande VS.

J Chem Theory Comput. 2012 Apr 10;8(4):1409-1414. Epub 2012 Mar 12.

25.

Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer.

Lin YS, Bowman GR, Beauchamp KA, Pande VS.

Biophys J. 2012 Jan 18;102(2):315-24. doi: 10.1016/j.bpj.2011.12.002.

26.

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.

Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS.

J Chem Theory Comput. 2011 Oct 11;7(10):3412-3419.

27.

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments.

Beauchamp KA, Ensign DL, Das R, Pande VS.

Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12734-9. doi: 10.1073/pnas.1010880108. Epub 2011 Jul 18.

28.

Progress and challenges in the automated construction of Markov state models for full protein systems.

Bowman GR, Beauchamp KA, Boxer G, Pande VS.

J Chem Phys. 2009 Sep 28;131(12):124101. doi: 10.1063/1.3216567.

29.

Mycobacterial infections in striped bass from Delaware Bay.

Ottinger CA, Brown JJ, Densmore CL, Starliper CE, Blazer VS, Weyers HS, Beauchamp KA, Rhodes MW, Kator H, Gauthier DT, Vogelbein WK.

J Aquat Anim Health. 2007 Jun;19(2):99-108. doi: 10.1577/H06-023.1.

PMID:
18201050
30.

Arrested development of the myxozoan parasite, Myxobolus cerebralis, in certain populations of mitochondrial 16S lineage III Tubifex tubifex.

Baxa DV, Kelley GO, Mukkatira KS, Beauchamp KA, Rasmussen C, Hedrick RP.

Parasitol Res. 2008 Jan;102(2):219-28. Epub 2007 Sep 22.

PMID:
17891544
31.

The effect of cohabitation of Tubifex tubifex (Oligochaeta: Tubificidae) populations on infections to Myxobolus cerebralis (Myxozoa: Myxobolidae).

Beauchamp KA, El-Matbouli M, Gay M, Georgiadis MP, Nehring RB, Hedrick RP.

J Invertebr Pathol. 2006 Jan;91(1):1-8.

PMID:
16321396
32.
33.

Phylogenetic comparison of the myxosporea based on an actin cDNA isolated from Myxobolus cerebralis.

Kelley GO, Beauchamp KA, Hedrick RP.

J Eukaryot Microbiol. 2004 Nov-Dec;51(6):660-3.

PMID:
15666723
34.

Prevalence and susceptibility of infection to Myxobolus cerebralis, and genetic differences among populations of Tubifex tubifex.

Beauchamp KA, Gay M, Kelley GO, El-Matbouli M, Kathman RD, Nehring RB, Hedrick RP.

Dis Aquat Organ. 2002 Aug 29;51(2):113-21.

35.

Molecular phylogeny of tubificid oligochaetes with special emphasis on Tubifex tubifex (Tubificidae).

Beauchamp KA, Kathman RD, McDowell TS, Hedrick RP.

Mol Phylogenet Evol. 2001 May;19(2):216-24.

PMID:
11341804
36.

'Candidatus Xenohaliotis californiensis', a newly described pathogen of abalone, Haliotis spp., along the west coast of North America.

Friedman CS, Andree KB, Beauchamp KA, Moore JD, Robbins TT, Shields JD, Hedrick RP.

Int J Syst Evol Microbiol. 2000 Mar;50 Pt 2:847-55.

PMID:
10758896
37.

Pericardial tamponade: an oncologic emergency.

Beauchamp KA.

Clin J Oncol Nurs. 1998 Jul;2(3):85-95. Review.

PMID:
10232148
38.

Sequence variation of the first internal spacer (ITS-1) of ribosomal DNA in ahermatypic corals from California.

Beauchamp KA, Powers DA.

Mol Mar Biol Biotechnol. 1996 Dec;5(4):357-62.

PMID:
8983201
39.

DEVELOPMENT, METAMORPHOSIS, AND SEASONAL ABUNDANCE OF EMBRYOS AND LARVAE OF THE ANTARCTIC SEA URCHIN STERECHINUS NEUMAYERI.

Bosch I, Beauchamp KA, Steele ME, Pearse JS.

Biol Bull. 1987 Aug;173(1):126-135. doi: 10.2307/1541867.

PMID:
29314987

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