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Items: 40

1.

Cholesterol-Dependent Bending Energy Is Important in Cholesterol Distribution of the Plasma Membrane.

Allender DW, Sodt AJ, Schick M.

Biophys J. 2019 Jun 18;116(12):2356-2366. doi: 10.1016/j.bpj.2019.03.028. Epub 2019 Apr 2.

PMID:
31023537
2.

Building Blocks of the Outer Membrane: Calculating a General Elastic Energy Model for β-Barrel Membrane Proteins.

Lessen HJ, Fleming PJ, Fleming KG, Sodt AJ.

J Chem Theory Comput. 2018 Aug 14;14(8):4487-4497. doi: 10.1021/acs.jctc.8b00377. Epub 2018 Jul 19.

3.

An anatomic transcriptional atlas of human glioblastoma.

Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD.

Science. 2018 May 11;360(6389):660-663. doi: 10.1126/science.aaf2666.

4.

Neuropathological and transcriptomic characteristics of the aged brain.

Miller JA, Guillozet-Bongaarts A, Gibbons LE, Postupna N, Renz A, Beller AE, Sunkin SM, Ng L, Rose SE, Smith KA, Szafer A, Barber C, Bertagnolli D, Bickley K, Brouner K, Caldejon S, Chapin M, Chua ML, Coleman NM, Cudaback E, Cuhaciyan C, Dalley RA, Dee N, Desta T, Dolbeare TA, Dotson NI, Fisher M, Gaudreault N, Gee G, Gilbert TL, Goldy J, Griffin F, Habel C, Haradon Z, Hejazinia N, Hellstern LL, Horvath S, Howard K, Howard R, Johal J, Jorstad NL, Josephsen SR, Kuan CL, Lai F, Lee E, Lee F, Lemon T, Li X, Marshall DA, Melchor J, Mukherjee S, Nyhus J, Pendergraft J, Potekhina L, Rha EY, Rice S, Rosen D, Sapru A, Schantz A, Shen E, Sherfield E, Shi S, Sodt AJ, Thatra N, Tieu M, Wilson AM, Montine TJ, Larson EB, Bernard A, Crane PK, Ellenbogen RG, Keene CD, Lein E.

Elife. 2017 Nov 9;6. pii: e31126. doi: 10.7554/eLife.31126.

5.

Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes.

Beaven AH, Sodt AJ, Pastor RW, Koeppe RE 2nd, Andersen OS, Im W.

J Chem Theory Comput. 2017 Oct 10;13(10):5054-5064. doi: 10.1021/acs.jctc.7b00400. Epub 2017 Sep 22.

6.

Palmitoylation Contributes to Membrane Curvature in Influenza A Virus Assembly and Hemagglutinin-Mediated Membrane Fusion.

Chlanda P, Mekhedov E, Waters H, Sodt A, Schwartz C, Nair V, Blank PS, Zimmerberg J.

J Virol. 2017 Oct 13;91(21). pii: e00947-17. doi: 10.1128/JVI.00947-17. Print 2017 Nov 1.

7.

Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model.

Sodt AJ, Beaven AH, Andersen OS, Im W, Pastor RW.

Biophys J. 2017 Mar 28;112(6):1198-1213. doi: 10.1016/j.bpj.2017.01.035.

8.

Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation.

Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W.

Biophys J. 2017 Mar 28;112(6):1185-1197. doi: 10.1016/j.bpj.2017.01.028.

9.

Cation-Selective Channel Regulated by Anions According to Their Hofmeister Ranking.

Gurnev PA, Roark TC, Petrache HI, Sodt AJ, Bezrukov SM.

Angew Chem Int Ed Engl. 2017 Mar 20;56(13):3506-3509. doi: 10.1002/anie.201611335. Epub 2017 Feb 15.

10.

Nonadditive Compositional Curvature Energetics of Lipid Bilayers.

Sodt AJ, Venable RM, Lyman E, Pastor RW.

Phys Rev Lett. 2016 Sep 23;117(13):138104. Epub 2016 Sep 23.

11.

A comprehensive transcriptional map of primate brain development.

Bakken TE, Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Dalley RA, Royall JJ, Lemon T, Shapouri S, Aiona K, Arnold J, Bennett JL, Bertagnolli D, Bickley K, Boe A, Brouner K, Butler S, Byrnes E, Caldejon S, Carey A, Cate S, Chapin M, Chen J, Dee N, Desta T, Dolbeare TA, Dotson N, Ebbert A, Fulfs E, Gee G, Gilbert TL, Goldy J, Gourley L, Gregor B, Gu G, Hall J, Haradon Z, Haynor DR, Hejazinia N, Hoerder-Suabedissen A, Howard R, Jochim J, Kinnunen M, Kriedberg A, Kuan CL, Lau C, Lee CK, Lee F, Luong L, Mastan N, May R, Melchor J, Mosqueda N, Mott E, Ngo K, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry S, Pendergraft J, Potekhina L, Reding M, Riley ZL, Roberts T, Rogers B, Roll K, Rosen D, Sandman D, Sarreal M, Shapovalova N, Shi S, Sjoquist N, Sodt AJ, Townsend R, Velasquez L, Wagley U, Wakeman WB, White C, Bennett C, Wu J, Young R, Youngstrom BL, Wohnoutka P, Gibbs RA, Rogers J, Hohmann JG, Hawrylycz MJ, Hevner RF, Molnár Z, Phillips JW, Dang C, Jones AR, Amaral DG, Bernard A, Lein ES.

Nature. 2016 Jul 21;535(7612):367-75. doi: 10.1038/nature18637. Epub 2016 Jul 13.

12.

Amphipathic Helices-Wedge? Or Nae Nae?

Lyman E, Sodt AJ.

Biophys J. 2016 Jan 5;110(1):1-2. doi: 10.1016/j.bpj.2015.11.3513. No abstract available.

13.

Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin.

Sodt AJ, Pastor RW, Lyman E.

Biophys J. 2015 Sep 1;109(5):948-55. doi: 10.1016/j.bpj.2015.07.036.

14.

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

Tao P, Sodt AJ, Shao Y, König G, Brooks BR.

J Chem Theory Comput. 2014 Oct 14;10(10):4198-4207. Epub 2014 Aug 15.

15.

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

Sodt AJ, Mei Y, König G, Tao P, Steele RP, Brooks BR, Shao Y.

J Phys Chem A. 2015 Mar 5;119(9):1511-23. doi: 10.1021/jp5072296. Epub 2014 Oct 30.

16.

The Curvature Induction of Surface-Bound Antimicrobial Peptides Piscidin 1 and Piscidin 3 Varies with Lipid Chain Length.

Perrin BS Jr, Sodt AJ, Cotten ML, Pastor RW.

J Membr Biol. 2015 Jun;248(3):455-67. doi: 10.1007/s00232-014-9733-1. Epub 2014 Oct 8.

17.

CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature.

Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD Jr, Pastor RW, Klauda JB.

Biophys J. 2014 Jul 1;107(1):134-45. doi: 10.1016/j.bpj.2014.05.034.

18.

A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.

Thompson CL, Ng L, Menon V, Martinez S, Lee CK, Glattfelder K, Sunkin SM, Henry A, Lau C, Dang C, Garcia-Lopez R, Martinez-Ferre A, Pombero A, Rubenstein JLR, Wakeman WB, Hohmann J, Dee N, Sodt AJ, Young R, Smith K, Nguyen TN, Kidney J, Kuan L, Jeromin A, Kaykas A, Miller J, Page D, Orta G, Bernard A, Riley Z, Smith S, Wohnoutka P, Hawrylycz MJ, Puelles L, Jones AR.

Neuron. 2014 Jul 16;83(2):309-323. doi: 10.1016/j.neuron.2014.05.033. Epub 2014 Jun 19.

19.

Molecular modeling of lipid membrane curvature induction by a peptide: more than simply shape.

Sodt AJ, Pastor RW.

Biophys J. 2014 May 6;106(9):1958-69. doi: 10.1016/j.bpj.2014.02.037.

20.

Transcriptional landscape of the prenatal human brain.

Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, Caldejon S, Carey A, Cuhaciyan C, Dalley RA, Dee N, Dolbeare TA, Facer BA, Feng D, Fliss TP, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Howard RE, Jochim JM, Kuan CL, Lau C, Lee CK, Lee F, Lemon TA, Lesnar P, McMurray B, Mastan N, Mosqueda N, Naluai-Cecchini T, Ngo NK, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry SE, Stevens A, Pletikos M, Reding M, Roll K, Sandman D, Sarreal M, Shapouri S, Shapovalova NV, Shen EH, Sjoquist N, Slaughterbeck CR, Smith M, Sodt AJ, Williams D, Zöllei L, Fischl B, Gerstein MB, Geschwind DH, Glass IA, Hawrylycz MJ, Hevner RF, Huang H, Jones AR, Knowles JA, Levitt P, Phillips JW, Sestan N, Wohnoutka P, Dang C, Bernard A, Hohmann JG, Lein ES.

Nature. 2014 Apr 10;508(7495):199-206. doi: 10.1038/nature13185. Epub 2014 Apr 2.

21.

The molecular structure of the liquid-ordered phase of lipid bilayers.

Sodt AJ, Sandar ML, Gawrisch K, Pastor RW, Lyman E.

J Am Chem Soc. 2014 Jan 15;136(2):725-32. doi: 10.1021/ja4105667. Epub 2014 Jan 3.

22.

Bending free energy from simulation: correspondence of planar and inverse hexagonal lipid phases.

Sodt AJ, Pastor RW.

Biophys J. 2013 May 21;104(10):2202-11. doi: 10.1016/j.bpj.2013.03.048.

23.

The tension of a curved surface from simulation.

Sodt AJ, Pastor RW.

J Chem Phys. 2012 Dec 21;137(23):234101. doi: 10.1063/1.4769880.

25.

An anatomically comprehensive atlas of the adult human brain transcriptome.

Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, Miller JA, van de Lagemaat LN, Smith KA, Ebbert A, Riley ZL, Abajian C, Beckmann CF, Bernard A, Bertagnolli D, Boe AF, Cartagena PM, Chakravarty MM, Chapin M, Chong J, Dalley RA, David Daly B, Dang C, Datta S, Dee N, Dolbeare TA, Faber V, Feng D, Fowler DR, Goldy J, Gregor BW, Haradon Z, Haynor DR, Hohmann JG, Horvath S, Howard RE, Jeromin A, Jochim JM, Kinnunen M, Lau C, Lazarz ET, Lee C, Lemon TA, Li L, Li Y, Morris JA, Overly CC, Parker PD, Parry SE, Reding M, Royall JJ, Schulkin J, Sequeira PA, Slaughterbeck CR, Smith SC, Sodt AJ, Sunkin SM, Swanson BE, Vawter MP, Williams D, Wohnoutka P, Zielke HR, Geschwind DH, Hof PR, Smith SM, Koch C, Grant SGN, Jones AR.

Nature. 2012 Sep 20;489(7416):391-399. doi: 10.1038/nature11405.

26.

Depth of α-synuclein in a bilayer determined by fluorescence, neutron reflectometry, and computation.

Pfefferkorn CM, Heinrich F, Sodt AJ, Maltsev AS, Pastor RW, Lee JC.

Biophys J. 2012 Feb 8;102(3):613-21. doi: 10.1016/j.bpj.2011.12.051. Epub 2012 Feb 7.

27.

Driving forces for transmembrane alpha-helix oligomerization.

Sodt AJ, Head-Gordon T.

Biophys J. 2010 Jul 7;99(1):227-37. doi: 10.1016/j.bpj.2010.03.071.

28.

An implicit solvent coarse-grained lipid model with correct stress profile.

Sodt AJ, Head-Gordon T.

J Chem Phys. 2010 May 28;132(20):205103. doi: 10.1063/1.3408285.

29.

Predicting accurate electronic excitation transfer rates via marcus theory with Boys or Edmiston-Ruedenberg localized diabatization.

Subotnik JE, Vura-Weis J, Sodt AJ, Ratner MA.

J Phys Chem A. 2010 Aug 26;114(33):8665-75. doi: 10.1021/jp101235a.

30.

Hartree-Fock exchange computed using the atomic resolution of the identity approximation.

Sodt A, Head-Gordon M.

J Chem Phys. 2008 Mar 14;128(10):104106. doi: 10.1063/1.2828533.

PMID:
18345876
31.

The limits of local correlation theory: electronic delocalization and chemically smooth potential energy surfaces.

Subotnik JE, Sodt A, Head-Gordon M.

J Chem Phys. 2008 Jan 21;128(3):034103. doi: 10.1063/1.2821124.

PMID:
18205484
32.

Localized orbital theory and ammonia triborane.

Subotnik JE, Sodt A, Head-Gordon M.

Phys Chem Chem Phys. 2007 Nov 7;9(41):5522-30. Epub 2007 Aug 29.

PMID:
17957308
33.

Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain.

Ng L, Pathak SD, Kuan C, Lau C, Dong H, Sodt A, Dang C, Avants B, Yushkevich P, Gee JC, Haynor D, Lein E, Jones A, Hawrylycz M.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):382-93.

PMID:
17666758
34.

Genome-wide atlas of gene expression in the adult mouse brain.

Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, Estin LK, Faber C, Facer BA, Fields R, Fischer SR, Fliss TP, Frensley C, Gates SN, Glattfelder KJ, Halverson KR, Hart MR, Hohmann JG, Howell MP, Jeung DP, Johnson RA, Karr PT, Kawal R, Kidney JM, Knapik RH, Kuan CL, Lake JH, Laramee AR, Larsen KD, Lau C, Lemon TA, Liang AJ, Liu Y, Luong LT, Michaels J, Morgan JJ, Morgan RJ, Mortrud MT, Mosqueda NF, Ng LL, Ng R, Orta GJ, Overly CC, Pak TH, Parry SE, Pathak SD, Pearson OC, Puchalski RB, Riley ZL, Rockett HR, Rowland SA, Royall JJ, Ruiz MJ, Sarno NR, Schaffnit K, Shapovalova NV, Sivisay T, Slaughterbeck CR, Smith SC, Smith KA, Smith BI, Sodt AJ, Stewart NN, Stumpf KR, Sunkin SM, Sutram M, Tam A, Teemer CD, Thaller C, Thompson CL, Varnam LR, Visel A, Whitlock RM, Wohnoutka PE, Wolkey CK, Wong VY, Wood M, Yaylaoglu MB, Young RC, Youngstrom BL, Yuan XF, Zhang B, Zwingman TA, Jones AR.

Nature. 2007 Jan 11;445(7124):168-76. Epub 2006 Dec 6.

PMID:
17151600
35.

Linear scaling density fitting.

Sodt A, Subotnik JE, Head-Gordon M.

J Chem Phys. 2006 Nov 21;125(19):194109.

PMID:
17129091
36.

A near linear-scaling smooth local coupled cluster algorithm for electronic structure.

Subotnik JE, Sodt A, Head-Gordon M.

J Chem Phys. 2006 Aug 21;125(7):074116.

PMID:
16942331
37.

Advances in methods and algorithms in a modern quantum chemistry program package.

Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert AT, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA Jr, Lochan RC, Wang T, Beran GJ, Besley NA, Herbert JM, Lin CY, Van Voorhis T, Chien SH, Sodt A, Steele RP, Rassolov VA, Maslen PE, Korambath PP, Adamson RD, Austin B, Baker J, Byrd EF, Dachsel H, Doerksen RJ, Dreuw A, Dunietz BD, Dutoi AD, Furlani TR, Gwaltney SR, Heyden A, Hirata S, Hsu CP, Kedziora G, Khalliulin RZ, Klunzinger P, Lee AM, Lee MS, Liang W, Lotan I, Nair N, Peters B, Proynov EI, Pieniazek PA, Rhee YM, Ritchie J, Rosta E, Sherrill CD, Simmonett AC, Subotnik JE, Woodcock HL 3rd, Zhang W, Bell AT, Chakraborty AK, Chipman DM, Keil FJ, Warshel A, Hehre WJ, Schaefer HF 3rd, Kong J, Krylov AI, Gill PM, Head-Gordon M.

Phys Chem Chem Phys. 2006 Jul 21;8(27):3172-91. Epub 2006 Jun 12. Review.

PMID:
16902710
38.

A Fast Implementation of Perfect Pairing and Imperfect Pairing Using the Resolution of the Identity Approximation.

Sodt A, Beran GJ, Jung Y, Austin B, Head-Gordon M.

J Chem Theory Comput. 2006 Mar;2(2):300-5. doi: 10.1021/ct050239b.

PMID:
26626518
39.

Unrestricted perfect pairing: the simplest wave-function-based model chemistry beyond mean field.

Beran GJ, Austin B, Sodt A, Head-Gordon M.

J Phys Chem A. 2005 Oct 13;109(40):9183-92.

PMID:
16332028
40.

Auxiliary basis expansions for large-scale electronic structure calculations.

Jung Y, Sodt A, Gill PM, Head-Gordon M.

Proc Natl Acad Sci U S A. 2005 May 10;102(19):6692-7. Epub 2005 Apr 21.

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