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Nifedipine-Induced Shock in Pregnancy With Aortic Stenosis.

Soares C, Gilson M.

Ann Intern Med. 2019 Oct 15. doi: 10.7326/L19-0481. [Epub ahead of print] No abstract available.


Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.

Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson M.

J Chem Theory Comput. 2019 Oct 11. doi: 10.1021/acs.jctc.9b00748. [Epub ahead of print]


Long-term Safety and Clinical Benefit of Mepolizumab in Patients With the Most Severe Eosinophilic Asthma: the COSMEX Study.

Khurana S, Brusselle GG, Bel EH, FitzGerald JM, Masoli M, Korn S, Kato M, Albers FC, Bradford ES, Gilson MJ, Price RG, Humbert M.

Clin Ther. 2019 Aug 22. pii: S0149-2918(19)30350-9. doi: 10.1016/j.clinthera.2019.07.007. [Epub ahead of print]


Beyond the disconnectivity hypothesis of schizophrenia.

Rolls ET, Cheng W, Gilson M, Gong W, Deco G, Lo CZ, Yang AC, Tsai SJ, Liu ME, Lin CP, Feng J.

Cereb Cortex. 2019 Aug 5. pii: bhz161. doi: 10.1093/cercor/bhz161. [Epub ahead of print]


Antitumor Activity of 1,18-Octadecanedioic Acid-Paclitaxel Complexed with Human Serum Albumin.

Callmann CE, LeGuyader CLM, Burton ST, Thompson MP, Hennis R, Barback C, Henriksen NM, Chan WC, Jaremko MJ, Yang J, Garcia A, Burkart MD, Gilson MK, Momper JD, Bertin PA, Gianneschi NC.

J Am Chem Soc. 2019 Jul 31;141(30):11765-11769. doi: 10.1021/jacs.9b04272. Epub 2019 Jul 18.


Network analysis of whole-brain fMRI dynamics: A new framework based on dynamic communicability.

Gilson M, Kouvaris NE, Deco G, Mangin JF, Poupon C, Lefranc S, Rivière D, Zamora-López G.

Neuroimage. 2019 Nov 1;201:116007. doi: 10.1016/j.neuroimage.2019.116007. Epub 2019 Jul 12.


A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site.

Nguyen C, Yamazaki T, Kovalenko A, Case DA, Gilson MK, Kurtzman T, Luchko T.

PLoS One. 2019 Jul 10;14(7):e0219473. doi: 10.1371/journal.pone.0219473. eCollection 2019.


Screening for and management of comorbidities after a nurse-led program: results of a 3-year longitudinal study in 769 established rheumatoid arthritis patients.

Gossec L, Soubrier M, Foissac F, Molto A, Richette P, Beauvais C, Ruyssen-Witrand A, Perdriger A, Chary-Valckenaere I, Mouterde G, Dernis E, Euller-Ziegler L, Flipo RM, Gilson M, Guis S, Mariette X, Pouplin S, Marhadour T, Schaeverbeke T, Sordet C, Fayet F, Dougados M.

RMD Open. 2019 Jun 14;5(2):e000914. doi: 10.1136/rmdopen-2019-000914. eCollection 2019.


Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking.

Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE.

Structure. 2019 Aug 6;27(8):1326-1335.e4. doi: 10.1016/j.str.2019.05.012. Epub 2019 Jun 27.


A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion.

Feng M, Gilson MK.

Biophys J. 2019 May 21;116(10):1898-1906. doi: 10.1016/j.bpj.2019.04.005. Epub 2019 Apr 11.


Entropic effects enable life at extreme temperatures.

Kim YH, Leriche G, Diraviyam K, Koyanagi T, Gao K, Onofrei D, Patterson J, Guha A, Gianneschi N, Holland GP, Gilson MK, Mayer M, Sept D, Yang J.

Sci Adv. 2019 May 1;5(5):eaaw4783. doi: 10.1126/sciadv.aaw4783. eCollection 2019 May.


Is self-assessment by patients of disease activity acceptable over the long term in rheumatoid arthritis? A 3-year follow-up of 771 patients.

Gossec L, Fayet F, Soubrier M, Foissac F, Molto A, Richette P, Beauvais C, Ruyssen-Witrand A, Perdriger A, Chary-Valckenaere I, Mouterde G, Dernis E, Euller-Ziegler L, Flipo RM, Gilson M, Balandraud N, Mariette X, Pouplin S, Marhadour T, Schaeverbeke T, Sordet C, Dougados M.

Rheumatology (Oxford). 2019 Aug 1;58(8):1498-1499. doi: 10.1093/rheumatology/kez094. No abstract available.


Simulating Water Exchange to Buried Binding Sites.

Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK.

J Chem Theory Comput. 2019 Apr 9;15(4):2684-2691. doi: 10.1021/acs.jctc.8b01284. Epub 2019 Mar 13.


D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings.

Gaieb Z, Parks CD, Chiu M, Yang H, Shao C, Walters WP, Lambert MH, Nevins N, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK.

J Comput Aided Mol Des. 2019 Jan;33(1):1-18. doi: 10.1007/s10822-018-0180-4. Epub 2019 Jan 10.


Transcranial Direct Current Stimulation Does Not Counteract Cognitive Fatigue, but Induces Sleepiness and an Inter-Hemispheric Shift in Brain Oxygenation.

Borragán G, Gilson M, Guerrero-Mosquera C, Di Ricci E, Slama H, Peigneux P.

Front Psychol. 2018 Nov 30;9:2351. doi: 10.3389/fpsyg.2018.02351. eCollection 2018.


Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder.

An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ.

Science. 2018 Dec 14;362(6420). pii: eaat6576. doi: 10.1126/science.aat6576.


Discovering de novo peptide substrates for enzymes using machine learning.

Tallorin L, Wang J, Kim WE, Sahu S, Kosa NM, Yang P, Thompson M, Gilson MK, Frazier PI, Burkart MD, Gianneschi NC.

Nat Commun. 2018 Dec 7;9(1):5253. doi: 10.1038/s41467-018-07717-6.


Toward Learned Chemical Perception of Force Field Typing Rules.

Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL.

J Chem Theory Comput. 2019 Jan 8;15(1):402-423. doi: 10.1021/acs.jctc.8b00821. Epub 2018 Dec 24.


Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD.

J Comput Aided Mol Des. 2018 Oct;32(10):937-963. doi: 10.1007/s10822-018-0170-6. Epub 2018 Nov 10.


Assessment of the long-term safety of mepolizumab and durability of clinical response in patients with severe eosinophilic asthma.

Khatri S, Moore W, Gibson PG, Leigh R, Bourdin A, Maspero J, Barros M, Buhl R, Howarth P, Albers FC, Bradford ES, Gilson M, Price RG, Yancey SW, Ortega H.

J Allergy Clin Immunol. 2019 May;143(5):1742-1751.e7. doi: 10.1016/j.jaci.2018.09.033. Epub 2018 Oct 23.


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.


Cognitive Fatigue, Sleep and Cortical Activity in Multiple Sclerosis Disease. A Behavioral, Polysomnographic and Functional Near-Infrared Spectroscopy Investigation.

Borragán G, Gilson M, Atas A, Slama H, Lysandropoulos A, De Schepper M, Peigneux P.

Front Hum Neurosci. 2018 Sep 20;12:378. doi: 10.3389/fnhum.2018.00378. eCollection 2018.


Distinct modes of functional connectivity induced by movie-watching.

Demirtaş M, Ponce-Alvarez A, Gilson M, Hagmann P, Mantini D, Betti V, Romani GL, Friston K, Corbetta M, Deco G.

Neuroimage. 2019 Jan 1;184:335-348. doi: 10.1016/j.neuroimage.2018.09.042. Epub 2018 Sep 17.


Lateralized rhythmic acoustic stimulation during daytime NREM sleep enhances slow waves.

Simor P, Steinbach E, Nagy T, Gilson M, Farthouat J, Schmitz R, Gombos F, Ujma PP, Pamula M, Bódizs R, Peigneux P.

Sleep. 2018 Dec 1;41(12). doi: 10.1093/sleep/zsy176.


Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.

Li A, Gilson MK.

J Chem Phys. 2018 Aug 21;149(7):072311. doi: 10.1063/1.5027439.


Nonparametric test for connectivity detection in multivariate autoregressive networks and application to multiunit activity data.

Gilson M, Tauste Campo A, Chen X, Thiele A, Deco G.

Netw Neurosci. 2017 Dec 1;1(4):357-380. doi: 10.1162/NETN_a_00019. eCollection 2018 Winter.


Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.

Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL.

Nat Commun. 2018 Aug 6;9(1):3085. doi: 10.1038/s41467-018-05406-y.


Framework based on communicability and flow to analyze complex network dynamics.

Gilson M, Kouvaris NE, Deco G, Zamora-López G.

Phys Rev E. 2018 May;97(5-1):052301. doi: 10.1103/PhysRevE.97.052301.


Automating Installation of the Integrating Biology and the Bedside (i2b2) Platform.

Wagholikar KB, Mendis M, Dessai P, Sanz J, Law S, Gilson M, Sanders S, Vangala M, Bell DS, Murphy SN.

Biomed Inform Insights. 2018 Jun 4;10:1178222618777749. doi: 10.1177/1178222618777749. eCollection 2018. Review.


Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.

Yin J, Henriksen NM, Muddana HS, Gilson MK.

J Chem Theory Comput. 2018 Jul 10;14(7):3621-3632. doi: 10.1021/acs.jctc.8b00318. Epub 2018 Jun 22.


Extracting orthogonal subject- and condition-specific signatures from fMRI data using whole-brain effective connectivity.

Pallarés V, Insabato A, Sanjuán A, Kühn S, Mantini D, Deco G, Gilson M.

Neuroimage. 2018 Sep;178:238-254. doi: 10.1016/j.neuroimage.2018.04.070. Epub 2018 May 22.


Motor-like Properties of Nonmotor Enzymes.

Slochower DR, Gilson MK.

Biophys J. 2018 May 8;114(9):2174-2179. doi: 10.1016/j.bpj.2018.02.008.


An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ.

Nat Genet. 2018 Apr 26;50(5):727-736. doi: 10.1038/s41588-018-0107-y.


Effective Connectivity in Depression.

Rolls ET, Cheng W, Gilson M, Qiu J, Hu Z, Ruan H, Li Y, Huang CC, Yang AC, Tsai SJ, Zhang X, Zhuang K, Lin CP, Deco G, Xie P, Feng J.

Biol Psychiatry Cogn Neurosci Neuroimaging. 2018 Feb;3(2):187-197. doi: 10.1016/j.bpsc.2017.10.004. Epub 2017 Oct 23.


Substrate-driven chemotactic assembly in an enzyme cascade.

Zhao X, Palacci H, Yadav V, Spiering MM, Gilson MK, Butler PJ, Hess H, Benkovic SJ, Sen A.

Nat Chem. 2018 Mar;10(3):311-317. doi: 10.1038/nchem.2905. Epub 2017 Dec 18.


Stereotypical modulations in dynamic functional connectivity explained by changes in BOLD variance.

Glomb K, Ponce-Alvarez A, Gilson M, Ritter P, Deco G.

Neuroimage. 2018 May 1;171:40-54. doi: 10.1016/j.neuroimage.2017.12.074. Epub 2017 Dec 30.


Task-related effective connectivity reveals that the cortical rich club gates cortex-wide communication.

Senden M, Reuter N, van den Heuvel MP, Goebel R, Deco G, Gilson M.

Hum Brain Mapp. 2018 Mar;39(3):1246-1262. doi: 10.1002/hbm.23913. Epub 2017 Dec 8.


Accounting for apparent deviations between calorimetric and van't Hoff enthalpies.

Kantonen SA, Henriksen NM, Gilson MK.

Biochim Biophys Acta Gen Subj. 2018 Mar;1862(3):692-704. doi: 10.1016/j.bbagen.2017.11.020. Epub 2017 Dec 6.


D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE.

J Comput Aided Mol Des. 2018 Jan;32(1):1-20. doi: 10.1007/s10822-017-0088-4. Epub 2017 Dec 4.


Analysis of fMRI data using noise-diffusion network models: a new covariance-coding perspective.

Gilson M.

Biol Cybern. 2018 Apr;112(1-2):153-161. doi: 10.1007/s00422-017-0741-y. Epub 2017 Dec 4.


Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T.

J Chem Theory Comput. 2018 Jan 9;14(1):418-425. doi: 10.1021/acs.jctc.7b00592. Epub 2017 Dec 8.


HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions.

Assaf KI, Florea M, Antony J, Henriksen NM, Yin J, Hansen A, Qu ZW, Sure R, Klapstein D, Gilson MK, Grimme S, Nau WM.

J Phys Chem B. 2017 Dec 14;121(49):11144-11162. doi: 10.1021/acs.jpcb.7b09175. Epub 2017 Dec 1.


Effective connectivity inferred from fMRI transition dynamics during movie viewing points to a balanced reconfiguration of cortical interactions.

Gilson M, Deco G, Friston KJ, Hagmann P, Mantini D, Betti V, Romani GL, Corbetta M.

Neuroimage. 2018 Oct 15;180(Pt B):534-546. doi: 10.1016/j.neuroimage.2017.09.061. Epub 2017 Oct 9.


Resting state networks in empirical and simulated dynamic functional connectivity.

Glomb K, Ponce-Alvarez A, Gilson M, Ritter P, Deco G.

Neuroimage. 2017 Oct 1;159:388-402. doi: 10.1016/j.neuroimage.2017.07.065. Epub 2017 Aug 3.


Testing inhomogeneous solvation theory in structure-based ligand discovery.

Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK.

Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):E6839-E6846. doi: 10.1073/pnas.1703287114. Epub 2017 Jul 31.


Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED.

J Comput Aided Mol Des. 2017 Aug;31(8):777. doi: 10.1007/s10822-017-0043-4. No abstract available.


Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters.

Henriksen NM, Gilson MK.

J Chem Theory Comput. 2017 Sep 12;13(9):4253-4269. doi: 10.1021/acs.jctc.7b00359. Epub 2017 Aug 4.


Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain.

Heinzelmann G, Henriksen NM, Gilson MK.

J Chem Theory Comput. 2017 Jul 11;13(7):3260-3275. doi: 10.1021/acs.jctc.7b00275. Epub 2017 Jun 13.


Attractive Interactions between Heteroallenes and the Cucurbituril Portal.

Reany O, Li A, Yefet M, Gilson MK, Keinan E.

J Am Chem Soc. 2017 Jun 21;139(24):8138-8145. doi: 10.1021/jacs.6b13005. Epub 2017 Jun 7.


Predicting Binding Free Energies: Frontiers and Benchmarks.

Mobley DL, Gilson MK.

Annu Rev Biophys. 2017 May 22;46:531-558. doi: 10.1146/annurev-biophys-070816-033654. Epub 2017 Apr 7. Review.

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