2019 Publications

 

Zhang S, Li H, Krieger JM, Bahar I. Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity. 2019 Apr 27. Molecular Biology and Evolution.
Tapia J, Saglam AS, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Faeder JR. MCell-R: A particle-resolution network-free spatial modeling framework. 2019. Modeling Biomolecular Site Dynamics; 1945: 203-229.
Sawant DV, Yano H, Chikina M, Zhang Q, Liao M, Liu C, Callahan DJ, Sun Z, Sun T, Tabib T, Pennathur A, Corry DB, Luketich JD, Lafyatis R, Chen W, Poholek AC, Bruno TC, Workman CJ, Vignali DAA. Adaptive plasticity of IL-10+ and IL-35+ Treg cells cooperatively promotes tumor T cell exhaustion. 2019 Apr 01. Nature Immunology.
Li Y, Cifuentes-Pagano E, DeVallance ER, de Jesus DS, Meijles DN, Koes D, Camacho CJ, Ross M, St Croix C, Pagano PJ. NADPH oxidase 2 inhibitors CPP11G and CPP11H attenuate endothelial cell inflammation & vessel dysfunction and restore mouse hind-limb flow. Redox Biol. 2019;22:101143. doi:10.1016/j.redox.2019.101143
Raghu VK, Zhao W, Pu J, Leader JK, Wang R, Herman J, Yuan, J, Benos PV, Wilson DO. Feasibility of lung cancer prediction from low-dose CT scan and smoking factor using causal models. Thorax. Published Online First: 12 March 2019. doi: 10.1136/thoraxjnl-2018-212638
Pei F, Li H, Liu B, Bahar I. Quantitative Systems Pharmacological Analysis of Drugs of Abuse Reveals the Pleiotropy of Their Targets and the Effector Role of mTORC1. Front Pharmacol. 2019;10:191. Published 2019 Mar 8. doi:10.3389/fphar.2019.00191
Abecassis I, Sedgewick AJ, Romkes M, Buch S, Nukui T, Kapetanaki MG, Vogt A, Kirkwood JM, Benos PV. PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy. Sci Rep. 2019;9(1):3309. Published 2019 Mar 1. doi:10.1038/s41598-019-39542-2
Pabon NA, Zhang Q, Cruz JA, Schipper DL, Camacho CJ, Lee REC. A network-centric approach to drugging TNF-induced NF-κB signaling. Nat Commun. 2019;10(1):860. Published 2019 Feb 26. doi:10.1038/s41467-019-08802-0
Mikulska-Rauminska K, Shrivastava I, Krieger, J, Zhang S, Li H, Bayir B, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. 2019 Feb 14. Journal of Chemical Information and Modeling.
Raza Q, Choi JY, Li Y, O’Dowd RM, Watkins SC, Chikina M, Hong Y, Clark NL, Kwiatkowski AV. Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila. PLoS Genet. 2019;15(2):e1007720. Published 2019 Feb 14. doi:10.1371/journal.pgen.1007720
Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. (2019) Allostery in Its Many Disguises: From Theory to Applications. Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. PMID: 30744993
Lee J Y, Krieger J, Herguedas B, Garcca-Nafrra J, Dutta A, Shaikh SA, Greger IH, Bahar I. (2019) Druggability Simulations and X-ray Crystallography Reveal a Ligand-binding Site in the GluA3 AMPA Receptor N-terminal Domain. Structure. doi:10.2139/ssrn.3188417
Wang Y, Cobanoglu MC, Li J, Hidvegi T, Hale P, Ewing M, Chu AS, Gong Z, Muzumdar R, Pak SC, Silverman GA, Bahar I, Perlumtter DH. (2019) An analog of glibenclamide selectively enhances autophagic degradation of misfolded α1-antitrypsin Z. PLoS ONE 14(1): e0209748. https://doi.org/10.1371/journal.pone.0209748
Asan A, Skoko JJ, Woodcock CC, Wingert BM, Woodcock SR, Normolle D, Huang Y, Stark JM, Camacho CJ, Freeman BA, Neumann CA. Electrophilic fatty acids impair RAD51 function and potentiate the effects of DNA-damaging agents on growth of triple-negative breast cells. (2019) Jan 11. Journal of Biological Chemistry, 294(2), 397-404.
Wang KZQ, Steer E, Otero PA, Bateman NW, Cheng MH, Scott AL, Wu C, Bahar I, Shih YT, Hsueh YP, Chu CT. PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. eNeuro. 2018;5(6):ENEURO.0466-18.2018. Published 2018 Jan 10. doi:10.1523/ENEURO.0466-18.2018
Cheikhi A, Wallace C, St Croix C, Cohen C, Tang W, Wipf P, Benos PV, Ambrosio F, Barchowsky A. Mitochondria are a substrate of cellular memory. (2019) Free Radical Biology and Medicine, 130, 528-541. https://doi.org/10.1016/j.freeradbiomed.2018.11.028
Sunseri J, King JE, Francoeur PG, Koes DR. Convolutional neural network scoring and minimization in the D3R 2017 community challenge. 2019. Journal of Computer-Aided Molecular Design; 33(1):19-34.

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