2017 Publications

Slide 1 Pociask DA, Robinson KM, Chen K, McHugh KJ, Clay ME, Huang GT, Benos PV, Janssen-Heininger YM, Kolls JK, Anathy V, Alcorn JF (2017) Epigenetic and Transcriptomic Regulation of Lung Repair during Recovery from Influenza Infection. Am J Pathol.  [Epub ahead of print].
carv-img Domazet-Loso T, Carvunis AR, M. Mar Alba, Sestak MS, Bakaric R, Neme R, Tautz D (2017) No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution Molecular Biology and Evolution 34(4):843-856.
Bahar I, Jernigan R, Dill K. (2017) Protein Actions: Principles & Modeling. New York, NY: Garland Science, Taylor & Francis Group
ddi-disco Kaltenmeier CT, Vollmer LL, Vernetti LA, Caprio L, Davis K, Korotchenko VN, Day BW, Tsang M, Hulkower KI, Lotze MT, Vogt A (2017) A tumor cell-selective inhibitor of mitogen-activated protein kinase phosphatases sensitizes breast cancer cells to lymphokine-activated killer cell activity. J Pharmacol Exp Ther.  [Epub ahead of print]

 

srep42296-f1 Vernetti L, Gough A, Baetz N, Blutt S, Broughman JR, Brown JA, Foulke-Abel J, Hasan N, In J, Kelly E, Kovbasnjuk O, Repper J, Senutovitch N, Stabb J, Yeung C, Zachos NC, Donowitz M, Estes M, Himmelfarb J, Truskey G, Wikswo JP, Taylor DL (2017) Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle. Sci Rep. 7:42296.
effect-of-dimerization Gur M, Cheng MH, Zomot E, Bahar I (2017) Effect of Dimerization on the Dynamics of Neurotransmitter: Sodium Symporters  J Phys Chem B [Epub ahead of print].
Ye Z, Needham PG, Estabrooks SK, Whitaker SK, Garcia BL, Misra S, Brodsky JL, Camacho CJ. (2017) Symmetry breaking during homodimeric assembly activates an E3 ubiquitin ligase. Sci Rep. 7(1):1789.
  Pabon NA, Camacho CJ. (2017) Probing protein flexibility reveals a mechanism for selective promiscuity. Elife 6. pii: e22889.
  Benos PV, Tosun BA, Manatakis DV, Vukmirovic M, Nguyen L, Yan X, Hu B, Deluliis G, Woolard T, Maya JD, Homer R, Kaminski N, Chennubhotla CS (2017) Towards Understanding Spatial Lung Tissue Heterogeneity In Idiopathic Pulmonary Fibrosis (IPF) A72. Mechanisms Driving Fibrosis A2384-A2384.

 

Narayanan C, Bernard DN, Bafna K, Choudhary OP, Chennubhotla CS, Agarwal PK, Doucet N (2017) Conformational Motions Impacting Function in an Enzyme Superfamily The FASEB Journal 31 (1 Supplement), 762.6-762.6

 

Jones T, Nguyen L, Tosun BA, Chennubhotla CS, Fine JL (2017) Computational Pathology versus Manual Microscopy: Comparison Based on Workflow Simulations of Breast Core Biopsies Laboratory Investigation 97, 398A-398A.

 

Overacre-Delgoffe AE, Chikina M, Dadey RE, Yano H, Brunazzi EA, Shayan G, Horne W, Moskovitz JM, Kolls JK, Sander C, Shuai Y, Normolle DP, Kirkwood JM, Ferris RL, Delgoffe GM, Bruno TC, Workman CJ, Vignali DAA. (2017) Interferon-γ Drives Treg Fragility to Promote Anti-tumor Immunity. Cell [Epub ahead of print]
Chikina M, Frieze A, Pegden W (2017) Assessing significance in a Markov chain without mixing. Proc Natl Acad Sci U S A. 114(11):2860-2864.
Kaya C, Cheng MH, Block ER, Sorkin A, Faeder JR, Bahar I (2017) Effect of Spatial Complexity on Dopaminergic Signaling Revealed from Multiscale Simulations Biophysical Journal 112 (3), 135a.

 

Soto-Gutierrez A, Gough A, Vernetti LA, Taylor DL, Monga SP. (2017) Pre-clinical and clinical investigations of metabolic zonation in liver diseases: The potential of microphysiology systems. Exp Biol Med (Maywood):1535370217707731. doi: 10.1177/1535370217707731. [Epub ahead of print] PMID: 28467181

 

Ragoza M, Hochuli J, Idrobo E, Sunseri J, Koes DR (2017) Protein-Ligand Scoring with Convolutional Neural Networks Journal of Chemical Information and Modeling 57 (4), 942-957
Sunseri J, Koes DR, Roy P, Gau D (2017) Characterization of Profilin Binding Kinetics using Ensemble Molecular Dynamics Simulations Biophysical Journal 112 (3), 287a

 

Koes DR, Vries J (2017) Error assessment in molecular dynamics trajectories using computed NMR chemical shifts Computational and Theoretical Chemistry 1099, 152-166
  Morel PA, Lee REC, Faeder JR Demystifying the cytokine network: Mathematical models point the way Cytokine [Epub ahead of print].
  Bergman S and Lezon TR. (2017). Modeling global changes induced by local perturbations to the HIV-1 capsid. J Mol Graphics Modelling 71:218-226 PMID: 27951510
  Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, Croix CS, Dar H, Liu B, Tyurin VA, Ritov VB, Kapralov OA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli R, Stockwell BR, Tyurina YY, Conrad M, Bayir H. (2017) Oxidized Arachidonic and Adrenic PEs Navigate Cells to Ferroptosis, Nature Chemical Biology,13:81-90
  D’Aiuto L, Williamson K, Dimitrion P, McNulty J, Brown CE, Dokuburra CB, Nielsen AJ, Lin WJ, Piazza P, Schurdak ME, Wood J, Yolken RH, Kinchington PR, Bloom DC, Nimgaonkar VL.
(2017) Comparison of three cell-based drug screening platforms for HSV-1 infection. Antiviral Res 2:136-140.
Bahreini A, Li Z, Wang P, Levine KM, Tasdemir N, Cao L, Weir HM, Puhalla SL, Davidson NE, Stern AM, Chu D, Park BH, Lee AV, Oesterreich S. (2017) Mutation site and context dependent effects of ESR1 mutation in genome-edited breast cancer cell models. Breast Cancer Res 19(1):60.

 

Lee-Montiel FT, George SM, Gough AH, Sharma AD, Wu J, DeBiasio R, Vernetti LATaylor DL. (2017) Control of oxygen tension recapitulates zone-specific functions in human liver microphysiology systems. Exp Biol Med (Maywood). 1:1535370217703978. [Epub ahead of print]

 

Nguyen L, Tosun AB, Fine J, Lee A, Taylor DL, Chennubhotla C. (2017) Spatial statistics for segmenting histological structures in H&E stained tissue images. IEEE Trans Med Imaging. [Epub ahead of print]

 

Vernetti L, Gough A, Baetz N, Blutt S, Broughman JR, Brown JA, Foulke-Abel J, Hasan N, In J, Kelly E, Kovbasnjuk O, Repper J, Senutovitch N, Stabb J, Yeung C, Zachos NC, Donowitz M, Estes M, Himmelfarb J, Truskey G, Wikswo JP, Taylor DL. (2017) Corrigendum: Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle. Sci Rep.7:44517.

 

Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla SC, Schurdak ME, Haney SA, Taylor DL. (2017) Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS Discov. (3):213-237.

 

Zhang J, Tian XJ, Chen YJ, Wang W, Watkins S, Xing J Cells Interpret Temporal Information From TGF-β Through A Nested Relay Mechanism bioRxiv, 134106

 

Sauerwald N, Zhang S, Kingsford C, Bahar I. (2017) Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings Nucleic Acids Research 45:3663-3673

 

Li H, Chang YY, Lee JY, Bahar I, Yang LW. (2017) DynOmics: dynamics of structural proteome and beyond Nucleic Acids Research.

 

Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y. (2017) Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis EBioMedicine 15:48-61 .

 

Mao G, Qu F, Angeli JP, Doll S, S. Croix C, Dar H, Liu B, Tyurin V, Ritov V, Kapralov O, Amoscato A, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli R, Stockwell B, Tyurina Y, Conrad M, Bayir H, Kagan V (2017) Oxidized Arachidonic and Adrenic Phosphatidylethanolamines Navigate Cells to Ferroptosis Nature Chemical Biology 13:81-90.
Cheng MH, Garcia-Olivares J, Wasserman S, DiPietro J, Bahar I (2017) Allosteric Modulation of Human Dopamine Transporter Activity under Conditions Promoting its Dimerization J Biol Chem [Epub ahead of print].
Cheng MH, Torres-Salazar D, Gonzalez-Suarez AD, Amara SG, Bahar I (2017) Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters. eLife [Epub ahead of print].
Hukriede N, Vogt A, de Caestecker M (2017) Drug Discovery to Halt the Progression of Acute Kidney Injury to Chronic Kidney Disease: A Case for Phenotypic Drug Discovery in Acute Kidney Injury Nephron [Epub ahead of print].
Matte-Martone C, Liu J, Zhou M, Chikina M, Green DR, Harty JT, Shlomchik WD (2017) Differential requirements for myeloid leukemia IFN-γ conditioning determine graft-versus-leukemia resistance and sensitivity J Clin Invest [Epub ahead of print].
Meslin C, Cherwin TS, Plakke MS, Small BS, Goetz BJ, Morehouse NI, Clark NL (2017) Structural complexity and molecular heterogeneity of a butterfly ejaculate reflect a complex history of selection Proc Natl Acad Sci U S A. [Epub ahead of print].
Li H, Sharma N, General IJ, Schreiber G, Bahar I (2017) Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling J Mol Biol. [Epub ahead of print].
Koes DR, Vries JK (2017) Evaluating Amber force fields using computed NMR chemical shifts Proteins [Epub ahead of print].
Ma S, Cheng MH, Guthrie DA, Newman AH, Bahar I, Sorkin A (2017) Targeting of dopamine transporter to filopodia requires an outward-facing conformation of the transporter Sci Rep 7(1):5399.
Shun T, Gough AH, Sanker S, Hukriede NA, Vogt A (2017) Exploiting Analysis of Heterogeneity to Increase the Information Content Extracted from Fluorescence Micrographs of Transgenic Zebrafish Embryos Assay Drug Dev Technol. Epub ahead of print].
Zhang Q, Chikina M, Szymczak-Workman AL, Horne W, Kolls JK, Vignali KM, Normolle D, Bettini M, Workman CJ, Vignali DAA (2017) LAG3 limits regulatory T cell proliferation and function in autoimmune diabetes Sci Immunol. 2(9).
Gough A, Vernetti L, Bergenthal L, Shun TY, Taylor DL (2017) The Microphysiology Systems Database for Analyzing and Modeling Compound Interactions with Human and Animal Organ Models Appl In Vitro Toxicol. 2(2):103-117.
Kulkarni S, Dolezal JM, Wang H, Jackson L, Lu J, Frodey BP, Dosunmu-Ogunbi A, Li Y, Fromherz M, Kang A, Santana-Santos L, Benos PV, Prochownik EV (2017) Ribosomopathy-like properties of murine and human cancers PLoS One 12(8):e0182705.
Faeder JR, Sheehan RP, Hawse WF, Gable MJ, Lee REC, Morel PA (2017) Unraveling how T cell antigen receptor signaling strength determines T cell differentiation using a combined experimental and computational approach The Journal of Immunology 
Tyurina YY, Shrivastava I, Tyurin VA, Mao G, Dar HH, Watkins S, Epperly M, Bahar I, Shvedova AA, Pitt B, Wenzel SE, Mallampalli RK, Sadovsky Y, Gabrilovich D, Greenberger JS, Bayır H, Kagan VE (2017) “Only a life lived for others is worth living:” Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions. Antioxid Redox Signal [Epub ahead of print].

 

Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA (2017) Improvements to the APBS biomolecular solvation software suite. Protein Sci [Epub ahead of print].

 

Mikulska-Ruminska K, Kulik AJ, Benadiba C, Bahar I, Dietler G, Nowak W (2017) Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Sci Rep 7(1):8852.
Suofu Y, Li W, Jean-Alphonse FG, Jia J, Khattar NK, Li J, Baranov SV, Leronni D, Mihalik AC, He Y, Cecon E, Wehbi VL, Kim J, Heath BE, Baranova OV, Wang X, Gable MJ, Kretz ES, Di Benedetto G, Lezon TR, Ferrando LM, Larkin TM, Sullivan M, Yablonska S, Wang J, Minnigh MB, Guillaumet G, Suzenet F, Richardson RM, Poloyac SM, Stolz DB, Jockers R, Witt-Enderby PA, Carlisle DL, Vilardaga JP, Friedlander RM (2017) Dual role of mitochondria in producing melatonin and driving GPCR signaling to block cytochrome c release. Proc Natl Acad Sci U S A [Epub ahead of print].
 

Nguyen L, Tosun AB, Fine JL, Taylor DL, Chennubhotla SC (2017) ARCHITECTURAL PATTERNS FOR DIFFERENTIAL DIAGNOSIS OF PROLIFERATIVE BREAST LESIONS FROM HISTOPATHOLOGICAL IMAGES Proc IEEE Int Symp Biomed Imaging 2017:152-155.

Koes DR, Dömling A, Camacho CJ (2017) AnchorQuery: Rapid online virtual screening for small-molecule protein-protein interaction inhibitors. Protein Sci. [Epub ahead of print].
Wingert BM, Oerlemans R, Camacho CJ (2017) Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges. J Comput Aided Mol Des. [Epub ahead of print].

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