2021 Publications

Sutkeviciuta I, Lee JY, White AD, Maria CS, Peña KA, Savransky S, Doruker P, Li H, Lei S, Kaynak B, Tu C, Clark LJ, Sanker S, Gardella TJ, Chang W, Bahar I* and Vilardaga JP*. (2021) Precise druggability of the PTH type 1 receptor. Nature Chem Biol. Online ahead of print.
Gau D, Vignaud L, Francoeur P, Koes DR, Guillonneau X, Roy P (2021) Inhibition of ocular neovascularization by novel anti-angiogenic compound. Exp Eye Res. 213:108861. doi: 10.1016/j.exer.2021.108861.
Cruz T, Jia M, Sembrat J, Tabib T, Agostino N, Bruno TC, Vignali D, Sanchez P, Lafyatis R, Mora AL, Benos PV, Rojas M (2021). Reduced Proportion and Activity of Natural Killer Cells in the Lung of Patients with Idiopathic Pulmonary Fibrosis Am J Respir Crit Care Med. Sep 1;204(5):608-610.
Belovich AN, Aguilar JI, Mabry SJ, Cheng MH, Zanella D, Hamilton PJ, Stanislowski DJ, Shekar A, Foster JD, Bahar I, Matthies HJG, Galli A (2021). A network of phosphatidylinositol (4,5)-bisphosphate (PIP 2) binding sites on the dopamine transporter regulates amphetamine behavior in Drosophila Melanogaster Mol Psychiatry. Aug;26 (8):4417-4430.
King JE, Koes DR (2021) SidechainNet: An all-atom protein structure dataset for machine learning. Protein. 89(11):1489-1496.
Kowalczyk A, Gbadamosi O, Kolor K, Sosa J, Andrzejczuk L, Gibson GA, Chikina M . . . Kiselyov K. (2021). Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter. Biochem J. doi:10.1042/bcj20210342
Chen F, Shi Q, Pei F, Vogt A, Porritt RA, Garcia G Jr, . . . Bahar I. (2021). A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection. Mol Syst Biol, 17(8), e10239.
Francoeur PG, & Koes DR. (2021). Correction to "SolTranNet-A Machine Learning Tool for Fast Aqueous Solubility Prediction". J Chem Inf Model. doi:10.1021/acs.jcim.1c00806
Cruz JA, Mokashi, CS, Kowalczyk GJ, Guo Y, Zhang Q, Gupta S, . . . Lee REC. (2021). A variable-gain stochastic pooling motif mediates information transfer from receptor assemblies into NF-κB. Sci Adv, 7(30). doi:10.1126/sciadv.abi9410
Erdem C, Lee AV, Taylor DL, & Lezon TR. (2021). Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells. PLoS Comput Biol, 17(6), e1009125. doi:10.1371/journal.pcbi.1009125
Tabib T, Huang M, Morse N, Papazoglou A, Behera R, Jia M, Benos PV . . . Lafyatis R. (2021). Myofibroblast transcriptome indicates SFRP2(hi) fibroblast progenitors in systemic sclerosis skin. Nat Commun, 12(1), 4384. doi:10.1038/s41467-021-24607-6
Molina LM, Zhu J, Li Q, Pradhan-Sundd T, Krutsenko Y, Sayed K, Benos PV . . . Monga SP. (2021). Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors. Cell Rep, 36(1), 109310. doi:10.1016/j.celrep.2021.109310\

Chen A, Jiang Y, Li Z, Wu L, Santiago U, Zou H, Cai C, Sharma V, Guan Y, McCarl LH, Ma J, Wu YL, Michel J, Shi Y, Konnikova L, Amankulor NM, Zinn PO, Kohanbash G, Agnihotri S, Lu S, Lu X, Sun D, Gittes GK, Wang Q, Xiao X, Yimlamai D, Pollack IF, Camacho CJ, Hu B (2021) Chitinase-3-like 1 protein complexes modulate macrophage-mediated immune suppression in glioblastoma. J Clin Invest, 131(16):e147552. doi: 10.1172/JCI147552.
Zhang Y, Zhang S, Xing J, & Bahar I. (2021). Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis. J Chem Phys, 154(19), 195102. doi:10.1063/5.0046710

Kaynak BT, Zhang S, Bahar I, & Doruker P. (2021). ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution. Bioinformatics. doi:10.1093/bioinformatics/btab496

King, J. E., & Koes DR. (2021). SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning. Proteins. doi:10.1002/prot.26169
Green H, Koes DR, & Durrant JD. (2021). DeepFrag: a deep convolutional neural network for fragment-based lead optimization. Chem Sci, 12(23), 8036-8047. doi:10.1039/d1sc00163a
Francoeur PG, & Koes DR. (2021). SolTranNet-A Machine Learning Tool for Fast Aqueous Solubility Prediction. J Chem Inf Model, 61(6), 2530-2536. doi:10.1021/acs.jcim.1c00331
Aggarwal S, Cheng MH, Salvino JM, Bahar I, & Mortensen OV. (2021). Functional Characterization of the Dopaminergic Psychostimulant Sydnocarb as an Allosteric Modulator of the Human Dopamine Transporter. Biomedicines, 9(6). doi:10.3390/biomedicines9060634
Mao W, Rahimikollu J, Hausler R, & Chikina M. (2021). DataRemix: a universal data transformation for optimal inference from gene expression datasets. Bioinformatics, 37(7), 984-991. doi:10.1093/bioinformatics/btaa745
Ramos I, Goforth C, Soares-Schanoski A, Weir DL, Samuels EC, Phogat S, Chikina M, . . . Letizia, A. G. (2021). Antibody Responses to SARS-CoV-2 Following an Outbreak Among Marine Recruits With Asymptomatic or Mild Infection. Front Immunol, 12, 681586. doi:10.3389/fimmu.2021.681586
Vogt A, Eicher SL, Myers TD, Hrizo SL, Vollmer LL, Meyer EM, & Palladino MJ. (2021). A High-Content Screening Assay for Small Molecules That Stabilize Mutant Triose Phosphate Isomerase (TPI) as Treatments for TPI Deficiency. SLAS Discov, 24725552211018198. doi:10.1177/24725552211018198
Aguilar JI, Cheng MH, Font J, Schwartz AC, Ledwitch K, Duran A, Bahar I . . . Galli A. (2021). Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia. Elife, 10. doi:10.7554/eLife.68039
Sun WY, Tyurin VA, Mikulska-Ruminska K, Shrivastava IH, Anthonymuthu T S, Zhai YJ, Bahar I . . . Kagan VE. (2021). Phospholipase iPLA(2)β averts ferroptosis by eliminating a redox lipid death signal. Nat Chem Biol, 17(4), 465-476. doi:10.1038/s41589-020-00734-x
McNutt AT, Francoeur P, Aggarwal R, Masuda T, Meli R, Ragoza M, . . . Koes DR. (2021). GNINA 1.0: molecular docking with deep learning. J Cheminform, 13(1), 43. doi:10.1186/s13321-021-00522-2
Kitsios GD, Kotok D, Yang H, Finkelman MA, Zhang Y, Britton N, Benos PV . . . Morris A. (2021). Plasma 1,3-beta-D-glucan levels predict adverse clinical outcomes in critical illness. JCI Insight. doi:10.1172/jci.insight.141277
Raghu VK, Horvat CM, Kochanek PM, Fink EL, Clark RSB, Benos PV, & Au AK. (2021). Neurological Complications Acquired During Pediatric Critical Illness: Exploratory "Mixed Graphical Modeling" Analysis Using Serum Biomarker Levels. Pediatr Crit Care Med. doi:10.1097/pcc.0000000000002776
Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Benos PV . . . Kaminski N. (2021). Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. Eur Respir J. doi:10.1183/13993003.02950-2020
Raghu VK, Ge X, Balajiee A, Shirer DJ, Das, I., Benos PV, & Chrysanthis PK. (2021). A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. IEEE/ACM Trans Comput Biol Bioinform, 18(3), 811-822. doi:10.1109/tcbb.2020.3019237
Kowalczyk GJ, Cruz JA, Guo Y, Zhang Q, Sauerwald N, & Lee REC. (2021). dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells. Bioinformatics, 37(5), 677-683. doi:10.1093/bioinformatics/btaa874
Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G Jr, . . . Bahar I. (2021). A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro. Structure. 29(9):951-962
Wingert B, Krieger J, Li H, & Bahar I. (2021). Adaptability and specificity: how do proteins balance opposing needs to achieve function? Curr Opin Struct Biol, 67, 25-32. doi:10.1016/j.sbi.2020.08.009
Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, . . . Bahar I. (2021). State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Prog Biophys Mol Biol, 160, 104-120. doi:10.1016/j.pbiomolbio.2020.08.006
Pei F, Shi Q, Zhang H, Bahar I. (2021) Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J Chem Inf Model [Online ahead of print].
Chesnokov MS, Halasi M, Borhani S, Arbieva Z, Shah BN, Oerlemans R, Khan I, Camacho CJ, Gartel AL (2021) Novel FOXM1 inhibitor identified via gene network analysis induces autophagic FOXM1 degradation to overcome chemoresistance of human cancer cells Cell Death Dis. 12(7): 704. doi: 10.1038/s41419-021-03978-0.
Boughton CK, Daly A, Thabit H, Hartnell S, Herzig D, Vogt A, . . . Hovorka R. (2021). Day-to-day variability of insulin requirements in the inpatient setting: observations during fully closed-loop insulin delivery. Diabetes Obes Metab. doi:10.1111/dom.14396
Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, . . . Bahar I. (2021). ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. Bioinformatics. doi:10.1093/bioinformatics/btab187
Gough A, Soto-Gutierrez A, Vernetti L, Ebrahimkhani MR, Stern AM, & Taylor DL (2021). Human biomimetic liver microphysiology systems in drug development and precision medicine. Nat Rev Gastroenterol Hepatol, 18(4), 252-268. doi:10.1038/s41575-020-00386-1
Lee CS, Berg JM, & Berg W A. (2021). Cancer Yield Exceeds 2% for BI-RADS 3 Probably Benign Findings in Women Older Than 60 Years in the National Mammography Database. Radiology, 204031. doi:10.1148/radiol.2021204031
Saputra E, Kowalczyk A, Cusick L, Clark N, & Chikina M. (2021). Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations in a phylogenetic context. Mol Biol Evol. doi:10.1093/molbev/msab068
Valenzi E, Yang H, Sembrat JC, Yang L, Winters S, Nettles R, Benos PV . . . Kitsios, G. D. (2021). Topographic heterogeneity of lung microbiota in end-stage idiopathic pulmonary fibrosis: the Microbiome in Lung Explants-2 (MiLEs-2) study. Thorax, 76(3), 239-247. doi:10.1136/thoraxjnl-2020-214770
Porritt RA, Paschold L, Noval Rivas M, Cheng MH, Yonker LM, Chandnani H, Bahar I . . . Arditi, M. (2021). HLA class I-associated expansion of TRBV11-2 T cells in Multisystem Inflammatory Syndrome in Children. J Clin Invest. doi:10.1172/jci146614
Brand RM, Moore BA, Zyhowski A, Siegel A, Uttam S, Metter EJ, . . . McGowan I. (2021). Tofacitinib inhibits inflammatory cytokines from ulcerative colitis and healthy mucosal explants and is associated with pSTAT1/3 reduction in T-cells. Am J Physiol Gastrointest Liver Physiol, 320(3), G396-g410. doi:10.1152/ajpgi.00383.2020
Parikh SB, Castilho Coelho N, & Carvunis AR. (2021). LI Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects. G3 (Bethesda), 11(2). doi:10.1093/g3journal/jkaa068
Folmsbee DL, Koes DR, & Hutchison GR. (2021). Evaluation of Thermochemical Machine Learning for Potential Energy Curves and Geometry Optimization. J Phys Chem A. doi:10.1021/acs.jpca.0c10147
Sorkina T, Cheng MH, Bagalkot TR, Wallace C, Watkins SC, Bahar I, & Sorkin A. (2021). Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity. J Biol Chem, 100430. doi:10.1016/j.jbc.2021.100430
Wacholder A, & Carvunis AR. (2021). New genes from borrowed parts. Science, 371(6531), 779-780. doi:10.1126/science.abf8493
Hrizo SL, Eicher SL, Myers TD, McGrath I, Wodrich APK, Venkatesh H, Vogt A . . . Palladino MJ. (2021). Identification of protein quality control regulators using a Drosophila model of TPI deficiency. Neurobiol Dis, 105299. doi:10.1016/j.nbd.2021.105299
Sun WY, Tyurin VA, Mikulska-Ruminska K, Shrivastava IH, Anthonymuthu TS, Zhai YJ, Bahar I, . . . Kagan VE. (2021). Phospholipase iPLA(2)β averts ferroptosis by eliminating a redox lipid death signal. Nat Chem Biol. doi:10.1038/s41589-020-00734-x
Cillo AR, Somasundaram A, Shan F, Cardello C, Workman CJ, Kitsios GD, Benos PV . . . Vignali DAA. (2021). Bifurcated monocyte states are predictive of mortality in severe COVID-19. bioRxiv. doi:10.1101/2021.02.10.430499
Stewart-Ornstein J, Iwamoto Y, Miller MA, Prytyskach MA, Ferretti S, Holzer P, . . . Lahav G. (2021). p53 dynamics vary between tissues and are linked with radiation sensitivity. Nat Commun, 12(1), 898. doi:10.1038/s41467-021-21145-z
Meirovitch H, & Bahar I. (2021). Harold A. Scheraga (10/18/1921-8/1/2020): A pioneering scientist who laid the foundations of protein science in the 20th century. Proc Natl Acad Sci USA, 118(8). doi:10.1073/pnas.2026796118
Wang H, Pei F, Vanyukov MM, Bahar I, Wu W, & Xing E P. (2021). Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. BMC Bioinformatics, 22(1), 50. doi:10.1186/s12859-021-03959-2
Bhullar KS, Son M, Kerek E, Cromwell CR, Wingert BM, Wu K, Camacho CJ, . . . Wu J. (2021). Tripeptide IRW Upregulates NAMPT Protein Levels in Cells and Obese C57BL/6J Mice. J Agric Food Chem. doi:10.1021/acs.jafc.0c07831
Tripathi S, Xing J, Levine H, & Jolly MK (2021). Mathematical Modeling of Plasticity and Heterogeneity in EMT. Methods Mol Biol, 2179, 385-413. doi:10.1007/978-1-0716-0779-4_28
Sakolish C, Reese CE, Luo YS, Valdiviezo A, Schurdak ME, Gough A, Taylor DL . . . Rusyn I (2021). Analysis of reproducibility and robustness of a human microfluidic four-cell liver acinus microphysiology system (LAMPS). Toxicology, 448, 152651. doi:10.1016/j.tox.2020.152651
Ramanathan A, Ma H, Parvatikar A, & Chennubhotla SC (2021). Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins. Curr Opin Struct Biol, 66, 216-224. doi:10.1016/j.sbi.2020.12.001
Vakirlis N, Acar O, Hsu B, Coelho NC, Van Oss SB, Wacholder A, . . . Carvunis AR, Camacho CJ(2021). Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun, 12(1), 200. doi:10.1038/s41467-020-20609-y
Cárdenes N, Sembrat J, Noda K, Lovelace T, Álvarez D, Bittar HET, Benos PV . . . Rojas, M. (2021). Human ex vivo lung perfusion: a novel model to study human lung diseases. Sci Rep, 11(1), 490. doi:10.1038/s41598-020-79434-4
Zheng F, Zhang S, Churas C, Pratt D, Bahar I, & Ideker T (2021). HiDeF: identifying persistent structures in multiscale 'omics data. Genome Biol, 22(1), 21. doi:10.1186/s13059-020-02228-4
Noval Rivas M, Porritt RA, Cheng MH, Bahar I, & Arditi M (2021). COVID-19-associated multisystem inflammatory syndrome in children (MIS-C): A novel disease that mimics toxic shock syndrome-the superantigen hypothesis. J Allergy Clin Immunol, 147(1), 57-59. doi:10.1016/j.jaci.2020.10.008
Dagvadorj J, Mikulska-Ruminska K, Tumurkhuu G, Ratsimandresy RA, Carriere J, Andres AM,Bahar I . . . Arditi M (2021). Recruitment of pro-IL-1α to mitochondrial cardiolipin, via shared LC3 binding domain, inhibits mitophagy and drives maximal NLRP3 activation. Proc Natl Acad Sci U S A, 118(1). doi:10.1073/pnas.2015632118
Anthonymuthu TS, Tyurina YY, Sun WY, Mikulska-Ruminska K, Shrivastava IH, Tyurin VA, Bahar I . . . Kagan VE (2021). Resolving the paradox of ferroptotic cell death: Ferrostatin-1 binds to 15LOX/PEBP1 complex, suppresses generation of peroxidized ETE-PE, and protects against ferroptosis. Redox Biol, 38, 101744. doi:10.1016/j.redox.2020.101744

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