2021 Publications

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\


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].
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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