2020 Publications

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
Francoeur PG, Masuda T, Sunseri J, Jia A, Iovanisci RB, Snyder I, & Koes DR (2020). Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design. J Chem Inf Model. doi:10.1021/acs.jcim.0c00411
Chen SY, Osimiri LC, Chevalier M, Bugaj LJ, Nguyen TH, Greenstein RA,Stewart-Ornstein, J, . . . El-Samad H (2020). Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics. Cell Syst. doi:10.1016/j.cels.2020.08.009
Bertolazzi G, Benos PV, Tumminello M, & Coronnello C (2020). An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs. BMC Bioinformatics, 21(Suppl 8), 201. doi:10.1186/s12859-020-3519-5
Song X, Zhou Z, Li H, Xue Y, Lu X, Bahar I, Kepp O, Hung MC, Kroemer G, and WanY (2020) Pharmacological suppression of B7-H4 glycosylation restores antitumor immunity in immune-cold breast cancers. Cancer Discovery, in press.
Zhang Y, Krieger JM, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I (2020) State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Progress in Biophysics and Molecular Biology, in press.
Mao W, Rahimikollu J, Hausler R, & Chikina M, (2020). DataRemix: a universal data transformation for optimal inference from gene expression datasets. Bioinformatics. doi:10.1093/bioinformatics/btaa745
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Faeder JR, . . . Hucka M (2020). SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol, 16(8), e9110. doi:10.15252/msb.20199110
Shin DH, Kim M, Kim Y, Jun I, Jung J, Nam JH, Cheng MH, . . . Lee MG (2020). Bicarbonate permeation through anion channels: its role in health and disease. Pflugers Arch, 472(8), 1003-1018. doi:10.1007/s00424-020-02425-x
Chikina M, & Pegden, W. (2020). Modeling strict age-targeted mitigation strategies for COVID-19. PLoS One, 15(7), e0236237. doi:10.1371/journal.pone.0236237
Paris KA, Santiago U, & CamachoCJ (2020). On the molecular mechanism of SARS-CoV-2 retention in the upper respiratory tract. bioRxiv. doi:10.1101/2020.07.29.227389
Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Benos PV, . . . McVerry BJ (2020). Respiratory Tract Dysbiosis is Associated With Worse Outcomes in Mechanically-Ventilated Patients. Am J Respir Crit Care Med. doi:10.1164/rccm.201912-2441OC
Chan LN, Murakami MA, Robinson ME, Caeser R, Sadras T, Lee J, Vogt A, . . . Müschen, M (2020). Signalling input from divergent pathways subverts B cell transformation. Nature, 583(7818), 845-851. doi:10.1038/s41586-020-2513-4
Tosun AB, Pullara F, Becich MJ, Taylor DL, Fine JL, & Chennubhotla SC (2020). Explainable AI (xAI) for Anatomic Pathology. Adv Anat Pathol, 27(4), 241-250. doi:10.1097/pap.0000000000000264
Berg WA, Berg JM, Sickles EA, Burnside ES, Zuley ML, Rosenberg RD, & Lee CS (2020).Cancer Yield and Patterns of Follow-up for BI-RADS Category 3 after Screening Mammography Recall in the National Mammography Database. Radiology, 296(1), 32-41. doi:10.1148/radiol.2020192641
Shi Q, Pei F, Silverman GA, Pak SC, Perlmutter DH, Liu B, & Bahar I (2020). Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis. Int J Mol Sci, 21(8). doi:10.3390/ijms21082855
Zhao J, Dar HH, Deng Y, St Croix CM, Li Z, Minami Y, Bahar I,, Shrivastava IH . . . Wenzel SE (2020). PEBP1 acts as a rheostat between prosurvival autophagy and ferroptotic death in asthmatic epithelial cells. Proc Natl Acad Sci U S A, 117(25), 14376-14385. doi:10.1073/pnas.1921618117
Chen YJ, Cheng YY, Wang W, Tian XJ, Lefever DE, Taft DA, . . . Xing J (2020). Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in. Biol Methods Protoc, 5(1), bpaa006. doi:10.1093/biomethods/bpaa006
Tian XJ, Zhou D, Fu H, Zhang R, Wang X, Huang S, . . . Xing J (2020). Sequential Wnt Agonist Then Antagonist Treatment Accelerates Tissue Repair and Minimizes Fibrosis. iScience, 23(5), 101047. doi:10.1016/j.isci.2020.101047
Hafner A, Reyes J, Stewart-Ornstein J, Tsabar M, Jambhekar A, & Lahav G (2020). Quantifying the Central Dogma in the p53 Pathway in Live Single Cells. Cell Syst, 10(6), 495-505.e494. doi:10.1016/j.cels.2020.05.001
Xing J (2020). Bidirectional interplay between physical and biological approaches on studying the epithelial-to-mesenchymal transition. Phys Biol, 17(2), 020201. doi:10.1088/1478-3975/ab73d0
Liu X, Feng B, Vats A, Tang H, Seibel W, Swaroop M, Schurdak M, . . . Chen Y (2020). Pharmacological clearance of misfolded rhodopsin for the treatment of RHO-associated retinitis pigmentosa. Faseb j. doi:10.1096/fj.202000282R
Yang J, Antin P, Berx G, Blanpain C, Brabletz T, Bronner M, Xing J, . . . Sheng G (2020). Guidelines and definitions for research on epithelial-mesenchymal transition. Nat Rev Mol Cell Biol, 21(6), 341-352. doi:10.1038/s41580-020-0237-9
Kosinski C, Herzig D, Laesser CI, Nakas CT, Melmer A, Vogt A, . . . Stettler C (2020). A Single Load of Fructose Attenuates the Risk of Exercise-Induced Hypoglycemia in Adults With Type 1 Diabetes on Ultra-Long-Acting Basal Insulin: A Randomized, Open-Label, Crossover Proof-of-Principle Study. Diabetes Care. doi:10.2337/dc19-2250
Tripyla A, Herzig D, Joachim D, Nakas CT, Amiet F, Andreou A, Vogt A . . . Bally L (2020). Performance of a factory-calibrated, real-time continuous glucose monitoring system during elective abdominal surgery. Diabetes Obes Metab. doi:10.1111/dom.14073
Jane EP, Premkumar DR, Thambireddy S, Golbourn B, Agnihotri S, Bertrand KC,Stern AM . . . Pollack IF (2020). Targeting NAD(+) Biosynthesis Overcomes Panobinostat and Bortezomib-Induced Malignant Glioma Resistance. Mol Cancer Res, 18(7), 1004-1017. doi:10.1158/1541-7786.Mcr-19-0669
Uttam S, Stern AM, Sevinsky CJ, Furman S, Pullara F, Spagnolo D, . . . Chakra Chennubhotla S (2020). Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks. Nat Commun, 11(1), 3515. doi:10.1038/s41467-020-17083-x
Gau D, Vignaud L, Allen A, Guo Z, Sahel J, Boone D,Koes DR . . . Roy P (2020). Disruption of profilin1 function suppresses developmental and pathological retinal neovascularization. J Biol Chem, 295(28), 9618-9629. doi:10.1074/jbc.RA120.012613
Nmezi B, Vollmer LL, Shun TY, Gough A, Rolyan H, Liu F, . . . Vogt A (2020). Development and Optimization of a High-Content Analysis Platform to Identify Suppressors of Lamin B1 Overexpression as a Therapeutic Strategy for Autosomal Dominant Leukodystrophy. SLAS Discov, 2472555220915821. doi:10.1177/2472555220915821
Wang T, Ma J, Hogan AN, Fong S, Licon K, Tsui B, Carvunis AR . . . Ideker T (2020). Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. Cell Syst. doi:10.1016/j.cels.2020.06.006
Konstantinidou M, Magari F, Sutanto F, Haupenthal J, Jumde VR, Ünver MY, Camacho CJ, . . . Dömling, A (2020). Rapid Discovery of Aspartyl Protease Inhibitors Using an Anchoring Approach. ChemMedChem, 15(8), 680-684. doi:10.1002/cmdc.202000024
Wierbowski SD, Wingert BM, Zheng J, & Camacho CJ (2020). Cross-docking benchmark for automated pose and ranking prediction of ligand binding. Protein Sci, 29(1), 298-305. doi:10.1002/pro.3784
Clark LJ, Krieger J, White AD, Bondarenko V, Lei S, Fang F, Bahar I . . . Vilardaga, J. P. (2020). Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation. Nat Chem Biol. doi:10.1038/s41589-020-0567-0
Kotok D, Yang L, Evankovich J W, Bain W, Dunlap D G, Shah F, Benos PV . . . Kitsios GD (2020). The evolution of radiographic edema in ARDS and its association with clinical outcomes: A prospective cohort study in adult patients. J Crit Care, 56, 222-228. doi:10.1016/j.jcrc.2020.01.012
Ge X, Raghu VK, Chrysanthis PK, Benos PV. (2020) CausalMGM: An Interactive Web-Based Causal Discovery Tool. Nucleic Acids Res. 2020 Jul 2; 48(W1):W597-W602. PMID: 32392295
Zheng F, Zhang S, Churas C, Pratt D, Bahar I, & Ideker T (2020). Decoding of persistent multiscale structures in complex biological networks. bioRxiv. doi:10.1101/2020.06.16.151555
Kaynak BT, Bahar I, & Doruker P (2020). Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions. Comput Struct Biotechnol J, 18, 1577-1586. doi:10.1016/j.csbj.2020.06.020
Krieger JM, Doruker P, Scott AL, Perahia D, & Bahar I (2020). Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods. Curr Opin Struct Biol, 64, 34-41. doi:10.1016/j.sbi.2020.05.013
Li F, Shrivastava IH, Hanlon P, Dagda RK, & Gasanoff ES (2020). Molecular Mechanism by which Cobra Venom Cardiotoxins Interact with the Outer Mitochondrial Membrane. Toxins (Basel), 12(7). doi:10.3390/toxins12070425
Ayoob JC, Kangas JD. (2020) 10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats. PLoS Comput Biol 16(6): e1007911.
Yang H, Benos PV, Kitsios GD. (2020) Protecting the lungs and hurting the kidneys: causal inference study for the risk of ventilation-induced kidney injury in ARDS Annals Transl Med.In press. Epub: 20-May-2020.
Zhou Z, Zhou H, Ponzoni L, Luo A, Zhu R, He M, Huang Y, Guan KL, Bahar I, Liu Z, Wan Y. EIF3H Orchestrates Hippo Pathway-mediated Oncogenesis Through an Unexpected Catalytic Control of YAP Stability. Cancer Res, in press.
Schurdak, M, Vernetti, L, Bergenthal, L, Wolter, Q K, Shun, T Y, Karcher, S, . . . Gough, A. (2020). Applications of the microphysiology systems database for experimental ADME-Tox and disease models. Lab Chip, 20(8), 1472-1492. doi:10.1039/c9lc01047e
Buschur KL, Chikina M, & Benos PV (2020). Causal network perturbations for instance-specific analysis of single cell and disease samples. Bioinformatics, 36(8), 2515-2521. doi:10.1093/bioinformatics/btz949
Meier I, Vogt AP, Meineri M, Kaiser HA, Luedi, MM, & Braun M (2020). Point-of-care ultrasound in the preoperative setting. Best Pract Res Clin Anaesthesiol, 34(2), 315-324. doi:10.1016/j.bpa.2020.04.010
Ponzoni L, Nguyen NH, Bahar I, Brodsky JL. Complementary Computational and Experimental Evaluation of Missense Variants in the ROMK Potassium Channel. PLOS Comp Biol. 2020 Apr 6;16(4):e1007749. PMID: 32251469
Li H, Doruker P, Hu G, Bahar I. Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophys J. 2020 Apr 7; 118: 1782-1794.
Gbotosho OT, Kapetanaki MG, Ross M, Ghosh S, Weidert F, Bullock GC, . . . Kato GJ (2020). Nrf2 deficiency in mice attenuates erythropoietic stress-related macrophage hypercellularity. Exp Hematol, 84, 19-28.e14. doi:10.1016/j.exphem.2020.02.005
Jane EP, Premkumar DR, Thambireddy S, Golbourn B, Agnihotri S, Bertrand KC, Mack SC, Myers MI, Chattopadhyay A, Taylor DL, Schurdak ME, Stern AM, Pollack IF. Targeting NAD+ biosynthesis overcomes panobinostat and bortezomib-induced malignant glioma resistance. Mol Cancer Res. 2020 Apr 1. PMID: 32238439
Li H, Pei F, Taylor DL, Bahar I. QuartataWeb: Integrated Chemical-protein-pathway Mapping for Polypharmacology and Chemogenomics. Bioinformatics, in press. 2020 Mar 28.
Schurdak M, Vernetti L, Bergenthal L, Wolter QK, Shun TY, Karcher S, Taylor DL, Gough A. Applications of the microphysiology systems database for experimental ADME-Tox and disease models. Lab Chip. 2020 Mar 25. [Epub ahead of print]
Konstantinidou M, Magari F, Sutanto F, Haupenthal J, Jumde VR, Ünver MY, Heine A, Camacho CJ, Hirsch AKH, Klebe G, Dömling A. Rapid Discovery of Aspartyl Protease Inhibitors Using an Anchoring Approach. ChemMedChem. 2020 Mar 18. PMID: 32187447
Gupta S, Lee REC, Faeder JR. Parallel Tempering with Lasso for model reduction in systems biology. PLoS Comput Biol. 2020 Mar 9; 16(3). PMID: 32150537
Thermozier S, Hou W, Zhang X, Shields D, Fisher R, Bayir H, Kagan V, Yu J, Liu B, Bahar I, Epperly MW, Wipf P, Wang H, Huq MS, and Greenberger JS. Anti-Ferroptosis Drug Enhances Total-Body Irradiation Mitigation by Drugs that Block Apoptosis and Necroptosis. Radiat Res. 2020 Mar 5. [Epub ahead of print]. PMID: 32134361
Weisel FJ, Mullett SJ, Elsner RA, Menk AV, Trivedi N, Luo W, Chikina M . . . Shlomchik MJ (2020). Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis. Nat Immunol, 21(3), 331-342. doi:10.1038/s41590-020-0598-4
Xing J. Bidirectional interplay between physical and biological approaches on studying the epithelial-to-mesenchymal transition. Phys Biol. 2020 Feb 28;17(2):020201. doi: 10.1088/1478-3975/ab73d0. No abstract available. PMID: 32109225
Ponzoni L, Peñaherrera DA, Oltvai ZN, Bahar I. Rhapsody: Predicting the pathogenicity of human missense variants. Bioinformatics. 2020 Feb 26. pii: btaa127. doi: 10.1093/bioinformatics/btaa127. [Epub ahead of print] PMID: 32101277
Zhang S, Chen F, Bahar I. Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation. Nucleic Acids Res. 2020 Feb 20;48(3):1131-1145. doi: 10.1093/nar/gkz1102. PMID: 31828312
Hafner A, Kublo L, Tsabar M, Lahav G, Stewart-Ornstein J. Identification of universal and cell-type specific p53 DNA binding. BMC Mol Cell Biol. 2020 Feb 18;21(1):5. doi: 10.1186/s12860-020-00251-8. PMID: 32070277
Vakirlis N, Carvunis AR, McLysaght A Elife. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. 2020 Feb 18;9. pii: e53500. doi: 10.7554/eLife.53500. PMID: 32066524.
Kapralov AA, Yang Q, Dar HH, Tyurina YY, Anthonymuthu TS, Kim R, St Croix CM, Mikulska-Ruminska K, Liu B, Shrivastava IH, Tyurin VA, Ting HC, Wu YL, Gao Y, Shurin GV, Artyukhova MA, Ponomareva LA, Timashev PS, Domingues RM, Stoyanovsky DA, Greenberger JS, Mallampalli RK, Bahar I, Gabrilovich DI, Bayır H, Kagan VE. Redox lipid reprogramming commands susceptibility of macrophages and microglia to ferroptotic death. Nat Chem Biol. 2020 Mar;16(3):278-290. doi: 10.1038/s41589-019-0462-8. Epub 2020 Feb 17. PMID: 32080625
Weisel FJ, Mullett SJ, Elsner RA, Menk AV, Trivedi N, Luo W, Wikenheiser D, Hawse WF, Chikina M, Smita S, Conter LJ, Joachim SM, Wendell SG, Jurczak MJ, Winkler TH, Delgoffe GM, Shlomchik MJ. Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis. Nat Immunol. 2020 Feb 17. doi: 10.1038/s41590-020-0598-4. [Epub ahead of print] PMID: 32066950
Sunseri J, Koes DR. libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications. J Chem Inf Model. 2020 Feb 12. doi: 10.1021/acs.jcim.9b01145. [Epub ahead of print] PMID: 32049525.
Granada AE, Jiménez A, Stewart-Ornstein J, Blüthgen N, Reber S, Jambhekar A, Lahav G. The effects of proliferation status and cell cycle phase on the responses of single cells to chemotherapy. Mol Biol Cell. 2020 Feb 12:mbcE19090515. doi: 10.1091/mbc.E19-09-0515. [Epub ahead of print]
Kowalczyk A, Partha R, Clark, NL, & Chikina M (2020). Pan-mammalian analysis of molecular constraints underlying extended lifespan. Elife, 9. doi:10.7554/eLife.51089
Kowalczyk A, Partha R, Clark NL, Chikina M. Pan-mammalian analysis of molecular constraints underlying extended lifespan.Elife. 2020 Feb 11;9. pii: e51089. doi: 10.7554/eLife.51089. PMID: 32043462
Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW 2nd, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun. 2020 Feb 7;11(1):781. doi: 10.1038/s41467-020-14500-z. PMID: 32034123
Kowalczyk A, Partha R, Clark NL, Chikina M. Pan-mammalian analysis of molecular constraints underlying extended lifespan. eLife. 2020 Feb 4. PMID: 32043462
Kessler MD, Loesch DP, Perry JA, Heard-Costa NL, Taliun D, Cade BE, Wang H, Daya M, Ziniti J, Datta S, Celedón JC, Soto-Quiros ME, Avila L, Weiss ST, Barnes K, Redline SS, Vasan RS, Johnson AD, Mathias RA, Hernandez R, Wilson JG, Nickerson DA, Abecasis G, Browning SR, Zöllner S, O'Connell JR, Mitchell BD; National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Population Genetics Working Group, O'Connor TD. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. Proc Natl Acad Sci U S A. 2020 Feb 4;117(5):2560-2569. doi: 10.1073/pnas.1902766117. Epub 2020 Jan 21. PMID: 31964835
Kim SH, Hahm ER, Singh KB, Shiva S, Stewart-Ornstein J, Singh SV. RNA--seq reveals novel mechanistic targets of withaferin A in prostate cancer cellss.Carcinogenesis. 2020 Jan 31. pii: bgaa009. doi: 10.1093/carcin/bgaa009. [Epub ahead of print] PMID: 32002539
Kooistra NHM, van Mourik MS, Rodríguez-Olivares R, Maass AH, Nijenhuis VJ, van der Werf R, Ten Berg JM, Kraaijeveld AO, Baan J Jr, Voskuil M, Vis MM, Stella PR. Late onset of new conduction disturbances requiring permanent pacemaker implantation following TAVI. Heart.2020 Jan 31. pii: heartjnl-2019-315967 doi: 10.1136/heartjnl-2019-315967 PubMed PMID: 32004313
Wierbowski SD, Wingert BM, Zheng J, Camacho CJ. Cross-docking benchmark for automated pose and ranking prediction of ligand binding.Protein Sci. 2020 Jan;29(1):298-305. doi: 10.1002/pro.3784. PubMed PMID: 31721338
Espeleta HC, Taylor DL, Kraft JD, Grant DM. Child maltreatment and cognitive vulnerabilities: Examining the link to posttraumatic stress symptoms. J Am Coll Health. 2020 Jan 16:1-8. doi: 10.1080/07448481.2019.1706538. [Epub ahead of print] PubMed PMID: 31929188
Kotok D, Yang L, Evankovich JW, Bain W, Dunlap DG, Shah F, Zhang Y, Manatakis DV, Benos PV, Barbash IJ, Rapport SF, Lee JS, Morris A, McVerry BJ, Kitsios GD. The evolution of radiographic edema in ARDS and its association with clinical outcomes: A prospective cohort study in adult patients. J Crit Care. 2020 Jan 13;56:222-228. doi: 10.1016/j.jcrc.2020.01.012. [Epub ahead of print] PMID: 32028223
Melamud E, Taylor DL, Sethi A, Cule M, Baryshnikova A, Saleheen D, van Bruggen N, FitzGerald GA. The promise and reality of therapeutic discovery from large cohorts.J Clin Invest. 2020 Jan 13. pii: 129196. doi: 10.1172/JCI129196. PubMed PMID: 31929188
Lee JY, Krieger JM, Li H, Bahar I. Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations.Protein Sci. 2020 Jan;29 doi: 10.1002/pro.3732 PubMed PMID: 31576621
Sorkin BC, Kuszak AJ, Bloss G, Fukagawa NK, Hoffman FA, Jafari M, Barrett B, Brown PN, Bushman FD, Casper SJ, Chilton FH, Coffey CS, Ferruzzi MG, Hopp DC, Kiely M, Lakens D, MacMillan JB, Meltzer DO, Pahor M, Paul J, Pritchett-Corning K, Quinney SK, Rehermann B, Setchell KDR, Sipes NS, Stephens JM, Taylor DL, Tiriac H, Walters MA, Xi D, Zappalá G, Pauli GF. Improving natural product research translation: From source to clinical trial.FASEB J.2020 Jan;34(1):41-65. doi: 10.1096/fj.201902143R. Epub 2019 Dec 10. PubMed PMID: 31914647

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