2020 Publications

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
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.
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.
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
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
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
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.
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. 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
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
Kowalczyk A, Partha R, Clark NL, Chikina M. Pan-mammalian analysis of molecular constraints underlying extended lifespan. eLife. 2020 Feb 4. PMID: 32043462
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
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
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
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
Buschur KL, Chikina M, Benos PV. Causal network perturbations for instance-specific analysis of single cell and disease samples.Bioinformatics. 2019 Dec 24. pii: btz949. doi: 10.1093/bioinformatics/btz949. PubMed PMID: 31873725

Other Years
‣ 2020 Publications
2019 Publications
2018 Publications
2017 Publications
2016 Publications
2015 Publications
2014 Publications
2013 Publications
2012 Publications
2011 Publications
2010 Publications
2009 Publications
2008 Publications
2007 Publications
2006 Publications
2005 Publications