2019 Publications

Berg J. Editor's note. Science. 2019 Oct 25;366(6464):432. doi: 10.1126/science.aaz9111. PubMed PMID: 31649187.
Berg J. On privilege. Science. 2019 Oct 25;366(6464):401. doi: 10.1126/science.aaz8977. PubMed PMID: 31649169.
Kohane I, Berg JM. Donald A. B. Lindberg (1933-2019). Science. 2019 Oct 4; 366(6461):37. doi: 10.1126/science.aaz3644. PubMed PMID: 31604294.
Berg J. Editorial expression of concern. Science. 2019 Sep 6;365(6457):991. doi: 10.1126/science.aaz2722. PubMed PMID: 31488679.
Berg J. Replication challenges. Science. 2019 Sep 6;365(6457):957. doi: 10.1126/science.aaz2701. PubMed PMID: 31488663.
McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI Insight. 2019 Oct 10. pii: 131597. doi: 10.1172/jci.insight.131597. [Epub ahead of print] PubMed PMID: 31600171.
Kitsios GD, Yang L, Manatakis DV, Nouraie M, Evankovich J, Bain W, Dunlap DG, Shah F, Barbash IJ, Rapport SF, Zhang Y, DeSensi RS, Weathington NM, Chen BB, Ray P, Mallampalli RK, Benos PV, Lee JS, Morris A, McVerry BJ. Host-Response Subphenotypes Offer Prognostic Enrichment in Patients With or at Risk for Acute Respiratory Distress Syndrome. Crit Care Med. 2019 Oct 18. doi: 10.1097/CCM.0000000000004018. [Epub ahead of print] PubMed PMID: 31634231.
Kim Y, Jun I, Shin DH, Yoon JG, Piao H, Jung J, Park HW, Cheng MH, Bahar I, Whitcomb DC, Lee MG. Regulation of CFTR Bicarbonate Channel Activity by WNK1: Implications for Pancreatitis and CFTR-Related Disorders. Cell Mol Gastroenterol Hepatol. 2019 Sep 24. pii: S2352-345X(19)30121-3. doi: 10.1016/j.jcmgh.2019.09.003. [Epub ahead of print] PubMed PMID: 31561038.
Lee JY, Krieger JM, Li H, Bahar I. Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations. Protein Sci. 2019 Oct 1. doi: 10.1002/pro.3732. [Epub ahead of print] PubMed PMID: 31576621.
Thermozier S, Zhang X, Hou W, Fisher R, Epperly MW, Liu B, Bahar I, Wang H, Greenberger JS. Radioresistance of Serpinb3a-/- Mice and Derived Hematopoietic and Marrow Stromal Cell Lines. Radiat Res. 2019 Sep;192(3):267-281. doi:10.1667/RR15379.1. Epub 2019 Jul 11. PubMed PMID: 31295086; PubMed Central PMCID: PMC6759811.
Chen L, Cruz A, Ramsey S, Dickson CJ, Duca JS, Hornak V, Koes DR, Kurtzman T. Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screeningPLoS One. 2019 Aug 20;14(8):e0220113. doi: 10.1371/journal.pone.0220113. eCollection 2019. PubMed PMID: 31430292.
Liu C, Chikina M, Deshpande R, Menk AV, Wang T, Tabib T, Brunazzi EA, Vignali KM, Sun M, Stolz DB, Lafyatis RA, Chen W, Delgoffe GM, Workman CJ, Wendell SG, Vignali DAA. Treg Cells Promote the SREBP1-Dependent Metabolic Fitness of Tumor-Promoting Macrophages via Repression of CD8+ T Cell-Derived Interferon-γ. Immunity. 2019 Aug 20;51(2):381-397.e6. doi: 10.1016/j.immuni.2019.06.017. Epub 2019 Jul 23. PubMed PMID: 31350177; PubMed Central PMCID: PMC6703933.
McDermott L, Koes D, Mohammed S, Iyer P, Boby M, Balasubramanian V, Geedy M, Katt W, Cerione R. GAC inhibitors with a 4-hydroxypiperidine spacer: Requirements for potencyBioorg Med Chem Lett. 2019 Aug 20:126632. doi: 10.1016/j.bmcl.2019.126632. [Epub ahead of print] PubMed PMID: 31474484.
Yablonska S, Ganesan V, Ferrando LM, Kim J, Pyzel A, Baranova OV, Khattar NK, Larkin TM, Baranov SV, Chen N, Strohlein CE, Stevens DA, Wang X, Chang YF, Schurdak ME, Carlisle DL, Minden JS, Friedlander RM. Mutant huntingtin disrupts mitochondrial proteostasis by interacting with TIM23Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16593-16602. doi: 10.1073/pnas.1904101116. Epub 2019 Jul 25. PubMed PMID: 31346086; PubMed Central PMCID: PMC6697818.
Mokashi CS, Schipper DL, Qasaimeh MA, Lee RECA System for Analog Control of Cell Culture Dynamics to Reveal Capabilities of Signaling NetworksiScience. 2019 Aug 8;19:586-596. doi: 10.1016/j.isci.2019.08.010. [Epub ahead of print] PubMed PMID: 31446223; PubMed Central PMCID: PMC6713801.
Bafna K, Narayanan C, Chennubhotla SC, Doucet N, Agarwal PK. Nucleotide substrate binding characterization in human pancreatic-type ribonucleasesPLoS One. 2019 Aug 8;14(8):e0220037. doi: 10.1371/journal.pone.0220037. eCollection 2019. PubMed PMID: 31393891; PubMed Central PMCID: PMC6687278.
Uttam S, Hashash JG, LaFace J, Binion D, Regueiro M, Hartman DJ, Brand RE, Liu Y. Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease. 2019 August. Cancer Prevention Research, 12(8):527-538
Tripathi S, Xing J, Levine H, Jolly MK, Mathematical Modeling of Plasticity and Heterogeneity in EMT, arXiv. 25 July 2019
Igoshin OA, Chen J, Xing J, Liu J, Elston TC, Grabe M, Kim KS, Nirody JA, Rangamani P, Sun SX, Wang H, Wolgemuth C. Biophysics at the coffee shop: lessons learned working with George Oster. 2019 July 22. Molecular Biology of the Cell; 30(16): 1882-1889.
Berg J. A Child of Apollo. 2019 July 19. Science; 365(6450): 203.
Argemi J, Latasa MU, Atkinson SR, Blokhin IO, Massey V, Gue JP, Cabezas J, Lozano JJ, Van Booven D, Bell A, Cao S, Vernetti LA, Arab JP, Ventura- Cots M, Edmunds LR, Fondevilla C, Starkel P, Dubuquoy L, Louvet A, Odena G, Gomez JL, Aragon T, Altamirano J, Caballeria J, Jurzcak MJ, Taylor DL, Berasain C, Wahlestedt C, Monga SP, Morgan MY, Sancho-Bru P, Mathurin P, Furuya S, Lackner C, Rusyn I, Shah VH, Thursz MR, Mann J, Avila MA, Bataller R. Defective HNF4alpha-dependent gene expression as a driver of hepatocellular failure in alcoholic hepatitis. Nat Commun. 2019;10(1):3126. Published 2019 Jul 16. doi:10.1038/s41467-019-11004-3.
Yeh CY, Ye Z, Moutal A, Gaur S, Henton AM, Kouvaros S, Saloman JL, Hartnett-Scott KA, Tzounopoulos T, Khannah R, Aizenman E, Camacho CJ. Defining the Kv2.1-syntaxin molecular interaction identifies a first-in-class small molecule neuroprotectant. 2019 July 15. Proceedings of the National Academy of Sciences of the United States of America.
Mandel J, Wang H, Normolle DP, Chen W, Yan Q, Lucas PC, Benos PV, Prochownik EV. Expression patterns of small numbers of transcripts from functionally- related pathways predict survival in multiple cancers. 2019 Jul 12. BMC Cancer; 19(1):686.
Fouquerel E, Barnes RP, Uttam S, Watkins SC, Bruchez MP, Opresko PL. Targeted and Persistent 8-Oxoguanine Base Damage at Telomeres Promotes Telomere Loss and Crisis. 2019 July 11. Molecular Cell, 75(1): 117 - 130
Qiu X, Zhang Y, Yang, Hosseinzadeh S, Wang L, Yuan R, Xu S, Ma Y, Replogle J, Darmanis S, Xing J, Weissman J, Mapping Vector Field of Single Cells, BioRxiv. 2019 July 9
Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang QJ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. 2019 Jul 5. PLOS Computational Biology; 15(7)
Cheng MH, Bahar I. Monoamine transporters: structure, intrinsic dynamics and allosteric regulation. 2019 July 03. Nature Structural & Molecular Biology; 26(7): 545-556.
Mao W, Zaslavsky E, Hartmann BM, Sealfon SC, Chikina M. Pathway-level information exterior (PLIER) for gene expression data. 2019 July. Nature methods; 16(7): 607-610.
Ngo M, Wechter N, Tsai E, Shun TY, Gough A, Schurdak ME, Schwacha A, Vogt A. A High-Throughput Assay for DNA Replication Inhibitors Based upon Multivariate Analysis of Yeast Growth Kinetics. 2019 July. SLAS Discovery; 24(6):669-681.
Berg J. DNA patents revisited. 2019 Jun 21. Science; 364(6446):1113.
Cheng MH, Ponzoni L, Sorkina T, Lee JY, Zhang She, SorkinA, Bahar I. Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations. 2019 Jun 20. Neuropharmacology; 107676.
Taylor DL, Gough A, Schurdak ME, Vernetti L, Chennubhotla CS, Lefever D, Pei F, Faeder JR, Lezon TR, Stern AM, Bahar I. Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology. 2019 June 15. Handbook of Experimental Pharmacology.
Kowalczyk A, Meyer WK, Partha R, Mao W, Clark NL, Chikina M. RERconverge: an R package for associating evolutionary rates with convergent traits. 2019 June 13. Bioinformatics.
Liu B, Gyori BM, Thiagarajan PS. Statistical Model Checking-Based Analysis of Biological Networks. 2019 Jun 12. Computational Biology; 30.
Hill J, Rastas P, Hornett EA, Neethiraj R, Clark N, Morehouse N, de la Paz Celorio-Mancera M Cols JC, Dircksen H, Meslin C, Keehnen N, Pruisscher P, Sikkink K, Vives M, Vogel H, Wiklund C, Woronik A, Boggs CL, Nylin S, Wheat CW. Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. 2019 June 12. Science Advances; 5(6):eaau3648.
Rashid S, Long Z, Sing S, Kohram M, Vashistha H, Navlakha S, Salman H, Oltvai ZN, Bar-Joseph Z. Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains. 2019 June 11. Proceedings of the National Academy of Sciences of the United States of America; 116(24): 11770-11775.
Miedel MT, Gavlock DC, Jia S, Gough A, Taylor DL, Stern AM. Modeling the Effect of the Metastatic Microenvironment on Phenotypes Conferred by Estrogen Receptor Mutations Using a Human Liver Microphysiological System. 2019 Jun 6. Sci Rep; 9(1):8341. doi:10.1038/s41598-019-44756-5
Sackton TB,Clark N. Convergent evolution in the genomics era: new insights and directions. 2019 June 3. Philosophical Transactions of the Royal Society B. 374(1777)
Singh M, Tian XJ, Donnenberg VS, Watson AM, Zhang J, Stabile LP, Watkins SC, Xing J, Sant S. Targeting the Temporal Dynamics of Hypoxia-Induced Tumor-Secreted Factors Halts Tumor Migration. 2019 June 1. Cancer Research; 79(11):2962-2977.
Wang W, Taft DA, Chen YJ, Zhang J, Wallace CT, Xu M, Watkins SC, Xing J. Learn to segment single cells with deep distance estimator and deep cell detector. 2019 May. Computers in Biology and Medicine; 108:133-141.
Kho DH, Uddin MH, Chatterjee M, Vogt A, Raz A, Wu GS. GP78 Cooperates with Dual-Specificity Phosphatase 1 To Stimulate Epidermal Growth Factor Receptor-Mediated Extracellular Signal-Regulated Kinase Signaling. 2019 May 14. Molecular and Cellular Biology; 39(11).
Zhou Z, Feng Z, Hu D, Yang P, Gur M, Bahar I, Cristofanilli M, Gradishar WJ, Xie X, Wan Y. A novel small-molecule antagonizes PRMT5-mediated KLF4 methylation for targeted therapy. 2019 May 14. EBioMedicine.
Partha R, Kowalczyk A, Clark N, Chikina M. Robust Method for Detecting Convergent Shifts in Evolutionary Rates. 2019 May 11. Molecular Biology and Evolution.
Zhang S, Li H, Krieger JM, Bahar I. Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity. 2019 Apr 27. Molecular Biology and Evolution.
Van Oss SB, Carvunis AR. De novo gene birth. 2019 May 23. PLoS Genetics; 15(5):e1008160. doi:10.1371/journal.pgen.1008160
Tapia J, Saglam AS, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Faeder JR. MCell-R: A particle-resolution network-free spatial modeling framework. 2019. Modeling Biomolecular Site Dynamics; 1945: 203-229.
Guowu L, Weiss SC, Vergara S, Camacho C, Calero G. Transcription with a laser: Radiation-damage free diffraction of RNA Polymerase II crystals. 2019 Apr 25. Methods.
Sawant DV, Yano H, Chikina M, Zhang Q, Liao M, Liu C, Callahan DJ, Sun Z, Sun T, Tabib T, Pennathur A, Corry DB, Luketich JD, Lafyatis R, Chen W, Poholek AC, Bruno TC, Workman CJ, Vignali DAA. Adaptive plasticity of IL-10+ and IL-35+ Treg cells cooperatively promotes tumor T cell exhaustion. 2019 Apr 01. Nature Immunology.
Li Y, Cifuentes-Pagano E, DeVallance ER, de Jesus DS, Meijles DN, Koes D, Camacho CJ, Ross M, St Croix C, Pagano PJ. NADPH oxidase 2 inhibitors CPP11G and CPP11H attenuate endothelial cell inflammation & vessel dysfunction and restore mouse hind-limb flow. Redox Biol. 2019;22:101143. doi:10.1016/j.redox.2019.101143
Raghu VK, Zhao W, Pu J, Leader JK, Wang R, Herman J, Yuan, J, Benos PV, Wilson DO. Feasibility of lung cancer prediction from low-dose CT scan and smoking factor using causal models. Thorax. Published Online First: 12 March 2019. doi: 10.1136/thoraxjnl-2018-212638
Zhang B, Li F, Chen Z, Shrivastava IH, Gasanoff ES, Dagda RK. Naja mossambica mossambica Cobra Cardiotoxin Targets Mitochondria to Disrupt Mitochondrial Membrane Structure and Function. 2019 March 8. Toxins; 11(3).
Pei F, Li H, Liu B, Bahar I. Quantitative Systems Pharmacological Analysis of Drugs of Abuse Reveals the Pleiotropy of Their Targets and the Effector Role of mTORC1. Front Pharmacol. 2019;10:191. Published 2019 March 8. doi:10.3389/fphar.2019.00191
Xing J, Tian XJ. Investigating epithelial-to-mesenchymal transition with integrated computational and experimental approaches. 2019 March 7. Physical Biology; 16(3):031001.
Zhang J, Chen H, Li R, Taft DA, Yao G, Bai F, Xing J. Spatial clustering and common regulatory elements correlate with coordinated gene expression. 2019 March 1. PLoS Comput Biol. 2019;15(3):e1006786. doi:10.1371/journal.pcbi.1006786
Abecassis I, Sedgewick AJ, Romkes M, Buch S, Nukui T, Kapetanaki MG, Vogt A, Kirkwood JM, Benos PV. PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy. Sci Rep. 2019;9(1):3309. Published 2019 March 1. doi:10.1038/s41598-019-39542-2
Pabon NA, Zhang Q, Cruz JA, Schipper DL, Camacho CJ, Lee REC. A network-centric approach to drugging TNF-induced NF-κB signaling. Nat Commun. 2019;10(1):860. Published 2019 Feb 26. doi:10.1038/s41467-019-08802-0
Mikulska-Rauminska K, Shrivastava I, Krieger, J, Zhang S, Li H, Bayir B, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. 2019 Feb 14. Journal of Chemical Information and Modeling.
Raza Q, Choi JY, Li Y, O’Dowd RM, Watkins SC, Chikina M, Hong Y, Clark NL, Kwiatkowski AV. Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila. PLoS Genet. 2019;15(2):e1007720. Published 2019 Feb 14. doi:10.1371/journal.pgen.1007720
Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. (2019) Allostery in Its Many Disguises: From Theory to Applications. Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. PMID: 30744993
Lee J Y, Krieger J, Herguedas B, Garcca-Nafrra J, Dutta A, Shaikh SA, Greger IH, Bahar I. (2019) Druggability Simulations and X-ray Crystallography Reveal a Ligand-binding Site in the GluA3 AMPA Receptor N-terminal Domain. Structure. doi:10.2139/ssrn.3188417
Wang Y, Cobanoglu MC, Li J, Hidvegi T, Hale P, Ewing M, Chu AS, Gong Z, Muzumdar R, Pak SC, Silverman GA, Bahar I, Perlumtter DH. (2019) An analog of glibenclamide selectively enhances autophagic degradation of misfolded α1-antitrypsin Z. PLoS ONE 14(1): e0209748. https://doi.org/10.1371/journal.pone.0209748
Asan A, Skoko JJ, Woodcock CC, Wingert BM, Woodcock SR, Normolle D, Huang Y, Stark JM, Camacho CJ, Freeman BA, Neumann CA. Electrophilic fatty acids impair RAD51 function and potentiate the effects of DNA-damaging agents on growth of triple-negative breast cells. (2019) Jan 11. Journal of Biological Chemistry, 294(2), 397-404.
Wang KZQ, Steer E, Otero PA, Bateman NW, Cheng MH, Scott AL, Wu C, Bahar I, Shih YT, Hsueh YP, Chu CT. PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. eNeuro. 2018;5(6):ENEURO.0466-18.2018. Published 2018 Jan 10. doi:10.1523/ENEURO.0466-18.2018
Cheikhi A, Wallace C, St Croix C, Cohen C, Tang W, Wipf P, Benos PV, Ambrosio F, Barchowsky A. Mitochondria are a substrate of cellular memory. (2019) Free Radical Biology and Medicine, 130, 528-541. https://doi.org/10.1016/j.freeradbiomed.2018.11.028
Sunseri J, King JE, Francoeur PG, Koes DR. Convolutional neural network scoring and minimization in the D3R 2017 community challenge. 2019. Journal of Computer-Aided Molecular Design; 33(1):19-34.

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