2018 Publications | Computational & Systems Biology

	Pulugulla SH, Workman R, Rutter NW, Yang Z, Adamik J, Lupish B, Macar DA, El Abdouni S, Esposito EX, Galson DL, Camacho CJ, Madura JD, Auron PE. A combined computational and experimental approach reveals the structure of a C/EBPβ-Spi1 interaction required for IL1B gene transcription. 2018 Dec 28. Journal of Biological Chemistry, 293(52), 19942-19956.
	Shen LL, Wang M, Zhou JL, Xing JH, Cui BK, Dai YC. Taxonomy and phylogeny of Postia. Multi-gene phylogeny and taxonomy of the brown-rot fungi: Postia (Polyporales, Basidiomycota) and related genera. Persoonia.. 2019 Jun;42:101-126. doi: 10.3767/persoonia.2019.42.05. Epub 2018 Nov 29. PubMed PMID: 31551616
	Krzysiak, T. C., Thomas, L., Choi, Y., Auclair, S., Qian, Y., Luan, S., Krasnow, S. M., Thomas, L. L., Koharudin, L. M. I., Benos, P. V., Marks, D. L., Gronenborn, A. M., Thomas, G. (2018). An Insulin-Responsive Sensor in the SIRT1 Disordered Region Binds DBC1 and PACS-2 to Control Enzyme Activity. Molecular Cell,72(6). doi:10.1016/j.molcel.2018.10.007
	Anthonymuthu, T. S., Kenny, E. M., Shrivastava, I., Tyurina, Y. Y., Hier, Z. E., Ting, H., Dar, H. H., Tyurin, V. A., Nesterova, A., Amoscato, A. A., Mikulska-Ruminska, K., Rosenbaum, J. C., Mao, G., Zhao, J., Conrad, M., Kellum, J. A., Wenzel, S. E., VanDemark, A. P., Bahar, I., Kagan, V. E., Bayır, H. (2018). Empowerment of 15-Lipoxygenase Catalytic Competence in Selective Oxidation of Membrane ETE-PE to Ferroptotic Death Signals, HpETE-PE. Journal of the American Chemical Society,140(51), 17835-17839. doi:10.1021/jacs.8b09913
	Dijk, L. V., Giladi, M., Refaeli, B., Hiller, R., Cheng, M. H., Bahar, I., & Khananshvili, D. (2018). Key residues controlling bidirectional ion movements in Na+/Ca2+ exchanger. Cell Calcium,76, 10-22. doi:10.1016/j.ceca.2018.09.004
	Raghu VK, Poon A, Benos PV. (2018). Evaluation of Causal Structure Learning Methods on Mixed Data Types. Proceedings of Machine Learning Research. 2018;92:48–65.
	Tyurina YY, Shrivastava I, Tyurin VA, Mao G, Dar HH, Watkins S, Epperly M, Bahar I, Shvedova AA, Pitt B, Wenzel SE, Mallampalli RK, Sadovsky Y, Gabrilovich D, Greenberger JS, Bayir H, Kagan VE. (2018) "Only a life lived for others is worth living:" Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions. Antioxid Redox Signal DOI:10.1089/ars.2017.7124 PMID: 28835115
	Beckwitt, C. H., Brufsky, A., Oltvai, Z. N., & Wells, A. (2018). Statin drugs to reduce breast cancer recurrence and mortality. Breast cancer research : BCR, 20(1), 144. doi:10.1186/s13058-018-1066-z
	Beckwitt CH, Clark AM, Ma B, Whaley D, Oltvai ZN, Wells A. Statins attenuate outgrowth of breast cancer metastases. 2018. British Journal of Cancer, 119(9), 1094-1105.
	Chakraborty S, Jiang C, Gau D, Oddo M, Ding Z, Vollmer L, Joy M, Schiemann W, Stolz DB, Vogt A, Ghosh S, Roy P. Profilin-1 deficiency leads to SMAD3 upregulation and impaired 3D outgrowth of breast cancer cells. 2018 Oct 15. British Journal of Cancer 119(9), 1106-1117.
	Dar, H. H., Tyurina, Y. Y., Mikulska-Ruminska, K., Shrivastava, I., Ting, H. C., Tyurin, V. A., Krieger, J., St Croix, C. M., Watkins, S., Bayir, E., Mao, G., Armbruster, C. R., Kapralov, A., Wang, H., Parsek, M. R., Anthonymuthu, T. S., Ogunsola, A. F., Flitter, B. A., Freedman, C. J., Gaston, J. R., Holman, T. R., Pilewski, J. M., Greenberger, J. S., Mallampalli, R. K., Doi, Y., Lee, J. S., Bahar, I., Bomberger, J. M., Bayır, H., … Kagan, V. E. (2018). Pseudomonas aeruginosa utilizes host polyunsaturated phosphatidylethanolamines to trigger theft-ferroptosis in bronchial epithelium. The Journal of clinical investigation, 128(10), 4639-4653.
	The ECCB 2018 Steering Committee, Artemis G Hatzigeorgiou, Pantelis Bagos, Panayiotis V Benos, Christoforos Nikolaou, Yves Moreau, Ioannis Kavakiotis; ECCB 2018: The 17th European Conference on Computational Biology, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i595–i598, https://doi.org/10.1093/bioinformatics/bty740
	Tilstra, J. S., Avery, L., Menk, A. V., Gordon, R. A., Smita, S., Kane, L. P., Chikina, M., Delgoffe, G. M., Shlomchik, M. J. (2018). Kidney-infiltrating T cells in murine lupus nephritis are metabolically and functionally exhausted. The Journal of clinical investigation, 128(11), 4884-4897.
	Manatakis DV, Raghu V, Benos PV; piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i848–i856, https://doi.org/10.1093/bioinformatics/bty591
	Reyes J, Chen JY, Stewart-Ornstein J, Karhohs KW, Mock CS, Lahav G. Fluctuations in p53 Signaling Allow Escape from Cell-Cycle Arrest. 2018 Aug 16. Molecular Cell, 71(4), 581-591.
	Meyer WK, Jamison J, Richter R, Woods SE, Partha R, Kowalczyk A, Kronk C, Chikina M, Bonde RK, Crocker DE, Gaspard J, Lanyon JM, Marsillach J, Furlong CE, Clark NL. Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals. 2019 Aug 10. Science, 361(6402, 591-594.
	Kitsios GD, Fitch A, Manatakis DV, Rapport SF, Li K, Qin S, Huwe J, Zhang Y, Doi Y, Evankovich J, Bain W, Lee JS, Methé B, Benos PV, Morris A, McVerry BJ (2018) Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients. Front Microbiol. 2018 Jul 10;9:1413. doi: 10.3389/fmicb.2018.01413.
	Rearick C, Ding F, Lin Y, Rose A, Sander C, Davis M, Benos PV, Tawbi HA, Tarhini AA, Kirkwood JM, Davar D (2018) Surveillance for melanoma (MEL): Results of a database study of stage I-III MEL . Journal of Clinical Oncology 36 (15_suppl), 9586-9586
	Ping P., Hermjakob H., Polson JS, Benos PV, Wang W.(2018) Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine Circulation Research. 2018 Apr 27;122(9):1290-1301. DOI: 10.1161/CIRCRESAHA.117.310967.
	Raghu VK, Ge X, Chrysanthis PK, Benos PV. (2017) Integrated Theory- and Data-driven Feature Selection in Gene Expression Data Analysis Proc Int Conf Data Eng. Apr 1525-1532. DOI: 10.1109/ICDE.2017.223.
	Pabon NA, Xia Y, Estabrooks SK, Ye Z, Herbrand AK, Sub E, Biondi RM, Assimon VA, Gestwicki JE, Brodsky JL, Camacho CJ, Bar-Joseph Z (2018) Predicting protein targets for drug-like compounds using transcriptomics. bioRxiv.
	Duff MR Jr, Borreguero JM, Cuneo MJ, Ramanathan A, He J, Kamath G, Chennubhotla SC, Meilleur F, Howell EE, Herwig KW, Myles DAA, Agarwal PK. Modulating Enzyme Activity by Altering Protein Dynamics with Solvent. Biochemistry. 2018 Jul 24;57(29):4263-4275. doi: 10.1021/acs.biochem.8b00424. 2018 Jul 24;57(29):4263-4275. PMID: 29901984
	Parvatikar A, Vacaliuc GS, Ramanathan A, Chennubhotla SC (2018) ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations. Biophys J. 2018 May 8;114(9):2040-2043. doi: 10.1016/j.bpj.2018.03.021. PMID: 29742397
	Lu C, Marx M, Zahid M, Lo CW, Chennubhotla SC, Quinn SP (2018) Stacked Neural Networks for end-to-end ciliary motion analysis. arXiv preprint arXiv:1803.07534
	Durden A, Loy AT, Reaves B, Fazli M, Courtney A, Quinn FD, Chennubhotla SC, Quinn SP (2018) Dynamic Social Network Modeling of Diffuse Subcellular Morphologies. PROC. OF THE 17th PYTHON IN SCIENCE CONF
	Nallu S, Hill JA, Don K, Sahagun C, Zhang W, Meslin C, Snell-Rood E, Clark NL, Morehouse NI, Bergelson J, Wheat CW, Kronforst MR (2018) The molecular genetic basis of herbivory between butterflies and their host plants. Nat Ecol Evol. 2018 Aug 3. doi: 10.1038/s41559-018-0629-9. PMID: 30076351
	Li X, George SM, Vernetti L, Gough AH, Taylor DL (2018) A glass-based, continuously zonated and vascularized human liver acinus microphysiologicalsystem (vLAMPS) designed for experimental modeling of diseases and ADME/TOX. Lab Chip. 2018 Jul 31. doi: 10.1039/c8lc00418h. 2018 Aug 21;18(17):2614-2631 PMID: 30063238
	Wang W, Taft DA, Chen YJ, Zhang J, Wallace CT, Xu M, Watkins SC, Xing J (2018) Learn to segment single cells with deep distance estimator and deep cell detector. arXiv preprint arXiv:1803.10829
	Zhang, J, Tian X, Chen Y, Wang W, Watkins S, Xing J. (2018) Pathway crosstalk enables cells to interpret TGF-β duration (2018). NPJ Systems Biology and Applications in press
	Singh M, Warita K, Warita T, Faeder JR, Lee REC, Sant S, Oltvai ZN (2018) Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors. Scientific Reports 8 (1)
	Hochuli J, Helbling A, Skaist T, Ragoza M, Koes DR (2018) Visualizing convolutional neural network protein-ligand scoring. Journal of Molecular Graphics and Modelling 84 , 96-108
	Molina L, Bell D, Tao J, Preziosi M, Pradhan-Sundd T, Singh S, Poddar M, Luo J, Ranganathan S, Chikina M, Monga SP (2018) Hepatocyte-Derived Lipocalin 2 Is a Potential Serum Biomarker Reflecting Tumor Burden in Hepatoblastoma. American Journal of Pathology 188 (8), 1895-1909
	Xu J, Ma H, Jin J, Uttam S, Fu R, Huang Y, Liu Y (2018) Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells. Cell Reports 24 (4), 873-882
	Rearick C, Ding F, Lin Y, Rose A, Sander C, Davis M, Benos PV, Tawbi HA, Tarhini AA, Kirkwood JM, Davar D (2018) Surveillance for melanoma (MEL): Results of a database study of stage I-III MEL . Journal of Clinical Oncology 36 (15_suppl), 9586-9586
	Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK (2018) Coloc-stats: A unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Research 46 (W1), W186-W193
	Ishikawa T, Hosaka YZ, Beckwitt C, Wells A, Oltvai ZN, Warita K (2018) Concomitant attenuation of HMG-CoA reductase expression potentiates the cancer cell growth-inhibitory effect of statins and expands their efficacy in tumor cells with epithelial characteristics. Oncotarget 9 (50), 29304-29315
	Ponzoni L, Zhang S, Cheng MH, Bahar I (2018) Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization. Philosophical Transactions of the Royal Society B: Biological Sciences 373 (1749)
	Berg J, Campbell P, Kiermer V, Raikhel N, Sweet D (2018) Joint statement on EPA proposed rule and public availability of data. Proceedings of the National Academy of Sciences of the United States of America 115 (24)
	Gupta S, Hainsworth L, Hogg J, Lee R, Faeder J (2018) Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology. Proceedings - 26th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2018 , 690-697
	Wingert BM, Camacho CJ (2018) Improving small molecule virtual screening strategies for the next generation of therapeutics. Current Opinion in Chemical Biology 44 , 87-92
	Chauhan BK, Medsinge A, Baumgartner MP, Scanga HL, Kamakari S, Gajdosova E, Camacho CJ, Nischal KK (2018) Case series: Pyramidal cataracts, intact irides and nystagmus from three novel PAX6 mutations. American Journal of Ophthalmology Case Reports 10 , 172-179
	Cheng MH, Kaya C, Bahar I (2018) Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter. Journal of Physical Chemistry B 122 (21), 5336-5346
	Ernst PB, Carvunis A-R (2018) Of mice, men and immunity: A case for evolutionary systems biology. Nature Immunology 19 (5), 421-425
	Narayanan C, Bernard DN, Bafna K, Gagne D, Chennubhotla CS, Doucet N, Agarwal PK (2018) Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily. Structure 26 (3), 426-436.e3
	Uttam S, Liu Y (2018) Fourier phase based depth-resolved nanoscale nuclear architecture mapping for cancer detection. Methods 136 , 134-151
	Jia S, Miedel MT, Ngo M, Hessenius R, Chen N, Wang P, Bahreini A, Li Z, Ding Z, Shun TY, Zuckerman DM, Taylor DL, Puhalla SL, Lee AV, Oesterreich S, Stern AM (2018) Clinically Observed Estrogen Receptor Alpha Mutations within the Ligand-Binding Domain Confer Distinguishable Phenotypes. Oncology (Switzerland) 94 (3), 176-189
	Dong Zhou, Haiyan Fu, Liangxiang Xiao, Hongyan Mo, Hui Zhuo, Xiaojun Tian, Lin Lin, Jianhua Xing, Youhua Liu (2018) Fibroblast-Specific β-catenin Signaling Dictates the Outcome of AKI. Journal of the American Society of Nephrology, ASN. 2017080903
	Wong VC, Bass VL, Bullock ME, Chavali AK, Lee REC, Mothes W, Gaudet S, Miller-Jensen K (2018) NF-κB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise. Cell Reports 22 (3), 585-599
	Schurdak ME, Pei F, Lezon TR, Carlisle D, Friedlander R, Taylor DL, Stern AM (2018) A quantitative systems pharmacology approach to infer pathways involved in complex disease phenotypes. Methods in Molecular Biology 1787 , 207-222
	Gough A, Shun TY, Taylor DL, Schurdak M (2018) Integrating analysis of cellular heterogeneity in high-content dose-response studies. Methods in Molecular Biology 1745 , 25-46
	Alison M Nagle, Cemal Erdem, Kevin Levine, Christos Sotiriou, Otto Metzger, D Lans Taylor, Timothy Lezon, Steffi Oesterreich, Adrian V Lee (2018) Abstract B158: Exploiting IGF1R pathway activation as a therapeutic strategy for E-cadherin deficient breast cancers. Molecular Cancer Therapeutics 17 (1 Supplement), B158-B158
	Jason A Hill, Ramprasad Neethiraj, Pasi Rastas, Nathan Clark, Nathan Morehouse, Maria de la Paz Celorio-Mancera, Jofre Carnicer Cols, Heinrich Dircksen, Camille Meslin, Kristin Sikkink, Maria Vives, Heiko Vogel, Christer Wiklund, Carol L Boggs, Soren Nylin, Christopher Wheat (2018) A butterfly chromonome reveals selection dynamics during extensive and cryptic chromosomal reshuffling. bioRxiv, 233700
	Nicolas A Pabon, Yan Xia, Samuel K Estabrooks, Zhaofeng Ye, Amanda K Herbrand, Evelyn Sub, Ricardo M Biondi, Victoria A Assimon, Jason E Gestwicki, Jeffrey L Brodsky, Carlos J Camacho, Ziv Bar-Joseph (2018) Proteome-scale detection of drug-target interactions using correlations in transcriptomic perturbations. bioRxiv, 254367
	Koes DR, Domling A, Camacho CJ (2018) AnchorQuery: Rapid online virtual screening for small-molecule protein–protein interaction inhibitors. Protein Science 27 (1), 229-232
	Kaya C, Cheng MH, Block ER, Bartol TM, Sejnowski TJ, Sorkin A, Faeder JR, Bahar I (2018) Heterogeneities in axonal structure and transporter distribution lower dopamine reuptake efficiency. eNeuro 5 (1)
	Vineet K Raghu, Joseph D Ramsey, Alison Morris, Dimitrios V Manatakis, Peter Sprites, Panos K Chrysanthis, Clark Glymour, Panayiotis V Benos (2018) Comparison of strategies for scalable causal discovery of latent variable models from mixed data. International Journal of Data Science and Analytics, 1-13
	Ji Young Lee, Zhiwei Feng, Xiang-Qun Sean Xie, Ivet Bahar (2018) Molecular Basis for the Functionality of γ-Secretase Inferred From Structure-Based Modeling and Druggability Simulations. Biophysical Journal 114 (3), 232a
	Hongchun Li, Nanaocha Sharma, Ignacio J General, Joseph M Salvino, Gideon Schreiber, Ivet Bahar (2018) Dynamic Modulation of Binding as a Mechanism for Regulating Interferon Signaling. Biophysical Journal 114 (3), 232a
	Ponzoni L, Bahar I (2018) Structural dynamics is a determinant of the functional significance of missense variants. Proceedings of the National Academy of Sciences of the United States of America 115 (16), 4164-4169
	Steinman J, Epperly M, Hou W, Willis J, Wang H, Fisher R, Liu B, Bahar I, McCaw T, Kagan V, Bayir H, Yu J, Wipf P, Li S, Huq MS, Greenberger JS (2018) Improved total-body irradiation survival by delivery of two radiation mitigators that target distinct cell death pathways. Radiation Research 189 (1), 68-83
	Tyurina YY, Shrivastava I, Tyurin VA, Mao G, Dar HH, Watkins S, Epperly M, Bahar I, Shvedova AA, Pitt B, Wenzel SE, Mallampalli RK, Sadovsky Y, Gabrilovich D, Greenberger JS, Bayir H, Kagan VE. (2018) "Only a life lived for others is worth living:" Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions.Antioxid Redox Signal DOI:10.1089/ars.2017.7124 PMID: 28835115
	Wingert BM, Oerlemans R, Camacho CJ (2018) Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges. Journal of Computer-Aided Molecular Design 32 (1), 287-297
	Krieger J, Lee JY, Greger IH, Bahar I (2018) Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions. Neuroscience Letters
	Gau D, Lewis T, McDermott L, Wipf P, Koes D, Roy P (2018) Structure-based virtual screening identifies a small-molecule inhibitor of the profilin 1–actin interaction. Journal of Biological Chemistry 293 (7), 2606-2616
	Raghu VK, Beckwitt CH, Warita K, Wells A, Benos PV, Oltvai ZN (2018) Biomarker identification for statin sensitivity of cancer cell lines. Biochemical and Biophysical Research Communications 495 (1), 659-665
	Keating SM, Taylor DL, Plant AL, Litwack ED, Kuhn P, Greenspan EJ, Hartshorn CM, Sigman CC, Kelloff GJ, Chang DD, Friberg G, Lee JSH, Kuida K. 2018 Mar 2. Opportunities and Challenges in Implementation of Multiparameter Single Cell Analysis Platforms for Clinical Translation. Clinical and Translational Science. doi: 10.1111/cts.12536. PMID: 29498218
	Beckwitt CH, Clark AM, Wheeler S, Taylor DL, Stolz DB, Griffith L, Wells A (2018) Liver 'organ on a chip'. Experimental Cell Research
	Saydmohammed M, Vollmer LL, Onuoha EO, Maskrey TS, Gibson G, Watkins SC, Wipf P, Vogt A, Tsang M (2018) A high-content screen reveals new small-molecule enhancers of ras/mapk signaling as probes for zebrafish heart development. Molecules 23 (7), 1-15
	Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei G-W, Holst MJ, McCammon JA, Baker NA (2018) Improvements to the APBS biomolecular solvation software suite. Protein Science 27 (1), 112-128