2016 Publications | Computational & Systems Biology

	Böhm S, Szakal B, Herken BW, Sullivan MR, Mihalevic MJ, Kabbinavar FF, Branzei D, Clark NL, Bernstein KA (2016) The Budding Yeast Ubiquitin Protease Ubp7 is a Novel Component Involved in S-phase Progression J Biol Chem 291(9):4442-52
	Berg JM, Berg WA (2016) No myth: Benefits of breast screening Nature 529(7586):283.
	Weisel FJ, Zuccarino-Catania GV, Chikina M, Shlomchik MJ (2016) A Temporal Switch in the Germinal Center Determines Differential Output of Memory B and Plasma Cells Immunity 44(1):116-30.
	Ziegler AB, Augustin H, Clark NL, Berthelot-Grosjean M, Simonnet MM, Steinert JR, Geillon F, Manière G, Featherstone DE, Grosjean Y (2016) The Amino Acid Transporter JhI-21 Coevolves with Glutamate Receptors, Impacts NMJ Physiology, and Influences Locomotor Activity in Drosophila Larvae Sci Rep 6:19692.
	Donovan RM, Tapia JJ, Sullivan DP, Faeder JR, Murphy RF, Dittrich M, Zuckerman DM (2016) Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories PLoS Comput Biol. 12(2):e1004611.
	Tejero J, Kapralov AA, Baumgartner MP, Sparacino-Watkins CE, Anthonymutu TS, Vlasova II, Camacho CJ, Gladwin MT, Bayir H, Kagan VE (2016) Peroxidase activation of cytoglobin by anionic phospholipids: Mechanisms and consequences Biochim Biophys Acta. 1861(5):391-401.
	Stern AM, Schurdak ME, Bahar I, Berg JM, Taylor DL (2016) A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine J Biomol Screen 21(6):521-34
	McDermott LA, Iyer P, Vernetti L, Rimer S, Sun J, Boby M, Yang T, Fioravanti M, O'Neill J, Wang L, Drakes D, Katt W, Huang Q, Cerione R (2016) Design and evaluation of novel glutaminase inhibitors Bioorg Med Chem. 24(8):1819-1839.
	Tao J, Xu E, Zhao Y, Singh S, Li X, Couchy G, Chen X, Zucman-Rossi J, Chikina M, Monga SP (2016) Modeling a Human HCC Subset in Mice Through Co-Expression of Met and Point-Mutant β-Catenin Hepatology [Epub ahead of print].
	Hain E, Camacho CJ, Koes DR (2016) Fragment oriented molecular shapes J Mol Graph Model. 66:143-54
	Sunseri J, Koes DR (2016) Pharmit: interactive exploration of chemical space Nucleic Acids Res 44(W1):W442-8
	Faeder JR, Morel PA (2016) Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments Biophys J. 110(8):1681-3.
	Xiao-Jun Tian, Hang Zhang, Jens Sannerud, Jianhua Xing (2016) Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design Proceedings of the National Academy of Sciences of the United States of America
	Sedgewick AJ, Shi I, Donovan RM, Benos PV (2016) Learning mixed graphical models with separate sparsity parameters and stability-based model selection BMC Bioinformatics Jun 6;17 Suppl 5:175.
	Chikina M, Robinson JD, Clark NL (2016) Hundreds of genes experienced convergent shifts in selective pressure in marine mammals Mol Biol Evol 33(9):2182-92
	Erdem C, Nagle AM, Casa AJ, Litzenburger BC, Wang YF, Taylor DL, Lee AV, Lezon TR (2016) Proteomic screening and lasso regression reveal differential signaling in insulin and insulin-like growth factor I pathways Mol Cell Proteomics 15(9):3045-57
	Suárez E, Adelman JL, Zuckerman DM (2016) Accurate estimation of protein folding and unfolding times: Beyond Markov state models J Chem Theory Comput. 12(8):3473–3481
	LaPorte MG, Wang Z, Colombo R, Garzan A, Peshkov VA, Liang M, Johnston PA, Schurdak ME, Sen M, Camarco DP, Hua Y, Pollock NI, Lazo JS, Grandis JR, Wipf P, Huryn DM (2016) Optimization of pyrazole-containing 1,2,4-triazolo-[3,4-b]thiadiazines, a new class of STAT3 pathway inhibitors Bioorg Med Chem Lett 26(15):3581-5
	Travers TS, Harlow L, Rosas IO, Gochuico BR, Mikul TR, Bhattacharya SK, Camacho CJ, Ascherman DP (2016) Extensive Citrullination Promotoes Immunogenicity of HSP90 through Protein Unfolding and Exposure of Cryptic Epitopes J Immunol 197(5):1926-36.
	Colombo R, Wnag Z, Han J, Balachandran R, Daghestani HN, Camarco DP, Vogt A, Day BW, Mendel D, Wipf P (2016) Total Synthesis and Biological Evaluation of Tubulysin Analogs J Org Chem 81(21):10302-10320.
	Clark AM, Ma B, Taylor DL, Griffith L, Wells A (2016) Liver metastases: Microenvironments and ex-vivo models. Exp Biol Med (Maywood) 241(15):1639-52.
	Harris La, Hogg JS, Tapia JJ, Sekar JA, Gupta S, Korsunsky I, Arora A, Barua D, Sheehan RP, Faeder JR (2016) BioNetGen 2.2 Advances in Rule-Based Modeling. Bioinformatics 32(21):3366-3368.
	Liu B, Liu Q, Yang L, Palaniappan SK, Bahar I, Thiagarajan PS, Ding JL (2016) Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways. Sci Signal 9(436):ra70.
	Gau D, Veon W, Zeng X, Yates N, Shroff SH, Koes DR, Roy P (2016) Threonine 89 Is an Important Residue of Profilin-1 That Is Phosphorylatable by Protein Kinase A. PLoS One 11(5):e0156313.
	Gearhart TL, Montelaro RC, Schurdak ME, Pilcher CD, Rinaldo CR, Kodadek T, Park Y, Islam K, Yurko R, Murques ET Jr, Burke DS (2016) Selection of a potential diagnostic biomarker for HIV infection from a random library of non-biological synthetic peptoid oligomers J Immunol Methods 435:85-9.
	Critchely-Thorne RJ, Duits LC, Prichard JW, Davison JM, Jobe BA, Campbell BB, Zhang Y, Repa KA, Reese LM, Li J, Diehl DL, Jhala NC, Ginsberg G, DeMarshall M, Foxwell T, Zaidi AH, Lansing Taylor D, Rustgi AK, Bergman JJ, Falk GW (2016) A Tissue Systems Pathology Assay for High-Risk Barrett's Esophagus. Cancer Epidemiol Biomarkers Prev. 25(6):958-68.
	Berg JM, Bhalla N, Bourne PE, Chalfie M, Drubin DG, Fraser JS, Greider CW, Hendricks M, Jones C, Kiley R, King S, Kirschner MW, Krumholz HM, Lehmann R, Leptin M, Pulverer B, Rosenzweig B, Spiro JE, Stebbins M, Strasser C, Swaminathan S, Turner P, Vale RD, VijayRaghavan K, Wolberger C. (2016) Scientific Community: Preprints for the life sciences. Science (6288):899-901.
	Gao Y, Liu Y, Hong L, Yang Z, Cai X, Chen X, Fu Y, Lin Y, Wen W, Li S, Liu X, Huang H, Vogt A, Liu P, Yin XM, Li M (2016) Golgi-associated LC3 lipidation requires V-ATPase in noncanonical autophagy Cell Death Dis 7(8):e2330.
	Agarwal PK, Doucet N, Chennubhotla C, Ramanathan A, Narayanan C (2016) Conformational Sub-states and Populations in Enzyme Catalysis Methods Enzymol 578:273-97.
	Kurkcuoglu Z, Bahar I, Doruker P (2016) ClustENM: ENM-based sampling of essential conformational space at full atomic resolution J Chem Theory Comput. 12(9):4549-62
	Okabe H, Yang J, Sylakowski K, Yovchev M, Miyagawa Y, Nagarajan S, Chikina M, Thompson M, Oertel M, Baba H, Monga SP, Nejak-Bowen KN (2016) Wnt signaling regulates hepatobiliary repair following cholestatic liver injury in mice Hepatology [Epud ahead of print]
	Jianhua Xing (2016) Neurons use physics for receptor selection Cell Systems 2:290
	Jingyu Zhang, Xiao-Jun Tian and Jianhua Xing (2016) Signal transduction pathways of EMT induced by TGF-Beta, SHH, and WNT and their crosstalks J. Clin. Med. 5:41
	Sunseri J, Ragoza M, Collins J, Koes DR (2016) A D3R prospective evaluation of machine learning for protein-ligand scoring. J Comput Aided Mol Des. 30(9):695-706.
	Pirrhadi S, Sunseri J, Koes DR (2016) Open source molecular modeling. J Mol Graph Model. 69:127-43
	Anandakrishnan R, Zhang Z, Donovan-Maiye R, Zuckerman DM (2016) Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process Proc Natl Acad Sci U S A. 113(40):11220-11225
	Clancy CJ, Meslin C, Badrane H, Cheng S, Losada LC, Nierman WC, Vergidis P, Clark NL, Nguyen MH (2016) Candida albicans Transcriptional Profiling Within Biliary Fluid From a Patient With Cholangitis, Before and After Antifungal Treatment and Surgical Drainage Open Forum Infect Dis. 3(3):ofw120.
	Chandran UR, Medvedeva OP, Barmada MM, Blood PD, Chakka A, Luthra S, Ferreira A, Wong KF, Lee AV, Zhang Z, Budden R, Scott JR, Berndt A, Berg JM, Jacobson RS (2016) TCGA Expedition: A Data Acquisition and Management System for TCGA Data PLoS One 11(10):e0165395.
	Sun Q, Loughran P, Shapiro R, Shrivastava IH, Antoine DJ, Li T, Yan Z, Fan J, Billiar TR, Scott MJ (2016) Redox-dependent regulation of hepatocyte AIM2 inflammasome activation in sterile liver injury in mice Hepatology [Epub ahead of print].
	Okabe H, Yang J, Sylakowski K, Yovchev M, Miyagawa Y, Nagarajan S, Chikina M, Thompson M, Oertel M, Baba H, Monga SP, Nejak-Bowen KN (2016) Wnt signaling regulates hepatobiliary repair following cholestatic liver injury in mice Hepatology 64(5):1652-1666.
	Tao J, Xu E, Zhao Y, Singh S, Li X, Couchy G, Chen X, Zucman-Rossi J, Chikina M, Monga SP (2016) Modeling a human hepatocellular carcinoma subset in mice through coexpression of met and point-mutant β-catenin Hepatology 64(5):1587-1605.
	Ye Z, Baumgartner MP, Wingert BM, Camacho CJ (2016) Optimal Strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge J Comp Aided Mol Des 30(9):695-706.
	Huang J, Woods P, Normolle D, Goff JP, Benos PV, Stehle CJ, Steinman RA (2016) Downregulation of estrogen receptor and modulation of growth of breast cancer cell lines mediated by paracrine stromal cell signals Breast Cancer Res Treat. [Epub ahead of print]
	Vernetti LA, Vogt A, Gough A, Taylor DL (2016) Evolution of Experimental Models of the Liver to Predict Human Drug Hepatotoxicity and Efficacy Clin Liver Dis. 21(1):197-214.
	Kagan VE, Mao G, Qu F, Angeli JP, Doll S, Croix CS, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayır H (2016) Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis Nat Chem Biol. [Epub ahead of print]
	Morel PA, Lee RE, Faeder JR (2016) Demystifying the cytokine network: Mathematical models point the way Cytokine. S1043-4666(16)30571-3.
	Bahreini A, Levine K, Santana-Santos L, Benos PV, Wang P, Andersen C, Oesterreich S, Lee AV (2016) Non-coding single nucleotide variants affecting estrogen receptor binding and activity Genome Med. 8(1):128.
	Bergman S, Lezon TR (2016) Modeling global changes induced by local perturbations to the HIV-1 capsid J Mol Graph Model. 71:218-226.
	Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor DL, Chennubhotla SC (2016) Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers J Pathol Inform 7:47.
	Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y (2016) Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis. EBioMedicine [Epub ahead of print].
	Lee REC, Qasaimeh MA, Xia X, Juncker D, Gaudet S (2016) NF-κB signalling and cell fate decisions in response to a short pulse of tumour necrosis factor. Scientific Reports 6, Article number: 39519.