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Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha Datta, Charles D. Johnson, "Examining de novo transcriptome assemblies via a quality assessment pipeline", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, no. 2, pp. 494-505, 2018.  (Journal Publication)  [More Details]  [Online]

M. Imani and U.M. Braga-Neto, "Particle Filters for Partially-Observed Boolean Dynamical Systems", Automatica, Vol. 87, Jan 2018, pp 238-250.  (Journal Publication)  [More Details]  [Online]

E. Atashpaz-Gargari, M.S. Reis, U.M. Braga-Neto, J. Barrera and E.R. Dougherty, "A fast Branch-and-Bound algorithm for U-curve feature selection", Pattern Recognition, Vol. 73, Jan 2018, pp. 172-188  (Journal Publication)  [More Details]  [Online]

A. Karbalayghareh, U.M. Braga-Neto, and E.R. Dougherty, "Intrinsically Bayesian robust classifier for single-cell gene expression trajectories in gene regulatory networks", BMC Systems Biology, Vol. 12 (Suppl 3), Mar 2018, p. 23.  (Journal Publication)  [More Details]  [Online]

A. Al Kawam, M. Alshawaqfeh, J. Cai, E. Serpedin and A. Datta, "Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies", BMC Bioinformatics  (Journal Publication)  [More Details]  [Online]

Yijie Wang and Xiaoning Qian, "Finding Low-Conductance sets with Dense interactions (FLCD) for better protein complex prediction", BMC Systems Biology, 11(S3): 22, 11 pages, doi: 10.1186/s12918-017-0405-5, 2017.  (Journal Publication)  [More Details]  [Online]

S Sridharan, R Varghese, V Venkatraj, and A Datta, "Hypoxia Stress Response Pathways: Modeling and Targeted Therapy", IEEE Journal of Biomedical and Health Informatics, Vol. 21, No. 3, 875-885, May 2017. DOI 10.1109/JBHI.2016.2559460.  (Journal Publication)  [More Details]  [Online]

R. Oliveira, M.T. Cordeiro, P. Moura, P. BaptistaFilho, U.M. Braga-Neto, E.T.A. Marques Júnior, L.H.V.G. Gil, "Serum cytokine/chemokine profiles in patients with dengue fever (DF) and dengue hemorrhagic fever (FHD) by using protein array", Journal of Clinical Virology, Vol. 89, Apr 2017, pp. 39-45.  (Journal Publication)  [More Details]  [Online]

P. Venkat, J. Hua, C. Sima, M. Cypert, M. Bittner and A. Datta, "Epiuorescent Imaging Study of the Effect of Anti-Diabetic Drug Metformin on Colorectal Cancer Cell Lines In Vitro", Journal of Cancer Research & Therapy,5(4):19-23, May 2017.  (Journal Publication)  [More Details]  [Online]

MeltemApaydin, Liang Xu, Bo Zeng, Xiaoning Qian, "Robust mutant strain design by pessimistic optimization", BMC Genomics, 18(S6): 677, 12 pages, doi: 10.1186/s12864-017-4025-7, 2017  (Journal Publication)  [More Details]  [Online]

M. Imani and U.M. Braga-Neto, "Gene regulatory network state estimation from arbitrary correlated measurements", EURASIP Journal on Advances in Signal Processing, Vol. 2018, Apr 2018, p. 22.  (Journal Publication)  [More Details]  [Online]

M. Imani and U.M. Braga-Neto, "Maximum-Likelihood Adaptive Filter for Partially-ObservedBoolean Dynamical Systems", IEEE Transactions on Signal Processing, Vol. 65, No. 2, Jan 2017, pp. 359-371.  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "CUFID-query: accurate network querying through estimation of network flow between query and target networks based on random walk", BMC Bioinformatics, 18(Suppl 14):500, 2017  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "CUFID-query: accurate network querying through estimation of network flow between query and target networks based on random walk", BMC Bioinformatics, 18(Suppl 14):500, 2017  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong and Byung-Jun Yoon, "SEQUOIA: Significance enhanced network querying through context-sensitive random walk and minimization of network conductance", BMC Systems Biology, 11(Suppl 3):20, 2017.  (Journal Publication)  [More Details]  [Online]

Chun-Chi Chen, Xiaoning Qian, and Byung-Jun Yoon, "Effective computational detection of piRNAs using n-gram models and support vector machine", BMC Bioinformatics, 18(Suppl 14):517. 2017.  (Journal Publication)  [More Details]  [Online]

Chun-Chi Chen, Noushin Ghaffari, Xiaoning Qian, and Byung-Jun Yoon, "Optimal hybrid sequencing and assembly: feasibility conditions for accurate genome reconstruction and cost minimization strategy", Computational Biology and Chemistry, 69, pp. 153–163, 2017  (Journal Publication)  [More Details]  [Online]

AseemPandey, Sheng Li Ding, Qing-Ming Qin, Rahul Gupta, Gabriel Gomez, Furong Lin, Xue-huaFeng, Luciana Fachini da Costa, Sankar P. Chaki, MadhuKatepalli, Elizabeth Case, Erin van Schaik, TabasumSidiq, Omar Khalaf, Angela Arenas, Koichi Kobayashi, James E. Samuel, Gonzalo Rivera, Robert C. Alaniz, Sing-Hoi Sze, Xiaoning Qian, Allison Rice-Ficht, William Russell, Thomas A. Ficht, Paul de Figueiredo, "Global reprogramming of host kinase signaling in response to fungal infection", Cell Host & Microbe, 21(5): 637–649.e1–e6, 2017. (Cover Page)  (Journal Publication)  [More Details]  [Online]

L.D. Mcclenny, M. Imani and U. M Braga-Neto, "BoolFilter: an R package for estimation and identification of Partially-Observed Boolean Dynamical Systems,", BMC Bioinformatics, Vol. 87, Jan 2018, pp 238-250.  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian and Edward R. Dougherty, "Bayesian regression with network prior: Optimal Bayesian filtering perspective", IEEE Transactions on Signal Processing, 64(23):6243-6253, 2016.  (Book Chapter)  [More Details]  [Online]

T. Chen and U.M. Braga-Neto, "Bayesian Estimation of the Discrete Coefficient of Determination", Special Issue on Bayesian Methods for Computational Systems Biology, EURASIP Journal of Bioinformatics and Systems Biology, 2016 Jan 15;2016(1):1.  (Journal Publication)  [More Details]  [Online]

SiamakZamaniDadanehand Xiaoning Qian, "Bayesian module identification from multiple noisy networks", EURASIP Journal on Bioinformatics and Systems Biology, 2016:5, 11 pages, doi: 10.1186/s13637-016-0038-9, 2016.  (Book Chapter)  [More Details]  [Online]

S. Khadraoui, M. Fnaiech, H. Nounou, M. Nounou, J. Guzinski, H. AbuRub, A. Datta, and S. P. Bhattacharyya, "Measurement-based control approach for tuning PID controllers: Application to induction machines", Journal of Control and Decision, Vol. 3, 179-196, 2016  (Journal Publication)  [More Details]  [Online]

S. Khadraoui, H. Nounou, M. Nounou, A. Datta, and S. P. Bhattacharyya, "Adaptive controller design for unknown systems using measured data", Asian Journal of Control, Vol. 18, no. 5, 1-14, 2016.  (Journal Publication)  [More Details]  [Online]

O. Arshad, P. Venkatasubramani, A. Datta and J. Venkatraj, "Using Boolean Logic Modeling of Gene Regulatory Networks to Exploit the Links between Cancer and Metabolism for Therapeutic Purposes", IEEE Journal of Biomedical and Health Informatics, Vol. 20, No. 1, 399-407, January 2016; DOI: 10.1109/JBHI.2014.2368391.  (Journal Publication)  [More Details]  [Online]

Meng Lu, Jianhua Z. Huang, Qian, "Sparse Exponential Family Principal Component Analysis", Pattern Recognition, 60: 681-691, 2016.  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model", BMC Bioinformatics, 17(Suppl 13):395, 2016.  (Journal Publication)  [More Details]  [Online]

Roozbeh Dehghannasiri, Byung-Jun Yoon, and Edward R. Dougherty, "Efficient experimental design for uncertainty reduction in gene regulatory networks", BMC Bioinformatics, 16(Suppl 13):S2, 2015.  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong and Byung-Jun Yoon, "Accurate multiple network alignment through context-sensitive random walk", BMC Systems Biology, 9(Suppl 1):S7, 2015.  (Journal Publication)  [More Details]  [Online]

Tao Hu, Juan Nunez-Iglesias, Shiv Naga Prasad Vitaladevuni, Lou Scheffer, Shan Xu, Mehdi Bolorizadeh, Harald F. Hess, Richard Fetter, and Dmitri B. Chklovskii, "Electron Microscopy Reconstruction of Brain Structure Using Sparse Representations Over Learned Dictionaries.", IEEE Trans. Med. Imaging 32(12):2179-2188 (2013)  (Journal Publication)  [More Details]  [Online]

Minna D Balbas, Michael J Evans, David J Hosfield, John Wongvipat, Vivek K Arora, Philip A Watson, Yu Chen, Geoffrey L Greene, Yang Shen, Charles L Sawyers, "Overcoming mutation-based resistance to antiandrogens with rational drug design", eLife 2013;2:e00499  (Journal Publication)  [More Details]  [Online]

Han K, Holder JL Jr, Schaaf CP, Lu H, Chen H, Kang H, Tang J, Wu Z, Hao S, Cheung SW, Yu P, Sun H, Breman AM, Patel A, Lu HC, Zoghbi HY., "SHANK3 overexpression causes manic-like behaviour with unique pharmacogenetic properties.", Nature. 2013 Nov 7;503(7474):72-7. doi: 10.1038/nature12630. Epub 2013 Oct 23.  (Journal Publication)  [More Details]  [Online]

Edward R Dougherty, "On the impoverishment of scientific education", EURASIP Journal on Bioinformatics and Systems Biology 2013, 2013:15  (Journal Publication)  [More Details]  [Online]

Chen, T. and Braga-Neto, "Maximum-Likelihood Estimation of the Discrete Coefficient of Determination in Stochastic Boolean Systems", IEEE Transactions on Signal Processing, vol.61, no.15, pp.3880,3894, Aug.1, 2013  (Journal Publication)  [More Details]  [Online]

Baker SA, Chen L, Wilkins AD, Yu P, Lichtarge O, Zoghbi HY., "An AT-hook domain in MeCP2 determines the clinical course of Rett syndrome and related disorders", Cell. 2013 Feb 28;152(5):984-96. doi: 10.1016/j.cell.2013.01.038  (Journal Publication)  [More Details]  [Online]

Xiangfang Li, Lijun Qian and Edward R Dougherty, "Dynamical modeling of drug effect using hybrid systems", EURASIP Journal on Bioinformatics and Systems Biology 2012, 2012:19  (Journal Publication)  [More Details]  [Online]

Tao Hu, A. Genkin and D.B. Chklovskii, "Computing sparse representations using a network of sparsely communicating nodes", Neural Computation 24, 2852 (2012)  (Journal Publication)  [More Details]  [Online]

Kessler JD, Kahle KT, Sun T, Meerbrey KL, Schlabach MR, Schmitt EM, Skinner SO, Xu Q, Li MZ, Hartman ZC, Rao M, Yu P, Dominguez-Vidana R, Liang AC, Solimini NL, Bernardi RJ, Yu B, Hsu T, Golding I, Luo J, Osborne CK, Creighton CJ, Hilsenbeck SG, Schiff R, Shaw CA, Elledge SJ, Westbrook TF., "A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis", Science. 2012 Jan 20;335(6066):348-53. doi: 10.1126/science.1212728. Epub 2011 Dec 8.  (Journal Publication)  [More Details]  [Online]

Hsu FH, Serpedin E, Hsiao TH, Bishop AJ, Dougherty ER, Chen Y., "Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer", BMC Genomics. 2012;13 Suppl 6:S13.   (Journal Publication)  [More Details]  [Online]

Xiangfang Li, Lijun Qian, Michael L. Bittner, Edward R. Dougherty, "Characterization of Drug Efficacy Regions Based on Dosage and Frequency Schedules", IEEE Trans. Biomed. Engineering 58(3): 488-498 (2011)  (Journal Publication)  [More Details]  [Online]

Ritwik Layek, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty, "Cancer therapy design based on pathway logic", Bioinformatics 27(4): 548-555 (2011)  (Journal Publication)  [More Details]  [Online]

Fryer JD, Yu P, Kang H, Mandel-Brehm C, Carter AN, Crespo-Barreto J, Gao Y, Flora A, Shaw C, Orr HT, Zoghbi HY., "Exercise and genetic rescue of SCA1 via the transcriptional repressor Capicua.", Science. 2011 Nov 4;334(6056):690-3. doi: 10.1126/science.1212673.  (Journal Publication)  [More Details]  [Online]

Zollanvari, A, Braga-Neto and Dougherty, E.R., "Joint Sampling Distribution Between Actual and Estimated Classification Errors for Linear Discriminant Analysis", Published in: Information Theory, IEEE Transactions on (Volume:56 , Issue: 2 ) Date of Publication: Feb. 2010 Page(s): 784 - 804 ISSN : 0018-9448 INSPEC Accession Number: 11152615 Digital Object Identifier : 10.1109/TIT.2009.2037034 Date of Current Version : 25 febrero 2010 Issue Date : Feb. 2010 Sponsored by : IEEE Information Theory Society  (Journal Publication)  [More Details]  [Online]

Youting Sun, Jianqiu Zhang, Ulisses Braga-Neto and Edward R Dougherty, "BPDA – A Bayesian peptide detection algorithm for mass spectrometry", BMC Bioinformatics 2010, 11:490 doi:10.1186/1471-2105-11-490  (Journal Publication)  [More Details]  [Online]

Y. Mishchenko*, Tao Hu*, J. Spacek, J. Mendenhall, K.M. Harris and D.B. Chklovskii, "Ultrastructural analysis of hippocampal neuropil from the connectomics perspective", Neuron 67, 1009, (2010)  (Journal Publication)  [More Details]  [Online]

Ulisses M. Braga-Neto and Edward R. Dougherty, "Exact Correlation between Actual and Estimated Errors in Discrete Classification", Published in: Journal Pattern Recognition Letters archive Volume 31 Issue 5, April, 2010 Pages 407-412   (Journal Publication)  [More Details]  [Online]

Ting Chen and Ulisses Braga-Neto, "Exact performance of CoD estimators in discrete prediction", Published in: · Journal EURASIP Journal on Advances in Signal Processing - Special issue on genomic signal processing archive Volume 2010, March 2010 Article No. 2   (Journal Publication)  [More Details]  [Online]

T. T. Vu and Braga-Neto, "Small-sample error estimation for bagged classification rules", Published in: · Journal EURASIP Journal on Advances in Signal Processing - Special issue on genomic signal processing archive Volume 2010, March 2010 Article No. 6   (Journal Publication)  [More Details]  [Online]

Dougherty, E. R., Sima, C., Hua, J., Hanczar, B., and Braga-Neto, U. M., "Performance of Error Estimators for Classification", Current Bioinformatics, Vol. 5, No. 1, 53-67, March, 2010.  (Journal Publication)  [More Details]  [Online]

Dougherty ER, Bittner ML., "Causality, randomness, intelligibility, and the epistemology of the cell", Curr Genomics. 2010 Jun;11(4):221-37  (Journal Publication)  [More Details]  [Online]

Youting Sun, Ulisses Braga-Neto and Edward R. Dougherty, "Impact of Missing Value Imputation on Classification for DNA Microarray Gene Expression Data – A Model-Based Study", Published in: ·Journal EURASIP Journal on Bioinformatics and Systems Biology Volume 2009, January 2009 Article No. 4   (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "Theory of DNA translocation through narrow ion channels and nanopores with charged walls", Physical Review E 78, 032901 (2008)  (Journal Publication)  [More Details]  [Online]

Tao Hu, R. Zhang and B.I. Shklovskii, "Electrostatic theory of viral self-assembly: a toy model", Physica A 387, 3059 (2008)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "How a protein searches for its specific site on DNA: role of intersegment transfer", Physical Review E 76, 051909 (2007)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "Kinetics of viral self-assembly: the role of ss RNA antenna", Physical Review E 75, 051901 (2007)  (Journal Publication)  [More Details]  [Online]

Y.J. Sun, W.S. Gao,Tao Hu and Q.J. Xing, "Photoelastic Waveguides Induced by Thin Film Composite Structure in InGaAsP/InP Double Heterostructures", Semiconductor Science and Technology 21, 575 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu, A.Yu. Grosberg and B.I. Shklovskii, "How proteins search for their specific sites on DNA: the role of DNA conformation", Biophysical Journal. 90, 2731 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu, A.Yu. Grosberg and B.I. Shklovskii, "Conductivity of a suspension of nanowires in a weakly conducting medium", Physical Review B 73, 155434 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "How does a protein search for the specific site on DNA: the role of disorder", Physical Review E 74, 021903 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "Hopping conductivity of a suspension of flexible wires in an insulator", Physical Review B 74, 174201 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "Theory of hopping conductivity of a suspension of nanowires in an insulator", Physical Review B 74, 054205 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu, Y. Fu, H. Zhang, S.L. Zhang, J. Ouyang and X.S. Zhao, "Temperature-dependent Raman Spectra of α-Fe2O3 Nano-wire and Bulk Material", Chinese Journal of Light Scattering 16, 303 (2004)  (Journal Publication)  [More Details]

Tao Hu, X. Lu, Y. Yan, Y. Fu, H. Zhang and S. L. Zhang, "Raman Spectroscopic Study on Iron Oxides Prepared by Oxidation of Iron", Spectroscopy and Spectral Analysis 24, 1072 (2004)  (Journal Publication)  [More Details]  [Online]

W.S. Gao, Q.J. Xing, Z.J. Yuan and Tao Hu, "W0.95Ni0.05 Compressive Strain Thin Film Stripe Window Induced Photoelastic Waveguide Structure in InGaAsP/InP Double Heterostructure", 2003 Chinese Phys. Lett. 20 1296 doi:10.1088/0256-307X/20/8/333  (Journal Publication)  [More Details]  [Online]