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Mohammadmahdi Rezaei Yousefi

  • Research Assistant Professor, Electrical & Computer Engr.
  • 205 Dreese Labs
    2015 Neil Ave
    Columbus, OH 43210

About

Education

Ph.D., Texas A&M University, 2013

Research areas

Genomic signal processing, intervention in gene regulatory networks, systems biology, bioinformatics, computational biology, system identification, stochastic systems and optimal control.

Biography

Dr. Yousefi received his master's degree in electrical engineering from the University of Tehran, Iran, in 2008 and his Ph.D. in electrical engineering from Texas A&M University, College Station, Texas and 2013, respectively. His Ph.D. research focused on designing optimal control strategies, taking into account probabilistic variabilities in tumor response to external interventions, for Markovian gene regulatory networks. He joined the Department of Electrical and Computer Engineering at The Ohio State University in June 2013 as a Research Assistant Professor. His current research interests include genomic signal processing and studying optimal intervention problems in gene regulatory networks from a probabilistic perspective.

Office

308 Dreese Laboratories

Honors

  • 2008-2009

    One-Time Scholarship. .

Books

2013

  • Yousefi,Mohammadmahdi,R. 2013. "Optimal Intervention in Markovian Genetic Regulatory Networks for Cancer Therapy." Texas A&M University.

2008

  • Yousefi,Mohammadmahdi,R. 2008. "Input Variable Selection in System Identification – Application in Time Series Prediction." University of Tehran.

Chapters

2016

  • Yousefi,Mohammadmahdi,R. 2016. "Optimal Intervention Methods for Markovian Gene Regulatory Networks." In Emerging Research in the Analysis and Modeling of Gene Regulatory Networks, edited by Ivanov,Ivan; Qian,Xiaoning; Pal,Ranadip, 161-208 - 161-208.

Journal Articles

2017

  • Dehghannasiri,Roozbeh; Xue,Dezhen; Balachandran,Prasanna,V; Yousefi,Mohammadmahdi,R; Dalton,Lori,A; Lookman,Turab; Dougherty,Edward,R, 2017, "Optimal Experimental Design for Materials Discovery." Computational Materials Science 129, 311–322 - 311–322.

2016

  • Dalton,Lori,A; Yousefi,Mohammadmahdi,R, 2016, "Data Requirements for Model Based Cancer Prognosis Prediction." Cancer Informatics (2016) 2015:Suppl. 5, 123-138 - 123-138.

2015

  • Yousefi,Mohammadmahdi,R; Dalton,Lori,A, 2015, "Optimal Cancer Prognosis Under Network Uncertainty." EURASIP Journal on Bioinformatics and Systems Biology 2015, no. 1, 1-15 - 1-15.
  • Dalton,Lori,A; Yousefi,Mohammadmahdi,R, 2015, "On Optimal Bayesian Classification and Risk Estimation Under Multiple Classes." EURASIP Journal on Bioinformatics and Systems Biology 2015, no. 8, 1-23 - 1-23.

2014

  • Yousefi,Mohammadmahdi,R; Dougherty,Edward,R, 2014, "A Comparison Study of Optimal and Suboptimal Intervention Policies for Gene Regulatory Networks in the Presence of Uncertainty." EURASIP Journal on Bioinformatics and Systems Biology 2014, no. 6, 1-13 - 1-13.

2013

  • 2013, "Optimal Intervention in Markovian Gene Regulatory Networks With Random-Length Therapeutic Response to Antitumor Drug.." IEEE transactions on bio-medical engineering 60, no. 12,
  • Yousefi,Mohammadmahdi,R; Dougherty,Edward,R, 2013, "Intervention in Gene Regulatory Networks With Maximal Phenotype Alteration." BIOINFORMATICS 29, no. 14, 1758-1767 - 1758-1767.
  • 2013, "Modeling the next generation sequencing sample processing pipeline for the purposes of classification." BMC BIOINFORMATICS 14,

2012

  • Yousefi,Mohammadmahdi,R; Dougherty,Edward,R, 2012, "Performance Reproducibility Index for Classification." BIOINFORMATICS 28, no. 21, 2824-2833 - 2824-2833.
  • Yousefi,Mohammadmahdi,R; Datta,Aniruddha; Dougherty,Edward,R, 2012, "Optimal Intervention Strategies for Therapeutic Methods With Fixed-Length Duration of Drug Effectiveness." IEEE TRANSACTIONS ON SIGNAL PROCESSING 60, no. 9, 4930-4944 - 4930-4944.

2011

  • Yousefi,Mohammadmahdi,R; Hua,Jianping; Dougherty,Edward,R, 2011, "Multiple-Rule Bias in the Comparison of Classification Rules." BIOINFORMATICS 27, no. 12, 1675-1683 - 1675-1683.
  • Amiri,Fatemeh; Yousefi,Mohammadmahdi,R; Lucas,Caro; Shakery,Azadeh; Yazdani,Nasser, 2011, "Mutual Information-Based Feature Selection for Intrusion Detection Systems." JOURNAL OF NETWORK AND COMPUTER APPLICATIONS 34, no. 4, 1184-1199 - 1184-1199.

2010

  • Yousefi,Mohammadmahdi,R; Hua,Jianping; Sima,Chao; Dougherty,Edward,R, 2010, "Reporting Bias When Using Real Data Sets to Analyze Classification Performance." BIOINFORMATICS 26, no. 1, 68-76 - 68-76.

2009

  • Yousefi,Mohammadmahdi,R; Kasmaei,Babak,S; Vahabie,A,Hossein; Lucas,Caro; Araabi,Babak,N, 2009, "Input Selection Based on Information Theory for Constructing Predictor Models of Solar and Geomagnetic Activity Indices." SOLAR PHYSICS 258, no. 2, 297-318 - 297-318.

Presentations

  • "Intervention in Gene Regulatory Networks with Maximal Phenotype Alteration." 2013,
  • "Multiple-Rule Bias in the Comparison of Classification Rules." 2011,
  • "Optimal Intervention Strategies for Cyclic Therapeutic Methods with Fixed-Length Duration of Effect." 2010,
  • "Control of Gene Networks and Reproducibility in Bioinformatics." 2014,
  • "Quantifying the Reporting Bias of Classification Performance on Real Data Sets." 2011,
  • "Optimal cancer prognosis under network uncertainty."
  • "Optimal Therapeutic Methods with Random-Length Response in Probabilistic Boolean Networks." 2012,
  • "Effects of Partial Reporting of Classification Results." 2010,
  • "Optimal Cancer Therapy Based on a Tumor Growth Inhibition Model." 2012,
  • "Combination of Singular Spectrum Analysis and Autoregressive Model for Short Term Load Forecasting." 2007,
  • "Modeling Cyclic and Acyclic Therapeutic Methods with Persistent Intervention Effect in Probabilistic Boolean Networks." 2011,
  • "Optimal Control of Gene Regulatory Networks with Uncertain Intervention Effects." 2014,
  • "Optimal Intervention Strategies for Cyclic Therapeutic Methods with Fixed-Length Duration of Effect." 2011,
  • "GPU Acceleration for Bayesian Control of Markovian Genetic Regulatory Networks." 2016,
  • "On Optimal Bayesian Classification and Risk Estimation Under Multiple Classes." 2015,
  • "Emergent Topological and Statistical Properties of Gene Regulatory Grids." 2015,
  • "Model-Based Cancer Prognosis." 2015,
  • "On the Limits of Data-Driven Cancer Prognosis Prediction." 2016,
  • "Emerging Properties of Gene Regulatory Networks and Grids." 2015,
  • "Optimal Control of Gene Regulatory Networks with Uncertain Intervention Effects." 2013,
  • "Compromised Intervention Policies for Phenotype Alteration." 2013,
  • "Overoptimism and Performance Reproducibility Issues in the Bioinformatics Studies." 2012,
  • "Bayesian Optimal Control of Markovian Genetic Regulatory Networks." 2013,
  • "Data Requirements for Model-Based Cancer Prognosis Prediction." 2016,

Papers in Proceedings

2016

  • "On the limits of data-driven cancer prognosis prediction." (4 2016).
  • Zhou,He; Hu,Jiang; Khatri,Sunil;Liu,Frank; Sze,Cliff Chin Ngai; Yousefi,Mohammadmahdi,R "GPU Acceleration for Bayesian Control of Markovian Genetic Regulatory Networks." in IEEE International Conference on Biomedical and Health Informatics (BHI). (2 2016). 304-307 - 304-307.

2015

  • Dalton,Lori,A; Yousefi,Mohammadmahdi,R. "On Optimal Bayesian Classification and Risk Estimation Under Multiple Classes (highlight paper)." in The 2nd International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2015), In conjunction with ACM-BCB 2015 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. (9 2015). N/A - N/A.
  • Ouma,Wilberforce Zachary; Yousefi,Mohammadmahdi,R; Doseff,Andrea,I; Grotewold,Erich "Emergent Topological and Statistical Properties of Gene Regulatory Grids (poster)." in 8th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges. (11 2015). P59 - P59.
  • "Optimal cancer prognosis under network uncertainty." (1 2015).
  • Ouma,Wilberforce Zachary; Lopez,Edgar; Yousefi,Mohammadmahdi,R; Doseff,Andrea,I; Grotewold,Erich "Emerging Properties of Gene Regulatory Grids (poster)." in ASPB Midwestern Section 2015 Meeting. (3 2015). N/A - N/A.

2014

  • Dalton,Lori,A; Yousefi,Mohammadmahdi,R "Optimal Bayesian Cancer Prognosis with Model-Constrained Robust Intervention." in IEEE Global Conference on Signal and Information Processing (GlobalSIP). (12 2014). 1382-1385 - 1382-1385.

2013

  • Yousefi,Mohammadmahdi,R; Dougherty,Edward,R "Bayesian Optimal Control of Markovian Genetic Regulatory Networks." in Asilomar Conference on Signals, Systems and Computers (ASILOMAR), 2013. (11 2013). 980-984 - 980-984.
  • Yousefi,Mohammadmahdi,R "Compromised Intervention Policies for Phenotype Alteration." in IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2013. (11 2013). 32-35 - 32-35.
  • "Optimal Control of Gene Regulatory Networks with Uncertain Intervention Effects." in IEEE Global Conference on Signal and Information Processing (GlobalSIP). (1 2013).

2012

  • Yousefi,Mohammadmahdi,R; Datta,Aniruddha; Dougherty,Edward,R "Optimal Therapeutic Methods with Random-Length Response in Probabilistic Boolean Networks." in IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2012. (12 2012). 50-53 - 50-53.
  • Yousefi,Mohammadmahdi,R; Datta,Aniruddha; Dougherty,Edward,R "Optimal Cancer Therapy Based on a Tumor Growth Inhibition Model." in IEEE Statistical Signal Processing Workshop (SSP), 2012. (8 2012). 568-571 - 568-571.

2011

  • Yousefi,Mohammadmahdi,R; Datta,Aniruddha; Dougherty,Edward,R. "Modeling Cyclic and Acyclic Therapeutic Methods with Persistent Intervention Effect in Probabilistic Boolean Networks." in IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2011. (12 2011). 38-41 - 38-41.
  • Yousefi,Mohammadmahdi,R; Datta, Aniruddha; Dougherty, Edward,R "Optimal Intervention Strategies for Cyclic Therapeutic Methods with Fixed-Length Duration of Effect." in Asilomar Conference on Signals, Systems and Computers (ASILOMAR), 2011. (11 2011). 1007-1011 - 1007-1011.

2010

  • Yousefi,Mohammadmahdi,R; Hua,Jianping; Sima,Chao; Dougherty,Edward,R "Effects of Partial Reporting of Classification Results." in IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2010. (11 2010). 1-4 - 1-4.

2007

  • Vahabie,A,Hossein; Yousefi,Mohammadmahdi,R; Araabi,Babak,N; Lucas,Caro; Barghinia,Saeedeh; Ansarimehr,P "Mutual Information Based Input Selection in Neuro-Fuzzy Modeling for Short Term Load Forecasting of Iran National Power System." in IEEE International Conference on Control and Automation (ICCA) 2007. (5 2007). 2710-2715 - 2710-2715.
  • Vahabie,A.,Hossein;Yousefi,Mohammadmahdi,R.;Araabi,Babak,N.;Lucas,Caro;Barghinia,Saeedeh;Ansarimehr,P. "Mutual Information Based Input Selection in Neuro-Fuzzy Modeling for Short Term Load Forecasting of Iran National Power System." JOURNAL: "Proceeding of the IEEE International Conference on Control and Automation (ICCA), 2007." in IEEE International Conference on Control and Automation (ICCA), 2007. (5 2007). 2710-2715 - 2710-2715.
  • Vahabie,A,Hossein; Yousefi,Mohammadmahdi,R; Araabi,Babak,N; Lucas,Caro; Barghinia,Saeedeh "Combination of Singular Spectrum Analysis and Autoregressive Model for Short Term Load Forecasting." in IEEE Power Tech, 2007. (7 2007). 1090-1093 - 1090-1093.
  • Yousefi,Mohammadmahdi,R; Mirmomeni,Masoud; Lucas,Caro "Input Variables Selection using Mutual Information for Neuro Fuzzy Modeling with the Application to Time Series Forecasting." in International Joint Conference on Neural Networks (IJCNN) 2007. (8 2007). 1121-1126 - 1121-1126.