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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." College Station: Texas A&M University.

2008

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

Chapters

Unknown

  • Yousefi,Mohammadmahdi,R. "Optimal Intervention Methods for Markovian Gene Regulatory Networks." In Emerging Research in the Analysis and Modeling of Gene Regulatory Networks, edited by Ivan Ivanov. Hershey: IGI Global, 2016.,

Journal Articles

2015

  • 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.
  • 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.

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.

2013

  • Yousefi,Mohammadmahdi,R; Datta,Aniruddha; Dougherty,Edward,R., 2013, "Optimal Intervention in Markovian Gene Regulatory Networks With Random-Length Therapeutic Response to Antitumor Drug." IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING 60, no. 12, 3542 - 3552.
  • Yousefi,Mohammadmahdi,R; Dougherty,Edward,R, 2013, "Intervention in Gene Regulatory Networks With Maximal Phenotype Alteration." BIOINFORMATICS 29, no. 14, 1758 - 1767.
  • Ghaffari,Noushin; Yousefi,Mohammadmahdi,R; Johnson,Charles,D; Ivanov,Ivan; Dougherty,Edward,R, 2013, "Modeling the Next Generation Sequencing Sample Processing Pipeline for the Purposes of Classification.." BMC BIOINFORMATICS 14, 307 -

2012

  • Yousefi,Mohammadmahdi,R; Dougherty,Edward,R, 2012, "Performance Reproducibility Index for Classification." BIOINFORMATICS 28, no. 21, 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.

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.
  • 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.

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.

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.

Unknown

  • Dalton,Lori,A; Yousefi,Mohammadmahdi,R, "Data Requirements for Model Based Cancer Prognosis Prediction." Cancer Informatics (2016)

Presentations

  • "Intervention in Gene Regulatory Networks with Maximal Phenotype Alteration." 2013, Presented at Student Research Week - Texas A&M University,
  • "Multiple-Rule Bias in the Comparison of Classification Rules." 2011, Presented at Texas A&M GSP Lab Seminars,
  • "Quantifying the Reporting Bias of Classification Performance on Real Data Sets." 2011, Presented at The Eighth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS 2011),
  • "Overoptimism and Performance Reproducibility Issues in the Bioinformatics Studies." 2012, Presented at Texas A&M GSP Lab Seminars,
  • "Optimal Intervention Strategies for Cyclic Therapeutic Methods with Fixed-Length Duration of Effect." 2010, Presented at Texas A&M GSP Lab Seminars,
  • "Combination of Singular Spectrum Analysis and Autoregressive Model for Short Term Load Forecasting." 2007, Presented at IEEE PowerTech 2007, Lausanne, SZ|SWZ
  • "Effects of Partial Reporting of Classification Results." 2010, Presented at IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Cold Spring Harbor, US|USA
  • "Modeling Cyclic and Acyclic Therapeutic Methods with Persistent Intervention Effect in Probabilistic Boolean Networks." 2011, Presented at IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), San Antonio, US|USA
  • "Optimal Cancer Therapy Based on a Tumor Growth Inhibition Model." 2012, Presented at IEEE Statistical Signal Processing Workshop (SSP’12), Ann Arbor, US|USA
  • "Optimal Therapeutic Methods with Random-Length Response in Probabilistic Boolean Networks." 2012, Presented at IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Washington, US|USA
  • "Compromised Intervention Policies for Phenotype Alteration." 2013, Presented at IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Houston, US|USA
  • "Control of Gene Networks and Reproducibility in Bioinformatics." 2014, Presented at Computational Biology Meetings, Columbus, US|USA
  • "Optimal Cancer Prognosis Under Network Uncertainty." 2014, Presented at ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB), Newport Beach, US|USA
  • "Optimal Intervention Strategies for Cyclic Therapeutic Methods with Fixed-Length Duration of Effect." 2011, Presented at Forty Fifth Asilomar Conference on Signals, Systems and Computers (ASILOMAR), Pacific Grove, US|USA
  • "Bayesian Optimal Control of Markovian Genetic Regulatory Networks." 2013, Presented at Forty Seventh Asilomar Conference on Signals, Systems and Computers (ASILOMAR), Pacific Grove, US|USA
  • "Optimal Control of Gene Regulatory Networks with Uncertain Intervention Effects." 2013, Presented at IEEE Global Conference on Signal and Information Processing (GlobalSIP’13), Austin, US|USA
  • "Optimal Control of Gene Regulatory Networks with Uncertain Intervention Effects." 2014, Presented at MBI Workshop for Young Researchers in Mathematical Biology,, Columbus, US|USA
  • "GPU Acceleration for Bayesian Control of Markovian Genetic Regulatory Networks." 2016, Presented at IEEE International Conference on Biomedical and Health Informatics (BHI), Las Vegas, US|USA
  • "On Optimal Bayesian Classification and Risk Estimation Under Multiple Classes." 2015, Presented at 2nd International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2015), In conjunction with ACM-BCB 2015, Atlanta, US|USA
  • "Emergent Topological and Statistical Properties of Gene Regulatory Grids." 2015, Presented at 8th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges, Philadelphia, US|USA
  • "Model-Based Cancer Prognosis." 2015, Presented at Computational Biology Laboratory, Columbus, US|USA
  • "On the Limits of Data-Driven Cancer Prognosis Prediction." 2016, Presented at IEEE International Conference on Biomedical and Health Informatics (BHI), Las Vegas, US|USA
  • "Emerging Properties of Gene Regulatory Networks and Grids." 2015, Presented at American Society of Plant Biologists, Midwestern Meeting, St. Louis, US|USA

Papers in Proceedings

2016

  • Yousefi,Mohammadmahdi,R; Dalton,Lori,A "On the Limits of Data-Driven Cancer Prognosis Prediction." in IEEE International Conference on Biomedical and Health Informatics (BHI). New York, (2 2016). 537 - 540.
  • 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). New York, (2 2016). 304 - 307.

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. Rockville, (3 2015). 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. Bethesda, (11 2015). P59 -
  • 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. New York, (9 2015). N/A -

2014

  • Yousefi,Mohammadmahdi,R; Dalton,Lori,A "Optimal Cancer Prognosis Under Network Uncertainty." in 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB),. New York, (9 2014). 682 - 683.
  • 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). New York, (12 2014). 1382 - 1385.

2013

  • Yousefi,Mohammadmahdi,R "Compromised Intervention Policies for Phenotype Alteration." in IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2013. New York, (11 2013). 32 - 35.
  • Yousefi,Mohammadmahdi,R; Ivanov,Ivan "Optimal Control of Gene Regulatory Networks with Uncertain Intervention Effects (invited)." in IEEE Global Conference on Signal and Information Processing (GlobalSIP), 2013. New York, (12 2013). 105 - 108.
  • Yousefi,Mohammadmahdi,R; Dougherty,Edward,R "Bayesian Optimal Control of Markovian Genetic Regulatory Networks." in Asilomar Conference on Signals, Systems and Computers (ASILOMAR), 2013. New York, (11 2013). 980 - 984.

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. NEW YORK, (12 2012). 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. NEW YORK, (8 2012). 568 - 571.

2011

  • 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. New York, (11 2011). 1007 - 1011.
  • 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. New York, (12 2011). 38 - 41.

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. NEW YORK, (11 2010). 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. NEW YORK, (5 2007). 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. NEW YORK, (7 2007). 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. NEW YORK, (8 2007). 1121 - 1126.
  • 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.