English Teacher Data

Amirhossein Manzourolajdad (Amir Manzour)

Washington, DC 20003

706-***-**** çamir.add03s@r.postjobfree.com

Curriculum Vitae

Analytical and visionary Bioinformatics Scientist with a Ph.D. in Bioinformatics and a Masters in Telecommunications Engineering combined with six years’ expertise in genetics and molecular biology, particularly relating to RNA switches, riboswitches, HIV Nef RNA, Next Generation Sequencing data, and gene/transcript differential expression. High skilled researcher with demonstrated project management expertise on different phases of a research project, from probabilistic modeling and algorithmic design/implementation to efficient and thorough analysis of large data sets. Establish effective working relationship with multidisciplinary teams; connect project teams with a large range of computational biology tools and relevant techniques.

SELECT ACHIEVEMENTS

• Proficient in Genotype-Phenotype studies including GWAS on SNP-Datasets.

• Expertise in Bioinformatics, Computational Biology, Biostatistics relating to Non-protein-coding RNA identification.

• Proficiency with development tools, including git, Unix-based shells, and IDEs/editors

• Fluency in programming and scripting languages and environments including Java, C#, SQL, R, Perl, Python, C++, Bash, Gnuplot, Netbeans, Eclipse, MS Visual Studio and SQL Server; superior working knowledge of relevant data analysis and visualization packages.

• Achievement Award, BIOCOMP’15 conference, Las Vegas, USA, 2015; Two-year Graduate Student Assistantship Award, UGA, USA (2009-2011).

• Ranked within top 700 amongst roughly 10000 participants in the national university’s examination of MS in Electrical Engineering in Iran, 2004

EDUCATION

Doctor of Philosophy (Ph.D.) in Bioinformatics, 2014 University of Georgia, Athens, GA

• Doctoral Dissertation: Ab initio Identification of Regulatory RNAs Using Information Theoretic Uncertainty Master of Science (M.S.) in Telecommunications Engineering, 2007 Isfahan University of Technology, Isfahan, Iran

• Master’s Thesis: Gene Mapping and Marker Clustering Using Shannon Mutual Information Bachelor of Science (B.S.) in Electrical Engineering, Electronics, 2003 University of Guilan, Rasht, Iran

• Capstone Project: Design and Implementation of a System Connecting a Device to PC via 8051 for Commercial Purposes RESEARCH EXPERIENCE

National Institute of Health, Bethesda, MD 2014-Present Research Fellow, National Institute of Arthritis and Musculoskeletal and Skin Diseases, (2018 – Present) Lead and support NIH research in Next Generation Sequencing for the Laboratory of Muscle Stem Cells and Gene Regulation. Manage comprehensive investigation and design of RNA-sequencing thorough analysis and visualization of large data sets. Contribute to study design and protocol development to enable novel experimentation. Manage multidimensional RNAseq data sets. Plan and execute multiple pipelines for RNA sequencing analyses and visualization including Single-end and Pair-end Read Mapping.

• Leverage Information Theory and Stochastic Context-free Grammars (SCFG) to develop multiple RNA structure models and predictions, achieving the identification of riboswitches involved in bacterial gene regulation and of genomic regions with high RNA plasticity in HIV.

Amirhossein Manzourolajdad (Amir Manzour)

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• Design and implementation of recursive algorithms for RNA structural analyses using dynamic programming techniques

• Oversee conditional probability techniques that support the identification of structural components of RNAs evolved for stabilizing an alternative conformation.

• Manage the analysis of large sequence data sets of Gene differential expression using cufflinks and isoform differential expression using rMATS and MISO.

• Designed and launched the stand-alone software in Rstudio, resulting in developing more in-dept analysis of differential expression and generating automated analysis pipelines.

• Facilitate efficient transfer of bioinformatics data from data sources to data users with benchmarking and data quality checks; Identify and test application/pipeline defects and fixes.

• Independently manage and evolve process for effectively using large-scale bioinformatics storage frameworks. Research Fellow, National Center for Biotechnology Information, (2016 – 2018) Led and managed groundbreaking research and initiatives across bioinformatics and computational biology research projects. Supported comprehensive NIH research and analysis of RNA structures including developing novel prediction methods for RNA Switches. Applied computational tools to research problems in molecular and structural biology, genetics, genomics, proteomics, phylogeny, and related fields.

• Created and executed automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics.

• Performed research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules including DNA and RNA.

• Coordinated and project managed multiple simultaneous research projects including data collection, data analysis, reporting, and publishing of biotechnology information worldwide. Visiting Postdoctoral Fellow, National Center for Biotechnology Information (2014 – 2016) Reconstructed a partial evolutionary history of viral strains collected from North American patients. Analyzed multiple RNA structures of a critical protein-coding region of HIV-1 known as Nef, resulting in the identification a key region whose RNA plasticity increased during the past few decades while amino acids of the corresponding region remained relatively conserved. Led and oversaw probabilistic modeling and visualizations and RNA structure analyses. Mentored laboratory assistants and graduate students in all key research areas including research methodology, laboratory procedures and policies.

Mobile Company of Iran IR-MCI, Tehran, Iran 2007 – 2008 Software Developer and Researcher

Led the development and launch of software network element maintenance including storing, validating, and cleaning large sets of data. Prepared automated reports using SQL and updated database for automated daily reports, data cleaning, and scheduled all reports. Manage research and analysis workflows and demonstrated ability to draw robust conclusions from complex datasets and presenting them in a clear and understandable way to a broad audience. Advanced Digital Communication Group, IUT, Isfahan, Iran 2005 Researcher

Led multiple digital communication research projects in including work on Simulation Projects: 802.11a Physical Layer. 4G, OFDM: a generalized tool for calculating BER and frame reception ratio. Launched multiple performance optimization strategies in Neural Networks including Base-band pulse-shape generator for 16QAM using adaptive network. Viterbi Algorithm (eliminating ISI), and Berlekamp’s BCH decoding algorithms. TEACHING EXPERIENCE

Amirhossein Manzourolajdad (Amir Manzour)

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Kish Language Institute Rasht, Iran 2000-2003

English Teacher

University of Guilan, Rasht, Iran 2001

Teaching Assistant in Electronics

PROFESSIONAL DEVELOPMENT

Ethics in Research Training for Postdocs, Office of Intramural Training and Education, NIH Management Bootcamp, Office of Intramural Training and Education, NIH Writing and Publishing a Scientific Paper, National Institute of Health Grant Writing, National Institute of Health

Scientists Teaching Science, National Institute of Health Lead Judge in Postbac Poster Day, National Institute of Health PUBLICATIONS

Peer Reviewed Journals

1. Manzourolajdad, A., Spouge, J.L. Structural prediction of RNA switches using conditional base pair probabilities. PLoS ONE, 14(6), June 12, 2019.

2. Manzourolajdad, A., Gonzalez, M., Spouge, J.L. Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic, PLoS ONE 11(9), Sept. 29, 2016. 3. Manzourolajdad, A., Arnold, J. Secondary Structural Entropy in RNA Switch (Riboswitch) Identification, BMC Bioinformatics, 2015, 16:133.

4. Manzourolajdad A., Wang, Y., Shaw, T.I., Malmberg, R.L. Information-theoretic uncertainty of SCFG modeled folding space of the non-coding RNA, Journal of Theoretical Biology, 2013, Vol. 318, 140- 163. 5. Wang, Y., Manzour, A., Shareghi, P., Shaw, T.I., Li, Y.W., Malmberg, R.L., Cai, L. Stable stem enabled shannon entropies distinguish non-coding RNAs from random backgrounds, BMC Bioinformatics,2012, 13 Suppl 5, S1. 6. Shaw, T.I., Manzour, A., Wang, Y., Malmberg, R.L., Cai, L. Analyzing modular RNA structure reveals low global structural entropy in microRNA sequences, Journal of Bioinformatics and Computational Biology, 2011, 9, 283-98. 7. Manzourolajdad, A., Saraee, M., Mirlohi, A., Javan, A., Genome-wide efficient Attribute Selection for Purely Epistatic Models via Shannon Entropy, The international journal of Business Intelligence and Data Mining, 2008. Vol. 3, No. 4, 390-408.

Book Chapters

1. Manzourolajdad, A. (2016). The application of grammar space entropy in RNA secondary structure modeling. In Emerging trends in applications and infrastructures for computational biology, bioinformatics, and systems biology, 2nd Edition. Elsevier.

CONFERENCES & PRESENTATIONS

Conferences

1. Manzourolajdad, A., Hafner, M., Do Empirical and Abstract Shannon Entropies Converge in Value? A Case in RNA Molecular Structure, First Intermountain Engineering, Technology and Computing (i-ETC) Conference, IEEE conference proceedings, Utah Valley University, Orem, UT, USA, 2020 2. Manzourolajdad A. The tendency of HIV-1 Nef to accommodate for high RNA conformational plasticity, Cold Spring Harbor Laboratory, USA, 2016

Amirhossein Manzourolajdad (Amir Manzour)

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3. Manzourolajdad A, Shannon’s Entropy of The Stochastic Context-Free Grammar and an Application to RNA Secondary Structure Modeling, Int'l Conf. Bioinformatics and Computational Biology (BIOCOMP'15), July 27-30, 2015. Las Vegas, USA, pp. 3-7.

4. Wang Y, Manzour A, Shareghi P, Shaw TI, Li YW, Malmberg RL, Cai L. Stable stem enabled shannon entropies distinguish non-coding RNAs from random backgrounds, Computational Advances in Bio and Medical Sciences, 2011, 184-189.

5. Shaw TI, Manzour A, Wang Y, Malmberg RL, Cai L. Analyzing modular RNA structure through shannon entropy reveals low global structural entropy in mirnas, Computational Systems Bioinformatics Conference, Proceedings, 2010. 9, 146-155.

6. Saraee M, Nikoofar H, Manzour A. Epistasy Search in Population-Based Gene Mapping Using Mutual Information, The IEEE Symposium on Signal Processing and Information Technology, 2007. 621-625. 7. Manzour A,Saraee M. Entropy-based epistasy search in SNP case-control studies, In Fourth International Conference on Fuzzy Systems and Knowledge Discovery, 2007. Haikou, China, pp. 21-26 8. Cancer Center, Howard University, 2015

APPOINTMENTS

1. Chair/Coordinator, International Conference on Bioinformatics and Computational Biology (BIOCOMP'15), July 27-30, 2015. Las Vegas, USA

2. Ad-Hoc Review, Bioinformatics, The Journal of Theoretical Biology, Scientific Reports 3. Secretary, Visiting Postdoctoral Fellows Committee, NIH PROFESSIONAL AFFILIATIONS

Institute of Bioinformatics, University of Georgia (2009 – 2014)

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