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Professional Summary

Master's student of biomedical engineering that focus on image analysis. Experienced in computer vision and machine learning. For the first time characterized biological images synthesized by deep generative models. Other achievements include developing a pipeline to extract the properties of objects in microscopy images for pathology study. Skilled in Python and Matlab.

Education
December 2018
Master of Science: Biomedical engineering
Carnegie Mellon University - Pittsburgh
  • Research focusing on realistic biomedical image processing and analysis.
  • QPA: 3.74/4.0
July 2017
Bachelor of Science: Biological science
Fudan University - Shanghai, China
  • Specialized in bioinformatics and genomics.
  • GPA: 3.26/4.0
Research
06/2018 to Current
Research Student Carnegie Mellon University Pittsburgh, Pennsylvania
  • Synthesized realistic biological images with generative adversarial networks. For the first time characterized the strengths and weaknesses of the networks in biological image synthesis.
  • Segmented microscopy images and extracted region properties of different organelles inside the cell. The data has revealed novel biological processes that caused Mucolipidosis (a disease that causes metabolic disorders).
  • Currently working on new network architectures that possess additional capability in biological image synthesis.
10/2016 to 05/2017
Research Assistant Chinese National Genome Center Shanghai
  • Carried out the genome-wide analysis of Echinococcus granulosus (human parasite) long non-coding RNA (lncRNA) and designed algorithms to organize and quantify genes. Proficiently used Python and R to screen and visualize large quantity of lncRNA expression data.
Projects

Optical character recognition using Neural networks

Feb. 2018 - Mar. 2018

  • Implemented artificial neural networks from scratch and achieved 90% accuracy in the image classification of handwriting letters.

Lucas-Kanade Tracking

Apr. 2018 - May. 2018

  • Implemented Lucas-Kanade algorithm from scratch to successfully track lesion site in Ultrasound video.
Publications

To be determined

Publications

To be determined

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Summary

I have experience in research using statistics and numerical analysis. My skills include explaining, analyzing, and coding solutions to a variety of problems of data science and applied mathematics.

Skill Highlights
  • Fluent in Python and experience with several mathematical libraries such as pandas, sciKit-learn, and Tensorflow.
  • Fluent in Matlab.
  • Experience in R, C++, and SAS/SQL.
  • Interpolation techniques, such as polynomial interpolation and Gaussian processes.
  • Mathematical optimization via gradient descent and Markov chain Monte Carlo methods.
  • Analysis and forecasting of time series.
  • Approximation of solutions to differential equations.
  • Theory and application of machine learning topics, ranging from classification/regression algorithms to clustering methods and dimensionality reduction techniques.
Experience
Analyst Intern
June 2019 to August 2019
Constellation Energy Baltimore, MD

Intern in the Pricing and Structuring team. Retrieved, cleaned, and inserted data sets into Constellation's system, and performed forecasting analysis on time series data. Data retrieval and insertion was completed in Python and MATLAB, while forecasting analysis was completed in Python with sciKit-learn and Tensorflow.

Experimental Particle Research Assistant
January 2015 to May 2017
IceCube Neutrino Observatory

Experimental work in particle physics. Extracted and read large data sets of muon and neutrino flux and analyzed their correlations with atmospheric temperature. Coding was completed in Python, and data extraction was done through remote servers with UNIX.

Education
Master of Science : Data Science, May 2020 University of Delaware Newark, DE, United States
Bachelor of Science : Applied Mathematics, 2018 University of Delaware Newark, DE, United States
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Skills
video production
Experience
Research Assistant
January 2017 to July 2017
Georgetown University School of Nursing and Health Studies
  • Communications Associate Georgetown University Center on Education and the Workforce, January 2018 - present, track media coverage, develop visual and written content for web and social media, collaborate on video production, and assist with overall team operations.
Research Assistant
July 2015
Fairfax County Office of Neighborhood and Community Services
  • Division 1A Athletic Directors' Association, Summer 2016, created database and wrote brief biographies for Division 1A athletic directors.
  • Fairfax County Youth Leadership Program-selected to represent McLean H.S.
  • as one of 30 high school students county-wide attended seminars, participated in community outreach events.
Education and Training
Spring 2018 Georgetown University College GPA: 3.6
Diploma : 2018 McLean High School McLean, Advanced GPA: 4.4 Deputy Sports Editor, The Hoya, Georgetown University student newspaper, spring *Assistant Sports Editor, The Hoya, Georgetown University student newspaper, current *Reporter, selected as member of The Hoya sports section, 2016-2017 *Mentor, Stride for College, work one-on-one with a first-generation college student in completing the college application process,
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Summary

Highly motivated, detail oriented recent college graduate seeking challenging opportunities in marketing/financial services.  You will find that I am a highly responsible, high energy person with exceptional interpersonal skills who works very well under pressure and enjoys interacting with the public both in person and on the phone.  

Education
Bachelor of Science: Marketing Quinnipiac University, Lender School Of Business Hamden, CT
  • Quantitative Courses Completed: Finance, Macro and Micro Economics, Business Statistics, Applied Calculus
  • Cumulative GPA: 3.2
Experience
Account Executive 03/2020 to 04/2020 Yelp Inc. New York, NY
  • Reached out to around 100 small/medium sized business in Canada via phone and email daily.
  • Wanted each business to become advertisers on Yelp and get their pages promoted for more viewership.
  • Went through a rigorous 2 week training to help overcome objections over the phone to keep the business owner on the line and engaged throughout the conversation.
Client Service Associate 10/2018 to 03/2019 Oppenheimer & Co. Inc. New York, NY
  • Worked on the Corporate Cash Management team and helped manage the day-to-day functions of a book totaling over $8 billion in corporate cash assets
  • Sent out prospecting letters and set up calls between our Managing Directors and potential new clients
  • Ran monthly portfolio summaries for clients including earned interest income, top holdings, and credit rating percentages of the total portfolio value
  • Responsible for sending out morning daily rates from various money market funds to select clients
  • Responsible for answering daily phone calls from clients and the movement of money in their accounts via wire or journal
Intern 12/2017 to 01/2018 Morgan Stanley Port Jefferson, NY
  • Worked under a Senior Financial Advisor who specialized in goals based wealth management.
  • Ran financial plans, asset allocation models, assisted in mutual fund research.
  • Assisted the FA in all aspects of his marketing efforts to help grow his business.
Client Associate 05/2017 to 08/2017 Wells Fargo Advisors Garden City, NY
  • Directly worked under four Financial Advisors, helped manage books totaling over $400 million.
  • Worked on a day to day basis with clients in person and over the phone.
  • Responsible for moving money between house held accounts, ACH money to checking accounts, and sending out checks to clients per request.
  • Made Excel Spreadsheets for each FA helping to organize their clients in a monetary or alphabetical order.
Research Assistant 01/2017 to 04/2017
  • Petnet is an Internet of Things (IoT) technology company and the creator of the SmartFeeder pet-feeding device. The SmartFeeder uses proprietary data and algorithms to feed the pet perfect portions and make optimal food recommendations for the pet.
  • Researched, collected, and prepared dog and cat breed data for inclusion in the Petnet "K-nearest neighbors" endemic pet food recommendation service. This service uses a pet's breed history and endemic food availability to determine which of the commercially available foods is the best fit for a dog or cat.
  • Mapped and determined an ingredient ontology for use in the endemic recommendation algorithm.
  • Worked directly with the VP of Food, Data, and Analytics.
Interests
  • Delta Tau Delta Fraternity- Quinnipiac Community Outreach Chair/New Member Education Committee
  • Organized and engaged in philanthropic fund raising events for our national philanthropy, Juvenile Diabetes Research Foundation (JDRF)
  • Organize teams for other philanthropic events around campus as well as encourage brothers to attend and donate to the cause
  • Help new members of our fraternity understand the foundation and history of Delta Tau Delta
Skills
Microsoft Word, PowerPoint, and Excel, and all aspects of Social Media
  • Articulate public speaker
  • Multi-media marketing
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Education
Ph.D.: Electrical Engineering North Carolina State University - Raleigh Current
  • GPA 4.00/4.00
Master of Science: Electrical Engineering Xi'an Jiaotong University - Xi'an, China Jun. 2014
  • GPA 88.5/100
Bachelor of Science: Electrical Engineering Zhejiang University - Hangzhou, China Jun. 2012
  • GPA 3.90/4.00
Research Experience
Research Assistant North Carolina State University - Raleigh, NC 09/2016 - Current

Strength:Power system energy management/Optimization

  • Develop distributed control methods tosolve the security-constrained economic dispatch problem, programming the distributed approaches in C and C++
  • Consider practical issues in battery applications, such as charging/discharging efficiency and degradation cost in the energy management problem
  • Develop distributed load balancing algorithm to maintain supply-demand balance when considering renewable forecast uncertainties and unexpected outages
Summer Intern California ISO - Folsom, CA 05/2017 - 08/2017
Strength: Data analysis using R and SQL
  • System level analysis: Analyze the trend of Congestion Revenue Rights (CRR) market performance by coming up with different system level indexes regarding to congestion rents, auction revenue and CRR payment
  • Constraint/CRR level analysis: calculate the CRR auction details on a per constraint/transmission element basis for representative set of months
  • Process more than 20 million market data to decipher the drivers of CRR revenue inadequacy and significant mismatches between auction price and payments
Research Assistant Total S.A. - Houston, Texas (working at NC STATE) 08/2015 - 09/2016

Strength: Microgrid modelling using Matlab

  • Develop a general microgrid model in Matlab Simulink, consisting of PV panels, wind turbines, storage devices, and loads, working in the grid connected mode
  • Perform sequential reliability assessment to quantify the System Average Interruption Duration Index (SAIDI) and Customer Average Interruption Duration Index (CAIDI)
  • Implement energy management algorithm in distributed controllers in Linux operating systems to maintain reliable operation of microgrids under contingencies
Research Assistant North Carolina State University - Raleigh, NC 09/2014 - 08/2015

Strength: Power flow analysis

  • Investigate the vulnerabilities of distributed energy management algorithms (e.g. distributed optimal power flow, distributed economic dispatch) to malicious cyber attacks, assuming distributed controllers are behaving abnormally
  • Conduct power flow analysis and analyze the economic and stability impacts of cyber attacks on electricity market
  • Respond to the malicious attacks by adjusting the system control signals and counteracting the malicious impacts
Summary
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Professional Summary
  • Cautious optimist biomedical research scientist with a strong background in cell-based biochemical assay- and microfluidic device development leading to the successful development of a novel, bio-analytical platform consisting of a unique, fluorescent, cell-permeable, peptide-based reporter and a droplet microfluidic device for high-throughput single cell analysis
  • Flexible team player and reliable collaborator in different aspects of interdisciplinary research demonstrated through successfully training  and managing 11 lab members to carry out 8 research projects in collaboration with 5 internal and external collaborators
  • Creative and self-motivated individual highly dedicated to biomedical research especially cancer diagnostics and drug discovery with demonstrated communication skills leading to 9 forthcoming publications and several public presentations at national and international conferences
Education
2018 Ph.D.: Chemical Engineering Louisiana State University | | Baton Rouge, LA, United States
  • Dissertation: Direct quantification of deubiquitinating enzyme activity in single intact cells

Supported through grants from the National Science Foundation (NSF, CBET 1509713) and the National Institute of Health (NIH, R03EB02935-01)

2014 Bachelor of Science: Chemical Engineering Sharif University of Technology | | Tehran, Iran
Skills
  • Cell culture and cryopreservation
  • Experienced in biochemical assay development
  • Fluorometry and fluorescent microscopy
  • Cell lysis and protein extraction
  • Advanced enzymology and kinetics analysis
  • Fluorescent peptide development
  • Microfluidic device development
  • Experimental statistics and single cell analysis
  • Project management
  • Strong communication skills
Experience
08/2014 - 12/2018 Graduate Research Assistant Louisiana State University | Baton Rouge, LA

Developed a novel bioanalytical platform including a fluorescent, cell-permeable, peptide-based reporter of deubiquitinating (dub) enzyme activity and a droplet microfluidic device for performing high-throughput screening  in single intact cells

  •  Independently and efficiently developed and performed cell-based biochemical assays to characterize a library of β-hairpin and D-chirality short sequences as cell penetrating peptides (CPPs) with enhanced protease resilience using fluorometry, fluorescent microscopy, CD spectroscopy, and degradation studies in cell lysates followed by RP-HPLC.
  •  Developed and performed fluorometric enzymology studies involving inhibition and dose response studies and fluorescent microscopy experiments to develop the first cell-permeable reporter of dub activity and demonstrate the application of this reporter in single intact cells.
  • Designed and fabricated a droplet microfluidic platform for high-throughput screening of intracellular events using fluorescent substrates.
  • Visualized data and performed statistical analysis and mathematical modeling using Origin Pro and COMSOL.
  • Developed and performed enzymology assays utilizing the novel dub reporter to identify a new class of dub inhibitors in collaboration with researchers at Pennington Biomedical Research Center (PBRC), Baton Rouge, LA.
  • Coupled the droplet microfluidic platform with a thiol acrylate-based hydrogel for tumor spheroid generation in collaboration with researchers at Pojman lab, LSU.
  • Generated and preserved frozen stocks of several cancer cell lines including HeLa, OPM-2, MDA-MB231, MCF-7, THP-1, K-562, U-937, and MM1S, and utilized them in biochemical assays.
  • Generated preliminary data for over 6 grant proposals.
  • Mentored 11 undergraduate and graduate researchers by training, supervising, and managing them to simultaneously generate experimental data for 8 projects and instructed them to present research at regional and national conferences.
  • Volunteered as a judge at LSU Discover Day (2017) annual undergraduate research symposium and judged 8 poster presentations.
  • Assisted with lab maintenance and inventory.
  • Presented work at 4 national and international conferences and wrote 9 research articles.
  • Shadowed hematologists and oncologists treating patients, collecting tumor biopsies, and running clinical trials at Oschner medical center, Baton Rouge, LA for 6 months to gain real-world insight into cancer treatment and clinical research.
Select Publications

" * " denotes co-first authors.  

(1) Safa, N.; Anderson, J. C.; Vaithiyanathan, M.; Pettigrew, J. H.;  Pappas, G.; Liu, D.; Gauthier, T.; Melvin, A. T., "CPProtectides: Rapid uptake of well-folded β-hairpin peptides with enhanced resistance to intracellular degradation", Peptide Science (forthcoming).
doi: 10.1002/pep2.24092
(2) Safa, N.; Vaithiyanathan, M.; Sombolestani, S.; Charles, S; Melvin, A. T., “High-throughput, single cell analysis of cell penetrating peptide uptake using a microfluidic droplet trapping array” (under review)
(3) Safa, N.; Pettigrew, J. H.; Liu, D.; Gauthier, T.; Melvin, A. T., “Direct quantification of deubiquitinating enzyme activity in intact cells using a protease resistant, cell permeable peptide-based reporter” (under review)
(4) Safa, N.; Pettigrew, J. H.; Kirkpatrick, C; Liu, D.; Gauthier, T.; Melvin, A. T., “Cell permeability and intracellular stability of D-chirality fluorescent peptides in mammalian cells” (under review)
(5)  Wortmann, W (III).; Kersker, N. D.; Safa, N.; Pojman, J.; Melvin, A. T.;  “Development of a thiol acrylate-based hydrogel for tumor spheroid generation in a microfluidic device” (in preparation)
(6)* Vaithiyanathan, M.; *Ramezani Bajgiran K.; Darapaneni, P.; Safa, N.; Elkhanoufi, R.; Dorman, J. A.; Melvin, A. T., “Luminescent Nanomaterials for Droplet Tracking in a Microfluidic Trapping Array”(under review)

(7) Sombolestani ,S.; Safa, N.; Anderson, J.C.; Rao, D.; Melvin, A. T., “Developing a microfluidic platform for visualizing oil film formation in gas-assisted gravity drainage (GAGD) Processes” (in preparation)

Awards
  • Dr. Charles E. Coates memorial conference travel award for attending microTAS international conference (2017)
  • Two LSU graduate student conference travel awards for attending BMES 2017 and microTAS 2017 conferences
  • Outstanding poster award at BMES 2016 National Meeting for the work "Rapid uptake and ubiquitination of fluorescent peptides in mammalian cells using a β- hairpin short sequence motif".
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Education and Training
September 2017
  • Previous Employer Graduate Research Assistant, College of Engineering, Civil & Environmental Engineering, The Pennsylvania State University, September 2013 - July 2017. Courses I teach at NYIT
  • ENGY 670 - Energy Technology in Perspective
  • ENGY 695 - Systems Engineering and Management
  • ENGY 730 - Computer Applications for Energy Management
2014
The Pennsylvania State University PA, USA PhD: Civil Engineering
  • GPA: 3.82/4.00, Thesis title: "Integration and Interoperability of Building Envelope Information and Energy Modeling". Research Adviser: Prof. Ali M. Memari, Teaching Assistant in "Design of Concrete Structures", "Design of Steel Structures", and "Structural Analysis by Matrix Methods", The Pennsylvania State University, 2015-16.
  • Teaching Assistant in "Statics" course, Amirkabir University of Technology, Iran, 2011-12.
  • Teaching Assistant in "Engineering Economics", Amirkabir University of Technology, Iran, 2007-10.
  • Taught COMFAR as an "Engineering Economics" Software, Amirkabir University of Technology, Iran, 2007-10.
13
Tehran University Iran M.Sc: Earthquake Engineering GPA: 3.54/4.00, Thesis title: "Experimental study of behavior of lightweight reinforced concrete beams under cyclic loads".
13
Consulting Engineer in Construction Material Institute of Tehran University Iran
  • Previous Teaching Experiences
  • Special lecturer and tutoring in "Building Enclosure Science and Design" on the topics of energy modeling and analysis, THERM, and WINDOW, The Pennsylvania State University, 2014-16.
  • Taught "Structural Analysis" as a temporary lecturer, The Pennsylvania State University
10
Amirkabir University of Technology (Tehran Polytechnic), New York Institute of Technology (NYIT) Iran B.Sc.: Civil Engineering
  • GPA: 3.10/4.00, Areas of Focus Energy Modeling and Smart Homes Structural
  • Buildings energy modeling and application of BIM in energy modeling
  • Building automation system
  • Smart grids and renewable energy resources
  • Building enclosure and energy retrofit
  • Smart homes and application of sensors, meters, and control systems
  • Experimental study and numerical modeling of the structural behavior, seismic behavior, and mechanical properties of normal and lightweight concrete (structural and non-structural). Current and Previous Employer Current Employer Assistant Professor
10
National Concrete Competition, Amirkabir Univ. of Tech
Skills
  • Proficient in:
  • BEopt
  • OpenStudio
  • THERM
  • WINDOW
  • WUFI
  • EnergyPlus
  • 3D Studio Max
  • SAP
  • SAFE
  • ETABS
  • AutoCAD
  • Revit
  • COMFAR
  • Familiar with:
  • Python
  • Visual Basic
  • MATLAB
  • C++
  • Artificial Neural Network (ANN), 4/5
  • 1/5
  • 3D Studio Max, AutoCAD, automation, Basic, C++, Computer Applications, Economics, energy efficient, Energy Management, English, Environmental Engineering, Focus, Fluent German, lecturer, materials, MATLAB, mechanical, WINDOW, Modeling, Network, Neural, Python, Research, Revit, SAP, simulation, Systems Engineering, Teaching, tutoring, Visual Basic
Experience
01/2013 - 01/2017
The Pennsylvania State University Research Assistant
  • Studied energy efficient smart homes and using BIM for energy modeling as part of the dissertation research topic.
  • Used Python to modify BIM files and C++ to modify source codes for energy simulation in OpenStudio and EnergyPlus.
  • Studied different methods and materials in building envelope energy retrofit of existing buildings as a research topic in Pennsylvania Housing Research Center (PHRC) and modeled a residential building in BEopt for energy simulation.
  • Studied the conventional and smart methods such as using different types of sensors for moisture management in residential buildings as a research topic in PHRC.
  • Studied on experiences learnt from U.S.
  • Solar Decathlon Competitions as a research topic in PHRC and categorized different mechanical, electrical, and envelope systems in participants' houses.
01/2010 - 01/2013
Tehran University Research Assistant
  • Studied on lightweight aggregates.
  • Managed groups of students in National Lightweight Concrete Competition.
  • Published papers and national technical reports on concrete material and additives.
01/2006 - 01/2010
Amirkabir University, Tehran Polytechnic Research Assistant
  • Worked on structural lightweight concrete (LECA aggregate) in a national project as a member of the technology group.
  • Managed to reduce the weight of concrete by 30% while maintaining the compressive strength.
  • Studied on non-structural lightweight concrete in the laboratory of concrete and structural materials using MANOVA and Artificial Neural Network (ANN) methods.
Interests
  • Academic Leadership and Working Experiences
  • One of the Advisors of Penn State team in Race to Zero competition for energy design and building science design, 2016.
  • Co-captain of Penn State team in Race to Zero competition and leader of Energy design and Building Science design teams, 2015. Honors and Awards
  • Editorial Board Member, Journal of Architectural Research and Development (JARD), since 2017.
  • Reviewer of Construction & Building Materials Elsevier journal, since 2017.
  • Reviewer of Journal of Architectural Engineering, ASCE, since 2017.
  • Reviewer of Emerald Insight Journal of Facilities, since 2018.
  • ASHRAE's student branch advisor (SBA) in New York Institute of Technology (NYIT).
Languages
English: Fluent German: Basic Knowledge
Additional Information
  • , Best Paper Award, for excellent paper presentation at the 14th annual College of Engineering Research Symposium organized by Engineering Graduate Student Council, April 4, 2017. Two-time winner of the Roger Glunt Graduate Fellowship in Residential Building Construction, The Pennsylvania State University, University Park, PA, 2015-16. Won two of the three excellent awards: Design Excellence and Systems Integration Excellence in Department of Energy Race to Zero Student Design Competition as a co-captain of the Penn State team and leader of the building enclosure and energy design teams, 2014-2015. Won the Best Technical Integration Award and also high scores for indoor air quality in U.S. Department of Energy Challenge Home Student Design Competition as a member of the Penn State team (building enclosure team), 2013-2014. Invited to become a member of The Pennsylvania State University chapter of Golden Key International Honour Society as the top 15% of the 2013 class. Ranked 2nd in the Second National Concrete Competition for non-structural lightweight concrete (gas concrete), Amirkabir University of Technology, Tehran, Iran, 2008. Ranked 110th (top 0.3%) among more than 35,500 participants in nationwide "Civil Engineering M.Sc. Entrance Exam", Iran, 2010. Finalist of Khwarizmi Competition (a national competition for young inventors) and the related article ranked in top 3 among many Iranian students' articles prepared for the "First Step to Noble Prize in Physics" contest, Poland, 2005.