IRFANULLAH DARWISH SALEH
Ann Arbor,Michigan
Summary
IRFANULLAH DARWISH SALEH
1232 Prospect St – Ann Arbor-MI 48104
irfanokeefe@gmail.com| darwish@umich.edu |415-413-8055 |www.linkedin.com/in/irfandarwishokeefe
Overview
10
10
years of professional experience
6
6
years of post-secondary education
2
2
Certifications
Work History
Quantitative Metabolomics & Bioinformatics
University of Michigan
11.2024 - Current
- Advisor: Dr. Tim Cernak | Department of Chemistry
Summary: I am currently working on an LC-MS-based metabolomics project at the University of Michigan, focused on distinguishing resistant from non-resistant hemlock trees using key m/z and retention time pairings. I am refining data workflows, validating m/z candidates, and developing bioinformatics pipelines. My work involves applying machine learning models such as PLS-DA and Random Forest to interpret data and identify significant patterns. The overarching goal is to integrate LC-MS, GC-MS, and NMR data using computational methods to detect reproducible patterns and clean noise, ultimately advancing metabolomics analysis techniques.
Key Achievements:
- Refined LC-MS data analysis workflows for metabolomics research.
- Validated m/z candidates and developed bioinformatics pipelines for data processing.
- Applied machine learning models (PLS-DA, Random Forest) to analyze complex metabolomics datasets.
- Collaborated on integrating LC-MS, GC-MS, and NMR data to enhance metabolomic analysis.
- Presented research findings in regular team meetings, fostering collaboration across departments.
Computational Medicine and Bioinformatics Research Assistant
University of Michigan Medical School
04.2023 - Current
- In my current lab, I am conducting bioinformatics research on mitochondrial DNA integration into nuclear DNA (numts)
- I designed a computational approach for determining guide-RNA k-mers for detecting non-reference numts to inform a Cas9-based molecular approach coupled with nanopore sequencing
- I began this project with limited bioinformatics experience but quickly mastered essential programming techniques and gained both conceptual and technical knowledge in the field
- This research contributed to an NIH R01 grant submission, and I am set to co-author an upcoming publication
- Navigated Great-Lakes computing cluster and managed operations of working directories
- Retrieved and loaded bioinformatics software packages and DNA data from external and internal data banks resources
- Assembled bioinformatics pipelines for gRNA-kmer generation and distribution analysis
- Wrote Bash and Python scripts for DNA sequence analysis
- Scheduled jobs on the Slurm workload manager using Terminal
- Gained robust bioinformatics terminology and principles comprehension
- Developed validation techniques for research accuracy
- Presented academic articles and research findings in weekly lab meetings, focusing on bioinformatics and computational medicine
- Collaborated consistently and effectively in a team setting
Molecular Genetics Research Assistant II
UT Southwestern Medical Center
03.2019 - 06.2021
- In 2018, I trained in advanced research in molecular genetics studying lipid-mediated signaling and ceramide-induced regulation of transmembrane proteins
- I helped design and maintain mouse models for testing the FAF1 gene's role in protecting cells from iron-catalyzed peroxidation
- Additionally, I designed and maintained mouse models with CREB3L1, CCR5, and TM4SF20 trans-genes
- I contributed to the research investigating the effects of Doxorubicin on ceramide accumulation and its impact on the activation of transcription factors like CREB3L1 and TM4SF20
- Performed genotyping, tissue collection, and analyzing genetic data for various transgenes
- Transgenic Mouse Line Development: Generated new knock-in and knock-out mouse lines utilizing CRISPR-Cas9, facilitating groundbreaking research on lipid-protein interactions and gene function
- Advanced Molecular Techniques: Demonstrated expertise in plasmid vector design and molecular cloning, significantly advancing the lab's genetic modification studies
- Molecular Isolation and Analysis: Proficiently isolated DNA, RNA, and proteins, and conducted comprehensive DNA sequencing to enhance the accuracy and depth of genetic analysis
- Animal Surgery and Dissection: Executed complex animal surgeries and dissections, ensuring high standards of care and precision in research procedures
- Mentorship and Training: Provided mentorship and hands-on training and guidance to a high school intern, fostering their knowledge and enthusiasm in molecular genetics and biomedical research
- Research Presentation Skills: Delivered literature reviews and research presentations during weekly team meetings, promoting an environment of knowledge sharing and collaborative problem-solving
- Team Collaboration: Thrived in a collaborative research setting, working effectively with multidisciplinary teams to achieve project milestones and contribute to the department's scientific endeavors
Computational Biophysics Research Assistant Intern
UT Southwestern Medical Center
11.2018 - 02.2019
- I developed computational algorithms to measure mobility properties of actin and CD36
- Mobility properties consisted of speed, velocity, density, polymerization, and de-polymerization
- I designed methods to analyze live cell videos using U-tracker for dynamic assessments of actin and CD36
- I independently learned MATLAB and adapted existing computational functions for new molecular targets
- Mastered MATLAB within a week to advance computational analysis
- Developed new computational methods for investigating molecular interaction properties between CD36 and Actin
- Analyzed data from single molecule Actin and CD36 interaction movies through uTrack and Qfsm software involving interactive coding
- Presented computational scientific articles at weekly group meetings
Cancer Metabolomics Research Assistant Intern
UT Southwestern Medical Center
07.2018 - 10.2018
- Supported data analysis for LC-MS and GC-MS metabolite profiling
- Prepared and processed metabolite samples and conducted genotyping assays for tumor tissue DNA
Information Technology Assistant
Wabash College
08.2015 - 12.2017
- Installed and maintained computers and software, performed diagnostics, and resolved technical issues for students and faculty
- Documented service actions and conducted hardware troubleshooting and virus removal
Biomedical Engineering Research Intern
Keck Graduate Institute
04.2017 - 09.2017
- In 2017, I transitioned to biomedical engineering, developing a microfluidic device to study blood-brain barrier integrity
- I designed and fabricated the device using AutoCAD and soft lithography, simulating physiological conditions to understand the effects of aged red blood cells as a function of blood-brain barrier integrity
- Installed and operated soft lithography machine, UV mask aligner, spin coater, plasma etcher, vacuum oven
- Trained PhD student to use microfluidic device development machines
- Implemented Python to program rotor pump with rate intervals for blood exchange
- Designed and developed a microfluidic platform to simulate blood brain barrier physical environment
Infectious Disease Research Intern
SRI International
04.2016 - 08.2016
- I investigated viral pathogen infections, including Influenza virus, Dengue Virus, Chikungunya, Zika, and HIV virus in cells and animal models
- Similarly, participated in mapping pharmaceutical compounds for efficacy in viral infections treatment models for existing infectious pathogens and diseases and tested preclinical pharmaceutical compounds for efficacy in viral-infected cells and animal models
- I characterized cellular and viral proteins associated with exacerbated Influenza infection during co-infection with the Dengue virus
- I assisted in the analysis of data extracted from the co-infection of animals and cells with Dengue and Influenza viruses
- Executed biochemical assays protocols in (A)BSL-1, (A)BSL-2 and (A)BSL-3 environments
- Analyzed virological data using Prism software and maintained lab instruments
- Collaborated with senior scientists in discussing research results and future plans to advance ongoing research projects
- Performed both routine and emergency maintenance of laboratory instruments including preparing stock reagents and maintaining cell cultures
Health Care Data Science Research Intern
Lodestone Logic
05.2015 - 08.2015
- Developed strategic models to evaluate US healthcare costs and analyzed pharmaceutical drug pricing using SPSS and Excel
- Identified and resolved data discrepancies to enhance data accuracy
Education
Bachelor of Arts - Chemistry, Computer Science
Wabash College
Crawfordsville, IN 01.2015 - 05.2018
Associate of Arts - General Studies (Biomedical Sciences)
Montgomery College
Rockville, MD 09.2011 - 12.2013
Profile
I studied Chemistry with a minor in Computer Science, integrating my passion for science with technology., My research journey spans Infectious Diseases, Biomedical Engineering, Molecular Genetics, and Computational Bioinformatics. I thrive on tackling complex ideas and contributing to advancements in these fields., I am eager to pursue higher education in Synthetic Organic Chemistry, specifically focusing on Natural Product Synthesis. I aim to integrate my interests in computational programming, artificial intelligence, and machine learning to improve innovation in this area., I am deeply passionate about hard work, fitness, and overall well-being. I believe in maintaining a balanced lifestyle that fosters both physical and cognitive health., I avidly explore current events and societal issues, staying informed about global concerns. I enjoy sharing insights with friends and colleagues, believing that knowledge is best when it's shared. In the grand scheme, I value and care about differences and challenges.
Certification
SRI International Biosafety Levels, BSL-3, 08/16/16, BSL-2, 08/16/16, BSL-1, 08/16/16
Technicalskills
IR, NMR, C^13-NMR, H^1-NMR, LC-MS, GC-MS, UV-Vis spectrophotometry, cell culture, confocal microscopy, fluorescence microscopy, flow cytometry, microfabrication, molecular cloning, protein purification, PCR, genotyping, immunoassays, algorithm design, data science, data structures, statistics, applied mathematics, web development, Bash, Linux, Python, HTML, Java, Mathematica, MATLAB, R, web development
Teaching Experience
High School Student Research Intern Mentor
UT Southwestern Medical Center, Dallas, TX | Apr 2020 – Aug 2020
- Mentored a high school summer intern on mouse breeding for transgenic lines, safety protocols in animal facilities, and experimental procedures.
- Provided hands-on training in PCR, genotyping, and primer design for DNA samples.
- Guided the intern through data translation and interpretation of genotyping results.
Awards
- Academic Scholarship, Edmund Burke School, 01/01/09, 12/31/11
- Exchange Study Academic Scholarship, U.S. Department of State, 01/01/09, 12/31/11
Timeline
Quantitative Metabolomics & Bioinformatics
University of Michigan
11.2024 - Current
Computational Medicine and Bioinformatics Research Assistant
University of Michigan Medical School
04.2023 - Current
Molecular Genetics Research Assistant II
UT Southwestern Medical Center
03.2019 - 06.2021
Computational Biophysics Research Assistant Intern
UT Southwestern Medical Center
11.2018 - 02.2019
Cancer Metabolomics Research Assistant Intern
UT Southwestern Medical Center
07.2018 - 10.2018
Biomedical Engineering Research Intern
Keck Graduate Institute
04.2017 - 09.2017
Infectious Disease Research Intern
SRI International
04.2016 - 08.2016
Information Technology Assistant
Wabash College
08.2015 - 12.2017
Health Care Data Science Research Intern
Lodestone Logic
05.2015 - 08.2015
Bachelor of Arts - Chemistry, Computer Science
Wabash College
01.2015 - 05.2018
Associate of Arts - General Studies (Biomedical Sciences)
Montgomery College
09.2011 - 12.2013
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