Hello, I'm

Alia Clark-Elsayed

Microbiologist and
Bioinformatics Scientist.

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Work Experience



Current Research

As a PhD candidate in the Cellular and Molecular Biology program at the University of Texas at Austin, I work at the intersection of computational biology and protein engineering. My research uses computational tools to advance protein design and optimization, particularly in developing novel biosensors for diagnostics.

My primary focus lies in the computational design and engineering of transcription factors capable of detecting clinically relevant molecules. This work has significant implications for medical diagnostics and therapeutic monitoring. I'm developing new approaches to create highly specific and sensitive biological sensors by combining computational prediction with experimental validation.

I've also pioneered high-throughput screening methods that allow for the simultaneous evaluation of libraries of protein variants. These innovative selections generate sequencing datasets to reveal crucial relationships between protein sequence and function. By analyzing these large-scale datasets, we can better understand the principles governing protein behavior and use this knowledge to guide future engineering efforts.

Industry Experience

Before beginning graduate school, I worked as a scientist on the Applications Development team at Inscripta, where I played a role in expanding the company's genome engineering platform. I developed novel applications for Inscripta's CRISPR-based technology, focusing on optimizing protocols and increasing the scope of possible genetic modifications.

My responsibilities included designing and executing high-throughput screening experiments to evaluate engineered strains. I independently developed selection methods to assess strain performance and established new workflows for phenotype characterization. This work involved building base strains, designing comprehensive genome-wide libraries, and implementing automated screening protocols. This experience strengthened my expertise in experimental design, high-throughput methods, and the practical implementation of genome engineering technologies.

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Technical Experience



Technical expertise

  • Computational protein design and modeling
  • High-throughput protein engineering and screening
  • Next-generation sequencing and data analysis
  • Machine learning applications in protein engineering
  • Molecular biology and biochemistry techniques

Skills
Experimental techniques
  • Molecular Biology: Plasmid assembly, purification, transformation; PCR and agarose gel electrophoresis; genome editing (CRISPR/Cas9, lambda red recombination)
  • DNA design: genetic libraries (promoter insertion, ribosome binding site, terminator, site-saturation mutagenesis) and circuit design
  • Protein: Bacterial protein production, purification (SDS-PAGE), enzyme activity assays

Computational tools
  • Programming: Python, Shell/Bash scripting
  • Computational Biology: Protein models (AlphaFold, Chai, ESM, RFAA, ProteinMPNN, LigandMPNN, RFDiffusion, FuncLib, FragFold, BindCraft), docking (DiffDock, GNINA), misc.(ChimeraX/PyMol)

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Education



I am currently pursuing my PhD in Cellular and Molecular Biology with a research track focus in Bioinformatics from the University of Texas at Austin. I am co-advised by Dr. Andrew Ellington and Dr. Edward Marcotte. My resarch focuses on the implementation of computational design tools into protein engineering workflows.

Before this, I earned my Bachelor of Arts in Molecular, Cellular, and Developmental Biology with Summa Cum Laude destinction with minors in French and Public Health from the University of Colorado Boulder. While there, I conducted research in the laboratory of Dr. Shelley Copley studying how bacteria evolve after the deletion of an essential gene. In this lab, I did my honors thesis titled "Comparing how Pseudomonas putida and Escherichia coli Evolve After Deletion of pdxB" which granted me this destinction. Through this work I gained valuable experience in experimental design and molecular biology techniques.

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Publications and Certifications



Here are the publications that I have been fortunate to work on:

Abbate, E.; Andrion, J.; Apel, A.; Biggs, M.; Chaves, J.; Cheung, K.; Ciesla, A.; Clark-ElSayed, A. ; Clay, M.; Contridas, R.; Fox, R.; Hein, G.; Held, D.; Horwitz, A.; Jenkins, S.; Kalbarczyk, K.; Krishnamurthy, N.; Mirsiaghi, M.; Noon, K.; Rowe, M.; Shepherd, T.; Tarasava, K.; Tarasow, T. M.; Thacker, D.; Villa, G.; Yerramsetty, K. Optimizing the Strain Engineering Process for Industrial-Scale Production of Bio-Based Molecules. Journal of Industrial Microbiology and Biotechnology 2023, 50 (1), kuad025. https://doi.org/10.1093/jimb/kuad025.

Dewachter, L.; Brooks, A. N.; Noon, K.; Cialek, C.; Clark-ElSayed, A.; Schalck, T.; Krishnamurthy, N.; Versées, W.; Vranken, W.; Michiels, J. Deep Mutational Scanning of Essential Bacterial Proteins Can Guide Antibiotic Development. Nat Commun 2023, 14 (1), 241. https://doi.org/10.1038/s41467-023-35940-3.

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