Lyla Atta > CV

MD-PhD Candidate

Johns Hopkins University

Research Experience

• PhD Candidate JEFworks lab, BME, JHU
  August 2020 - Present.
  Developing statistical and computational tools for the analysis of spatially resolved transcriptomics data.
• Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. bioRxiv 2023 under review.
• VeloViz: RNA-velocity informed embeddings for visualizing cellular trajectories. Bioinformatics 2021. Software and tutorials.
• Computational challenges and opportunities in spatially resolved transcriptomic data analysis. Nature Communications 2021.
• Characterizing cell-type spatial relationships across length scales in spatially resolved omics data. bioRxiv, 2023, under review..
• Alignment of spatial transcriptomics data using diffeomorphic metric mapping. Nature Communications, 2023..
• Soluble PD-L1 reprograms blood monocytes to prevent cerebral edema and facilitate recovery after ischemic stroke. Brain Behavior and Immunity, 2023. accepted..
• Reference-free cell-type deconvolution of pixel-resolution spatially resolved transcriptomics data. Nature Communications, 2022..
• Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma. Cancer Cell 2021.
• Graduate Rotation Student Elana Fertig Lab, JHU
  July 2020 - August 2019.
  Statistical models to simulate immune cell single-cell RNA sequencing.
• Research Associate Scott Manalis Lab, MIT
  June 2017 - June 2018.
  Investigated single cell biophysical measurements and gene expression as markers of immune checkpoint inhibitor therapy in melanoma.
• Undergraduate Researcher Douglas Lauffenburger Lab, MIT
  March 2017 - June 2017.
  Investigated signaling networks underlying resistance to targeted cancer therapy.
• Tested dose dependent effects of drug combinations on Triple Negative Breast Cancer (TNBC) cell lines.
• Developed mathematical growth model comparing TNBC cell line drug response.
• Analyzed bulk gene expression to identify mediators of non-genetic resistance to EGFR pathway inhibitors.
• Data Science Coursework Statistics and Data Science, MIT
  Fall 2016.
  Network Analysis of Phosphoproteomic Data in Glioblastoma.
• Created graphical models of protein signaling interactions based on receptor tyrosine kinase phosphorylation data from GBM mouse models.
• Implemented graphical network analysis approaches to identify differences between tumor and control network models.
• Identified significant changes in signaling networks between tumor and control and identified cytoskeletal proteins marking these changes.
• Undergraduate Researcher Ron Weiss Lab, MIT
  November 2014 - March 2016.
  Synthetic mammalian circuit for in vivosensing and response to extracellular biomarkers.
• Automated, distribution-based clustering of flow cytometry data in Matlab.
• Designed an antibody-based extracellular platform for in vivo detection of biomarkers and transduction of an intracellular response.
• Collaborated to build detection platform using recombinant gene cloning techniques and tested functionality in Human Embryonic Kidney cells using flow cytometry and confocal microscopy.

Teaching

• Introduction to Data Analysis and Visualization
  20 students, Biomedical Engineering, JHU.
  Spring 2023, Spring 2024.
  Developed and taught lesson plans, guided independent student projects for 4-credit January intersession-term elective.
• Critical Appraisal of Clinical Studies
  20 student, 30 students, School of Medicine, JHU.
  Fall 2022, Fall 2023.
  Developed and taught lesson plan, led student discussion for first-year medical school selective focused on critical appraisal of randomized-control trials and cohort studies.
• Genomic Data Visualization
  5 Students, Biomedical Engineering, JHU.
  Spring 2022.
  Developed and taught guest lecture, graded homework and exams, provided feed- back for improvement.
• Critical Appraisal of COVID-19 Therapeutics Trials
  15 Students, School of Medicine, JHU.
  Fall 2020.
  Developed and taught lesson plan, led student discussion for first-year medical school selective focused on critical appraisal of COVID-19 therapeutic trials.
• Analysis of Biomolecular and Cellular Systems (20.320)
  40 Students, Biological Engineering, MIT.
  Fall 2016.
  Developed and taught lesson plans, created supplementary course notes, problem set and exam solutions for undergraduate core biological engineering course focused on mechanistic modeling of biomolecular reactions using differential equations in Matlab.

Activities and Projects

• HEAL Refugee Health and Asylum Collaborative
  JHU School of Medicine
  April 2022 - present
  Assisted with and drafted affidavits for 10 forensic physical and psychological evaluations for asylum applicants.
• Arabic-English interpretation for 2 forensic physical and psychological evaluations for asylum applicants.
Translated client orientation documents into Arabic to help Arabic-speaking clients prepare for evaluations.
• Open Case Studies
  JHU School of Medicine
  November 2021 - March 2022
  Contributed to Educators Guide for using Open Case Studies for data science instruction.
• JHU Medical School Admissions Committee
  JHU School of Medicine
  August 2021 - March 2022
  Interviewed 31 JHUSOM applicants, reviewed and summarized applications, and provided admission input to faculty admissions committee.
• Greater Boston Pandemic Fabrication Team
  March 202 - September 2021
  Co-led design and testing of Powered Air-Purifying Respirators to address COVID-19 PPE shortages. (Kothakonda et. al.
• Center for RISC
  University of Chicago
  July 2020 - September 2020
  Adapted data science curriculum for use by students with limited programming experience.
• Independent Student Analysis Committee
  JHU School of Medicine
  March 2020
  Analyzed student survey to identify strengths and areas of improvement in medical school experience for LCME re-accreditation process.
  Recommended strategies to improve pre-clinical curriculum, diversity and inclusion, student mistreatmet based on student survey results.
• Student Curriculum Review Team
  JHU School of Medicine
  August 2018 - March 2020
  Analyzed evaluations for medical school pre-clinical courses to identify strengths and weaknesses.
  Organized student town hall to solicit student feedback to improve pre-clinical Genetics and Metabolism courses.
  Designed and analyzed a student survey assessing effectiveness of the Student Curriculum Review Team in facilitating curricular improvements. (Kumar et. al.)
  
• Medical School Peer Advising Leader
  JHU School of Medicine
  March 2019 - March 2020
  Coordinated matching of 120 first-year medical school students to second-year mentors.
  Organized social and educational events facilitating exhange of advice through multiple transitions in medical school pre-clinical curriculum.
  
• Qualified Bilingual Staff Speaker
  Johns Hopkins Medicine
  March 2020 - present
  Qualified to communicate in Arabic with patients within the scope of clinical student role.
  
• Undergraduate Board President
  Biological Engineering, MIT.
  February 2016 - March 2017
  Established first annual BE Research Symposium for students to present their research.
  Planned, administered, and analyzed the first feedback survey and forum soliciting feedback from graduating seniors and presented results to faculty committee.
  Led a weeklong Freshman Pre-orientation Program for students interested in biological engineering.
  Created a sophomore orientation program for students starting the Biological Engineering major.