by Boaz Goldberg
Introduction
This summer, I had the incredible opportunity to work with the Xiao Lab at the Johns Hopkins School of Medicine funded by a PURA fellowship. My role involved conducting research related to the computational modeling of gene regulation in bacteria as regulated by genome topology. I was able to develop a computational model, simulate a variety of genetic setups with this model, analyze the resulting data, present my research at an internationally attended conference, and am currently working to get my research published in PLOS computational. This experience allowed me to further the research I had been performing this past academic year as well as contribute significantly to my academic, professional, and personal growth.
Key Experiences
My primary task during my research internship was to analyze data resulting from a computational model of gene expression that I had been working on throughout the previous academic year. This included determining the most biologically relevant regimes in our parameters space to study, iterating through numerous conditions within said region, and seeing how each parameter influences the simulation results (specifically, transcriptional rate and noise). This allows us to make predictions on the regulatory roles of various biological factors on gene expression, most importantly DNA topoisomerase activities and topological domain length. One of the most exciting parts about my fellowship was the opportunity to present my research at the 2024 Topoisomerases in Biology and Medicine Conference. Preparing for this presentation required me to distill complex scientific concepts into a concise, complete, and visually interesting poster, which was an interesting and challenging experience. The feedback I received from other professionals in the field was invaluable and helped refine my research further. This experience has been critical not only in guiding my future research but also in giving me a better picture of what academic collaboration looks like in general, allowing me to make better informed career choices with more experience under my belt.
Skills and Knowledge Gained
Throughout the internship, I developed a wide range of skills. Technically, I honed my abilities in computational modeling, data analysis, and scientific writing. I used various programming languages and analysis softwares in order to perform my research, including python, R and BASH. I also gained experience in adobe illustrator in order to generate figures to present my research, both in poster, presentation, and paper forms. In addition to technical skills, I also enhanced several soft skills. Effective communication was crucial, especially when presenting my research and collaborating with my team. I learned to convey complex information clearly and concisely, which is a vital skill in any professional setting. Through several conversations with the rest of my lab, I learned how to prioritize what information I choose to share in our group meetings as well as how to present this information effectively. Time management and adaptability were other key skills I developed, as balancing multiple projects and meeting tight deadlines required careful planning and flexibility, especially when considering my other time commitments such as studying for the MCAT, volunteering at Union Memorial Hospital, and completing the required assignments for the Life Design Summer Experience Practicum.
Impact of OKRs
Setting and working towards OKRs significantly influenced my fellowship experience and what I have taken out of this experience moving forward. One of my primary objectives was to produce publication-quality results. This goal drove me to maintain a high standard of work throughout the internship. By setting specific key results, I was able to hold myself accountable to several figures that will contribute to a publication in the near future. Another important OKR was to gain broad exposure to social sciences topics, including economics, sociology, and politics. I set this goal mainly for personal interest in gaining an exposure to a broader range of fields than I have previously. I have started listening to podcasts on economic and social issues (Freakonomics) as well as keeping up with the news better than I previously had. I have found this goal to not only be interesting but also to contribute to my ability to make more informed decisions in the future. Finally, the OKR of developing skills in interacting with patients through my volunteering at Union Memorial Hospital. I have found that I have become much more comfortable interacting with patients over the course of this Summer, and have found more effective ways to get patients to open up to me in our conversations. I have found this not only to be valuable to me to get better prepared for a future career in medicine, but also valuable for my patients who often struggle with isolation when stuck in the hospital for extended periods of time, sometimes with little to no visits from family members.
Lessons Learned
One of the major lessons I learned during my practicum was the importance of perseverance and continuous improvement. Research is inherently iterative, and encountering setbacks is a natural part of the process. I encountered numerous setbacks during the course of my research, ranging from personal mistakes (such as missing issues during the debugging process until after running simulations) to unpredictable complications (such as unexpected computational or experimental results). Learning to view challenges as opportunities for growth was a valuable lesson that will undoubtedly serve me well in my future career. I also learned the significance of effective mentorship and collaboration. Working closely with my research mentor and other team members taught me the value of seeking feedback and being open to different perspectives. This collaborative approach not only improved the quality of my work but also made the research process more enjoyable and fulfilling.
Future Applications
The skills and knowledge I gained during this internship will be crucial for my future career. My technical skills in a variety of programming and presentation software will be invaluable in my future work as I continue in computational research and continue presenting information in a variety of contexts. Additionally, the soft skills I enhanced, such as communication and time management, will be invaluable in any professional context. Whether in academia or medicine, the ability to effectively convey ideas and manage multiple projects will be essential. This requires the ability to manage not only my own time, but also the ability to collaborate with others effectively, which relies heavily on communication skills. I have found that communication is central to scientific research, and that my engaging with this communication in a variety of contexts and media has been incredibly valuable to my development of my communication abilities. These communication abilities will allow me to better interact with both patients and colleagues as I move forward.
Conclusion
My summer internship at the Xiao Lab was a transformative experience that provided numerous opportunities for growth and learning. From developing computational models to presenting at conferences, each experience has contributed to my personal and professional development. I have gained valuable experience, developed new skills, met new people, and grown in a way that will be incredibly beneficial to my future career and life in general. I plan to apply my new knowledge, technical abilities, and soft skills to my future in academic medicine.
