Keynote Talk
DiamondHacks 2024, La Jolla, California
The mission of DiamondHacks is to bring together hackers from diverse backgrounds to develop innovative solutions to real world problems.
Talks
Invited Talks
Improving HIV incidence estimation through integration of molecular data with epidemic modeling
AntiViral Research Center (AVRC), La Jolla, California (virtual)
In February 2024, I was invited to be a guest speaker in the HIV & Global Health Rounds organized by the AntiViral Research Center (AVRC) at UC San Diego. My talk, jointly presented with Natasha Martin and Ravi Goyal, was titled Improving HIV incidence estimation through integration of molecular data with epidemic modeling.
Real-time genomic surveillance of pathogens through bioinformatics applications
Computational Tools for Decoding Microbial Ecosystems (ESE/GE/BI/IDS 184 Winter 2024), California Institute of Technology (Caltech), Pasadena, California
In February 2024, I was invited by Professor Smruthi Karthikeyan to give a guest lecture in the Winter 2024 offering of ESE/GE/BI/IDS 184: Computational Tools for Decoding Microbial Ecosystems. I gave a talk titled Real-time genomic surveillance of pathogens through bioinformatics applications.
Real-time genomic surveillance of pathogens through bioinformatics applications
1st Meeting of the Pan American Health Organization (PAHO) Genomic Surveillance Regional Networks (PAHOGen), Brasilia, Brazil (virtual)
The Pan American Health Organization (PAHO) is the specialized international health agency for the Americas. It works with countries throughout the region to improve and protect people’s health. PAHO engages in technical cooperation with its member countries to fight communicable and noncommunicable diseases and their causes, to strengthen health systems, and to respond to emergencies and disasters. To advance these goals, PAHO promotes technical cooperation between countries and works in partnership with ministries of health and other government agencies, civil society organizations, other international agencies, universities, social security agencies, community groups, and other partners. PAHO promotes the inclusion of health in all public policies and the engagement of all sectors in efforts to ensure that people live longer, healthier lives, with good health as their most valuable resource. Under the leadership of its 51 member countries and territories, PAHO sets regional health priorities and mobilizes action to address health problems that respect no borders and that, in many cases, jeopardize the sustainability of health systems. PAHO wears two institutional hats: it is the specialized health agency of the Inter-American System and also serves as Regional Office for the Americas of the World Health Organization (WHO), the specialized health agency of the United Nations. From its Washington, D.C., headquarters, 27 country offices and three specialized centers in the region, PAHO promotes evidence-based decision-making to improve and promote health as a driver of sustainable development. I was invited to give a talk at the 1st Meeting of the PAHO Genomic Surveillance Regional Networks (PAHOGen). My talk was titled Real-time genomic surveillance of pathogens through bioinformatics applications.
Improving HIV incidence estimation through integration of molecular data with epidemic modeling
San Diego Center for AIDS Research (CFAR), UC San Diego, La Jolla, California
In November 2023, I was invited to be a guest speaker in the seminar series organized by the San Diego Center for AIDS Research (CFAR) at UC San Diego. My talk, jointly presented with Natasha Martin and Ravi Goyal, was titled Improving HIV incidence estimation through integration of molecular data with epidemic modeling.
A scalable approach for detecting exam similarity in CS courses
Department of Computer Science, UC Davis, Davis, California
The UC Davis Department of Computer Science invited me to give a talk titled A scalable approach for detecting exam similarity in CS courses.
Massively-scalable tools for real-time viral molecular surveillance
Lawrence Livermore National Laboratory (LLNL), Livermore, California
I was invited by the Lawrence Livermore National Laboratory (LLNL) to give a talk titled Massively-scalable tools for real-time viral molecular surveillance.
Bioinformatics, AI, and Games
Sony Interactive Entertainment (PlayStation), San Mateo, California
I was invited by Sony Interactive Entertainment (PlayStation) to give a talk about computational viral molecular epidemiology titled Bioinformatics, AI, and Games.
Computational Methods in Viral Molecular Epidemiology
San Diego Diplomacy Council, San Diego, California (virtual)
I was invited by the San Diego Diplomacy Council to give a talk about computational methods in viral molecular epidemiology for the delegation of Middle Eastern and North African healthcare experts.
ViralConsensus: Fast and memory-efficient viral consensus calling
Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore (virtual)
I was invited by the Department of Laboratory Medicine at the National University Hospital, Singapore to give a talk about ViralConsensus (Moshiri, 2023), a tool I developed for massively-scalable viral consensus sequence generation.
Massively scalable reference-guided Multiple Sequence Alignment of viral genomes
COVID Information Commons (CIC), Columbia University, New York City, New York (virtual)
The COVID Information Commons (CIC) is an open website to facilitate knowledge sharing and collaboration across various COVID research efforts, initiated by the NSF Convergence Accelerator. The initial focus of the CIC website is on NSF-funded COVID Rapid Response Research (RAPID) projects. The CIC serves as a resource for researchers, students and decision-makers from academia, government, not-for-profits and industry to identify collaboration opportunities, to leverage each other’s research findings, and to accelerate the most promising research to mitigate the broad societal impacts of the COVID-19 pandemic.
Panelist
Exploring HyFlex Perspectives Through Research and Practice, UC Riverside, Riverside, California (hybrid)
In March 2023, I was invited to be a guest speaker in the panel discussion that was part of the Exploring HyFlex Perspectives Through Research and Practice meeting organized by the XCITE Center for Teaching and Learning at UC Riverside.
Computational Methods in Viral Molecular Epidemiology
Pandemic Response to Emerging Pathogens, Antimicrobial Resistance and Equity (PREPARE) Institute, UC San Diego, La Jolla, California (virtual)
In February 2023, I was invited to be a guest speaker in the seminar series organized by the Pandemic Response to Emerging Pathogens, Antimicrobial Resistance and Equity (PREPARE) Institute at UC San Diego. My talk was titled Computational Methods in Viral Molecular Epidemiology.
Panelist
SASE West Regional Conference, La Jolla, California
The Society of Asian Scientists and Engineers (SASE) hosts annual regional conferences that aim for students from chapters in the West Region to come together for a day of networking, professional and personal development, discovering programs from other chapters, and more. I was invited as a UC San Diego Computer Science & Engineering professor to speak on a panel about academic vs. industry career paths.
Applications of Bioinformatics in the Real-Time Molecular Surveillance of Viral Pathogens
Emerging Infectious Diseases Seminar, Columbia University, New York City, New York (virtual)
In Fall 2022, I was invited to be a guest speaker in the Emerging Infectious Diseases seminar series at Columbia University, organized by Stephen Morse.
A scalable approach for detecting exam similarity in CS courses
Algorithms for Computing and Education (ACE) Lab, UC Berkeley, Berkeley, California (virtual)
The UC Berkeley Algorithms for Computing and Education (ACE) Lab brings together an interdisciplinary group of researchers from Computer Science, the iSchool, and the Graduate School of Education, working at the intersection of education and computing. Our projects involve novel educational software that helps educators educate better and students learn better, spanning traditional, online, and hybrid learning. I was invited to give a talk in the ACE Lab Talk Series titled A scalable approach for detecting exam similarity in CS courses.
Panelist
Career Night for Computer Science, Sweetwater Union High School District, Chula Vista, California (virtual)
The Sweetwater Union High School District (SUHSD) is a school district headquartered in Chula Vista, California. SUHSD is one of the most ethnically and economically diverse districts in California: approximately 87% of students belong to an ethnic minority group and over 40% of students qualify for the free or reduced lunch program. I am an alumnus of SUHSD (Bonita Vista High School class of 2011). The College and Career Readiness/CTE department of SUHSD coordinated a virtual districtwide Career Night Series, which was intended for 7th-12th grade students and their parents. On March 2, 2022, the Career Night Series held a panel to discuss career paths in Computer Science, and I was an invited panelist.
Keynote Talk
Bioinformatics Exchange (BEx) 2022, La Jolla, California (virtual)
The Bioinformatics Exchange (BEx) brings together leading faculty and Bioinformatics graduate students at the University of California, San Diego to discuss and present their work in this exciting area of research. This annual one day symposium offers a unique opportunity for students in the Bioinformatics and Systems Biology Program, as well as students interested in Bioinformatics, to get acquainted with the wide spectrum of research topics in the field.
Transforming education through Massive Adaptive Interactive Texts (MAITs)
Digital Education Hackathon (DigiEduHack) 2021, Ljubljana, Slovenia (virtual)
The International Research Centre on Artificial Intelligence (IRCAI), under the auspices of the United Nations Educational, Scientific and Cultural Organization (UNESCO), has been asked through the Government of Slovenia by Directorate-General for Education, Youth, Sport and Culture (DG EAC) to host, during the Slovenian presidency to the European Council (Jul-Dec 2021), the main stage of the Digital Education Hackathon (DigiEduHack), a flagship initiative of the Digital Education Action Plan. DigiEduHack is an EIT initiative under the European Commission’s Digital Education Action Plan, led by EIT Climate-KIC and coordinated by Aalto University. This year the main stage event is hosted by the Slovenian Presidency of the Council of the European Union in cooperation with the International Research Center on Artificial Intelligence (IRCAI) under the auspices of UNESCO. DigiEduHack is a series of online and in-person hackathons taking place all around the world on 9-10 November 2021, focusing on co-creating digital education solutions for a more sustainable world. DigiEduHack is free, inclusive, sustainable, open to anyone worldwide. DigiEduHack aims at fostering user-driven, co-created solutions, ranging from concepts or ideas to fully implementable apps. Stakeholders from the whole educational spectrum, as well as NGOs, startups, libraries, research labs, or ministries, engage in DigiEduHack in a bid to identify and solve key challenges in digital education. I gave an invited talk at DigiEduHack 2021 titled Transforming education through Massive Adaptive Interactive Texts (MAITs).
Applications of Bioinformatics in the Real-Time Molecular Surveillance of Viral Pathogens
Genomic Epidemiology Webinar, Pan American Health Organization (PAHO), Washington, D.C. (virtual)
The Pan American Health Organization (PAHO) is the specialized international health agency for the Americas. It works with countries throughout the region to improve and protect people’s health. PAHO engages in technical cooperation with its member countries to fight communicable and noncommunicable diseases and their causes, to strengthen health systems, and to respond to emergencies and disasters. To advance these goals, PAHO promotes technical cooperation between countries and works in partnership with ministries of health and other government agencies, civil society organizations, other international agencies, universities, social security agencies, community groups, and other partners. PAHO promotes the inclusion of health in all public policies and the engagement of all sectors in efforts to ensure that people live longer, healthier lives, with good health as their most valuable resource. Under the leadership of its 51 member countries and territories, PAHO sets regional health priorities and mobilizes action to address health problems that respect no borders and that, in many cases, jeopardize the sustainability of health systems. PAHO wears two institutional hats: it is the specialized health agency of the Inter-American System and also serves as Regional Office for the Americas of the World Health Organization (WHO), the specialized health agency of the United Nations. From its Washington, D.C., headquarters, 27 country offices and three specialized centers in the region, PAHO promotes evidence-based decision-making to improve and promote health as a driver of sustainable development. I was invited to give a talk at the Genomic Epidemiology Webinar hosted by PAHO. My talk was titled Applications of Bioinformatics in the Real-Time Molecular Surveillance of Viral Pathogens.
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes
Virus Evolution and Molecular Epidemiology (VEME) Workshop 2021, Gainesville, Florida (virtual)
Combating viral spread and their associated disease burden is a tremendous challenge requiring significant research efforts and dedicated measures, informing public health, veterinary care, and agriculture strategies. Viral sequence data is a major asset in the characterization of pathogens. Understanding the processes that generate genetic diversity assists in the struggle against viral infections and enhances our understanding of past evolutionary and epidemiological events. It can also help in the identification of the origins of new epidemics, in monitoring the effectiveness of therapeutic strategies, and eventually in predicting the behavior of viral epidemics. Advances in bioinformatics have led to improved approaches to investigating viral outbreaks that have been successfully applied to viruses including the Human immunodeficiency viruses (HIV), the Ebola virus, the Dengue and Zika viruses, the Chikungunya virus and the Influenza virus.
Optimizing high-performance cloud computing to enable real-time high-throughput SARS-CoV-2 whole genome sequence analysis
Virus Evolution and Molecular Epidemiology (VEME) Workshop 2021, Gainesville, Florida (virtual)
Combating viral spread and their associated disease burden is a tremendous challenge requiring significant research efforts and dedicated measures, informing public health, veterinary care, and agriculture strategies. Viral sequence data is a major asset in the characterization of pathogens. Understanding the processes that generate genetic diversity assists in the struggle against viral infections and enhances our understanding of past evolutionary and epidemiological events. It can also help in the identification of the origins of new epidemics, in monitoring the effectiveness of therapeutic strategies, and eventually in predicting the behavior of viral epidemics. Advances in bioinformatics have led to improved approaches to investigating viral outbreaks that have been successfully applied to viruses including the Human immunodeficiency viruses (HIV), the Ebola virus, the Dengue and Zika viruses, the Chikungunya virus and the Influenza virus.
Ten Simple Rules for Attending Your First Conference
Natural Sciences Seminar, Division of Natural Sciences, New College of Florida, Sarasota, Florida (virtual)
The New College of Florida hosts a Natural Sciences Seminar series (via the Division of Natural Sciences). I was invited to co-host a talk in this seminar series with Liz Leininger, in which we presented our recent manuscript, Ten Simple Rules for Attending Your First Conference.
COVID-19 Genomic Analysis
Research Running on Cloud Compute & Emerging Technologies (RRoCCET) 2021, San Diego, California (virtual)
RRoCCET is a hub for researchers seeking to overcome the increasing inadequacy of traditional research computing infrastructure by means of migration to the public cloud. This conference is a success-driven, methods-focused event hosted and attended by researchers looking for solution paths: feasible, tractable implementation plans informed by existing case studies. I was invited to give a talk at the RRoCCET 2021 conference. My talk was titled COVID-19 Genomic Analysis.
Bioinformatics workflows in viral amplicon sequencing
Micron Technology, Inc., Boise, Idaho (virtual)
Micron Technology, Inc. is an American producer of computer memory and computer data storage including dynamic random-access memory, flash memory, and USB flash drives. In an effort to fight the COVID-19 pandemic, I have partnered with Micron, and I gave a talk to their engineers titled Bioinformatics workflows in viral amplicon sequencing.
Legacy Lecture
Scholars Society at UCSD, La Jolla, California (virtual)
The Scholars Society at UCSD annually selects one professor to deliver a Legacy Lecture with the following prompt: “If this were your last lecture, what would you want to share with everyone?”. I was selected to deliver the 2021 Legacy Lecture.
Scalable methods in viral molecular epidemiology
Workshop on Pandemic Preparedness, UC National Laboratory Fees Program (virtual)
The UC National Laboratory Fees Research Program enhances partnerships between UC researchers and laboratory scientists at Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL). In April 2021, they held a Workshop on Pandemic Preparedness, and I was an invited speaker.
Tech Talk
SD Hacks 2021, La Jolla, California (virtual)
SD Hacks has been one of the largest hackathons in California since its inception back in 2015 and is excited to be celebrating its 5th anniversary.
RAPID: Real-time phylogenetic inference and transmission cluster analysis of COVID-19
COVID Information Commons (CIC), Columbia University, New York City, New York (virtual)
The COVID Information Commons (CIC) is an open website to facilitate knowledge sharing and collaboration across various COVID research efforts, initiated by the NSF Convergence Accelerator. The initial focus of the CIC website is on NSF-funded COVID Rapid Response Research (RAPID) projects. The CIC serves as a resource for researchers, students and decision-makers from academia, government, not-for-profits and industry to identify collaboration opportunities, to leverage each other’s research findings, and to accelerate the most promising research to mitigate the broad societal impacts of the COVID-19 pandemic.
Enabling scalable online learning through the development of Massive Adaptive Interactive Texts (MAITs)
Distance Education Symposium 2020, Northern Caribbean University, Mandeville, Jamaica (virtual)
The Distance Education Center of Northern Caribbean University (NCU) aims to achieve the following: (1) provide online learning opportunities that will result in certificates, diplomas and degrees being awarded, (2) facilitate professional development courses and programmes online that are relevant and distinctive for the upskilling of communities, (3) maintain a high standard of online delivery that will ensure graduates being recognized as educated citizens in society, (4) ensure that graduates acquire the skills and competencies necessary to perform effectively and efficiently in various environments, (5) improve content delivery via technology innovation, (6) increase enrollment through satellite/extension sites, and (7) improve online diversification of programming to satellite and online students.
A Viral Analysis Workflow
TheOpenCode Foundation, San Diego, California (virtual)
TheOpenCode is a not-for-profit organization that aims to provide students from low-income families the education and resources required to pursue a career in computer science. Through their bootcamps, accelerators, and other programs, they reach people from around the world. As a guest speaker, I ran a workshop titled A Viral Analysis Workflow, in which I demonstrated how to run a standard phylogenetic inference workflow using an example dataset of full SARS-CoV-2 genome assemblies.
Scientists using AI to track, predict epidemics like COVID-19
Arirang News: Global Insight, South Korea (virtual)
Arirang TV is an English-language South Korean television network based in Seoul and aimed at an overseas audience. The channel airs different programming in different countries, but generally airs news, cultural programs, educational shows and documentaries. Global Insight is a program on Arirang News that hosts live talks with experts, opinion leaders, and interesting people on global issues. I was invited to speak on Global Insight in a segment titled Scientists using AI to track, predict epidemics like COVID-19.
Algorithms in Viral Phylogenetics and Molecular Epidemiology
Micron Technology, Inc., Boise, Idaho (virtual)
Micron Technology, Inc. is an American producer of computer memory and computer data storage including dynamic random-access memory, flash memory, and USB flash drives. In an effort to fight the COVID-19 pandemic, I have partnered with Micron, and I gave a talk to their engineers titled Algorithms in Viral Phylogenetics and Molecular Epidemiology.
Keynote Talk
SD Hacks 2019, La Jolla, California
SD Hacks has been one of the largest hackathons in California since its inception back in 2015 and is excited to be celebrating its 5th anniversary. The focus of SD Hacks 2019 was Sustainability, Health and Wellness, and Education.
Scalable methods for molecular epidemiology of rapidly-evolving pathogens
Colloquium and Distinguished Lecture Series, Computer Science and Engineering, UC San Diego, La Jolla, California
I was invited to give a talk at the Colloquium and Distinguished Lecture Series hosted by the UC San Diego Department of Computer Science and Engineering. In my talk, titled Scalable methods for molecular epidemiology of rapidly-evolving pathogens, I discussed my teaching philosophy, contributions to diversity, and research interests.
Massively scalable tools for the analysis of viral epidemics
Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, Pennsylvania
I was invited to give a talk at the seminar series hosted by the Temple University Institute for Genomics and Evolutionary Medicine (iGEM). In my talk, titled Massively scalable tools for the analysis of viral epidemics, I discussed various methods I have developed for studying viral epidemics, namely FAVITES, TreeCluster, TreeSwift, and TreeN93.
Standardized Environments using JupyterHub
Data Science Hub, San Diego Supercomputer Center, La Jolla, California
The Data Science Hub at the San Diego Supercomputer Center is a community hub where experts from SDSC and other units of the university can apply their experience in building and participating in collaborative, multi-disciplinary data science teams to help provide solutions to regional, national, and global challenges, including smart cities, precision medicine, advanced manufacturing, and data center automation. My talk was titled Standardized Environments using JupyterHub.
The Era of Online Learning
TEDxUCSD 2017, La Jolla, California
The TEDx Program is designed to help communities, organizations and individuals to spark conversation and connection through local TED-like experiences. At TEDx events, a screening of TED Talks videos — or a combination of live presenters and TED Talks videos — sparks deep conversation and connections at the local level. TEDx events are planned and coordinated independently, under a free license granted by TED. I was invited to speak at TEDxUCSD 2017, and my talk was titled The Era of Online Learning. The recording can be found here.
Campus Talks
Professor Talk
Eta Kappa Nu (HKN), UC San Diego, La Jolla, California
Eta Kappa Nu (IEEE-HKN) is the official engineering student honor society of IEEE and is dedicated to encouraging and recognizing excellence in IEEE fields of interest. HKN uniquely honors ECE, CSE, MAE, BENG, MATH-CS, COGS-ML and DSC students who have achieved substantial success academically, possess leadership qualities and have noteworthy character. Members consist of students, alumni, faculty, and professionals who have demonstrated exceptional academic and professional accomplishments. At UCSD (Kappa Psi chapter), HKN hosts a diverse range of workshops and events to promote technical, professional, and academic development. Through these initiatives, we aim to inspire continuous growth and provide invaluable resources to help our members thrive in their respective fields.
Chalk Talk
Undergraduate Bioinformatics Club (UBIC), UC San Diego, La Jolla, California
The Undergraduate Bioinformatics Club (UBIC) represents UCSD’s undergraduates who are studying in or interested in the diverse field of bioinformatics. Through a combination of events, programs, and projects, their mission is to educate and contribute to the education and aspirations of every bioinformatics student at UCSD. The UBIC Chalk Talk is a seminar series encompassing a wide-range of Bioinformatics applications from eminent researchers for all-levels of undergraduates.
Panelist
Professor Panel, Computer Science & Engineering Society (CSES) at UC San Diego, La Jolla, California
The Computer Science & Engineering Society (CSES) at UC San Diego student organization hosted a “Professor Panel,” during which undergraduate students in the audience asked questions about various topics, ranging from pursuing research, success in courses, graduate school, etc. I was invited to speak as a panelist.
The Academic Career Path
Summer Internship Symposium, Department of Biomedical Informatics, UC San Diego, La Jolla, California
The UC San Diego Health Department of Biomedical Informatics (DBMI) held its annual Summer Internship Symposium.
The Academic Career Path
Summer Internship (Virtual) Symposium, Department of Biomedical Informatics, UC San Diego, La Jolla, California (virtual)
The UC San Diego Health Department of Biomedical Informatics (DBMI) held its annual Summer Internship (Virtual) Symposium.
Panelist
Introduction to Research Panel, Women in Computing (WIC) at UC San Diego, La Jolla, California
The Women in Computing (WIC) at UC San Diego student organization hosted an “Introduction to Research Panel.” I was invited to speak as a panelist.
Panelist
The Bioengineering Experience 2022, La Jolla, California
The Biomedical Engineering Society (BMES) at UC San Diego hosts an annual event called “The Bioengineering Experience” that is meant to highlight the different career paths, connections, and opportunities one can develop and utilize during their time here. Our event will include presentations from current professors, past alumni, and bioengineering organizations. I was invited as a past alumnus to provide advice to undergraduates interested in Bioinformatics.
Professor Panelist
First-Year Experience: Coding in Biology, Undergraduate Bioinformatics Club (UBIC), UC San Diego, La Jolla, California (virtual)
The Undergraduate Bioinformatics Club (UBIC) at UCSD is an organization that represents the undergraduates at UCSD who are studying in or interested in the diverse field of bioinformatics. Through a combination of events, programs, and projects, their mission is to educate and contribute to the education and aspirations of every bioinformatics student at UC San Diego.
Faculty Panelist
Society of Asian Scientists & Engineers (SASE), UC San Diego, La Jolla, California (virtual)
The Society of Asian Scientists & Engineers (SASE) at UCSD is a pre-professional organization dedicated to promoting professional development and preparing undergraduates for their futures, whether it be graduate school, research in a lab, an engineer, or anything in-between. SASE helps students by organizing professional events and workshops, such as their annual networking event Dining with Professionals, resume workshops, and more.
Faculty Panelist
Office of Undergraduate Admissions, UC San Diego, La Jolla, California (virtual)
The UC San Diego Office of Undergraduate Admissions held a Virtual Fall Showcase in October 2021. I was invited to speak on a Faculty Panel at the event.
Guest Speaker
Meet the Profs, EnVisionaries, UC San Diego, La Jolla, California (virtual)
EnVisionaries at UC San Diego is a student organization that aims to (1) educate students in Engineering, Visual Arts, design, and manufacturing processes, (2) support the Envision Maker Studio and other UCSD maker studios working directly with Envision Maker Studio in their goals to provide students with an environment to connect theory with practice, (3) provide a forum for the discussion and exchange of ideas related to Engineering, Visual Arts, and the development of the maker studios, and (4) provide a platform of integration for non-arts or engineering students to learn and work within maker spaces. They held a series of “Meet the Profs” Q&A sessions, and I was invited to speak at one.
The Academic Career Path
Summer Internship (Virtual) Symposium, Department of Biomedical Informatics, UC San Diego, La Jolla, California (virtual)
The UC San Diego Health Department of Biomedical Informatics (DBMI) held its 11th annual Summer Internship (Virtual) Symposium in August 2021. I gave a talk titled The Academic Career Path, in which I provided a general overview of the career path from undergraduate education all the way through obtaining a faculty position (e.g. Bachelor’s, Ph.D., post-doc, faculty), and I provided general recommendations for opportunities to take advantage of at each stage of the path.
Faculty Panelist
Summer Transfer Series, Computer Science & Engineering, UC San Diego, La Jolla, California (virtual)
The Computer Science & Engineering Department at UC San Diego held a series of webinars for transfer students in the department: the CSE Summer Transfer Series. I was invited to speak on a panel during one of the webinars of the series, during which the panel discussed various departmental and university-wide opportunities to engage in undergraduate research.
Faculty Panelist
Virtual Transfer Summer Prep Program, Jacobs School of Engineering, UC San Diego, La Jolla, California (virtual)
The Jacobs School of Engineering (JSOE) at UC San Diego hosts an annual Transfer Prep program, which is a virtual 5-day program held over the summer for incoming transfer engineering students. This free program provides incoming students with the opportunity to acclimate to campus life, build skills and habits necessary for success in engineering, and develop community amongst their peers before beginning their courses in the fall. In 2021, due to the COVID-19 pandemic, Transfer Prep was offered as a virtual program, and I participated in the “Virtual Coffee Chats” portion of the program, which was a networking event for incoming transfer students to have their first interactions with faculty and gain a better understanding of the diversity in research within the engineering departments.
Guest Speaker
Twitch Live Stream, Computer Science & Engineering, UC San Diego, La Jolla, California (virtual)
The Computer Science & Engineering Department at UC San Diego holds a series of Twitch Live Streams between the Department Chair and various guests to discuss various topics of interest to students and to the general public. I was the co-host of the inaugural Live Stream of this series, during which I discussed my research, reflected on my path to academia, and gave advice for professional development for students.
Scalable tools for viral molecular epidemiology
Summer Seminar Series, Bioinformatics and Systems Biology, UC San Diego, La Jolla, California (virtual)
The Bioinformatics and Systems Biology (BISB) Graduate Program at UC San Diego held a Summer Seminar Series in 2021. I gave a talk titled Scalable tools for viral molecular epidemiology.
COVID-19 Phylogenetics and Molecular Epidemiology
Information Technology Services (ITS), UC San Diego, La Jolla, California (virtual)
A Lunch & Learn Session is a UC San Diego IT Services (ITS) activity held in an informal setting to communicate information, increase visibility, meet new members, know their leaders and/or share knowledge with one another about continuous improvement and related topics. I gave a talk titled COVID-19 Phylogenetics and Molecular Epidemiology.
Student-Faculty Mixer Panelist
Tau Beta Pi, UC San Diego, La Jolla, California (virtual)
In May 2021, the UC San Diego Tau Beta Pi Engineering Honors Society hosted a Student-Faculty Mixer, and I was invited to speak on the faculty panel at the event.
STEM Faculty Q&A Panelist
Tau Beta Pi (TBP) and Society of Asian Scientists & Engineers (SASE), UC San Diego, La Jolla, California (virtual)
The UCSD Chapter of Tau Beta Pi (TBP) is a prominent engineering honors society that focuses on serving their members and the public to promote integrity and excellence in engineering. The Society of Asian Scientists & Engineers (SASE) at UCSD is a pre-professional organization dedicated to promoting professional development and preparing undergraduates for their futures, whether it be graduate school, research in a lab, an engineer, or anything in-between. SASE helps students by organizing professional events and workshops, such as their annual networking event Dining with Professionals, resume workshops, and more. In May 2021, in honor of Asian American and Pacific Islander (AAPI) Heritage Month, TBP and SASE held a collaborative event focused on AAPI representation in academia and research. One part of this event consisted of a Q&A Panel for students to ask STEM faculty members from AAPI backgrounds about their experiences in academia and research.
Science and Engineering Student-Faculty Mixer Panelist
Associated Students Office of Academic Affairs, UC San Diego, La Jolla, California (virtual)
In May 2021, the UC San Diego Associated Students Office of Academic Affairs hosted a Science and Engineering Student-Faculty Mixer, and I was invited to speak on the faculty panel at the event.
Ask Me Anything (AMA) Panelist
Electrical and Computer Engineering Undergraduate Student Council (ECE USC), UC San Diego, La Jolla, California (virtual)
The Electrical and Computer Engineering Undergraduate Student Council (ECE USC) is the voice of Electrical and Computer Engineering (ECE) students at UC San Diego. Through community building, networking, and leadership, the council strives to effect change within the department and campus at large though various events and programs. In February 2021, ECE USC hosted an AMA (Ask Me Anything) panel consisting of professors in various departments within the Jacobs School of Engineering (JSOE), during which students could ask seek advice from their professors. ECE USC invited me to represent the Computer Science & Engineering (CSE) Department.
Hidden Markov Models
Speaker Series, ACM AI, UC San Diego, La Jolla, California (virtual)
ACM AI is a UCSD student organization aiming to build a community of AI enthusiasts at UCSD and connect that community to the broader AI network. They also strive to keep AI fun and accessible to all. To achieve this goal, ACM AI hosts many workshops, competitions, networking events, research talks, and reading groups. In February 2021, ACM AI invited me to give a lecture on Hidden Markov Models.
Video Game Console Hacking, a History
Speaker Series, ACM Cyber, UC San Diego, La Jolla, California (virtual)
ACM Cyber is a UCSD student organization designed to expand the knowledge of cybersecurity for all students. As part of their mission, they host various workshops, panel discussions, capture the flag events, and other programs covering the latest in cybersecurity. In February 2021, ACM Cyber invited me to give a talk about the history of video game console hacking and security, titled Video Game Console Hacking, a History. I reached out to the popular video game console security YouTuber, ModernVintageGamer, who delivered the talk with me as a co-speaker.
Ask Me Anything (AMA)
Undergraduate Bioinformatics Club (UBIC), UC San Diego, La Jolla, California (virtual, Reddit)
The Undergraduate Bioinformatics Club (UBIC) represents UCSD’s undergraduates who are studying in or interested in the diverse field of bioinformatics. Through a combination of events, programs, and projects, their mission is to educate and contribute to the education and aspirations of every bioinformatics student at UCSD. Throughout the 2020-2021 academic year, UBIC hosted a series of Reddit AMAs (Ask Me Anything), during which students could post questions on Reddit to be answered by a predetermined guest speaker. I was the first guest of the AMA series (see the Reddit post and the recording of the AMA).
Chalk Talk
Undergraduate Bioinformatics Club (UBIC), UC San Diego, La Jolla, California
The Undergraduate Bioinformatics Club (UBIC) represents UCSD’s undergraduates who are studying in or interested in the diverse field of bioinformatics. Through a combination of events, programs, and projects, their mission is to educate and contribute to the education and aspirations of every bioinformatics student at UCSD. The UBIC Chalk Talk is a seminar series encompassing a wide-range of Bioinformatics applications from eminent researchers for all-levels of undergraduates.
Mathematical Modeling of Viral Evolution and Epidemiology
Seminar Series, Halıcıoğlu Data Science Institute, UC San Diego, La Jolla, California
I was invited to give a talk at the seminar series hosted by the Halıcıoğlu Data Science Institute. In my talk, titled Mathematical Modeling of Viral Evolution and Epidemiology, I discussed my research efforts in the field of computational molecular viral epidemiology, namely with respect to HIV.
Panelist
The Bioengineering Experience 2019, La Jolla, California
The Biomedical Engineering Society (BMES) at UC San Diego hosts an annual event called “The Bioengineering Experience” that is meant to highlight the different career paths, connections, and opportunities one can develop and utilize during their time here. Our event will include presentations from current professors, past alumni, and bioengineering organizations. I was invited as a past alumnus to provide advice to undergraduates interested in Bioinformatics.
FAVITES: FrAmework for VIral Transmission and Evolution Simulation
Bioinformatics Exchange (BEx) 2018, La Jolla, California
The Bioinformatics Exchange (BEx) brings together leading faculty and Bioinformatics graduate students at the University of California, San Diego to discuss and present their work in this exciting area of research. This annual one day symposium offers a unique opportunity for students in the Bioinformatics and Systems Biology Program, as well as students interested in Bioinformatics, to get acquainted with the wide spectrum of research topics in the field. I gave a talk that focused on statistical modeling of viral epidemics, namely the FAVITES simulation framework that I developed.
Phylogenetics and Education
Bioinformatics and Systems Biology Boot Camp 2018, La Jolla, California
The week-long boot camp for incoming first year students of the Bioinformatics and Systems Biology Graduate Program aims to 1) introduce new students to the Program, its faculty and students, the courses, and research opportunities, (2) foster student community and collaboration among students of the first year class, and to students in upper classes, (3) convey the bar for the core curriculum and key classes, as well as the research excitement and work ethic characteristic of the program’s best students, and (4) provide incoming students with an opportunity to remedy deficiencies prior to taking the core classes. I gave a talk that focused on algorithms in phylogenetics as well as methods in teaching.
Panelist
Bioinformatics Industry + Academia Symposium 2018, La Jolla, California
The Undergraduate Bioinformatics Club (UBIC) at UC San Diego hosts a yearly Bioinformatics Symposium in which faculty members, researchers, and industry professionals are invited to speak about their experiences in the field as well as to answer any questions the members of UBIC may have. I spoke as an undergraduate researcher who had gone through the graduate school application process.
Panelist
The Bioengineering Experience 2018, La Jolla, California
The Biomedical Engineering Society (BMES) at UC San Diego hosts an annual event called “The Bioengineering Experience” that is meant to highlight the different career paths, connections, and opportunities one can develop and utilize during their time here. Our event will include presentations from current professors, past alumni, and bioengineering organizations. I was invited as a past alumnus to provide advice to undergraduates interested in Bioinformatics.
Guest Speaker
UC San Diego Bioinformatics Podcast, La Jolla, California
The Undergraduate Bioinformatics Club (UBIC) at UC San Diego runs the UCSD Bioinformatics Podcast, which is a series in which they interview various graduate students, faculty, and researchers at UC San Diego. I was the first invited guest on the podcast, and my interview can be found here.
Phylogenetics
Bioinformatics Exchange (BEx) 2017, La Jolla, California
The Bioinformatics Exchange (BEx) brings together leading faculty and Bioinformatics graduate students at the University of California, San Diego to discuss and present their work in this exciting area of research. This annual one day symposium offers a unique opportunity for students in the Bioinformatics and Systems Biology Program, as well as students interested in Bioinformatics, to get acquainted with the wide spectrum of research topics in the field.
Panelist
Bioinformatics Industry + Academia Symposium 2017, La Jolla, California
The Undergraduate Bioinformatics Club (UBIC) at UC San Diego hosts a yearly Bioinformatics Symposium in which faculty members, researchers, and industry professionals are invited to speak about their experiences in the field as well as to answer any questions the members of UBIC may have. I spoke as an undergraduate researcher who had gone through the graduate school application process.
Panelist
The Bioengineering Experience 2017, La Jolla, California
The Biomedical Engineering Society (BMES) at UC San Diego hosts an annual event called “The Bioengineering Experience” that is meant to highlight the different career paths, connections, and opportunities one can develop and utilize during their time here. Our event will include presentations from current professors, past alumni, and bioengineering organizations. I was invited as a past alumnus to provide advice to undergraduates interested in Bioinformatics.
A two-state model of tree evolution and its applications to Alu retrotransposition
Population and Medical Genetics Seminar, UC San Diego, La Jolla, California
The Population and Medical Genetics Seminar is a bi-weekly seminar series hosted by faculty members of the Bioinformatics and Systems Biology Graduate Program at UC San Diego.
Panelist
Bioinformatics Industry + Academia Symposium 2016, La Jolla, California
The Undergraduate Bioinformatics Club (UBIC) at UC San Diego hosts a yearly Bioinformatics Symposium in which faculty members, researchers, and industry professionals are invited to speak about their experiences in the field as well as to answer any questions the members of UBIC may have. I spoke as an undergraduate researcher who had gone through the graduate school application process.
Panelist
The Bioengineering Experience 2016, La Jolla, California
The Biomedical Engineering Society (BMES) at UC San Diego hosts an annual event called “The Bioengineering Experience” that is meant to highlight the different career paths, connections, and opportunities one can develop and utilize during their time here. Our event will include presentations from current professors, past alumni, and bioengineering organizations. I was invited as a past alumnus to provide advice to undergraduates interested in Bioinformatics.
Panelist
Bioinformatics Industry + Academia Symposium 2015, La Jolla, California
The Undergraduate Bioinformatics Club (UBIC) at UC San Diego hosts a yearly Bioinformatics Symposium in which faculty members, researchers, and industry professionals are invited to speak about their experiences in the field as well as to answer any questions the members of UBIC may have. I spoke as an undergraduate researcher who had gone through the graduate school application process.