Staff Spotlight: Cindy Chan
Cindy Chan started her position as the managing director of MMLI on Aug 5, taking over from Ron Payne. Cindy joins us from the lab of Professor Stephen P. Long where she did her postdoctoral research to improve photosynthesis in sugarcane and energycane using genetic engineering. Besides postdoc-ing, she worked part time as the data manager of the RIPE project in the past 3 years. In her new role as managing director, she hopes to further improve the efficiency of MMLI management/administration to better support the research goals of MMLI. She was drawn to MMLI wanting to learn more about how small molecule making process can be accelerated using AI methods, and how we could safely democratize molecular innovation, as well as to use this opportunity to learn about research administration. [Click above to read more!]
Trainee Spotlight: Vikas Upadhyay
Vikas Upadhyay is a graduate student in the lab of Dr. Costas Maranas where he is currently working on the design of computational tools for chemical synthesis planning, with a focus on biosynthesis, which is a complex task requiring the consideration of numerous factors, including thermodynamics, novel reaction identification, and enzyme selection/design—often necessitating enzyme engineering to enhance activity for novel reactions. He is also exploring ways to incorporate chemical reaction space alongside biological reaction space, aiming to leverage the strengths of both in synthesis planning. Originally from India, Vikas completed his undergraduate degree in Chemical Engineering at IIT Hyderabad where he developed a strong interest in optimization algorithms. This fascination grew as he realized that many ML and AI algorithms are essentially sophisticated networks of optimization techniques, leading him to pursue a PhD in Chemical Engineering. [Click above to read more!]
MMLI Staff Spotlight: Cindy Chan!
What is your background/what did you do before your current role?
I have a BSc. (Honours) in Biotechnology from the University Malaysia Sabah and worked as a marketing executive and then a high school teacher for a couple of years before flying to Europe to do an Erasmus Mundus Masters in Forensic Science. Following that, I did a PhD in plant sciences at the University of Cambridge studying morphology and physiology of the green alga. Upon completion of my PhD, I joined the lab of Professor Stephen P. Long for my postdoctoral research to improve photosynthesis in sugarcane and energycane using genetic engineering. Besides postdoc-ing, I worked part time as the data manager of the RIPE project in the past 3 years.
What is your current position? What drew you to MMLI and what are your goals for the position?
I started my position as the managing director of MMLI on Aug 5, taking over from Ron Payne.
Goals: I’d hope to further improve the efficiency of MMLI management/administration to better support the research goals of MMLI. I want to learn more about how small molecule making process can be accelerated using AI methods, and how we could safely democratize molecular innovation. I also want to use this opportunity to learn about research administration.
How do you like to spend your free time? (or what would you do for fun if you had more free time!)
As a foodie, I enjoy trying out good food, and making them. I spend most of my free time with my kitkatz (grey dilute torties) and my Brit husband.
Fun fact (or extremely average fact) about yourself you would like to share.
I’m a born and bred Malaysian, speak multiple languages and lived in a few different countries (Malaysia (of course!), South Korea (briefly for internship), Spain, Portugal, the UK, and now the US) over the past 20 years. Come chat with me about languages and science and education systems around the world!
MMLI Trainee Spotlight: Let’s meet Vikas Upadhyay
What is your background/what did you do before your current role?
I am originally from India and completed my undergraduate degree in Chemical Engineering at IIT Hyderabad. During my undergrad, I developed a strong interest in optimization algorithms. This fascination grew as I realized that many ML and AI algorithms are essentially sophisticated networks of optimization techniques. My passion for these algorithms led me to pursue a PhD in Chemical Engineering at Pennsylvania State University with Dr. Costas Maranas, where I am currently working on the design of computational tools for chemical synthesis planning, with a focus on biosynthesis. Biosynthesis planning is a complex task requiring the consideration of numerous factors, including thermodynamics, novel reaction identification, and enzyme selection/design—often necessitating enzyme engineering to enhance activity for novel reactions. I am also exploring ways to incorporate chemical reaction space alongside biological reaction space, aiming to leverage the strengths of both in synthesis planning.
What is your current position/short description of what you are working on right now with MMLI.
A critical aspect of this work involves the need for high-quality data to train these tools, where Large Language Models (LLMs) coupled with Retrieval-Augmented Generation (RAG) techniques can play a significant role in mining literature-verified data. Additionally, linking these computational tools with high-throughput experimentation systems allows for the rapid testing of synthesis pathways and the assessment of enzymes for novel substrate activity. This approach can generate high-fidelity data that further enhances model accuracy. Currently, I am particularly excited about using reinforcement learning combined with biophysics-driven synthesis pathway design to gain a deeper understanding of pathway design, moving beyond solely data-driven methods. In parallel, I am working on developing enzyme engineering tools that predict high-quality mutant sequences with the potential for higher activity for novel reactions. Additionally, We are working on an algorithm to understand biochemical reaction mechanisms, which could help in designing new-to-nature enzymes based on desired reaction/conversion.
What drew you to MMLI (or your lab)?
My journey into the world of optimization, ML/AI, and their applications naturally drew me to projects that challenge the status quo in chemical synthesis planning. The interdisciplinary nature of MMLI, coupled with its collaborative environment, has been the perfect setting for me to explore and expand my research in leveraging algorithms for understating chemistry, which aligns perfectly with MMLI’s focus on AI for chemistry. The opportunity to apply my expertise in optimization/ML/AI algorithms to solve complex problems in chemistry and biology, as well as the real-life application of such tools to synthesize a wide range of chemicals efficiently and economically is what excites me most about being part of MMLI.
What has been your favorite part of being a part of MMLI?
My favorite part of being a part of MMLI has been the opportunity to collaborate and learn from leading experts across various disciplines, including Chemistry, Computer Science, Chemical Engineering, Synthetic Biology, Metabolic Engineering, and Education. These interactions have significantly enriched my approach to tackling hard complex problems. Another aspect I’ve particularly enjoyed is working with UI/UX designers to develop user-friendly websites for the tools we create. This experience has taught me the importance of considering user experience in tool development—ensuring that a tool is intuitive and accessible is just as crucial as its technical functionality. I found it especially rewarding to collaborate with the NCSA team on designing novoStoic2.0 as part of the AlphaSynthesis platform for MMLI. Additionally, my role as the Leadership Chair of the MMLI-SPC allowed me to work closely with other graduate students in planning and executing events for MMLI, further enhancing my leadership and organizational skills. Overall, MMLI has broadened my skill set in ways I never anticipated.
How do you like to spend your free time?
I find hiking and exploring nature to be the perfect way to unwind and gain fresh perspectives on my work. I’m also into photography, though I don’t get to do it as often as I’d like since it can be time-consuming—still, it’s something I truly enjoy (I’d be happy to share some of my photos if you’re interested!). Psychology and philosophy are other passions of mine, and When I’m not out in nature or behind the lens, I dive into books that understand/explore human behavior. Cooking is another activity I really enjoy, especially experimenting with new recipes. The funny part is that while I love cooking, I’m not as keen on eating what I make—so it gives me the perfect excuse to invite friends over, which also helps me maintain that essential human connection. And when I’m not doing any of those things, you’ll probably find me either reading a research article or reading manga (especially One Piece), or let’s be honest, procrastinating like any typical graduate student.
Fun fact (or extremely average fact) about yourself you would like to share.
A fun fact about me is that I have a bit of a talent for getting lost—intentionally! Whether I’m in a new city or out on a hike, I love to wander off the beaten path and discover hidden gems. It’s all about the adventure and finding those unexpected spots that you can’t plan for. This sense of exploration probably spills over into my work, where I’m always eager to dive into uncharted territory and uncover new insights. Just like in my research, sometimes the best discoveries happen when you’re not exactly sure where you’re going, but you’re enjoying the journey!
This adventurous spirit has also shaped my research journey, which has taken me across three different countries—India, Japan, and the United States. While I don’t have a collection of lab coats (the perks of experimental research!), I’ve gathered a diverse set of experiences and perspectives. Each place has its unique approach to science and collaboration, and blending these different viewpoints has been incredibly rewarding.