MOLECULE MAKER - Key Persons
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Member of the Executive Committee
- Graduate Student
Dr. Shukla's research is focused on understanding the complex biological processes using novel physics-based models and techniques. The main goals of his lab are to develop a platform for integrating novel evolution-based methods for understanding protein function, elucidating mechanistic insights to regulate plant growth and development in context of global climate change, and understanding complex manipulation of signaling networks in both plants and humans by small molecules. Under this broad umbrella of computational molecular sciences, Shukla group integrates ideas from a wide range of disciplines to answer questions that are tied together by a vision of "Dynamic" biology and its role in engineering products for human health, energy and environment.
Bryan Amador Bryan is a graduate student in the Computing and Information Science PhD program at Rochester Institute of Technology, where he is currently in his third year and a member of the Document and Pattern Recognition Lab (DPRL). In the DPRL lab, they research systems that recognize and retrieve information from documents, images, and videos. Bryan's area of research is Math Information Retrieval, where the goal is to develop tools that facilitate users' access to mathematical content. Right now, he is most excited to work on modeling the task of formula search as a graph embedding and retrieval problem taking advantage of the visual and semantic content of formulas. [Click above to read more!]
Carl Edwards is a graduate student in Heng Ji's group at the Siebel School of Computing and Data Science, University of Illinois. Carl is currently prototyping the new mCLM model in MMLI. He has a double major in honors computer science and honors mathematics from the University of Tennessee and is planning to graduate from his PhD at Illinois this year. [Click to read more]
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Executive
- Member of the Executive Committee
Job Titles:
- Managing Director
- Managing Director of MMLI
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!]
Job Titles:
- Donald B. Broughton Professor
- Executive Committee
Costas Maranas is the Donald B. Broughton Professor in the Department of Chemical Engineering at Pennsylvania State University. His research group is part of the retrosynthesis team. They are working towards developing automated workflows for the discovery of synthesis pathways to target chemicals using enzymatic conversions. As part of this effort they have developed a suite a software tools including novoStoic2.0, dGPredictor and EnzRank. [Click above to read more!]
Job Titles:
- Education & Curriculum Consultant
Job Titles:
- Graduate Student
- Trainee Spotlight
David Friday is a graduate student in Thrust 4 working in the Jackson Lab using computer simulations (DFT or MD) to predict properties of light-absorbing materials (for solar cells) and employing machine learning methods (regression or Bayesian Optimization) to optimize materials toward experimental target properties. [Click above to read more!]
Job Titles:
- Member of the Executive Committee
- Undergrad Student
Job Titles:
- Associate Professor
- Member of the Executive Committee
- Associate Professor in the Department of Chemical and Biomolecular
Diwakar Shukla is an associate professor in the Department of Chemical and Biomolecular Engineering at the University of Illinois at Urbana-Champaign. He is also an affiliate faculty at the Center for Biophysics and Quantitative Biology, Department of Plant Biology, Bioengineering and Chemistry. His research work focuses on understanding the complex molecular processes in chemical and biomolecular systems using computational and experimental techniques. His research group is interested in deciphering the protein sequence-structure-dynamics-function relationship and its regulation. In MMLI, he works with Huimin Zhao's group to understand these relationships for enzymes, particularly in predicting properties such as specificity and selectivity. [Click to read more]
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Director
- Director of the MMLI
He is the Steven L. Miller Chair of chemical and biomolecular engineering, and professor of chemistry, biochemistry, biophysics, and bioengineering at the University of Illinois at Urbana-Champaign (UIUC), director of NSF AI Institute for Molecule Synthesis, and Editor in Chief of ACS Synthetic Biology. [Click above to read more]
He is the Steven L. Miller chair of chemical and biomolecular engineering, and professor of chemistry, biochemistry, biophysics, and bioengineering at the University of Illinois at Urbana-Champaign (UIUC), director of NSF AI Institute for Molecule Synthesis(moleculemaker.org), and Editor in Chief of ACS Synthetic Biology. He received his B.S. degree in Biology from the University of Science and Technology of China in 1992 and his Ph.D. degree in Chemistry from the California Institute of Technology in 1998 under the guidance of Nobel Laureate Dr. Frances Arnold. Prior to joining UIUC in 2000, he was a project leader at the Industrial Biotechnology Laboratory of the Dow Chemical Company. He was promoted to full professor in 2008. Dr. Zhao has authored and co-authored over420 research articles and over 30 issued and pending patent applications with several being licensed by industry. In addition, he has given plenary, keynote, or invited lectures in over 460 international meetings, universities, industries, and research institutes. Dr. Zhao received numerous research and teaching awards and honors such as AI ChE FP&B Division Award, ECI Enzyme Engineering Award, ACS Marvin Johnson Award, and SIMB Charles Thom Award. His primary research interests are in the development and applications of synthetic biology, machine learning, and laboratory automation tools to address society's most daunting challenges in health, energy, and sustainability.
Job Titles:
- Assistant Professor
- Assistant Professor in the Chemistry Department at UIUC
Dr. Nick Jackson is an Assistant Professor in the Chemistry department at UIUC and is working in Thrust 4 on the closed-loop design of organic electronics with Marty Burke, Charles Schroeder, and Ying Diao (and all of their excellent students!). [Click above to read more!]
Job Titles:
- Trainee Spotlight
- Visiting Scholar in the Chemistry Department at UIUC
Elena Burlova is a Visiting Scholar in the Chemistry department at UIUC and is working in Thrust 2 in the Denmark Lab. She joined MMLI in June 2022 to work as a research programmer and to do regression modeling for enantioselective catalysis. [Click above to read more!]
Job Titles:
- Member of the Executive Committee
Job Titles:
- Research Assistant Professor
Ganesh Sivaraman recently joined MMLI as a Research Assistant Professor after working at Argonne National Laboratory as part of the Argonne Leadership Computing Data Science Program. His focus at MMLI is bringing together the best of AI and the chemical sciences. [Click above to read more!]
Job Titles:
- Professor at Computer Science Department
Heng Ji is a professor at Computer Science Department and part of Thrust 1 in MMLI. Her esearch focuses on Natural Language Processing, especially on Multimedia Multilingual Information Extraction, Knowledge-enhanced Large Language Models and Vision-Language Models, AI for Science and Science-inspired AI. There exist approximately 166 billion small molecules, with 970 million deemed druglike. Despite this vast pool, only a tiny portion of molecules are currently approved across global healthcare systems. This scarcity underscores the urgent need for innovative approaches, motivating me to contribute significantly to molecule function discovery with advanced AI technologies. Many of these technologies can be applied to other domains such as new material discovery. [Click above to read more!]
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Computer Scientist
- Executive
Jiawei Han is a computer scientist, focusing on data mining, machine learning and text mining. His group has been working on information extraction and text mining from scientific literature. He was drawn to MMLI by its interest in MMLI data/text mining from chemistry data, including chemistry science literature and says that his favorite part of being a part of MMLI is working with his students and other colleagues in chemistry on various research problems. In his free time, he likes to travel and reading broadly. [Click above to read more!]
Job Titles:
- Member of the Executive Committee
- Trainee Spotlight
Job Titles:
- Member of the Executive Committee
- Associate Director for Software, NCSA
Job Titles:
- Member of the Executive Committee
Job Titles:
- Lead Software Engineer
- Lead Research Software Engineer at the National Center for Supercomputing Applications
- Lead Software Engineer at the National Center for Supercomputing Applications
- Researcher Spotlight
Matt Berry is an the lead research software engineer at the National Center for Supercomputing Applications at the University of Illinois who has been leading a team of NCSA researchers to support the development and deployment of MMLI AlphaSynthesis tool suit. [Click to read more]
Matt is a Lead Software Engineer at the National Center for Supercomputing Applications at the University of Illinois. His work with the MMLI focuses on supporting the dynamic database.
Job Titles:
- Tiara Torres - Flores
- Trainee Spotlight
Tiara Torres-Flores is a 3rd year PhD student in the Chemical and Biomolecular Engineering Department. She is currently a part of the MMLI Thrust 4 working on automated synthesis of oligothiophenes for rapid discovery of organic photovoltaic (OPV) materials and is particularly interested in understanding the factors controlling protodeboronation rates for Suzuki-Miyaura cross-coupling reactions applied to sequence-defined oligomers of different chain lengths. [Click above to read more!]
Tiara is a 3rd year PhD student in the Chemical and Biomolecular Engineering Department. She is currently a part of the MMLI Thrust 4 working on automated synthesis of oligothiophenes for rapid discovery of organic photovoltaic (OPV) materials and is particularly interested in understanding the factors controlling protodeboronation rates for Suzuki-Miyaura cross-coupling reactions applied to sequence-defined oligomers of different chain lengths.
What is your background? I did my B.S. in Chemical Engineering at the University of Puerto Rico at Mayaguez with a curricular sequence in Visual Arts. During that time, I started my research journey with OPVs, hydrogel synthesis for biomedical applications, and worked at Eli Lilly as a process engineer.
What drew you to MMLI? Although my background was in chemical engineering, I was always drawn to synthetic organic chemistry and the MMLI offered the opportunity for me to seamlessly combine both. I was excited to be at the center of cutting-edge chemistry, automation, and AI.
Job Titles:
- Graduate Student
- Trainee Spotlight
Mohit Anand Mohit Anand is Ph.D candidate at Penn State University in the Maranas group, which explores metabolic modeling, protein design, and synthesis planning. His research focuses on developing computational tools for synthesis planning, recently investigating language models to predict synthetic pathways. Fascinated by the intersection of AI and chemistry, he was drawn to MMLI after watching a documentary on AlphaFold, which he believed would transform enzyme chemistry-a belief later validated by a Nobel Prize awarded to its creators. At MMLI, he values the freedom to explore innovative ideas and collaborate with talented individuals, gaining insights from speakers at symposiums and retreats. [Click above to read more!]
Job Titles:
- Graduate Student
- Trainee Spotlight
Nolan Green is a 4th year PhD candidate in the Chemical and Biomolecular Engineering Department. Originally from originally from Erie, PA, he graduated in 2020 from Wake Forest University and is currently working in Dr. Marty Burke's lab developing a small molecule mimic of hemoglobin. He also works with MMLI's Thrust 5 to implement AI/ML and automated organic synthesis into the undergraduate curriculum at UIUC. [Click above to read more!]
Job Titles:
- Member of the Executive Committee
- Undergraduate Student
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Member of the Executive Committee
Job Titles:
- Professor
- Professor at Rochester Institute of Technology
Richard Zanibbi is a professor at Rochester Institute of Technology, coming to RIT and MMLI from a postdoc fellow position at the Centre for Pattern Recognition and Machine Intelligence at Concordia University in Montreal, Canada. Richard directs the Document and Pattern Recognition Lab, which helps MMLI identify new methods to extract molecules from PDFs.[Click above to read more!]
Job Titles:
- Member of the Executive Committee
- Professor
Karn Pamar is a MMLI postdoc working in the lab of Professor Scott Denmark. He works to ameliorate enantioselective catalysis using previously developed and novel machine learning tools. Karn was born in Vancouver, BC, Canada and completed his B.Sc. in Alberta at the University of Calgary and then moved to the University of Saskatchewan in Saskatoon to complete his Ph.D. From there, he decided to explore the American prairies and ended up in Illinois, which is not as cold as Sask! [Click above to read more!]
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Member of the Executive Committee
- Visiting Education
- Visiting Education Lead
Shelley Wagner is Visiting Education Lead in Thrust 5 (Workforce Development). Before joining MMLI, she was a high school science teacher for 14 years with background in special education. [Click to read more]
Job Titles:
- Member of the Executive Committee
- Graduate Student
Siru Ouyang is a graduate student in Jiawei Han's group at the Siebel School of Computing and Data Science, University of Illinois. In MMLI, her research focuses on Natural Language Processing and Machine Learning in MMLI. She graduated with a Bachelor's degree from the IEEE honored class at Shanghai Jiao Tong University (SJTU) in 2022 and joined Han's group the same year. [Click to read more]
Job Titles:
- Member of the Executive Committee
- Graduate Student
Tianhao Yu is a graduate student in Huimin Zhao's group working to develop a functionally conditioned protein generative model in MMLI after earning a B.S. in Chemical Engineering at the University of Rochester. He's currently on the job market as he wraps up his PhD work in Zhao lab.
Job Titles:
- Member of the Executive Committee
- Graduate Student
- Trainee Spotlight
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!]
Job Titles:
- Member of the Executive Committee
- Graduate Student
Job Titles:
- Associate Professor, University Scholar and Dow Chemical Company
Ying Diao is an Associate Professor, University Scholar and Dow Chemical Company Faculty Scholar in Department of Chemical and Biomolecular Engineering at University of Illinois at Urbana-Champaign, the Co-Chair of Molecular Science and Engineering in the Beckman Institute of Advanced Science and Technology, and a Thrust Lead of the Molecular Maker Lab Institute - an NSF AI Institute. She received her Ph.D. degree in Chemical Engineering from MIT in 2012. Her doctoral thesis was on understanding heterogeneous nucleation of pharmaceuticals by designing polymeric substrates. In her subsequent postdoctoral training at Stanford University, she pursued research in the thriving field of printed electronics. Diao group, started in 2015 at Illinois, focuses on understanding assembly of organic functional materials and innovating printing approaches that enable structural control down to the molecular and nanoscale. [Click to read more]
Job Titles:
- Member of the Executive Committee
- Graduate Student