Karolak Lab
Postdoctoral posting available here and under Opportunities. Reach out if you are interested in applying for postdoctoral researcher position or fellowships and looking for the host.
Also if interested in PhD program in Cancer Biology under Dr. Karolak mentorship at Moffitt.
Undergraduate students - reach out if interested in internships.
Follow us on Twitter: @amkarolak (our group) and @ml4onco (ML Department).
Spring 2025:
Ella Lawrence and Mouktik Isukapalli have been selected to train as interns with SPARK at the Moffitt Cancer Center and Research Institute for the summer of 2025. SPARK is a highly competitive and prestigious Summer Program for the Advancement of Research Knowledge at Moffitt Cancer Center. They plan to join the experimental and clinical labs. Congratulations!!
More information can be found at: https://www.moffitt.org/education/research-education-and-training/office-of-undergraduate-and-visiting-scholar-affairs/spark/
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On March 19, Kat presents at the ML research in progress seminar series EMERGE. She discusses fusion of molecular dynamics with machine learning to predict and understand binding site mutation-induced resistance using KRAS G12C secondary mutations as an example.
Excellent presentation and engaging discussion with the ML team members. Plus visit from the spring breakers on the MolAI team: Tiff (UPenn), Meghna (JHU), and Ella (UF).
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On February 20, we visited City of Hope Cancer Center in both Monrovia and Duarte locations. Great time and friends. Once again, looking forward to our next project together.
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The week of February 15-19, we’re excited to be at the Biophysical Society Annual Meeting in Los Angeles. Kat and Trieu received their travel awards, presented posters, and Kat gave a flash talk.
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Aleks had a privilege to speak to and interact with the University of South Florida students during the 2nd Moffitt Cancer Center Career Day @ USF Health on 2/12. Discussed our focus + opportunities to join.
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On January 23, Aleks discusses the structure of QS and ML at Moffitt, as well as our lab's research, to the students in the Cancer Biology Class at University of South Florida. The invitation came from Dr. Sandy Westerheide, Associate Professor in the Department of Molecular Biosciences. Great Q&A session!
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Fall 2024:
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We welcome Ella Lawrence to the Molecular AI Team! Ella is a freshman in Chemistry at University of Florida!
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Aleks presents on the AI innovations in molecular design at the inaugural Drug Discovery Chemistry Europe Conference in Barcelona, Spain in the AI section:
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Kat's abstract gets selected for a talk at the 2025 Annual Biophysical Society Meeting in LA!
Well done Kat! Congratulations on this recognition, looking forward to your talk :).
Both Kat and Trieu will present the Posters + both received the Travel Awards!
Titles of their presentations:
MUTATIONS IN DRUG BINDING SITES: INTEGRATING COMPUTATIONAL CHEMISTRY AND MACHINE LEARNING TO UNDERSTAND MUTATION-INDUCED RESISTANCE - Kat
MOLECULAR DESIGN WITH GENERATIVE AI: A TRANSFORMER GRAPH VARIATIONAL AUTOENCODER APPROACH - Trieu
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Trieu gets accepted to the 2025 Summer MERCK’s Internship Program in Boston!
So well done and deserved. Congratulations Trieu, Molecular AI Group wishes you best of luck and looking forward to your scientific adventures!
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We welcome Edith Behrens to the Molecular AI Team! Edie is a junior at Chemical Engineering at USF and will research in our Lab for academic credit (Advanced Undergraduate Research Course) at USF.
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November 14-15: We present at the 2nd Machine Learning Workshop in Memory of Dr. Robert Gillies at Moffitt. Posters by Kat and Mouktik, and talk by Aleks.
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October 28-30: Most of our Molecular AI trainees presented at this year 5th annual ORIEN Scientific Summit and 2nd Data Science Symposium hosted by ORIEN in Tampa.
Day1: Rohit and Mouktik on using the ORIEN dataset for PDAC stratification, Trieu on genAI TGVAE model for molecular design.
Day2: Kat and Tiffany (Ella virtually) on mutation-induced resistance in cancer.
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October 24 - 25: Trieu was selected to give a talk about TGVAE during the panel discussion (well done!) and Kat presented the poster on mutation-induced resistance in cancer at the 2nd the AI+X Symposium at USF Research Park.
Photos by Kat, more pics to come!
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October 24 - 25: Aleks was honored to speak about our and MCC research and goals plus discuss collaborations and educational opportunities for undergraduates, master and PhD students at Stevens Institute of Technology in Hoboken, NJ.
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Trieu represents our group at the Quantitative Science Division Annual Oktoberfest at Moffitt. His poster was on the transformer model for molecular design. Pics with other ML members including this year poster awardee, Piyawan from Yi Luo's lab.
Summer 2024:
Kat, Tiffany, and Ella presents at the Machine Learning Department Research in Progress EMERGE Meeting on the Importance of Mutation-Induced Resistance in Cancer. Thank you for presenting and thanks to Kat for mentoring our interns this summer.
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Check out Trieu's preprint on the TGVAE model at bioRxiv: https://doi.org/10.1101/2024.07.22.604603. Congrats Trieu on your first author first publication with Molecular AI!
Trieu presents on his Transformer Graph Variational Autoencoder (TGVAE) model in application to a design of novel molecules at the July 18th Screening and Proteomics Initiative for Novel Targets and Drugs (SPRINTD) meeting at Moffitt.
Quite an accomplishment and significant work.
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Group lunch (from the left: the USF Bull, and then Trieu, Ella, Kat, Tiffany, Mouktik, missing Meghna and Rohit). Happy Summer Everyone!
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Kat presents at the Screening and Proteomics Initiative for Novel Targets and Drugs (SPRINTD) meeting on the 3D structure modeling of EWS/FLI1 and EWS/ATF1 fusion proteins. (June 6) Very well done Kat!
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Aleks discusses research in our Molecular AI Group at the 1st Prescriptomics and Personalized Medicine Conference at Caparica, Lisbon, Portugal– Invited Talk (May 12)
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Our 2024 Moffitt Scientific Symposium posters were presented by Meghna and Trieu (May 8):
M.Manjith, A.Karolak. Investigating Role of Mucins, Biofilm-Related Biomarkers, to Predict Response to Therapy in Colorectal Cancer. Moffitt Scientific Symposium (5/2024)
T.Nguyen, D.Imbody, E.Haura, A.Karolak. Transformer Graph Variational Autoencoder for De Novo Drug Design. Moffitt Scientific Symposium (5/2024)
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May 7: Trieu presents at the Machine Learning Department Research in Progress EMERGE Meeting. Title: Transformer Graph Variational Autoencoder for De Novo Drug Design.
We also say farewell to Adam, who moves to a new position and summer internship. Good luck Adam!
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Spring 2024:
Our group welcomes Kat Mizgalska, PhD student from USF, who will continue her graduate studies in our group. Also, welcome to Mouktik Isukapalli, undergraduate student from USF.
Welcome Kat and Mouktik! Happy to have you!
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We present our work at a number of meetings this semester:
T.Nguyen, A.Karolak Transformer Graph Variational Encoder for De Novo Drug Design. Trieu gave a talk at the ODSi Meeting (4/2024). Superb work + well presented!
A.Karolak Machine Learning and Molecular AI at Moffitt – Invited Panelist:
- at the Breakout Session on AI in Healthcare, 3rd GNSI Tampa Summit, USF (3/2024)
- at the Florida Polytechnic University, (3/2024)
A.Karolak In Control of Your Career Trajectory – Virtual Postdoc Event at Moffitt (2/2024)
M.Stitou, T.Nguyen, A.Karolak Poster on: Integrating Artificial Intelligence and Chemistry for Cancer Research: From Mutational Signatures to De Novo Drug Design – 2nd Annual Bioengineering at Moffitt Meeting (2/2024)
M.Stitou, A.Karolak KRAS acquired resistance – Talk at the ODSi Meeting (2/2024)
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Meghna also gets accepted to John Hopkins University. She will major in Cellular and Molecular Biology. Congratulations!!
The Society for Science announces that Meghna Manjith has been named a top 300 Scholar in the 83rd Regeneron Science Talent Search —the nation’s oldest and most prestigious science and mathematics competition for high school seniors She also received 3rd place at the Florida State Science and Engineering Fair in the Mathematics and Computational Sciences Division. Well done and deserved!
Fall 2023:
In December, we welcome Meghna Manjith and Rohit Veligeti!
Group outing to NASA/KSC and the Thanksgiving brunch (with current and future) lab members:
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We present our work on AI for pharmacophore modeling and Heterogeneous colorectal cancer at the Quantitative Science Division 2nd Annual Oktoberfest at Moffitt:
Trieu Nguyen, Mourad Stitou, Denis J. Imbody, Eric B. Haura, and Aleksandra Karolak on: "AI-enabled Pharmacophore-Guided Drug Design: A Novel Approach for Targeting Double KRAS G12C/Y96C Mutation"
Adam Wojtulewski, Yoga Balagurunathan, Daniel A. Anaya, and Aleksandra Karolak on: "The Heterogeneity in Survival among Patients with Metastatic Colorectal Cancer".
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We welcome two new members: Triệu Nguyễn and Dr. Mourad Stitou to our Molecular AI team. Happy to have you!
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Aleks presents and discusses our work on IPMNs at the AACR Special Conference on Pancreatic Cancer in Boston.
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Aleks gives an invited talk and presents our work on AI in peritoneal carcinomatosis at the Moffitt GI PM Retreat.
Summer 2023:
We present and discuss our work at Epigenetics and Genetics in Cancer Gordon Research Conference in Italy and at the Screening and Proteomics Initiative for Novel Targets and Drugs Platform (SPRINTD) at the Molecular Medicine Program at Moffitt.
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Archi Marrapu and Adam Wojtulewski join us for the summer internship. Welcome Adam and Archi! (here with Sara after Summer Interns research presentations)
Spring 2023:
Work done by Matthew Froid in dr. Basanta's and our lab was presented at the March edition of EMERGE ML research in progress meetings. The abstract was accepted to the poster presentation at Moffitt Symposium in May. Well done Matthew!
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Sara Del Valle joins our team. She is the youngest team member, taking HCC courses while at high school. Also already accepted to the undergraduate program in three universities. Welcome Sara!
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Matthew Froid joins our team for 10 weeks long rotations. He is a PhD Candidate in the Cancer Biology Program at Moffitt in Dr. David Basanta team at IMO. Welcome Matthew!
Fall 2022:
Nam Nguyen proposed a project and led the team on the The eXplainable Quantum-Classical AI-based (XQC-AI) tool for clinical decision support during the Bio-Data Club’s 4th Annual Hackathon at Moffitt. His work was recognized and received the third place! :)
Congratulations Nam, well done!
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Our ML Department together with Dr. David Basanta and the IMO Department at Moffitt hosted Dr. Russ Rockne. Russ is the Associate Professor in the Department of Computational and Quantitative Medicine and Director of the Division of Mathematical Oncology at City of Hope Cancer Center in Duarte, CA. See Twitter for the snapshots of his talk and visit.
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We were busy presenting Nam's work at the conferences. See Twitter posts for pictures and details.
Talk & Poster:
N.Nguyen, J.Fleming, P.McDonald, KC.Chen, A.Karolak Intelligent Personalized Risk Prediction for Intraductal Papillary Mucinous Neoplasms of Pancreas
- The Gillies Machine Learning in Image Analytics Workshop, Clearwater, FL (11/2022)
- International Society for Computational Biology RSGDREAM Meeting, Las Vegas, NV (11/2022)
- American Pancreas Association Annual Meeting, Orlando, FL (11/2022)
- Oktoberfest Scientific Celebration, Moffitt Cancer Center (10/2022)
Poster:
N.Nguyen, A.Karolak, KC.Chen Advancing Modeling and Biomedicine using Quantum Machine Intelligence
- International Society for Computational Biology RSGDREAM Meeting, Las Vegas, NV (11/2022)
- Oktoberfest Scientific Celebration, Moffitt Cancer Center (10/2022)
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Bi Zhao, Applied Research Scientist in our lab, moved to the independent position at USF Health. We wish you many successes and good work environment!
Summer 2022:
Anne Greene, a former volunteer in our group and a recent USF graduate with Master of Science in Bioinformatics and Computational Biology is now a Data Analyst in the GIO department at Moffitt in the lab of Dr. Jenny Permuth.
Congrats Anna!
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Katherine Rodriguez, our former group member and a recent graduate of the University of South Florida (Bachelor's of Science in Biomedical Sciences and a minor in Aging Sciences), is now a research technician in the Bhat Laboratory for the Morsani College of Medicine, USF.
Congrats Katherine on your new adventure!
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Aleks presented 'A Framework for Mutational Signature Analysis Based on DNA Shape Parameters' at the 2022 Computational Chemistry Gordon Research Conference on Multiscale Modeling of Complex Systems including AI and ML applications for Drug Design in Castelldefels, Barcelona, Spain.
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We welcome two new members: Dr. Bi Zhao and PhD Candidate Nam Nguyen!
Bi earned her PhD in Cell and Molecular Biology from USF and her postdoctoral training took place at the Virginia Commonwealth. Her experience is in data science, machine learning, and protein structural and functional research.
Nam is a PhD Candidate in the Department of Electrical Engineering at USF graduating in 2023. He has experience in algorithmic designs for classical and quantum AI applied to cancer research.
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Aleks presented at the ODSi-Moffitt seminars and GI Pancreas Working Group at Moffitt on the ‘Machine learning and computational modeling for cancer research’.
Spring 2022:
With Anna and Katherine graduating this month, we are looking forward to having Dr. Bi Zhao joining us in June and Nam Nguyen in July.
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Happy to announce we have received the Quantitative Science Team Award on RNA splicing in collaboration with dr. Timothy Shaw and dr. Paul Stewart at Moffitt. Reach out if you you are interested in working on Data Integration and Biomarker Discovery.
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Anna Greene pursuing MSc in Bioinformatics and Computational Biology at USF joined our team as a student volunteer. Happy to have you Anna!
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Katherine Rodriguez pursuing BS in Biomedical Sciences joined our team. Welcome Katherine!