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Jeffrey A. Ruffolo
Researcher, Profluent Bio
Joined
September 2022
Names
Jeffrey A. Ruffolo
(Preferred)
,
Jeffrey Ruffolo
Emails
****@jhu.edu
(Confirmed)
,
****@profluent.bio
(Confirmed)
Personal Links
Homepage
Google Scholar
ORCID
Career & Education History
Researcher
Profluent Bio
(profluent.bio)
2023
–
Present
PhD student
Whiting School of Engineering
(engineering.jhu.edu)
2019
–
2023
Undergrad student
University of Missouri
(missouri.edu)
2014
–
2019
Advisors, Relations & Conflicts
No relations added
Expertise
protein design
2019
–
Present
protein structure prediction
2019
–
Present
antibodies
2019
–
Present
Publications
E1: Retrieval-Augmented Protein Encoder Models
Sarthak Jain
,
Joel Beazer
,
Jeffrey A. Ruffolo
,
Aadyot Bhatnagar
,
Ali Madani
ICML 2026 FM4LS Workshop Poster
Readers:
Everyone
Scaling Unlocks Broader Generation and Deeper Functional Understanding of Proteins
Aadyot Bhatnagar
,
Sarthak Jain
,
Joel Beazer
,
Samuel C. Curran
,
Alexander M. Hoffnagle
,
Kyle Shan Ching
,
Michael Martyn
,
Stephen Nayfach
,
Jeffrey A. Ruffolo
,
Ali Madani
NeurIPS 2025 spotlight
Readers:
Everyone
Conditional Enzyme Generation Using Protein Language Models with Adapters
Jason Yang
,
Aadyot Bhatnagar
,
Jeffrey A. Ruffolo
,
Ali Madani
Submitted to ICLR 2025
Readers:
Everyone
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion
Alex Morehead
,
Jeffrey Ruffolo
,
Aadyot Bhatnagar
,
Ali Madani
NeurIPS 2023 Workshop on Machine Learning in Structural Biology
Readers:
Everyone
ProGen2: Exploring the Boundaries of Protein Language Models
Erik Nijkamp
,
Jeffrey Ruffolo
,
Eli N Weinstein
,
Nikhil Naik
,
Ali Madani
22 Sept 2022 (modified: 15 Jan 2026)
ICLR 2023 Conference Withdrawn Submission
Readers:
Everyone
Co-Authors
Aadyot Bhatnagar
Alex Morehead
Alexander M. Hoffnagle
Ali Madani
Eli N Weinstein
Erik Nijkamp
Jason Yang
Joel Beazer
Kyle Shan Ching
Michael Martyn
Nikhil Naik
Samuel C. Curran
Sarthak Jain
Stephen Nayfach