James Fraser

PREreviews

1. James Fraser and 1 other author reviewed On-target mutations confer resistance to WRN helicase inhibitors in Microsatellite Unstable Cancer Cells

   • Oncology
   • Pathology and Forensic Medicine
   • Molecular Biology

   Review published

   June 2, 2026

   Preprint server

   bioRxiv

2. James Fraser and Sofia Bali reviewed Anticipating on-target resistance to WRN inhibitors in microsatellite unstable cancers

   Review published

   June 2, 2026

   Preprint server

   bioRxiv

3. James Fraser, Karson Chrispens, and 1 other author reviewed Density-guided AlphaFold3 uncovers unmodelled conformations in β ₂ -microglobulin

   • Materials Chemistry
   • Molecular Biology
   • Genetics

   Review published

   May 31, 2026

   Preprint server

   bioRxiv

4. Andres Olavarrieta Colasurdo, James Fraser, Brian Cheung, and Varvara Shvareva reviewed De novo design of protein nanoparticles with integrated functional motifs

   • Molecular Biology
   • Ecology
   • Structural Biology

   Review published

   May 30, 2026

   Preprint server

   bioRxiv

5. Andoni I Asencor, Jonah Frazier, James Fraser, and Brian Cheung reviewed Towards pharmacokinetic profile predictions for monoclonal antibodies using sequence based machine learning derived parameters and compartmental modeling

   • Radiology, Nuclear Medicine and Imaging
   • Molecular Biology

   Review published

   May 23, 2026

   Preprint server

   bioRxiv

6. Barbara S. Perez, James Fraser, Parmis Abdoli, and 1 other author reviewed Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery

   • Microbiology
   • Pharmacology
   • Molecular Biology

   Review published

   May 22, 2026

   Preprint server

   bioRxiv

7. Bivas Nag, James Fraser, Jane E. Oberhauser, and Brian Cheung reviewed TissueFormer: Extending single-cell foundation models to predict population-level phenotypes

   • Molecular Biology
   • Biophysics

   Review published

   May 22, 2026

   Preprint server

   bioRxiv

8. Beau Lonnquist, Adam Fillion, James Fraser, and Brian Cheung reviewed Zero-shot design of a de novo metalloenzyme

   • Renewable Energy, Sustainability and the Environment
   • Organic Chemistry
   • Molecular Biology

   Review published

   May 21, 2026

   Preprint server

   bioRxiv

9. James Fraser and ziyue zou reviewed DeepDOX1: A Dual-Drive Framework Integrating Deep Learning and First-Principles Physics for Drug-Protein Affinity Prediction

   • Computational Theory and Mathematics
   • Molecular Biology

   Review published

   March 11, 2026

   Preprint server

   bioRxiv

10. Sofia Bali, Alexander, Alex Tong, and James Fraser reviewed PathDiffusion: modeling protein folding pathway using evolution-guided diffusion

    • Molecular Biology
    • Atomic and Molecular Physics, and Optics
    • Computational Mathematics

    Review published

    February 24, 2026

    Preprint server

    bioRxiv

11. James Fraser and 1 other author reviewed X-ray Crystallography-Guided Design and Synthesis of Cyclopentyl Heteroaryl Carboxylic Acid based Inhibitors of the SARS-CoV-2 Nsp3 Macrodomain (Mac1)

    • Molecular Biology
    • Organic Chemistry

    Review published

    February 20, 2026

    Preprint server

    ChemRxiv

12. James Fraser and Joseph Bondy-Denomy reviewed Generative design of novel bacteriophages with genome language models

    • Ecology
    • Molecular Biology

    Review published

    September 22, 2025

    Preprint server

    bioRxiv

13. James Fraser, Stephanie A. Wankowicz, and Karson Chrispens reviewed AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network

    • Molecular Biology
    • Materials Chemistry
    • Atomic and Molecular Physics, and Optics

    Review published

    July 16, 2025

    Preprint server

    bioRxiv

14. Gyuna, James Fraser, JINGYOU RAO, and 1 other author reviewed Distinct energetic blueprints diversify function of conserved protein folds

    • Molecular Biology
    • Genetics

    Review published

    July 3, 2025

    Preprint server

    bioRxiv

15. CJ San Felipe, James Fraser, and 1 other author reviewed The temperature dependence of binding entropy is a selective pressure in protein evolution

    • Molecular Biology
    • Physical and Theoretical Chemistry

    Review published

    June 26, 2025

    Preprint server

    bioRxiv

16. Karson Chrispens, Isaiah Hazelwood, and James Fraser reviewed Have protein-ligand cofolding methods moved beyond memorisation?

    • Computational Theory and Mathematics
    • Materials Chemistry
    • Molecular Biology

    Review published

    June 20, 2025

    Preprint server

    bioRxiv

17. Karson Chrispens, Stephanie A. Wankowicz, and James Fraser reviewed Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

    Review published

    June 20, 2025

    Preprint server

    bioRxiv

18. Nikhil Gupta, James Fraser, and 2 other authors reviewed Oligomerization enables the selective targeting of intrinsically disordered regions by small molecules

    • Molecular Biology

    Review published

    June 16, 2025

    Preprint server

    bioRxiv

19. Isaiah Hazelwood, James Fraser, Willow Coyote-Maestas, and 1 other author reviewed Energetic and structural control of polyspecificity in a multidrug transporter

    • Physical and Theoretical Chemistry
    • Molecular Biology

    Review published

    May 15, 2025

    Preprint server

    bioRxiv

20. Karson Chrispens and James Fraser reviewed InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

    • Artificial Intelligence
    • Molecular Biology

    Review published

    January 24, 2025

    Preprint server

    bioRxiv

21. James Fraser, Rishav Mitra, and Priyanka Bajaj reviewed Computational enzyme design by catalytic motif scaffolding

    • Molecular Biology

    Review published

    December 14, 2024

    Preprint server

    bioRxiv

22. CJ San Felipe, James Fraser, and Jessica Flowers reviewed Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation

    • Sensory Systems
    • Mechanical Engineering
    • Physical and Theoretical Chemistry

    Review published

    December 3, 2024

    Preprint server

    bioRxiv

23. James Fraser, Jessica Flowers, and 1 other author reviewed Seeing Double: Molecular dynamics simulations reveal the stability of certain alternate protein conformations in crystal structures

    • Materials Chemistry
    • Molecular Biology

    Review published

    December 1, 2024

    Preprint server

    bioRxiv

24. James Fraser and ziyue zou reviewed Effects of residue substitutions on the cellular abundance of proteins

    • Molecular Biology
    • Materials Chemistry

    Review published

    October 29, 2024

    Preprint server

    bioRxiv

25. James Fraser reviewed Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography

    • Materials Chemistry
    • Molecular Biology

    Review published

    September 23, 2024

    Preprint server

    bioRxiv

26. James Fraser reviewed Bioorthogonal labeling of chitin in pathogenic Candida species reveals biochemical mechanisms of hyphal growth and homeostasis

    • Infectious Diseases
    • Organic Chemistry
    • Food Science

    Review published

    September 22, 2024

    Preprint server

    bioRxiv

27. James Fraser and Avi J. Samelson reviewed Massively parallel genetic perturbation reveals the energetic architecture of an amyloid beta nucleation reaction

    • Physiology
    • Molecular Biology

    Review published

    September 22, 2024

    Preprint server

    bioRxiv

28. James Fraser, Jessica Flowers, and 1 other author reviewed Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex

    • Molecular Biology
    • Cell Biology

    Review published

    September 1, 2024

    Preprint server

    bioRxiv

29. James Fraser, Luisa Vasconcelos, Liyi Cheng, Samantha Lish, S. Chan Baek, Lang Ding, Alexandra Probst, Naiya Phillips, William Grubbe, Youchen Guan, and 2 other authors of HHMI Transparent and Accountable Peer Review Training Program reviewed Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants

    • Infectious Diseases
    • Ecology

    Review published

    March 4, 2024

    Preprint server

    bioRxiv

30. Christian Macdonald, James Fraser, David Byun, and Jeffrey Zheng reviewed The herbicide acetochlor causes lipid peroxidation by inhibition of glutathione peroxidase 4

    • Molecular Biology
    • Plant Science

    Review published

    August 11, 2023

    Preprint server

    bioRxiv

31. Christian Macdonald, James Fraser, Ivan Chavez, Dani Rodea, and Ashraya Ravikumar reviewed Decoding the Cure-all Effects of Ginseng

    • Molecular Biology
    • Pharmacology
    • Geriatrics and Gerontology

    Review published

    June 30, 2023

    Preprint server

    bioRxiv

32. Christian Macdonald, James Fraser, Ilayda Alkislar, and Nicholas Freitas reviewed Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network

    • Molecular Biology
    • Physical and Theoretical Chemistry

    Review published

    June 30, 2023

    Preprint server

    bioRxiv

33. Stephanie Wankowicz, Lena Bergmann, and James Fraser reviewed The mineralocorticoid receptor forms higher order oligomers upon DNA binding

    • Endocrinology, Diabetes and Metabolism
    • Genetics
    • Molecular Biology

    Review published

    June 23, 2023

    Preprint server

    bioRxiv

34. Christian Macdonald and James Fraser reviewed The conserved protein CBA1 is required for vitamin B ₁₂ uptake in different algal lineages

    • Molecular Biology
    • Rheumatology
    • Plant Science

    Review published

    June 1, 2023

    Preprint server

    bioRxiv

35. Christian Macdonald, James Fraser, Zhengya Liu, and Catherine Shin reviewed Phosphorylation of pyruvate dehydrogenase marks the inhibition of in vivo neuronal activity

    • Cellular and Molecular Neuroscience
    • Social Psychology
    • Cognitive Neuroscience

    Review published

    May 26, 2023

    Preprint server

    bioRxiv

36. Christian Macdonald, James Fraser, and Sonya Lee reviewed Higher-order epistasis creates idiosyncrasy, confounding predictions in protein evolution

    • Genetics
    • Molecular Biology

    Review published

    October 14, 2022

    Preprint server

    bioRxiv