Claire McWhite

Claire McWhite

Assistant Professor, Department of Molecular and Cellular Biology. Protein language models and bioinformatics.

CV

Claire Darnell McWhite, Ph.D.

clairemcwhite@arizona.edu | clairemcwhite.github.io | @clairemcwhite | +1 240-418-2083

Research interests

Interpretability of Large Language Models of biomolecules and gene expression, Agentic programming, Algorithms for bioinformatics, Big Data

Positions

(2024-current) Assistant Professor (Tenure-track) Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA

(2025) Expert Consultant for LincSwitch Therapeutics, LLC

(2020-2024) Lewis-Sigler Scholar Princeton University, Princeton, NJ, USA

Editorial Responsibilities

Professional Affiliations

Degrees

Other Research Experiences

(2014-2020) The University of Texas at Austin Department of Molecular Biosciences

(2010-2014) Rice University Department of Chemical and Biomolecular Engineering

(2008-2012) National Cancer Institute, National Institutes of Health, Bethesda, MD

Publications

  1. A Shamail and CD McWhite, “Representing biological concepts as directions in foundation model embeddings”, bioRxiv, 10.64898/2026.10.10.758204, 2026
  2. M Catalano, G Pepe, G Ausiello, C McWhite, G Gambosi, M Helmer-Citterich, PF Gherardini, “Cross-Attention Over RNA And Protein Sequences Enables Generalizable Interaction Prediction”, bioRxiv, 2026.04.22.720174, 2026
  3. V Dang, B Voigt, D Yang, G Hoogerbrugge, M Lee, RM Cox, O Papoulas, CD McWhite, R Pradeep, JC Leggere, BA Neely, RS Gray, EM Marcotte, “A cross-vertebrate brain protein interaction map identifies conserved neural and non-neural complexes”, Cell Reports 45 (6), 117422, 2026
  4. RM Cox, O Papoulas, S Shril, C Lee, TP Gardner, ZT Ansari, AM Battenhouse, M Lee, K Drew, CD McWhite, D Yang, JC Leggere, D Durand, F Hildebrandt, JB Wallingford, EM Marcotte, “A protein interactome for the last eukaryotic common ancestor illuminates the biochemical basis of modern genetic diseases”, Cell Genomics 6 (6), 101254, 2026
  5. A Shamail and CD McWhite, “A General Algorithm for Detecting Higher-Order Interactions via Random Sequential Additions”, arXiv:2511.21614, 2025
  6. A Shamail and CD McWhite, “Automated Protein Motif Localization using Concept Activation Vectors in Protein Language Model Embedding Space”, arXiv:2511.21614, 2025
  7. R Shaw, SD Love, CD McWhite, “Evaluating pretrained protein language model embeddings as proxies for functional similarity”, Journal of Molecular Evolution, 1–12, 2025
  8. S Majidian, A Hadziahmetovic, F Langschied, S Pascarelli, … CD McWhite, … et al., “Quest for orthologs in the era of data deluge and AI: challenges and innovations in orthology prediction and data integration”, Journal of Molecular Evolution, 1–18, 2025
  9. H Xu, R Bierman, D Akey, C Koers, T Comi, CD McWhite, JM Akey, “Landscape of human protein-coding somatic mutations across tissues and individuals”, bioRxiv, 2025.01.07.631808, 2025. In Review at Science
  10. CD McWhite, W Sae-Lee, Y Yuan, AL Mallam, NA Gort-Freitas, S Ramundo, M Onishi, EM Marcotte, “Alternative proteoforms and proteoform-dependent assemblies in humans and plants”, Molecular Systems Biology, 1–19, 2024
  11. ES Wallner, A Mair, D Handler, CD McWhite, SL Xu, L Dolan, DC Bergmann, “Spatially resolved proteomics of the Arabidopsis stomatal lineage identifies polarity complexes for cell divisions and stomatal pores”, Developmental Cell, 10.1016/j.devcel.2024.03.001, 2024
  12. CD McWhite, I Armour-Garb, M Singh, “Leveraging protein language models for accurate multiple sequence alignment”, Genome Research, 33(7):1145-1153, 2023
  13. M Kafri, W Patena, L Martin, L Wang, G Gomer, AK Sirkejyan, A Goh, AT Wilson, SE Gavrilenko, M Breker, A Roichman, CD McWhite, JD Rabinowitz, FR Cross, M Wuhr, MC Jonikas, “Systematic identification and characterization of novel genes in the regulation and biogenesis of photosynthetic machinery”, Cell 186 (25), 5638–5655.e25, 2023
  14. L Wang, W Patena, KA Van Baalen, Y Xie, ER Singer, S Gavrilenko, M Warren-Williams, L Han, HR Harrigan, LD Hartz, V Chen, VTNP Ton, S Kyin, HH Shwe, MH Cahn, AT Wilson, M Onishi, J Hu, DJ Schnell, CD McWhite, MC Jonikas, “A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways”, Cell, S0092-8674(23)00676-1, 2023
  15. V de Crecy-Lagard, …, CD McWhite, …, “A roadmap for the functional annotation of protein families: a community perspective”, Database, baac062, 2022
  16. W Sae-Lee, CL McCafferty, EJ Verbeke, PC Havugimana, O Papoulas, CD McWhite, JR Houser, K Vanuytsel, G Murphy, K Drew, A Emili, DW Taylor, EM Marcotte, “The protein organization of a red blood cell”, Cell Reports 40(3):111103, 2022
  17. CD McWhite, O Papoulas, K Drew, V Dang, JC Leggere, W Sae-Lee, EM Marcotte, “Co-Fractionation Mass Spectrometry to Identify Protein Complexes”, STAR Protocols 2:1, 2021
  18. A Zeileis, JC Fisher, K Hornik, R Ihaka, CD McWhite, P Murrell, R Stauffer, CO Wilke, “colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes”, Journal of Statistical Software, 96:1, 2020
  19. K Drew, C Lee, RM Cox, V Dang, CC Devitt, CD McWhite, O Papoulas, RL Huizar, EM Marcotte, JB Wallingford, “A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery”, Developmental Biology 467:1-2, 2020
  20. CD McWhite, O Papoulas, K Drew, RM Cox, V June, OX Dong, T Kwon, C Wan, ML Salmi, SJ Roux, KS Browning, ZJ Chen, PC Ronald, EM Marcotte, “A pan-plant protein complex map reveals deep conservation and novel assemblies”, Cell 181:2, 2020
  21. CD DuPai, CD McWhite, CB Smith, R Garten, S Maurer-Stroh, CO Wilke, “Influenza passaging annotations: what they tell us and why we should listen”, Virus Evolution 5 (1), vez016, 2019
  22. W Zhao, B Bachhav, CD McWhite, L Segatori, “A yeast selection system for the detection of proteasomal activation”, Protein Engineering, Design and Selection 31 (11), 437–445, 2018
  23. AH Kachroo, JM Laurent, A Akhmetov, M Szilagyi-Jones, CD McWhite, A Zhao, EM Marcotte, “Systematic bacterialization of yeast genes identifies a near-universally swappable pathway”, eLife 6:e25093, 2017
  24. KS Drew, C Lee, RL Huizar, F Tu, B Borgeson, CD McWhite, Y Ma, JB Wallingford, EM Marcotte, “Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes”, Molecular Systems Biology 13:932, 2017
  25. BJ Liebeskind, CD McWhite, EM Marcotte, “Towards Consensus Gene Ages”, Genome Biology and Evolution 8 (6): 1812–1823, 2016
  26. CD McWhite, AG Meyer, CO Wilke, “Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin”, Virus Evolution 2 (2):vew026, 2016
  27. BJ Liebeskind, CD McWhite, EM Marcotte, “Applications of comparative evolution to human disease genetics”, Current Opinion in Genetics & Development 35, 16–24, 2015
  28. W Zhao, M Bonem, CD McWhite, JJ Silberg, L Segatori, “Sensitive detection of proteasomal activation using the Deg-On mammalian synthetic gene circuit”, Nature Communications 5, 2014
  29. A Demelash, P Rudrabhatla, HC Pant, X Wang, ND Amin, CD McWhite, X Naizhen, RI Linnoila, “Achaete-scute homologue-I (ASH1) stimulates migration of lung cancer cells through Cdk5/p35 pathway”, Molecular Biology of the Cell 23 (15), 2856–2866, 2012

Grants and Scholarships

Academic Service

Student supervision

Student Committees

Refereeing

Grant Panels

Awards

Published Scientific Software

Conferences and Seminars

Posters

Teaching Experience

Outreach

Language

English, Italian (fluent)