CV
Claire Darnell McWhite
cmcwhite@princeton.edu | clairemcwhite.github.io | @clairemcwhite | Scholar page
Lewis-Sigler Scholar, Princeton University
Protein-centric comparative biology, natural language models of protein structure and function
Ph.D. Cell and Molecular Biology
Education
- University of Texas at Austin, Cell and Molecular Biology Ph.D. program, Computational Biology (2014-2020)
- Rice University, Class of 2014, B.S. Biochemistry and Cell Biology
Research Experience
Princeton University
Advisors: Mona Singh, Martin Jonikas, Joshua Akey
The University of Texas at Austin Department of Molecular Biosciences
- Dr. Edward Marcotte Research Group (2014-) Projects relating to computational prediction of protein complexes, including 1) conserved complexes of plants and 2) comparative evolution of protein organization across eukaryotes.
- Dr. Claus Wilke Research Group (2/2015-8/2015) Projects relating to uncovering sources of artifacts in computational evolutionary rate measurement of influenza evolution.
- Dr. John Wallingford Research Group (11/2014-2/2015) Projects relating to functionally replacing genes in multicellular organisms with genes from single celled organisms.
Rice University Department of Chemical and Biomolecular Engineering
- (2010-2014) Dr. Laura Segatori Research Group, Cell and Protein Engineering Laboratory. Projects relating to the discovery of novel proteasome activating compounds and genes in mammalian and yeast models.
National Cancer Institute, National Institutes of Health, Bethesda, MD
- (2008-2012) Dr. Ilona Linnoila Research Group, Experimental Pathology Section, Projects related to lung epithelial cells in abnormal lesions and chemical injury.
Publications
- CD McWhite, M Singh, “Vector-clustering Multiple Sequence Alignment: Aligning into the twilight zone of protein sequence similarity with protein language models”, BioRXiv 2022.10.21.513099, 2022
- 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”, BioRXiv 2022.09.21.508930, 2022
- L Wang, W Patena, KA Van Baalen, Y Xie, ER Singer, S Gavrilenko, M WarrenWilliams, L Han, HR Harrigan, V Chen, VTNP Ton, S Kyin, HH Shwe, MH Cahn, AT Wilson, J Hu, DJ Schnell, CD McWhite, M Jonikas, “A Chloroplast Protein Atlas Reveals Novel Structures and Spatial Organization of Biosynthetic Pathways”, BioRXiv 2022.05.31.493820v1, 2022
- V de Crécy-Lagard, …, CD McWhite, …, “A roadmap for the functional annotation of protein families: a community perspective”, Database baac062, 2022
- W Sae-Lee W, 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
- 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
- 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
- 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 RNAassociated proteins in vivo provides insights into vertebrate ciliary beating machinery”, Developmental Biology 467:1-2, 2020
- 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
- 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
- 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
- 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
- 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
- BJ Liebeskind, CD McWhite, EM Marcotte, “Towards Consensus Gene Ages”, Genome Biology and Evolution 8 (6): 1812-1823, 2016
- 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
- CD McWhite, BJ Liebeskind, EM Marcotte, “Applications of comparative evolution to human disease genetics”, Current Opinion in Genetics & Development 35, 16-24, 2015
- 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
- A Demelash, P Rudrabhatla, HC Pant, X Wang, ND Amin, CD McWhite, X Naizhen, RI Linnoila, “Achaete-scute homologue-1 (ASH1) stimulates migration of lung cancer cells through the Cdk5/p35 pathway”, Molecular Biology of the Cell 23 (15), 2856-2866, 2012
Talks
- Mendel Early Career Symposium, Invited talk, Vienna BioCenter, 2022
- Systems, Synthetic, and Physical Biology Seminar, Rice University, 2022
- International Society for Computational Biology Webinar seminar, Virtual, 2022
- Western Photosynthesis Conference, Invited talk, remote, 2022
- Plant Cell Atlas, Invited talk, remote, 2021
- Polyploidy Webinar, remote, 2020
- Computing on Phenotypes, Invited talk, Iowa State University, Ames, IA, 4/2019
- First International Plant Systems Biology Conference, Roscoff, France, 9/2018
Teaching
- Instructor - QCB455/MOL455/COS455 Introduction to Genomics and Computational Molecular Biology, Princeton, Fall 2020, 2021, 2022
- Teacher’s Assistant - Advanced Bash Scripting Short Course, UT Austin, Spring 2019
- Teacher’s Assistant - Intro to Next-Generation Sequencing Short Course, UT Austin, Spring 2018
- Co-instructor - Peer-led Biocomputing Working Group: Python/Bash, UT Austin, Spring 2017
- Lecturer (data visualization in R) - Peer-led Biostatistics Seminar, UT Austin, Fall, 2016
- Open Coding Hour - Assist graduate students with programming issues, UT Austin. Fall 2016 - Spring 2019
- Teacher’s Assistant - BCH339N Systems Biology & Bioinformatics, Spring, UT Austin, 2016
Fellowhips and scholarships
- Lewis-Sigler Scholar, Princeton University, 2020-
- NIH F31 Graduate Fellowship, “Proteomics of ciliopathy protein complexes” Impact score: 10, Percentile: 1% , 2018-2020
- Graduate School Summer Fellowship, Summer, 2017
- Honorable Mention, NSF Graduate Research Fellowship Program (2016)
- Spring/Fall Graduate Fellowship, UT Austin (8/2014-5/2015)
- National Merit Scholarship (8/2010-5/2014)
- Trustee’s Distinguished Scholarship, Rice University (8/2010-5/2014)
- Century Scholarship for Research, Rice University (8/2010-5/2012)
Honors
- Princeton Engineering Commendation for Outstanding Teaching, 2021
- Best Talk, First International Plant Systems Biology Conference, Fall, 2018
- Student Choice Award, UT Austin Natural Sciences Council’s Art in Science Display, 3/2017
- Visualizing Science Competition, 2nd Place, UT Austin College of Natural Sciences, 11/2016
- Graduate Student Research Award, Society of Systemic Biologists, 7/2016
- Selected Artist, Evolution Art Exhibition, Art.Science.Gallery, 6/2016
- Best Poster, UT Austin Institute for Cellular and Molecular Biology Retreat, 9/2015
- Best Poster, Big Data in Biology Symposium, Center for Computational Biology and Bioinformatics, Austin, Texas, 5/2015
Software
- colorblindr: An R package to aid design of colorblind-interpretable figures
- colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes
Outreach
- Introduction to Alphafold2, Fall 2022
- Introduction to Data Visualization in R, Fall 2019
- Introduction to Network Visualization, Austin R Users Group, Spring, 2018
- Speaker at BAHFest Texas, A festival of bad ad-hoc hypotheses, Spring, 2018
Posters
- US HUPO, Charleston, SC, 3/2022
- US HUPO, remote, 2021
- The Society for Molecular Biology and Evolution, Austin, TX, 7/2017
- Quest for Orthologs Meeting, Los Angeles, CA, 5/2017
- Omics Approaches to Study the Proteome Keystone Conference, Breckenridge, CO, 1/2017
- Plant Biology, Austin, TX, 7/2016
- Evolution, Austin, TX, 6/2016
- Quest for Orthologs Meeting, Barcelona, Spain, 5/2015
- Big Data in Biology Symposium, Austin, TX, 5/2015
- Rice Undergraduate Research Symposium, 4/2011, 4/2012, 4/2013
- NIH Summer Research Symposium, 8/2011
Groups
- Quest for Orthologs Consortium
- Plant Cell Atlas