Theobald lab publications at PubMed


Heather M. Frank, Sanket Walujkar, Richard M. Walsh, Jr., Willem J. Laursen, Douglas L. Theobald, Paul A. Garrity, and Rachelle Gaudet (2024)
"Structural basis of ligand specificity and channel activation in an insect gustatory receptor."
Cell Reports 43(4):114035.
bioRχiv doi:10.1101/2023.12.19.572336

Michael A. Sennett and Douglas L. Theobald (2024)
"Extant Sequence Reconstruction: The accuracy of ancestral sequence reconstructions evaluated by extant sequence cross-validation."
Journal of Molecular Evolution 92:181-206.


Yerdos A. Ordabayev, Larry J. Friedman, Jeff Gelles, and Douglas L. Theobald (2022)
"Bayesian machine learning analysis of single molecule fluorescence colocalization image data."
eLife 2022;11:e73860.
bioRχiv doi:10.1101/2021.09.30.462536

John B. Stiller, Renee Otten, Daniel Häussinger, Pascal S. Rieder, Douglas L. Theobald, and Dorothee Kern (2022)
"Structure determination of high-energy states in a dynamic protein ensemble."
Nature 603 (7901): 528-535.

Lys Sanz Moreta, Ola Rønning, Ahmad Salim Al-Sibahi, Jotun Hein, Douglas L. Theobald, and Thomas Hamelryck (2022)
"Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder."
ICLR 2022 (Tenth International Conference on Learning Representations)
[ICLR 2022 pdf]


Christoffer H. Norn, Ingemar André, and Douglas L. Theobald (2021)
"A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices."
Protein Science 30(10):2057-2068. [pdf]


Lys Sanz Moreta, Ahmad Salim Al-Sibahi, Douglas L. Theobald, William Bullock, Basile Nicolas Rommes, Andreas Manoukian, and Thomas Hamelryck (2019)
"A probabilistic programming approach to protein structure superposition."
2019 IEEE Conference On Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) [pdf]


Jacob D. Wirth, Jeffrey I. Boucher, Joseph R. Jacobowitz, Scott Classen, and Douglas L. Theobald (2018)
"Functional and structural resilience of the substrate loop in the evolution of Plasmodium lactate dehydrogenase."
Biochemistry 57(45):6434-6442. [pdf]


Lindsey B. Lamarche, Ramasamy P. Kumar, Melissa M. Trieu, Erin L. Devine, Douglas L. Theobald, and Daniel D. Oprian (2017)
"Purification and characterization of RhoPDE, a retinylidene/phosphodiesterase fusion protein and potential optogenetics tool from the choanoflagellate Salpingoeca rosetta."
Biochemistry 56(43):5812-5822.

Melissa M. Trieu, Erin L. Devine, Lindsey B. Lamarche, Aaron E. Ammerman, Jordan A. Greco, Robert R. Birge, Douglas L. Theobald, and Daniel D. Oprian (2017)
"Expression, purification, and spectral tuning of RhoGC, a retinylidene/guanylyl cyclase fusion protein and optogenetics tool from the aquatic fungus Blastocladiela emersonii."
Journal of Biological Chemistry 292:10379-10389.

Vy Nguyen, Christopher Wilson, Marc Hömberger, John Stiller, Roman Agafonov, Steffen Kutter, Justin English, Douglas L. Theobald, and Dorothee Kern (2017)
"Evolutionary drivers of thermoadaptation in enzyme catalysis."
Science 355(6322):289-294.


Erin L. Devine, Douglas L. Theobald, and Daniel D. Oprian (2016)
"Relocating the active-site lysine in rhodopsin: 2. Evolutionary intermediates."
Biochemistry 55(34):4864-4870. [pdf, pdf]

Phillip A. Steindel, Emily H. Chen, Jacob D. Wirth, and Douglas L. Theobald (2016)
"Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases."
Protein Science 25(7):1319-1331. [Open Access, pdf]

Douglas L. Theobald (2016)
"Presenilin adopts the ClC channel fold."
Protein Science 25(7):1363-1365. [Open Access, pdf]


Chris Wilson, Roman Agafonov, Marc Hömberger, Steffen Kutter, Adelajda Zorba, Jackson Halpin, Vanessa Buosi, Renee Otten , David Waterman, Douglas L. Theobald, and Dorothee Kern (2015)
"Using ancient protein kinases to unravel a modern cancer drug's mechanism."
Science 347(6224):882-886. [pdf]

Thomas Hamelryck, Wouter Boomsma, Jesper Ferkinghoff-Borg, Jes Frellsen, John Haslett, John T. Kent, Kanti V. Mardia, and Douglas L. Theobald (2015)
"Proteins, physics, and probabilities: An outline of a Bayesian formulation of the protein folding problem."
Geometry Driven Statistics,
Ian L. Dryden and John T. Kent, Editors,
Wiley Series in Probability and Statistics,
John Wiley and Sons, Chichester.
ISBN 978-3-642-27224-0


Jeffrey I. Boucher, Joseph R. Jacobowitz, Brian C. Beckett, Scott Classen, and Douglas L. Theobald (2014)
"An atomic resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases."
eLife 2014;10.7554/eLife.02304 [Open Access]

Kristine A. Mackin, Richard A. Roy, and Douglas L. Theobald (2014)
"An empirical test of convergent evolution in rhodopsins."
Molecular Biology and Evolution, 31(1):85-95. [Open Access, pdf]


Lina Ni, Peter Bronk, Elaine C. Chang, April M. Lowell, Juliette O. Flam, Vincent C. Panzano, Douglas L. Theobald, Leslie C. Griffith, and Paul A. Garrity (2013)
"A gustatory receptor paralog controls rapid warmth avoidance in Drosophila."
Nature, 500(7464):580-584. [pdf]

Erin L. Devine, Daniel D. Oprian, and Douglas L. Theobald (2013)
"Relocating the active-site lysine in rhodopsin and implications for evolution of the retinylidene proteins."
Proceedings of the National Academy of Sciences USA, 110(33):13351-13355. [pdf]

Dmitry Lyumkis, Axel Brilot, Douglas L. Theobald, and Nikolaus Grigorieff (2013)
"Likelihood-based classification of cryo-EM images using FREALIGN."
Journal of Structural Biology, 183(3):377-388. [pdf]

Kanti V. Mardia, Christopher J. Fallaize, Stuart Barber, Richard M. Jackson, and Douglas L. Theobald (2013)
"Bayesian alignment of similarity shapes."
The Annals of Applied Statistics, 7(2):989-1009. [pdf]


Douglas L. Theobald and Phillip A. Steindel (2012)
"Optimal simultaneous superpositioning of multiple structures with missing data."
Bioinformatics 28(15):1972-1979. [pdf]

Douglas L. Theobald (2012)
"Likelihood and empirical Bayes superpositions of multiple macromolecular structures."
Bayesian Methods in Structural Bioinformatics,
Thomas Hamelryck, Kanti V. Mardia, and Jesper Ferkinghoff-Borg, Editors,
Statistics for Biology and Health Series ,
Springer Verlag, New York.
March 31, 2012
ISBN 978-3-642-27224-0 [pdf]


Douglas L. Theobald (2011)
"On universal common ancestry, sequence similarity, and phylogenetic structure:
The sins of P-values and the virtues of Bayesian evidence."

Biology Direct 6:60 [Open Access, pdf, alt pdf]
Highly Accessed

Kene Piasta, Douglas L. Theobald, and Chris Miller (2011)
"Potassium-selective block of barium permeation through single KcsA channels."
Journal of General Physiology 138(4):421-436. [pdf]

Douglas L. Theobald and Kanti V. Mardia (2011)
"Full Bayesian analysis of the generalized non-isotropic Procrustes problem with scaling."
In Next Generation Statistics in Biosciences,
Arief Gusnanto, Kanti V. Mardia, and Christopher J. Fallaize, Editors, pp 41-44,
Proceedings of the 30th Leeds Annual Statistical Research (LASR) Workshop,
July 5-7, 2011
Department of Statistics, University of Leeds, UK.
ISBN: 978-0-85316-302-2

Pu Liu, Dimitris K. Agrafiotis, and Douglas L. Theobald (2011)
"Fast determination of the optimal rotation matrix for macromolecular superpositions. Reply."
Journal of Computational Chemistry 32(1):185-186. [Open Access, pdf]


Douglas L. Theobald (2010)
"Was the universal common ancestry proved? Reply"
Nature 468(7326):E10. [pdf]

Douglas L. Theobald (2010)
"A formal test of the theory of universal common ancestry."
Nature 465(7295):219-222. [pdf]

Mike Steel and David Penny (2010)
News and Views — "Origins of life: Common ancestry put to the test."
Nature 465(7295):168-169.

Kyeongjin Kang, Stefan R. Pulver, Vince C. Panzano, Elaine C. Chang, Leslie C. Griffith, Douglas L. Theobald, and Paul A. Garrity (2010)
"Analysis of Drosophila TRPA1 reveals an ancient origin for human chemical nociception."
Nature 464(7288):597-600. [pdf]

Douglas L. Theobald and Chris Miller (2010)
"Membrane transport proteins: Surprises in structural sameness."
Nature Structural and Molecular Biology 17(1):2-3. [pdf]

Douglas L. Theobald (2010)
"Dawkins' missing link."
Review of The Greatest Show on Earth,
by Richard Dawkins, (2009), Free Press, New York.
Reports of the National Center for Science Education 30(3):37-38.

Pu Liu, Dimitris K. Agrafiotis, and Douglas L. Theobald (2010)
"Fast determination of the optimal rotation matrix for macromolecular superpositions."
Journal of Computational Chemistry 31(7):1561-1563. [Open Access, pdf]
The QCProt C code for determining rapid least-squares rotations.


Douglas L. Theobald (2009)
"A nonisotropic Bayesian approach to superpositioning multiple macromolecules."
In Statistical Tools for Challenges in Bioinformatics,
Arief Gusnanto, Kanti V. Mardia, and Christopher J. Fallaize, Editors, pp 55-59,
Proceedings of the 28th Leeds Annual Statistical Research (LASR) Workshop,
July 7-9, 2009
Department of Statistics, University of Leeds, UK. [pdf, pdf, LASR 2009 full proceedings]
ISBN: 978-0-85316-280-3


Douglas L. Theobald* and Deborah S. Wuttke (2008)
* corresponding author
"Accurate structural correlations from maximum likelihood superpositions."
PLoS Computational Biology 4(2):e43. [Open Access, pdf]


Douglas L. Theobald (2007)
"Punctuated equilibrium."
International Encyclopedia of the Social Sciences, 2nd Edition,
Darity WA, Editor in Chief,
MacMillan Library Reference, Detroit, pp. 629-631. [pdf]


Douglas L. Theobald* and Deborah S. Wuttke (2006)
* corresponding author
"Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem."
Proceedings of the National Academy of Sciences USA 103(49):18521-18527. [Open Access, pdf]

Douglas L. Theobald* and Deborah S. Wuttke (2006)
* corresponding author
"THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures."
Bioinformatics 22(17):2171-2172. [Open Access, pdf]
Supplementary Material [pdf]


Douglas L. Theobald and Deborah S. Wuttke (2005)
"Divergent evolution within protein superfolds inferred from profile-based phylogenetics."
Journal of Molecular Biology 354(3):722-737. [PMC, pdf]

Douglas L. Theobald (2005)
"Rapid calculation of RMSDs using a quaternion-based characteristic polynomial."
Acta Crystallographica A 61(4):478-480. [Open Access, pdf]
The QCP C code for determining rapid RMSDs.


Douglas L. Theobald and Deborah S. Wuttke (2004)
"Prediction of multiple tandem OB-fold domains in telomere end-binding proteins Pot1 and Cdc13."
Structure 12(10):1877-1879. [pdf]

Rachel M. Mitton-Fry, Emily M. Anderson, Douglas L. Theobald, Leslie W. Glustrom, and Deborah S. Wuttke (2004)
"Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13."
Journal of Molecular Biology 338(2):241-55. [ScienceDirect, pdf]


Douglas L. Theobald, Rachel B. Cervantes, Victoria Lundblad, and Deborah S. Wuttke (2003)
"Homology among telomeric end-protection proteins."
Structure 11(9):1049-1050. [ScienceDirect, pdf]

Douglas L. Theobald and Steve C. Schultz (2003)
"Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes."
EMBO Journal 22(16): 4314-4324. [PMC, pdf]

Douglas L. Theobald, Rachel M. Mitton-Fry, and Deborah S. Wuttke (2003)
"Nucleic acid recognition by OB-fold proteins."
Annual Review of Biophysics and Biomolecular Structure 32(16):115-133. [PMC, pdf]