2022
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.
doi:10.7554/eLife.73860
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.
doi:10.1038/s41586-022-04468-9
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)
https://openreview.net/pdf?id=FZoZ7a31GCW
[ICLR 2022 pdf]
2021
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]
doi:10.1002/pro.4155
2019
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]
doi:10.1109/CIBCB.2019.8791469
2018
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]
doi:10.1021/acs.biochem.8b00913
2017
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.
doi:10.1021/acs.biochem.7b00519
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.
doi:10.1074/jbc.M117.789636
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.
doi:10.1126/science.aah3717
2016
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]
doi:10.1021/acs.biochem.6b00478
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]
doi:10.1002/pro.2904
Douglas L. Theobald (2016)
"Presenilin adopts the ClC channel fold."
Protein Science
25(7):1363-1365.
[Open Access, pdf]
doi:10.1002/pro.2919
2015
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]
doi:10.1126/science.aaa1823
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
2014
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]
doi:10.7554/eLife.02304
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]
doi:10.1093/molbev/mst171
2013
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]
doi:10.1038/nature12390
PMC3758369
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]
doi:10.1073/pnas.1306826110
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]
doi:10.1016/j.jsb.2013.07.005
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]
doi:10.1214/12-AOAS615
2012
Douglas L. Theobald and Phillip A. Steindel (2012)
"Optimal simultaneous superpositioning of multiple structures with missing data."
Bioinformatics
28(15):1972-1979.
[pdf]
doi:10.1093/bioinformatics/bts243
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]
doi:10.1007/978-3-642-27225-7_8
2011
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]
doi:10.1186/1745-6150-6-60
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]
doi:10.1085/jgp.201110684
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]
doi:10.1002/jcc.21606
2010
Douglas L. Theobald (2010)
"Was the universal common ancestry proved? Reply"
Nature
468(7326):E10.
[pdf]
doi:10.1038/nature09483
Douglas L. Theobald (2010)
"A formal test of the theory of universal common ancestry."
Nature
465(7295):219-222.
[pdf]
doi:10.1038/nature09014
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]
doi:10.1038/nature08848
Douglas L. Theobald and Chris Miller (2010)
"Membrane transport proteins: Surprises in structural sameness."
Nature Structural and Molecular Biology
17(1):2-3.
[pdf]
doi:10.1038/nsmb0110-2
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]
doi:10.1002/jcc.21439
The QCProt
C code
for determining rapid least-squares rotations.
2009
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
2008
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]
doi:10.1371/journal.pcbi.0040043
2007
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]
2006
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]
doi:10.1073/pnas.0508445103
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]
doi:10.1093/bioinformatics/btl332
Supplementary Material [pdf]
2005
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]
doi:10.1016/j.jmb.2005.08.071
Douglas L. Theobald (2005)
"Rapid calculation of RMSDs using a quaternion-based characteristic polynomial."
Acta Crystallographica A
61(4):478-480. [Open Access,
pdf]
doi:10.1107/S0108767305015266
The QCP
C code
for determining rapid RMSDs.
2004
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]
doi:10.1016/j.str.2004.07.015
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]
doi:10.1016/j.jmb.2004.01.063
2003
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]
doi:10.1016/S0969-2126(03)00183-7
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]
doi:10.1093/emboj/cdg415
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]
doi:10.1146/annurev.biophys.32.110601.142506