Publications



PubMed

Theobald lab publications at PubMed



2017


Vy Nguyen, Chrisopher Wilson, Marc Homberger, 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 Homberger, 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
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]
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