In review
Dmitry Lyumkis, Axel Brilot, Douglas L. Theobald, and Nikolaus Grigorieff
"Likelihood-based classification of cryo-EM images using FREALIGN."
In review at
Journal of Structural Biology
Douglas L. Theobald
"Presenilin adopts the ClC channel fold."
In review at
Bioinformatics
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."
In review at
Nature
At Brandeis
2013
Erin L. Devine, Daniel D. Oprian, and Douglas L. Theobald (2013)
"Relocating the active-site lysine in rhodopsin."
In review at
PNAS
Kristine A. Mackin, Richard A. Roy, and Douglas L. Theobald (2013)
"An empirical test of convergent evolution in rhodopsins."
In review at
Molecular Biology and Evolution
Kanti V. Mardia, Christopher J. Fallaize, Stuart Barber, Richard M. Jackson, & Douglas L. Theobald (2013)
"Bayesian alignment of similarity shapes."
The Annals of Applied Statistics,
in press
[Open Access pdf]
2012
Douglas L. Theobald & Phillip A. Steindel (2012)
"Optimal simultaneous superpositioning of multiple structures with missing data."
Bioinformatics
28(15):1972-1979
[Open Access]
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, & 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 & 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, Dmitri K. Agrafiotis, & 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]
2010
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 & 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 & 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 & Chris Miller (2010)
"Membrane transport proteins: Surprises in structural sameness."
Nature Structural & 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, Dmitri K. Agrafiotis, & 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.
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 & Deborah S. Wuttke (2008)
"Accurate structural correlations from maximum likelihood superpositions."
PLoS Comput Biol
4(2):e43. [Open Access,
pdf]
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]
At the University of Colorado at Boulder
2006
Douglas L. Theobald & Deborah S. Wuttke (2006)
"Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem."
Proc Natl Acad Sci U S A
103(49):18521-18527. [Open Access,
pdf]
Douglas L. Theobald & Deborah S. Wuttke (2006)
"THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures."
Bioinformatics
22(17):2171-2172. [Open Access,
pdf]
Supplementary Material [pdf]
2005
Douglas L. Theobald & Deborah S. Wuttke (2005)
"Divergent evolution within protein superfolds inferred from profile-based phylogenetics."
J Mol Biol
354(3):722-737. [PMC,
pdf]
Douglas L. Theobald (2005)
"Rapid calculation of RMSDs using a quaternion-based characteristic polynomial."
Acta Crystallogr A
61(4):478-480. [Open Access,
pdf]
The QCP
C code
for determining rapid RMSDs.
2004
Douglas L. Theobald & 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 & Deborah S. Wuttke (2004)
"Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13."
J Mol Biol
338(2):241-55. [ScienceDirect,
pdf]
2003
Douglas L. Theobald, Rachel B. Cervantes, Victoria Lundblad & Deborah S. Wuttke (2003)
"Homology among telomeric end-protection proteins."
Structure
11(9):1049-1050. [ScienceDirect,
pdf]
Douglas L. Theobald & 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 & Deborah S. Wuttke (2003)
"Nucleic acid recognition by OB-fold proteins."
Annu Rev Biophys Biomol Struct
32(16):115-133. [PMC,
pdf]