Software

Exon Visualization Applet (Early Beta)

Neuron Simulation Applet

code for the 2004 covariance papers

(new version 1.1 released Sept. 2, 2005. Requires Java 1.5)

code for Scheme 4 and PINC

 

Recent Publications

T. Hamp, J. Jones and A.A. Fodor.
Targeting the V1-V2 region of the 16S rRNA gene yields improved measures of microbial community composition in a pyrosequencing survey of a wastewater treatment plant.
In revision, Applied and Environmental Microbiology.

N. Sanapereddy, T. Hamp, L. Gonzalez and H. Hilger, A.A. Fodor and S.M. Clinton.
Molecular Diversity of a North Carolina Wastewater Treatment Plant As Revealed by Pyrosequencing.
In press, Applied and Environmental Microbiology.

Reid RW, Fodor AA
Determining gene expression on a single pair of microarrays.
BMC Bioinformatics. 2008, 9:489.

Gharaibeh RZ, Fodor AA, Gibas CJ
Using Probe Secondary Structure Information to Enhance Affymetrix GeneChip Background Estimates.
Comput Biol Chem. 2007 April ; 31(2): 92–98.
pdf

Fodor AA, Tickle TL, Richardson C
Towards the uniform distribution of null p-values on microarrays.
Genome Biol. 2007, 8(5):R69.
pdf

Pyott SJ, Meredith AL, Fodor AA, Vázquez AE, Yamoah EN, Aldrich RW
Cochlear function in mice lacking the BK channel alpha, beta1, or beta4 subunits.
J Biol Chem . 2007 Feb 2; 282 (5): 3312-24 . Epub 2006 Nov 29
pdf
Andrea L Meredith, Steven W Wiler, Brooke H Miller, Joseph S Takahashi, Anthony A Fodor, Norman F Ruby, Richard W Aldrich
BK calcium-activated potassium channels regulate circadian behavioral rhythms and pacemaker output
Nature Neuroscience, 9, 1041-1049, 2006
Anthony A. Fodor, Richard W. Aldrich.

Statistical Limits to the Identification of Ion Channel Domains by Sequence Similarity
JGP 127(6), 755-766, 2006
pdf
Anthony A. Fodor, Richard W. Aldrich.
On Evolutionary Conservation of Thermodynamic Coupling in Proteins.
JBC 279(18):19046-19050, 2004
pdf
John P. Dekker, Anthony Fodor, Richard Aldrich and Gary Yellen.
A pertubation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments.
Bioinformatics 20:1565-1572, 2004
Supplementary Materials
pdf
Anthony A. Fodor and Richard W. Aldrich.
Influence of Conservation on Calculations of Amino Acid Covariance in Multiple Sequence Alignments.
Proteins 56(2): 211-221, 2004
Supplementary Materials
pdf