efg's Research Notes
July 2001 - Oct 2008


Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock

Mary-Lee Dequéant, Sebastian Ahnert, Herbert Edelsbrunner, Thomas M. A. Fink, Earl F. Glynn, Gaye Hattem, Andrzej Kudlicki, Yuriy Mileyko, Jason Morton, Arcady R. Mushegian, Lior Pachter, Maga Rowicka, Anne Shiu, Bernd Sturmfels, Olivier Pourquié. PLoS ONE 3(8): e2856 doi:10.1371/journal.pone.0002856, 2008. PubMed.

A Flexible Template Boundary Element in the RNA Subunit of Fission Yeast Telomerase

Jessica A. Box, Jeremy T. Bunch1, David C. Zappulla, Earl F. Glynn and Peter Baumann, Journal of Biological Chemistry (in press), 2008.  Supplementary information. PubMed.

Prevention of the neurocristopathy Treacher Collins syndrome through inhibition of p53 function

Natalie C Jones, Megan L Lynn, Karin Gaudenz, Daisuke Sakai, Kazushi Aoto, Jean-Phillipe Rey, Earl F Glynn, Lacey Ellington, Chunying Du, Jill Dixon, Michael J Dixon & Paul A Trainor, Nature Medicine, 14, 125-133, 2008PubMed.

A Complex Oscillating Network of Signaling Genes Underlies the Mouse
Segmentation Clock

Mary-Lee Dequéant, Earl Glynn, Karin Gaudenz, Matthias Wahl, Jie Chen, Arcady Mushegian, Olivier Pourquié, Science, 314(5805): 1595-1598, 2006PubMed.

Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms

EF Glynn, J Chen, AR Mushegian

Bioinformatics, 1 Feb 2006; 22: 310-316.   Supplementary information. PubMed.

Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae

EF Glynn, PC Megee, HG Yu, C Mistrot, E Unal, DE Koshland, JL DeRisi, JL Gerton
PLoS Biology, Vol 2, Issue 9, Sept 2004.  Supplementary information. PubMed.


Analyzing Olfactory Response Data in ABF Files

Stowers R/Bioconductor Discussion Group, 25 Sept 2008

Error Analysis and Propagation of Errors

Bioinformatics Weekly Seminar, 7 May 2008

Cluster Computing with R

Stowers R/Bioconductor Discussion Group, 18 Dec 2007

Using Color in R

Stowers R/Bioconductor Discussion Group, 17 July 2007

Fourier Analysis and Image Processing

Bioinformatics Weekly Seminar, 14 Feb 2007, and previously at
Foundations of Image Processing Seminar on 29 Sept 2006
hosted by Stowers Advanced Instrumentation and Physics group.

Nonlinear Curve Fitting

Bioinformatics Department meeting, 11 Oct 2006.

Characterization of Chronic Fatigue Syndrome
Using Affective Disorder and Immune System Pathways

Earl F. Glynn, Hua Li, Chris Seidel, Frank Emmert-Streib, Jie Chen,
Arcady R. Mushegian  

CAMDA 2006 Conference, 9 June 2006

Using Lomb-Scargle Periodograms to Identify Periodic Genes in Somitogenesis

Bioinformatics Weekly Seminar, 29 March 2006.

Software Tools for Scientific Data Analysis and Visualization:
R and Bioconductor

Stowers Science Club, 20 May 2005.

Genome-wide Mapping of the Cohesin Complex in Yeast

Stowers Core Facility Journal Club, 9 May 2005.

Logic Regression

Bioinformatics Weekly Seminar, 2 March 2005.

Searching for Periodic Gene Expression Patterns
Using Lomb-Scargle Periodograms

Earl F. Glynn, Arcady R. Mushegian, Jie Chen

CAMDA 2004 Conference , 11 Nov 2004.

Wavelets:  Denoising of Yeast Cohesin Binding Data

Bioinformatics Weekly Seminar, 9 July 2003.

Introduction to Image Processing

Stowers Science Club, 8 March 2002.


FCSExtract utility reads Flow Cytometery Standard (FCS) data from a binary FCS file and converts it to an ASCII text format, which can be read by a variety of software analysis packages.  [Windows]  An example of working with this data in R is provided.  [UNIX or Windows]   FCSExtract and FCSViewer are not related in any way and work on entirely different FCS data files.


FCSViewer utility reads Fluorescence Correlation Spectroscopy (FCS) data, a proprietary Zeiss format, and displays the two channels of data over a specified time interval. Updated to work with new Zeiss ConfoCor 3 data format, as well as older ConfoCor 2 format.   [Windows] FCSExtract and FCSViewer are not related in any way and work on entirely different FCS data files.

HemavetCSV utility creates a single comma-separated values (CSV) file with summary information from a directory of Hemavet files.  [Windows]  Available on request.


Detecting periodic patterns in unevenly-spaced gene expression time series
using Lomb-Scargle periodograms.  R Code.  [UNIX or Windows]

PeakFinder was developed to find cohesin binding sites represented by the peaks in yeast chromatin immunoprecipitation (ChIP) microarray data, but can be applied to plot any measurement against a parameter such as genome coordinate, to interactively analyze the measurement plot, and to annotate the peaks on the basis of local properties of the curve.  [Windows]

TiffTags displays the "tag" fields in a TIFF (tagged image file format) file. TiffTags was created to troubleshoot problem TIFF files and implement code in Windows to display certain TIFFs. [Windows]

TweenMotif is an interactive Windows program for visualizing the locations of a specified target motif within a set of sequences, as well as the gaps between the repeating motifs. The program creates a summary table of the frequency counts of the gap sequences that can be pasted into an Excel spreadsheet for further analysis

ZeissToSGI converts from a Zeiss AxioVision TIFF file to one that can be read by the SoftWoRx software on SGI machines. [Windows]

Technical Notes
Embarrassingly Parallel Computations Using the Sun Grid Engine

R TechNotes and R Graphics Gallery   [UNIX or Windows]
(under construction)

Working with Affy GeneChip Sequence and Annotation Files in Access

Also see:
Affy GeneChip MOE430A: Probe Sequences in a ProbeSet Example

Working notes for using PHYLIP programs "neighbor" and "consense" to explore bootstrap support for clusters in tree

Understanding CAMDA '06 Data

Also see: Characterization of Chronic Fatigue Syndrome
Using Affective Disorder and Immune System Pathways

Miscellaneous Links / Information Resources

Science Computing
Bioinformatics   Microarrays Image Processing
Life Sciences Computer Science / Computational Techniques
Physical Sciences Information Technology for Bioinformatics
Mathematics & Statistics Scientific Software Application Notes

Earl F. Glynn
Scientific Programmer

Mushegian Lab
Bioinformatics Center

31 Oct 2008