efg's Research Notes

Publications
	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, 2008. PubMed.
	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, 2006. PubMed.
	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.

Publications

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, 2008. PubMed.

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, 2006. PubMed.

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.

Presentations
	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 andImmune 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.

Presentations

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 andImmune 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.

Software
FCSExtract	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	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	HemavetCSV utility creates a single comma-separated values (CSV) file with summary information from a directory of Hemavet files. [Windows] Available on request.
Lomb-Scargle	Detecting periodic patterns in unevenly-spaced gene expression time series using Lomb-Scargle periodograms. R Code. [UNIX or Windows]
PeakFinder	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	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]
ZeissToSGI	ZeissToSGI converts from a Zeiss AxioVision TIFF file to one that can be read by the SoftWoRx software on SGI machines. [Windows]

Software

FCSExtract

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

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

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

Lomb-Scargle

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

PeakFinder

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

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]

ZeissToSGI

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
	Working notes for using PHYLIP programs "neighbor" and "consense" to explore bootstrap support for clusters in tree
	Understanding CAMDA '06 Data

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

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

Understanding CAMDA '06 Data

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

Science

Computing

Bioinformatics Microarrays

Image Processing

Life Sciences

Computer Science / Computational Techniques

Physical Sciences

Information Technology for Bioinformatics

Mathematics & Statistics

Scientific Software Application Notes