University of Michigan
UM Health System
Kellogg Eye Center
UM SPH Epidemiology
Research Publications and Presentations
Below you will find links to a selection of the most recent publications and presentations produced by the researchers and staff in Dr. Julia Richards lab here at the Kellogg Eye Center:
- Rozsa FW, Reed DM, Scott KM, Pawar H, Moroi SE, Kijek TG, Krafchak CM, Othman MI, Vollrath D, Elner VM, Richards JE. (2006). Gene expression profile of human trabecular meshwork cells in response to long-term dexamethasone exposure. Mol Vis. 2006 Feb 27;12:125-41. PMID: 16541013.
- Woodroffe A, Krafchak CM, Fuse N, Lichter PR, Moroi SE, Schertzer R, Downs CA, Duren WL, Boehnke M, Richards JE. (2006). Ordered subset analysis supports a glaucoma locus at GLC1I on chromosome 15 in families with earlier adult age at diagnosis. Exp Eye Res. 2006 Jun;82(6):1068-74. Epub 2005 Nov 18. PMID: 16298363.
- Krafchak CM, Pawar H, Moroi SE, Sugar A, Lichter PR, Mackey DA, Mian S, Nairus T, Elner V, Schteingart MT, Downs CA, Kijek TG, Johnson JM, Trager EH, Rozsa FW, Mandal MN, Epstein MP, Vollrath D, Ayyagari R, Boehnke M, Richards JE. (2006). Mutations in TCF8 cause posterior polymorphous corneal dystrophy and ectopic expression of COL4A3 by corneal endothelial cells. Am J Hum Genet. 2005 Nov; 77(5):694-708. Epub 2005 Sep 14. PMID: 16252232.
- Shimizu S, Krafchak C, Fuse N, Epstein MP, Schteingart MT, Sugar A, Eibschitz-Tsimhoni M, Downs CA, Rozsa F, Trager EH, Reed DM, Boehnke M, Moroi SE, Richards JE. (2004). A locus for posterior polymorphous corneal dystrophy (PPCD3) maps to chromosome 10. Am J Med Genet A. 2004 Nov 1;130(4):372-7. PMID: 15384081.
- Gonçalo R. Abecasis, Beverly M. Yashar, Yu Zhao, Noor M. Ghiasvand, Sepideh Zareparsi, Kari E. H. Branham, Adam C. Reddick, Edward H. Trager, Shigeo Yoshida, John Bahling, Elena Filippova, Susan Elner, Mark W. Johnson, Andrew K. Vine, Paul A. Sieving, Samuel G. Jacobson, Julia E. Richards, and Anand Swaroop (2004). Age-Related Macular Degeneration: A High-Resolution Genome Scan for Susceptibility Loci in a Population Enriched for Late-Stage Disease. Am. J. Hum. Genet., 74:482-494.
- Sayoko E. Moroi MD, PhD, Parag A. Gokhale MD, Miriam T. Schteingart MD, Alan Sugar MD, Catherine A. Downs MS, Satoko Shimizu MD, Charles Krafchak MPH, Nobuo Fuse MD, Susan G. Elner MD, Victor M. Elner MD, PhD, Andrew Flint MD, Michael P. Epstein PhD, Michael Boehnke PhD, and Julia E. Richards PhD (2003), Clinicopathologic correlation and genetic analysis in a case of posterior polymorphous corneal dystrophy . American Journal of Ophthalmology, Vol. 135, Issue 4: 461-470.
- R. M. Ayala-Lugo, P. R. Lichter, H. S. Pawar, A. Aledavood, S. E. Moroi, C. A. Downs, T. M. Guckian, W. C. Bromley, C. T. Ntim-Amponash, A. Mendoza, V. Azocar, E. J. Maul, B. F. Boyd, S. B. Lewis, J. E. Richards: Optineurin (OPTN) screening in Primary Open Angle-Glaucoma (POAG). Presented at the Annual Meeting of American Academy of Ophthalmology, Anaheim, CA, 2003.
Software Publications and Presentations
- Trager, EH (2006). International Text Layout & Typography: The Big & Future Picture presented at the Gnome Live! Text Layout Summit in Boston, October, 2006.
- Trager, EH (2005). The Penguin and Unicode: The State of Unicode and Internationalization in Linux presented at the International Unicode Conference 27 in Berlin, April, 2005.
- Trager, EH (2004). Madeline Version 0.935 Software Documentation
- Trager, EH (2004). Using Open Standards and Open Source Software in the battle to create a superior clinical and research data system presented at the PHP Quebec 2004 conference in Montreal.
Tools
Web Tools
This section provides links to web-based tools developed in-house.
Cicada
Cicada is a data entry and retrieval system for marker data used in genetic linkage analyses written by Ed Trager. You can find out more about Cicada here .
Access to Cicada is restricted to authorized researchers at the Kellogg Eye Center. Unauthorized access attempts are logged. Contact Ed Trager if you need access.
Sequence Chromatogram Assistant
The Sequence Chromatogram Assistant is a web-based tool designed to streamline the creation of publication-ready sequence chromatogram graphics. The tool basically runs EMBOSS's ABIView tool for you after you have specified starting and ending bases for the region of interest. The tool modifies the Postscript created by ABIView so that you have less manual work to do to produce publication-ready graphics.
Sequence Chromatogram Assistant
Tiana
Tiana is a web-based tool by Ed Trager for rapidly importing tabular data (from spreadsheets, for example) into a database where the data can be examined using the full power of SQL. The tool currently consists of two parts: an importer, and an inspector. For each column in a table, the inspector displays distinct values, counts, and percentages. This allows one to rapidly discern extreme values, non-standardized abbreviations or codes, and other subtle problems that often plague data sets.
Access to Tiana is restricted to authorized researchers at the Kellogg Eye Center. Unauthorized access attempts are logged. Contact Ed Trager if you need access.
Online Chinese-English Dictionary 网上简繁体汉英词典
A number of online Chinese and Chinese-English dictionaries exist on the web. This one, developed by Ed Trager based on the publically-available CEDICT data, presents results in both simplified (简体字) and traditional characters (繁體字), provides pronounciation in both pinyin (拼音) and zhuyin fuhao (注音符號), and uses carefully constructed search algorithms. These features should make the dictionary useful to mainland, Taiwan, and overseas Chinese, as well as to all students of Chinese.
Software
Madeline
Madeline is a program written by Ed Trager for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. Madeline converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. We are pleased to release Madeline under the GNU General Public License (GPL).
Madeline 2.0 Pedigree Drawing Engine
Older Versions of Madeline
The stable version (v. 0.935) now detects simple Mendelian inheritance inconsistencies, provides publication-quality multipoint LOD score plotting based on the output from programs like Simwalk2, and features many other improvements.
Madeline v. 0.936 BETA VERSION FOR TESTING DATED 2004.11.04
This new version of Madeline is a bug fix release with some significant improvements as well. Requires a modern, standards-compliant C++ compiler with a good STL implementation such as GNU GCC version 3.3 or better. New features include:
-
Smart table selection allows you to open up data tables without having to specify the
.mfhfiles..mfhare created automatically when they don't exist without having to runrecognizemanually. Implementation of this feature has also eliminated some show-stopping segmentation faults. -
Directory listing.
List filesnow lists the files in your current working directory. You need no longer resort to usingsystem "ls -l"as was previously required. - Increased use of C++ STL containers in the code base has resulted in better code, better memory management, and the elimination of show-stopping bugs.
Despite these improvements, please note that this version is still considered a beta version for testing until we have been able to test it more extensively. For documentation, please refer to version 0.935 below.
Madeline v. 0.935
This is the stable version. It features numerous improvements over v. 0.933.
- Madeline 0.935 Documentation (2004.07.15)
- Madeline 0.935 Tutorial (2004.07.15)
- Notes on compiling Madeline v. 0.935 (2004.07.15)
- Madeline v. 0.935 FAQ (2004.07.21)
- Progress on Madeline 0.935 Feature Set
- LOD Plots in Madeline 0.935
Download Madeline 0.935 Stable Version
Old Version: Madeline v. 0.933
This is the old version which is still available for download by the internet public at large.
- Documentation (v. 0.933)
- Slide Presentation (v. 0.933)
- Note on Compiling and Installing (v. 0.933)
- Example of reading LINKAGE files in Madeline (v. 0.933)
Download Madeline 0.933 Old Version
Shuffle
Shuffle is a utility written by Ed Trager in optimized C++ to randomly shuffle a DNA sequence any number of times. The program uses a high-quality portable random number generator presented in Press et al.'s Numerical Recipes in C with a period greater than 2 x 1018. In addition, the program obtains seeds for the random number generator from an entropy pool present on the compute server.
- Shuffle Documentation
- shuffle-1.01.tar.gz Shuffle version 1.01 in tarred gzip format.
Gt
Gt is an X11 text file and non-blocking process output viewer written by Ed Trager. It can be used with Madeline for viewing log files and process output. Gt may be included as part of the Madeline v. 0.935 distribution. Requires GTK+ 1.2 libraries.
- Gt Documentation
- gt-0.010.tar.gz Gt v. 0.010 in tarred gzip format.
Edith
Edith is a professional X11 editor for UNIX and Linux platforms written by Annius V. Groenink that has some particularly nice features for manipulating columns, highlighting multiple items of data, searching using regular expressions, and other features that are extremely useful for editing data files. Compared to an editor like vi, Edith has a much easier learning curve, but still has a fairly extensive set of powerful features useful for advanced data manipulation.
This editor does not originate from our lab here, but we like it a lot and highly recommend that you use this program as the editor to use with Madeline.
The Gladiator Project
Gladiator
Gladiator is a new web-based clinical and genetics data entry system being developed by Ed Trager and Ritu Khanna for joint use in the research labs of Dr. Anand Swaroop and Dr. Julia Richards here at the Kellogg Eye Center. Although initially designed for use in these two labs, our long-term goal is to make Gladiator useful for managing the clinical and genetics data for eye disease studies in general.
Unicode
Unicode Primer
Unicode solves the problem of multiple computer encodings for all of the world's scripts, scientific, and mathematical symbols by assigning unique code points in a code space that is much larger than what extended ASCII could accomodate. If your work requires that you reach a global audience in one capacity or another, then you'll want to know about Unicode!
A Quick Primer On Unicode and Software Internationalization Under Linux and UNIX
Unicode Font Guide for Free/Libre Open Source Operating Systems
As Linux and the Open Source philosophy and technologies upon which Linux is based have begun to penetrate new markets world wide, numerous governmental, non-governmental, commercial, and private organizations have been collaborating to provide high-quality Unicode-based fonts to support native language computing. The following is a selective guide to Unicode-based fonts arranged geographically and by script. While ideal for use on free/libre Open Source operating systems, these fonts can also be used on Windows and Mac OSX platforms.
Unicode Font Guide for Free/Libre Open Source Operating Systems
LASi Postscript Printing Engine Project
LASi is a library written by Larry Siden that provides a C++ stream output interface
( with operator << ) for creating Postscript documents that can contain
characters from any of the scripts and symbol blocks supported in
Unicode and by Owen Taylor's
Pango layout engine. The library accomodates right-to-left
scripts such as Arabic and Hebrew as easily as left-to-right scripts. Indic and Indic-derived
Complex Text Layout (CTL) scripts, such as Devanagari, Thai, Lao, and Tibetan are supported
to the extent provided by Pango and by the OpenType fonts installed on your system. All of this
is provided without need for any special configuration or layout calculation on the programmer's part.
LASi is now being maintained by Ed Trager and Ritu Khanna here at the Kellogg Eye Center.
LASi Documentation Download LASi 1.0.4
Uv Editor
Uv (Uniview) is a lightweight text editor that supports UTF-8 unicode, and provides a small set of advanced text and file manipulation abilities. We decided to start writing Uv after realizing that we were using multiple different text editors, each for different purposes, because no one text editor provided all the features we required.
Uv Documentation uv-1.0.tar.gz
Documentation and Links
Quality Control in the Linkage Analysis Data Pipeline
In February of 2003, Ed Trager gave a talk to a group of graduate training grant recipients from the Department of Biostatistics on quality control issues and solutions for preparing linkage data for statistical analysis. This link will take you to the slides used in that presentation.
Quality Control in the Linkage Analysis Data Pipeline
Richards Lab Bioinformatics Software Documentation
These are links to the documentation distributed with various packages that are available on our servers:
Unix Tutorials
Sooner or later, researchers in the life sciences often need to move beyond the limited world of computing on a standard Windows PC and tackle the initially daunting, but in the long run rewarding, world of Unix-based computing.
The following link from the Electronic Engineering Department at the University of Surrey, Guildford, UK, is a highly recommended "how to" resource that will help you come up to speed on UNIX quickly:
Our link below will provide you with a conceptual overview, as well as in-depth coverage of some of the more important tools that you will need to know to work in a modern, secure UNIX-based computing environment:
Richlab UNIX-based Computing Resources Tutorial
The above tutorial includes, but is not limited to, the following topics:
The following link provides baseline instructions for using Phred, Phrap, and Polyphred in the Richlab Unix computing environment:
Phred/Phrap/Polyphred Instructions (PDF)
Convenient Lab Links
- NCBI - National Center for Biotechnology Information
- Daly, Kruglyak, Lander et al.'s Genehunter page at Rockefeller University
- School of Public Health Center for Statistical Genetics
- NCBI's FASTLINK home page
- Phil Green et al.'s Crimap documentation page at Rockefeller University
- MAP-O-MAT automated marker-based linkage mapping server at Rutgers University
- Marshfield Clinic genetic map builder and related resources
- MEGA 2 data handling program documentation
- Eric Sobel's Simwalk2
- Gonçalo Abecasis' MERLIN page at the Center for Statistical Genetics, Ann Arbor
- Gonçalo Abecasis' MERLIN Quick Reference Sheet
- Phred/Phrap/Consed page at the University of Washington
- Polyphred page at the University of Washington.
- EMBOSS European Molecular Biology Open Software Suite page formerly at the UK Human Genome Mapping Project Resource Centre and now on Sourceforge
- HaploPainter
People
Principle Investigator
Dr. Julia Richards
The research program of Dr. Julia Richards focuses on the underlying causes of hereditary eye disease. Her research has a long-term emphasis on the group of diseases classified as glaucoma, one of the leading causes of irreversible blindness in the United States. Several recent breakthroughs in gene mapping and cloning have resulted from her collaborations with glaucoma specialist Paul R. Lichter, MD, biostatistician Michael Boehnke, PhD, and researchers at other institutions including Stanford, University of Oklahoma, and UCSF.
Her work on characterizing specific glaucoma genes and their role in glaucoma and related phenomena is paralleled by efforts to better understand the clinical characteristics associated with particular genes and mutations. Studies at the level of genes, cells, animals and people all assist in our efforts to sort through the underlying causes of the hereditary glaucomas and evaluate the relationships between the glaucomas and a variety of abnormal developmental processes, both ocular and non-ocular. Genome scanning, positional candidate cloning, gene mapping, mutation screening, expression studies including promoter analysis and studies of protein products, cell culture and transgenic animal models of human disease, computer informatics, clinical characterization, genetic counseling and patient education all contribute to advances in understanding the underlying causes of glaucoma and relating those findings to clinical practice.
Select Publications
- Gonçalo R. Abecasis, Beverly M. Yashar, Yu Zhao, Noor M. Ghiasvand, Sepideh Zareparsi, Kari E. H. Branham, Adam C. Reddick, Edward H. Trager, Shigeo Yoshida, John Bahling, Elena Filippova, Susan Elner, Mark W. Johnson, Andrew K. Vine, Paul A. Sieving, Samuel G. Jacobson, Julia E. Richards, and Anand Swaroop (2004). Age-Related Macular Degeneration: A High-Resolution Genome Scan for Susceptibility Loci in a Population Enriched for Late-Stage Disease. Am. J. Hum. Genet., 74:482-494.
- Sayoko E. Moroi MD, PhD, Parag A. Gokhale MD, Miriam T. Schteingart MD, Alan Sugar MD, Catherine A. Downs MS, Satoko Shimizu MD, Charles Krafchak MPH, Nobuo Fuse MD, Susan G. Elner MD, Victor M. Elner MD, PhD, Andrew Flint MD, Michael P. Epstein PhD, Michael Boehnke PhD, and Julia E. Richards PhD (2003), Clinicopathologic correlation and genetic analysis in a case of posterior polymorphous corneal dystrophy . American Journal of Ophthalmology, Vol. 135, No. 4: 461-470.
- Satoko Shimizu, MD, Paul R. Lichter, MD, A. Tim Johnson, MD, PhD, Zhaohui Zhou, PhD, Misao Higashi, BS, Maria Gottfredsdottir, MD, Mohammad Othman, PhD, Sayoko Moroi, MD, PhD, Frank W. Rozsa, PhD, Robert M Schertzer, MD, Margo S. Clarke, MD, Arthur L. Schwartz, MD, Catherine A. Downs, MS, Douglas Vollrath, MD, PhD, and Julia E. Richards, PhD. (2002). Age-dependent prevalence of mutations at the GLC1A Locus in primary open-angle glaucoma . American Journal of Ophthalmology, Vol. 130, No. 2: 165-177.
- Douglas Vollrath, Virna L. Jaramillo-Babb, Mark V. Clough, Ian McIntosh, Kathleen M Scott, Paul R. Lichter and Julia E. Richards (1998). Loss-of-function mutations in the LIM-homeodomain gene, LMX1B, in nail-patella syndrome . Human Molecular Genetics, Vol. 7, No. 7: 1091-1098.
Staff
Ed Trager Hemant Pawar David Reed Frank Rozsa Kathy Scott