Dr. Julia Richards
The research program of Dr. Julia Richards, PhD focuses on the underlying causes of hereditary eye disease and the normal processes of ocular aging. 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 identification of disease genes, disease risk factors, and risk factors associated with endophenotypes, have resulted from her collaborations with glaucoma specialists Paul R. Lichter, MD, Sayoko Moroi, MD, PhD, and Joshua Stein, MD, MS, and biostatistical geneticists Michael Boehnke, PhD, and Jun Li, PhD, and researchers at other institutions including Stanford, University of Oklahoma, and UCSF. Over the years she has collaborated with researchers from Ghana, Peru, Australia, Canada, Japan, Korea, and Taiwan, and more recently has expanded her international collaborations through interaction with the International Glaucoma Genetics Consortium. She contributed three of the twelve populations in the ten-center NEIGHBOR genome-wide association study (GWAS) that has led to breakthroughs in identification of common SNPs associated with open-angle glaucoma its endophenotypes as well as novel pathways associated with glaucoma.
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. Linkage analysis, genome wide association studies, whole exome sequencing, expression profiling all contribute to our search for the underlying causes of inherited eye disease.
Research Publications and Presentations
- Dr. Julia Richards complete bibliography.
Below you will find links to a selection of representative publications and presentations produced by the researchers and staff in Dr. Julia Richards lab here at the Kellogg Eye Center:
- Stein JD, Kim DS, Niziol LM, Talwar N, Nan B, Musch, Richards JE. Differences in Rates of Glaucoma Among Asian Americans Compared With Other Races and Among Individuals of Different Asian Ethnicities. Ophthalmology. 2011;118:1031-7. PMCID: PMC3109193
- Moroi SE, Raoof DA, Reed DM, Zöllner S, Qin Z, Richards, JE. Progress toward Personalized Medicine for Glaucoma. Expert Review of Ophthalmology; 2009;4:145-161. PMCID: PMC3728985,
- Rozsa FW, Scott K, Pawar H, Moroi S, Richards JE. Effects of timolol on MYOC, OPTN, and WDR36 RNA levels. Arch Ophthalmol; 2008;126:86-93. PMID: 18195223
- Ayala-Lugo RM, Pawar H, Reed DM, Lichter PR, Moroi SE, Page M, Eadie J, Azocar V, Maul E, Ntim-Amponash C, Bromley W, Obeng-Nyarkoh E, Johnson AT, Guckian Kijek T, Downs CA, Johnson JM, Perez-Grossmann R, Guevara-Fujita ML, Fujita R, Wallace MR, Richards JE. Variation in Optineurin (OPTN) Allele Frequencies Between and Within Populations Mol Vis; 2007;13:151-163. PMCID2533035
- Mimiwati Z, Mackey DA, Craig JE, Mackinnon JR, Rait JL, Liebelt JE, Ayala-Lugo R, Vollrath D, Richards JE. Nail-patella syndrome and its association with glaucoma: a review of eight families. Br J Ophthalmol; 2006;90:1505-9. PMCID: PMC1857543
- 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.
- 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.
- Thompson DA, McHenry CL, Li Y, Richards JE, Othman MI, Schwinger E, Vollrath D, Jacobson SG, Gal A. Retinal dystrophy due to paternal isodisomy for chromosome 1 or chromosome 2, with homoallelism for mutations in RPE65 or MERTK, respectively. Am J Hum Genet 2002;70(1):224-229.
- 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.
- Othman MI, Sullivan SA, Skuta GL, Cockrell DA, Stringham HM, Downs CA, Fornes A, Mick A, Boehnke M, Vollrath D, Richards JE. Autosomal dominant nanophthalmos (NNO1) with high hyperopia and angle closure glaucoma maps to chromosome 11. Am J Hum Genet 1998;63:1411-1418.
- Rozsa F, Othman MI, Shimizu S, Lichter PR, Johnson AT, Scott K, Nguyen TD, Polansky JR, Richards JE. GLC1A mutations point to regions of potential functional importance on the TIGR/MYOC protein. Mol Vis 1998;4:20
- 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.
- Richards JE, Lichter PR, Boehnke M, Uro JLA, Torrez D, Wong D, Johnson AT. Mapping of a gene for autosomal dominant juvenile-onset open-angle glaucoma to chromosome 1q. Am J Hum Genet 1994;54: 62-70.
Current Lab Members
- Julia E. Richards, PhD
- Ed Trager, MS
- Frank Rozsa
- Sarah Garnai
- Christine Rygiel, MPH, MB (ASCP)
- Melissa Cloutier
- Michelle Daoud
Past Lab Members
- Katy Downs, MS
- Kathleen Scott
- Alyce Whipp
- Misao Higashi
- Theresa Kijek
- Hemant Pawar
- David Reed
- Rosa Ayala
- Kanjana Soongswang
- Kimberly Warner
- Michele Ford
- Linda Hosman
- Dorothy Giebel
- Emily Bird
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.
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).
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
.mfhare created automatically when they don't exist without having to run
recognizemanually. Implementation of this feature has also eliminated some show-stopping segmentation faults.
List filesnow lists the files in your current working directory. You need no longer resort to using
system "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)
- LOD Plots in Madeline 0.935
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)
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.
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-0.010.tar.gz Gt v. 0.010 in tarred gzip format.
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 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 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!
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. This resource is now on unifont.org:
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.
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.
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.
Richards Lab Bioinformatics Software Documentation
These are links to the documentation distributed with various packages that are available on our servers:
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:
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:
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