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Contributors to the RDP

Director
James R. Cole, Ph.D.
colej@msu.edu

Jim is a Research Assistant Professor with The Center for Microbial Ecology at MSU. He oversees the website, database, and development.

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Benli Chai, Ph.D.
chaibenl@msu.edu

Benli is Curator and Bioinformatics Specialist. He received his Ph.D. in Molecular Biology from the Department of Crop and Soil Sciences at Michigan State University in 1999. He previously had been a sequence curator in the Mouse Genome Informatics group in the Jackson Laboratory during 2000-2001. Benli received his M.Eng. in Bioinformatics in 2009.

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Ryan J. Farris
farrisry@msu.edu

Ryan was the RDP's Systems Programmer during our creation/phase-in of RDP's SOAP Web Services, the Pyrosequencing Pipeline and the RDP Classifier SourceForge project.

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Jordan Fish
fishjord@msu.edu

Jordan took over as RDP's Systems Programmer upon Ryan's move to North Carolina. He has been instrumental in streamlining existing RDP tools and creating new tools to deal with Functional Gene data.

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Karl Fogel
kfogel@red-bean.com

Karl, with some assistance by Jim Blandy, wrote a prototype sequence editor named ALE, based on the emacs editor. ALE development is no longer occurring.
Web: http://www.red-bean.com/kfogel/

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George Garrity, Sc.D
garrity@msu.edu

George is an MSU Dept. of Microbiology faculty member and former Editor-in-Chief of Bergey's Manual of Systematic Bacteriology. He serves as an RDP Faculty Advisor.
Web: http://www.bergeys.org/

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Graduate Students

Adithya M. Bandela is a Master's student in Computer Science and Engineering. He is currently working on an automated sequence scanner which is capable of detecting anomalous sequences before they get added into RDP's database each month. Sequences detected as anomalous are flagged as being of 'suspect quality'.
Sunandana Chandra worked as an undergraduate at the RDP since 2000 and earned a Master's Degree with a Graduate Research Assistantship through the RDP in 2004. She was responsible for annotating and curating ribosomal RNA sequences, and creating acceptance tests for RDP's tools and services. Sue now works at NIH in Bethesda, MD.
Jim Hughes and Uday, as part of their master's thesis projects, wrote the web-based form interface to the RDP's dbms that is used in-house by RDP staff to update sequence annotation.
Li Bing analyzed a new alignment algorithm for her master's thesis.

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Scott Harrison, Ph.D.
scotth@wayne.edu

Scott was instrumental in helping to deploy the Taxomatic/SOSCC resource. He is currently working as a college instructor at Wayne State University.

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Russ Hougland
hougland@uiuc.edu

As an employee of the University of Illinois' Computing and Communications Services Office, Russ provided system administration and server support after Mike McCaughey left the RDP. He continues from time to time to provide support for auxiliary RDP needs.

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Wen-Min Kuan

Wen-Min wrote a program to interconvert sequence and annotation data in a variety of formats. She also wrote a prototype Prolog-based Facts Editor.

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Siddique Kulam
siddiq15@msu.edu

Siddique was responsible for RDP tools code maintenance. Some of his projects included the Weighbor-Joining tool in Phylip interface for the RDP 9.0 release Tree Builder. Siddique now works for the State of Michigan.

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Niels Larsen, Ph.D.
niels@cme.msu.edu

Niels is the author of many important programs used by the RDP: PAL (PreALign), Sequence Match and Chimera Check (SimRank), Probe Match (Check Probe), Distance Matrix, and Alignment Slices. He is currently working with Integrated Genomics, Inc.

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Tim Lilburn, Ph.D.
lilburn@msu.edu

Tim participates in the curation of RDP's annotation data and sequence alignments. He also is a member of the RDP outreach team, and facilitates a joint RDP-Bergey's Manual Trust treeing project.

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Michael Maciukenas

Mike wrote TreeTool, a unix-based tree viewing and editing program. He is currently at the NCSA at the University of Illinois.

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Tom Macke
macke@scripps.edu

Tom, along with the assistance of other early RDP participants, principally Robin Gutell, wrote an initial alignment editor, named "ae". He subsequently developed the next generation alignment editor, "AE2", still used in-house by RDP staff.

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Bonnie Maidak, Ph.D.
maidak@ncbi.nlm.nih.gov

Bonnie oversaw the editing of all annotation data and the alignment of all SSU sequences for several years. She also provided user support. Bonnie has now moved on to the NCBI.

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Terrence L. Marsh, Ph.D.
marsht@msu.edu

Terence L. Marsh is a Research Asst. Professor in the Center for Microbial Ecology and the Department of Microbiology at MSU. His laboratory has contributed to the develpoment of T-RFLP as a tool of community analysis. He participated in the construction of the T-RFLP and TAP-TRFLP analysis functions of the RDP as well as the RDP tutorial.
Web: http://mmg.msu.edu/114.html

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Michael J. McCaughey, Ph.D.
mrmike@clickbang.com

Mike created the original E-mail and WWW servers of the RDP, served as system administrator, and answered technical user support queries. He currently has his own computer consulting company, Click! Consulting.

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Donna M. McGarrell
dmcgarre@msu.edu

Donna joined RDP in March 2002 as web designer. She is a former elementary/jr. high computer teacher. She works with the programmers/analysts to create and maintain various sites for CME.
Web: http://www.msu.edu/~dmcgarre/

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Gary J. Olsen, Ph.D.
gary@phylo.life.uiuc.edu

Gary co-created the RDP with Carl Woese, another faculty member of the Department of Microbiology at the University of Illinois. Gary wrote many programs and scripts to create trees, modify data, and other additional utilities.
Web: http://mcb.illinois.edu/faculty/profile/gjo

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Ross Overbeek, Ph.D.
overbeek@mcs.anl.gov

Ross co-wrote the fastDNAml code and several wrapper scripts used to generate the RDP phylogenetic trees, as well as authoring a fine pattern matcher which is used in the RDP-II Check Probe function. He also coordinated the first RDP ftp server. Ross is affiliated with Argonne National Laboratory. 

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Chuck Parker
cparker@nvs-inc.com

Chuck was the RDP-II web site administrator for several years and was responsible for answering users' technical questions. He was also responsible for developing useful online tools for the RDP, like the RDP sequence browser and Phylip interface for Release 8.1. He is currently working with a startup company.

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Sakti Pramanik, Ph.D.
pramanik@cse.msu.edu

Sakti is a MSU Dept. of Computer Science faculty member and serves as a RDP Faculty Advisor. He oversaw the development of RDP's object-oriented database.
Web: http://www.cse.msu.edu/~pramanik/

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Paul Saxman
saxman@umich.edu

Paul wrote the RDP's Java T-RFLP analysis tool as an undergraduate. He was a systems administrator for CAEN at the University of Michigan.

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Tom Schmidt, Ph.D.
tschmidt@msu.edu

Tom is a MSU Dept. of Microbiology faculty member and serves as a RDP Faculty Advisor. His research goals are to identify and understand patterns of microbial diversity in nature.
Web: http://mmg.msu.edu/127.html

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Mitchell Sogin, Ph.D.
sogin@evol5.mbl.edu

Mitch earned his Ph.D. with Carl Woese and started using rRNA sequences to investigate the evolutionary relationships among protists. He contributed the first SSU eukaryotic alignments to the RDP. He is at the Marine Biological Laboratory in Woods Hole, Massachusetts.
Web: http://jbpc.mbl.edu/labs-sogin.html

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Jason Stredwick
stredwic@msu.edu

During 1999, Jason participated in the development of XML-based tools to extract, parse, and load GenBank data into the RDP-II's object-oriented database. He left the RDP-II in August 1999 and is now working on computer simulators.

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Oliver Strunk

Oliver wrote the Java code for the RDP taxonomy browser (Release 8).

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Jim Tiedje, Ph.D.
tiedjej@msu.edu

Jim is the Director of the Center for Microbial Ecology at MSU and the head of the RDP-II project.
Web: http://cme.msu.edu/tiedjelab/jtiedje.shtml

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Undergraduate Students

Previous undergraduate students who assisted the RDP were: Chris Opron, Michael Griffith, Christopher Bannigan, Sibbir Noman, Zachary Wahl, Tammy Nelson, Bradley Strader, Michelle Vorwald, and Amy Capelli.

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Qiong Wang
wangqion@msu.edu

Qiong joined the RDP in June 2002 after receiving her Master's in Computer Science from MSU. She is interested in Bioinformatics and developed RDP naïve Bayesian Classifier and FrameBot (a frameshift detection and correction tool) and many other programs. She is also responsible for RDP database and web site maintenance. Qiong completed a Master's Degree in Pediatrics from Tongji Medical University in 1997.

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Carl R. Woese, Ph.D.
carl@phylo.life.uiuc.edu

Carl initially recognized the usefulness of ribosomal RNA sequences to determine phylogenetic relationships. His lab generated many of the original rRNA small subunit sequences, and his hands created the SSU prokaryotic alignment during the initial stages of the RDP. He is still at the University of Illinois at Urbana-Champaign.
Web: http://www.igb.illinois.edu/about/archaea

 

Questions/comments: rdpstaff@msu.edu
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