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Lonnie Welch

Stuckey Professor
Biomedical Engineering,Electrical Engineering and Computer Science,Center for Scientific Computing and Immersive Technologies
STKR 354
welch@ohio.edu
Phone: 740.593-.1575

http://light.ece.ohio.edu/~reggen/2012/

Professor Lonnie R. Welch is the Stuckey Professor of Electrical Engineering and Computer Science at Ohio University, a member of the Graduate Faculties of the Biomedical Engineering Program and of the Molecular and Cellular Biology Program, director of the Bioinformatics Laboratory at Ohio University, and the founder and Chair of the Great Lakes Bioinformatics Conference (an official conference of the International Society on Computational Biology). His research has been sponsored by the National Human Genome Research Institute, the Ohio Plant Biotechnology Consortium, NASA, the National Science Foundation, the Defense Advanced Research Projects Agency, and the Ohio Board of Regents. He is the principal investigator of the $9M Bioinformatics Program of the Ohio Board of Regents. Dr. Welch is founder and co-chair of the ISMB Special Interest Group on Bioinformatics for Regulatory Genomics (BioRegSIG).


Research Interests: Bioinformatics, Computational regulatory genomics, Machine learning, High performance computing

All Degrees Earned: Ph.D., 1990, M.S.1987, B.S. 1985, Computer and Information Science, the Ohio State University.

Publications:

Lee Nau, Frank Drews, Lonnie Welch, A Scalable Multicore Implementation of the TEIRESIAS Algorithm, 12th Bioinformatics Open Source Conference (BOSC), July 2011, Vienna, Austria.

Lonnie Welch, Russell Schwartz, Fran Lewitter, Report from the ISCB Education Committee: A Draft Curriculum for Bioinformatics, Third Annual RECOMB Conference on Bioinformatics Education (RECOMB-BE), an ISMB/ECCB 2011 Satellite Meeting, July 2011, Vienna, Austria.

J Lichtenberg , A. Yilmaz, K. Kurz, X. Liang, C. Nelson, T. Bitterman, E. Stockinger, E. Grotewold, and L. Welch, Encyclopedias of DNA Elements for Plant Genomes, in Advances in Genomic Sequence Analysis and Pattern Discovery, Laura Elnitski, Helen Piontkivska and Lonnie Welch (Editors), World Scientific Publishers, Hackensack, NJ, 2011.

Lonnie R. Welch, Laura M. Koehly, and Laura Elnitski (2011). Shared Regulatory Motifs in Promoters of Human DNA Repair Genes. In Inna Kruman (Editor), DNA Repair (pp. 67-84). Rijeka, Croatia: Intech.

Advances in Genomic Sequence Analysis and Pattern Discovery (Science, Engineering, and Biology Informatics Vol. 7). Laura Elnitski (Editor), Helen Piontkivska (Editor), Lonnie R. Welch (Editor). World Scientific Publishing Company. 2011 Jan 17.

Lichtenberg J, Kurz K, Liang X, Al-ouran R, Neiman L, Nau LJ, Welch JD, Jacox E, Bitterman T, Ecker K, Elnitski L, Drews F, Lee SS, Welch LR. WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. BMC Bioinformatics. 2010 Dec 21;11 11 Suppl 12:S6. PubMed PMID: 21210985; PubMed Central PMCID: PMC3040532.

Genome-wide detection of a TFIID localization element from an initial human disease mutation. Yang MQ, Laflamme K, Gotea V, Joiner CH, Seidel NE, Wong C, Petrykowska HM, Lichtenberg J, Lee S, Welch L, Gallagher PG, Bodine DM, Elnitski L. Nucleic Acids Res. 2011 Mar;39(6):2175-87. Epub 2010 Nov 11.

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E. Nucleic Acids Res. 39(Database issue):D1118-22. 2011 Jan.

Regulatory network nodes of check point factors in DNA repair pathways. Laura Elnitski, Jens Lichtenberg, Lonnie R. Welch. BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology 529-536. 2010 Aug.

A bioinformatics approach to the identification, classification, and analysis of hydroxyproline-rich glycoproteins. Showalter AM, Keppler B, Lichtenberg J, Gu D, Welch LR. Plant Physiology 153:485-513. 2010 Apr.

Scalable parallel word search in multicore/multiprocessor systems. Frank Drews, Jens Lichtenberg, Lonnie Welch. The Journal of Supercomputing Volume 51, Number 1, 58-75. 2010 Jan.

An integrated bioinformatics approach to the discovery of cis-regulatory elements involved in plant gravitropic signal transduction. X. Liang, K. Shen, J. Lichtenberg, S.E. Wyatt, and L.R. Welch. International Journal of Computational Bioscience 1:33-54. 2010.

The word landscape of the non-coding segments of the Arabidopsis thaliana genome. Lichtenberg J, Yilmaz A, Welch JD, Kurz K, Liang X, Drews F, Ecker K, Lee SS, Geisler M, Grotewold E, Welch LR. BMC Genomics 10:463. 2009 Oct 8.

Word-based characterization of promoters involved in human DNA repair pathways. Lichtenberg J, Jacox E, Welch JD, Kurz K, Liang X, Yang MQ, Drews F, Ecker K, Lee SS, Elnitski L, Welch LR. BMC Genomics 10(Suppl 1):S18. 2009 Jul 7.

Construction of Genomic Regulatory Encyclopedias: Strategies and Case Studies. Jens Lichtenberg, Mohit Alam, Thomas Bitterman, Frank Drews, Klaus Ecker, Laura Elnitski, Susan Evans, Matt Geisler, Erich Grotewold, Dazhang Gu, Edwin Jacox, Kyle Kurz, Stephen S. Lee, Xiaoyu Liang, Pooja M. Majmudar, Paul Morris, Chase Nelson, Eric Stockinger, Joshua D. Welch, Sarah Wyatt, Alper Yilmaz, and Lonnie R. Welch. In Proceedings of the 2009 Ohio Collaborative Conference on Bioinformatics (OCCBIO '09). IEEE Computer Society, Washington, DC, USA, 65-70. 2009.

The SiteSeeker motif discovery tool. Ecker K, Lichtenberg J, Welch L. In Silico Biol Volume 9, Number 1-2, 11-22. 2009.

Discovery of regulatory elements in Oomycete orthologs. Jens Lichtenberg, Paul Morris, Klaus Ecker, and Lonnie Welch. The 2008 International Conference on Bioinformatics and Computational Biology, Las Vegas. 2008 Jul.

Application of bioinformatics and scalable computing to perform proteomic analysis of stomach tissue from diabetic mice. Edward O. List, Darlene E. Berryman, Amanda J. Palmer, Elahu Gosney, Shigeru Okada, Bruce Kelder, Jens Lichtenberg, Lonnie R. Welch and John J. Kopchick. Journal of Scalable Computing: Practice and Experience 8(2):173-183. 2007 Jun.

Patents:

Program Control For Resource Management Architecture and Corresponding Programs, US patent application 09/864821, US patent no. 7,096,248, patent issued 08-2006.

System for Monitoring and Reporting Performance of Hosts and Applications and Selectively Configuring Applications in a Resource Managed System, US patent application 09/864830, US patent number 7,051,098, patent issued 5-2006.

Resource Allocation Decision Function for Resource Management Architecture and Corresponding Programs, US patent application 09/864825, pending approval.

Awards:

2010 Alumnus of the Year, Claymont High School (for demonstrated lifetime leadership and abilities in chosen field)

2001 Stuckey Professorship, Ohio University (for outstanding accomplishments in research and teaching)

1998 Outstanding Young Faculty Member, University of Texas at Arlington

1998 Aegis Excellence Award, United States Navy (for contributions in dynamic resource management to the Navy's High Performance Distributed Computing (HiPer-D) and AdCon-21 projects)