Professor Lonnie R. Welch received a Ph.D. in Computer and Information Science from the Ohio State University. Currently, he is the Stuckey Professor of Electrical Engineering and Computer Science at Ohio University, and he is a member of the Graduate Faculties of the Biomedical Engineering Program and of the Molecular and Cellular Biology Program.  Dr. Welch performs research in the areas of bioinformatics, computational regulatory genomics, machine learning and high performance computing.  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.  Dr. Welch has more than twenty years of research experience in the area of high performance computing.  In his graduate work at Ohio State University, he developed high performance 3-D graphics rendering algorithms, and he invented a parallel virtual machine for object-oriented software.  For 15 years, his research focused on middleware and optimization algorithms for high performance computing; this work produced three successive generations of adaptive resource management middleware for high performance real-time systems, and resulted in two patents and more than 150 publications. Currently, Professor Welch directs the Bioinformatics Laboratory at Ohio University, where he performs research in the area of computational regulatory genomics.  His team develops algorithms and software tools, which they apply to reverse engineer the genetic and epigenetic regulatory control systems of a variety of organisms.

Dr. Welch is the founder and Chair of the Great Lakes Bioinformatics Conference (an official conference of the International Society on Computational Biology).  As Founding Chair of the Great Lakes Bioinformatics Consortium, an Affiliated Regional Group of the International Society on Computational Biology, Dr. Welch has been an active member of the Regional Affiliates Committee of the ISCB. Additionally, he serves on the ISCB's Board of Directors, Education Committee (Vice Chair), and Conferences Committee.   He is the Principal Investigator of the $9M Bioinformatics Program of the Ohio Board of Regents.  Prof. Welch is founder and Co-Chair of the ISMB Special Interest Group on Bioinformatics for Regulatory Genomics (BioRegSIG). 

Selected Publications

1. Lonnie R. Welch, Russell Schwartz, Fran Lewitter, A Report of the Curriculum Task Force of the ISCB Education Committee
   PLOS Computational Biology, June 2012
   
   
2. Lee Nau, Frank Drews, Lonnie Welch, A Scalable Multicore Implementation of the TEIRESIAS Algorithm, 12th Bioinformatics Open Source Conference (BOSC), July 2011, Vienna, Austria.
   
   
3. 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.
   
   
4. 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.
   
   
5. 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.
   
   
6. 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.
   
   
7. 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.
   
   
8. 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.
   

   
   

9. 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.
   
   
10. 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.
    
    

11. 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.
    

    
    

12. 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.
    
    
13. 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.
    
    
14. 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.
    

    
    

15. 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.
    
    
16. The SiteSeeker motif discovery tool.
    Ecker K, Lichtenberg J, Welch L.  In Silico Biol Volume 9, Number 1-2, 11-22. 2009.
    
    
17. 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.
    

    
    

18. 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.
    
    

Research Topics

• Bioinformatics
• Computational regulatory genomics
• Machine learning
• High performance computing