2009 Publications

J. Lichtenberg, A. Yilmaz, J. D. Welch, K. Kurz, X. Liang, F. Drews, K. Ecker, S. S. Lee, M. Geisler, E. Grotewold, L. R. Welch, "The word landscape of the non-coding segments of the Arabidopsis thaliana genome," BMC Genomics 2009, 10:463.
Full article

Jens Lichtenberg, Edwin Jacox, Joshua D Welch, Kyle Kurz, Xiaoyu Liang, Mary Q Yang, Frank Drews, Klaus Ecker, Stephen S Lee, Laura Elnitski, Lonnie R Welch, "Word-based Characterization of Promoters involved in Human DNA-repair Pathways," BMC Genomics 2009, 10:S18.
Full article

Jens Lichtenberg, Mohit Alam, Thomas Bitterman, Frank Drews, Klaus Ecker, Laura Elnitski, Susan Evans, 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, "Construction of Genomic Regulatory Encyclopedias: Strategies and Case Studies," Proceedings of the Ohio Collaborative Conference on Bioinformatics, IEEE Computer Society press, June 2009.

2008 Publications

J. Lichtenberg, E. Jacox, M.Q. Yang, L. Elnitski, and L. Welch, "Word-Based Characterization of Promoters from Human DNA Repair Pathways," GENOME INFORMATICS, Cold Spring Harbor Laboratory/Wellcome Trust Joint Conference, Hinxton, UK, September 10 - 14, 2008.

F. Drews, E. Petri, J. Lichtenberg, and L. Welch, "Scalable Parallel Word Search in Multi-Core/Multiprocessor Systems," The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), Las Vegas, July, 2008.

Jens Lichtenberg, Paul Morris, Klaus Ecker, and Lonnie Welch, "Discovery of Regulatory Elements in Oomycete Orthologs," The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), Las Vegas, July, 2008.

J. Lichtenberg, E. Jacox, M.Q. Yang, L. Elnitski, and L. Welch,  "Word-based Characterization of the Bidirectional Promoters from the Human DNA-repair Pathways," The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), Las Vegas, July, 2008.

K. Ecker and L. Welch, "The SiteSeeker Motif Discovery Tool," The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), Las Vegas, July, 2008.

Kaiyu Shen, Sarah Wyatt and Lonnie Welch, "Finding cis-regulatory elements involved in plant gravitropic signal transduction," Ohio Collaborative Conference on Bioinformatics, Toledo, Ohio, June 2008.

Sarah Wyatt, Kaiyu Shen, and Lonnie Welch, "Grappling with the Gravity Box," Ohio Collaborative Conference on Bioinformatics, Toledo, Ohio, June 2008.

Chase Nelson, Lonnie Welch and Eric Stockinger, "Using WordSeeker to identify regulatory elements in CBF genes from the Triticeae," Ohio Collaborative Conference on Bioinformatics, Toledo, Ohio, June 2008.

Jens Lichtenberg and Lonnie Welch, "Clustering of Motif Discovery Data to Identify Transcription Factor Binding Sites," Ohio Collaborative Conference on Bioinformatics, Toledo, Ohio, June 2008.

Paul Morris, Jens Lichtenberg, Lonnie Welch, "In Silico Identification of Regulatory Elements in Oomycete Genomes using WordSeeker," Oomycete Molecular Genetics Workshop, Birnam, UK, May 2008.

2007 Publications

Klaus Ecker, Dazhang Gu and Lonnie R. Welch, "SiteSeeker – A Motif Discovery Tool," 7th IEEE International Conference on Bioinformatics and Bioengineering, Boston, October 2007.

Laura Elnitski and Lonnie R. Welch, "New Frontiers in Computational Genomics: Identification of Novel Functional Elements and Genome-scale Pattern Analysis" (an editorial), Scalable Computing: Practice and Experience, 8(3):i–vii (September 2007).

Lonnie Welch, Eric Petri, and Dazhang Gu, "WordSeeker: Discovering Genome-wide Patterns," Ohio Collaborative Conference on Bioinformatics, Miami, Ohio, July 2007.

Dazhang Gu, Lonnie Welch, Allan Showalter, "The Classification of Hydroxyproline-Rich Glycoproteins Using Machine Learning," poster, Ohio Collaborative Conference on Bioinformatics, Miami, Ohio, July 2007.

Shuhua Du, Susan Evans, Dazhang Gu, Lonnie Welch, "Discovering Conserved Domain and 3D Structure for Ovca1 Proteins," poster, Ohio Collaborative Conference on Bioinformatics, Miami, Ohio, July 2007.

Dazhang Gu, Lonnie Welch, Pooja Majmudar, Susan Evans, "Discovering the Presence of P53 Motif Binding Site in Cancer Related Genes," poster, Ohio Collaborative Conference on Bioinformatics, Miami, Ohio, July 2007.

Dazhang Gu, Lonnie Welch, Sarah Wyatt, Klaus Ecker, "Toward a Methodology for Discovery of Regulatory Motifs in Plants," poster, Ohio Collaborative Conference on Bioinformatics, Miami, Ohio, July 2007.

Dazhang Gu, Lonnie Welch, Sarah Wyatt, and Klaus Ecker, "Toward a Methodology for Discovery of Regulatory Motifs in Plants," poster, International Symposium on Bioinformatics Research and Applications (ISBRA), Atlanta, GA, May 2007.

Allan M. Showalter, Brian Keppler, Jason Yerardi, Tom Conley, Lonnie R. Welch, and Dazhang Gu, "A Bioinformatics Approach to the Identification, Classification, and Analysis of Hydroxyproline-Rich Glycoproteins," poster, International Symposium on Bioinformatics Research and Applications (ISBRA), May 2007, Atlanta, GA.

Jens Lichtenberg and Lonnie Welch, "Design Pattern for Protein Identification," poster, International Symposium on Bioinformatics Research and Applications (ISBRA), Atlanta, GA, May 2007.

Jens Lichtenberg, Lonnie Welch, John Kopchick, Shigeru Okada, Lucila Sackmann-Sala, and Sudha Sankaran, "Post-translational Modification Analysis," 4th Annual Ohio Mass Spectrometry Symposium, March 2007, Columbus, Ohio.

Jens Lichtenberg and Lonnie Welch, "Design Pattern for Protein Identification," 4th Annual Ohio Mass Spectrometry Symposium, March 2007, Columbus, Ohio.

Jens Lichtenberg and Lonnie Welch, "Pattern Language for Biomarker Discovery," poster, 4th Annual Ohio Mass Spectrometry Symposium, March 2007, Columbus, Ohio.