Dr. Erich Baker

Dr. Erich Baker
Chair, Department of Computer Science; Professor, Bioinformatics
Website
High Res Photo
CV

Chair, Department of Computer Science
Professor, Bioinformatics

Education

  • PhD, University of Tennessee (2000)
  • MS, Barry University (1996)
  • BA, University of Notre Dame (1994)
Academic Specialization: Bioinformatics

Dr. Baker continues to drive the direction of research in bioinformatics. His early background in bench science in the area of immunology, and a transformative postdoctoral position in early genome integration, with specific emphasis in computation, data integration and harmonization, gives Dr. Baker a broad background in systems biology, data management, and bioinformatics. His focus as a PI-, co-PI-, or co-investigator on several large, distributed informatics and data mining projects has been pivotal in establishing best practices in multi-domain data integration and distributed collaborations, and investigating novel algorithm approaches in exploring a diversity of omic datasets. Applications resulting from these experiences cover well-documented LIMS and data integration systems that attempt to bring the data and analytic tools of biology closer to domain experts. 

 

 

Publications

  • Hill, D. P., Harper, A., Malcolm, J., McAndrews, M. S., Mockus, S. M., Patterson, S. E., Reynolds, T., Baker, E. J., Bult, C. J., Chesler, E. J., & Blake, J. A. (2019). Cisplatin- resistant triple-negative breast cancer subtypes: Multiple mechanisms of resistance. BMC Cancer, 19(1), 1039. https://doi.org/10.1186/s12885-019-6278-9.
  • Jason Bubier, David Hill, Gaurab Mukherjee, Timothy Reynolds, Erich J. Baker, Alexander Berger, Jake Emerson, Judith A Blake, Elissa J. Chesler. Curating Gene Sets: Challenges and Opportunities for Integrative Analysis. Database. Volume 2019. 2019, baz036, https://doi.org/10.1093/database/baz036.
  • Bubier, Jason, Sutphin, George, Reynolds, Timothy, Korstanje, Ron, Fuksman-Kumpa, Axis, Baker, Erich, Langston, Michael, and Chesler, Elissa. Integration of heterogeneous functional genomics data in gerontology research identifies genes and pathway underlying aging across species. PLoS ONE 14(4): e0214523. https://doi.org/10.1371/journal.pone.0214523.
  • Moore, Sharon, Baker, Erich, Grant, Kathy, Gonzales, Steven, Zollinger, Elizabeth, and Radunskaya, Ami. Time for a Drink? A Mathematical Model of Non-Human Primate Alcohol Consumption. Frontiers in Applied Mathematics and Statistics. 2019 Feb 22. Vol. 5. https://doi.org/10.3389/fams.2019.00006.
  • Dozier BL, Stull CA, Baker EJ, Ford MM, Jensen JP, Finn DA, and Grant KA. Chronic ethanol drinking increases during the luteal menstrual cycle phase in rhesus monkeys: implication of progesterone and related neurosteroids. Psychopharmacology (Berl). 2019 Jan 15. pp 1- 12. doi: 10.1007/s00213-019-5168-9.
  • Phillips, Charles, Wang, Kai, Baker, Erich, Bubier, Jason, Chesler, Elissa, and Langston, Michael. On Finding and Enumerating Maximal and Maximum k-Partite Cliques in k-Partite Graphs. Algorithms. 2019, 12(1), 23. https://doi.org/10.3390/a12010023.
  • Bubier, Jason, Sutphin, George, Reynolds, Timothy, Korstanje, Ron, Fuksman-Kumpa, Axis, Baker, Erich, Langston, Michael, and Chesler, Elissa. Integration of heterogeneous functional genomics data in gerontology research identifies genes and pathway underlying aging across species. BioRxiv, October, 2018. https://doi.org/10.1101/451013. [Preprint]
  • Bubier, Jason, Vivek Philip, Christopher Quince, James Campbell, Yanjiao Zhou, Tatiana Vishnivetskaya, Suman Duvvuru, Rachael Hageman Blair, Juliet Ndukum, Kevin D Donohue, Charles Phillips, Carmen Foster, David Mellert, George Weinstock, Cymbeline T Culiat, Erich J Baker, Michael A Langston, Bruce O’Hara, Anthony V Palumbo, Mircea Podar, Elissa J Chesler. Systems Genetic Discovery of Host-Microbiome Interactions Reveals Mechanisms of Microbial Involvement in Disease. BioRxiv, January 1, 2018. https://doi.org/10.1101/349605. [Preprint]
  • S M Ashiqul Islam, Christopher Michel Kearney and Erich Baker. Classes, Databases, and Prediction Methods of Pharmaceutically and Commercially Important Cystine-Stabilized Peptides. Toxins 2018, 10(6), 251. https://doi.org/10.3390/toxins10060251.
  • S.M. Ashiqul Islam, Christopher Michel Kearney & Erich J. Baker. Assigning biological function using hidden signatures in cystine-stabilized peptide sequences. Scientific Reports volume 8, Article number: 9049 (2018). DOI:10.1038/s41598-018-27177-8.
  • Islam SMA, Heil BJ, Kearney CM, Baker EJ. Protein classification using modified n-grams and skip-grams. Bioinformatics. 2018 May 1;34(9):1481-1487. doi: 10.1093/bioinformatics/btx823. PubMed PMID: 29309523
  • SM Ashiqul Islam, Christopher Michel Kearney, Ankan Choudhury, Erich J. Baker. Protein Classification using Modified N-Gram and Skip-Gram Models: Extended Abstract. The 8th ACM International Conference. 2017. DOI: 10.1145/3107411.3108193.
  • Baker EJ, Walter NA, Salo A, Rivas Perea P, Moore S, Gonzales S, Grant KA. Identifying Future Drinkers: Behavioral Analysis of Monkeys Initiating Drinking to Intoxication is Predictive of Future Drinking Classification. Alcohol Clin Exp Res. 2017 Mar;41(3):626-636. doi: 10.1111/acer.13327.
  • Bubier JA, Langston MA, Baker EJ, Chesler EJ. Integrative Functional Genomics for Systems Genetics in GeneWeaver.org. Methods Mol Biol. 2017;1488:131-152.
  • Akinyeke T, Weber SJ, Davenport AT, Baker EJ, Daunais JB, Raber J. Effects of alcohol on c-Myc protein in the brain. Behav Brain Res. 2017 Mar 1;320:356-364. doi: 10.1016/j.bbr.2016.11.009.
  • Jason A. Bubier, Troy D. Wilcox, Jeremy J. Jay, Michael A. Langston, Erich J. Baker, Elissa J. Chesler. Cross-Species Integrative Functional Genomics in GeneWeaver Reveals a Role for Pafah1b1 in Altered Response to Alcohol. Frontiers in Behavioral Neuroscience 01/2016; 10. DOI:10.3389/fnbeh.2016.00001
  • Erich Baker, Jason A. Bubier, Timothy Reynolds, Michael A. Langston, Elissa J. Chesler. GeneWeaver: data driven alignment of cross-species genomics in biology and disease. Nucleic Acids Research 12/2015; 44(D1):gkv1329. DOI:10.1093/nar/gkv1329
  • S M Ashiqul Islam, Tanvir Sajed, Christopher Michel Kearney, Erich J Baker. PredSTP: A highly accurate SVM based model to predict sequential cystine stabilized peptides. BMC Bioinformatics 07/2015; 16(210):1. DOI:10.1186/s12859-015-0633-x
  • Jason A Bubier, Charles A Phillips, Michael A Langston, Erich J Baker, Elissa J Chesler. GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data. Mammalian Genome 06/2015; 26(9). DOI:10.1007/s00335-015-9575-x
  • Speegle, G., Baker, E. Integration of Big Data Components for NoSQL Problems, Proceedings of the 2014 International Conference on Advances in Big Data Analytics, 2014. 128-134.
  • Erich J. Baker, Jonathan Farro, Steven Gonzales, Christa Helms and Kathy grant. Chronic alcohol self-administration in monkeys shows long-term quantity/frequency categorical stability. ACER. 2014 Nov;38(11):2835-43.
  • Charles A Phillips, Erich J Baker, Elissa J Chesler, Michael A Langston. Algorithmic tools for tripartite data analysis. BMC Bioinformatics 09/2014; 15(Suppl 10):P32-P32. DOI:10.1186/1471-2105-15-S10-P32
  • Pablo Rivas-Perea, Erich Baker, Greg Hamerly, Bryan F Shaw. Detection of leukocoria using a soft fusion of expert classifiers under non-clinical settings. BMC Ophthalmology 09/2014; 14(1):110. DOI:10.1186/1471-2415-14-110
  • EJ Baker, C Culpepper, C Philips, J Bubier, M Langston and EJ Chesler. Identifying common components across biological network graphs using a bipartite data model. GLBIO. BMC Proceedings 2014, 8(Suppl 6):S4.
  • Daunais, Davenport, Helms, Gonzales, Hemby, Friedman, Farro, Baker and Grant. Monkey alcohol tissue research resource: banking tissues for alcohol research. ACER. 2014 Jul;38(7):1973-81.
  • Yun Zhang, Charles A. Philips, Gary L. Rogers, Erich J. Baker, Elissa J. Chesler and Michael A. Langston. On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types. BMC Bioinformatics. 2014. 15(1):110.
  • Elissa J. Chesler and Erich J. Baker. Contributions of genomic and informatics approaches to understanding alcohol dependence: from genes to networks. Neurobiology of Alcohol Dependence. 2014:523-537.
  • Jeremy J Jay, Erich J Baker and Elissa J Chesler. A Context-Driven Gene Prioritization Method for Web-based Function Genomics. Bioinformatics Research and Applications, Springer. 161-172, 2013
  • Erich J. Baker. The Bioinformatics of Behavioral Neuroscience. International Review of Neurobiology. 2012. 103:19-38.
  • Erich J. Baker, Jeremy Jay, Jason Bubier, Michael Langston and Elissa Chesler. The Ontological Discovery Environment: A web-based system for integrative functional genomics analysis. Nucleic Acids Research. 2012. 40(1) D1067-1076.
  • Erich J. Baker and Elissa J. Chesler The importance of open source integrative genomics to drug discovery. Current Opinions in Drug Discovery. 2010. 13(3):310-316.
  • Erich J. Baker, Zuopan Li, Jeremy Jay, Vivek Philip, Yun Zhang, Michael A. Langston, Elissa J. Chesler Ontological discovery environment: A system for integrating gene-phenotype associations. Genomics, 2009. 94:377-387.
  • Baker, L.E. and Baker, E.J. Reuniting Families: using phenotypic and genotypic forensic evidence to identify unknown immigrant remains. Journal of Forensic Science, 2008 53(1).
  • Baker, E.J., Lin, Guan, Liu, Huadong, and Kosuri, R. NFU-enabled FASTA: Distributing bioinformatics applications over wide-area networks. Source Code for Biology and Medicine, 2007 Nov 26;2:8.
  • Kirov SA, Peng X, Erich Baker, Schmoyer D, Zhang B and Snoddy J. GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments for sets of genes and gene products. BMC Bioinformatics. 2005 Mar 24;6(1):72.
  • Erich Baker, B. Jackson, L. Galloway, et. al. MuTrack: an on-line distributed database for phenotypic discovery in mutagenized mice. BMC Bioinformatics. 2004 5:11.
  • Baker, E.J., Gerrard, D., Bamberger, E.G., Lozzio, C.B., and Ichiki, A.T.. HL-60-conditioned media induces myeloperoxidase in K-562 leukemia cells. Leukemia Research, 26:1017-1025, 2002.
  • Baker, E.J., Ichiki, A.T., Day, N.E., Andrews, R.B., Bamberger, E.G., and Lozzio, C.B. Simultaneous flow cytometric measurement of K-562 megakaryocytic differentiation and CD56+ large granular lymphocyte cytotoxicity. Journal of Immunological Methods. 253(1-2):37-44, 2001.
  • Baker, E.J., Ichiki, A.T., Hodge J.W., Sugantharaj, D., Bamberger, E.G., and Lozzio, C.B. PMA-treated K-562 leukemia cells mediate a TH2-specific expansion of CD4+ T cells in vitro. Leukemia Research 24:1049-1057, 2000.
  • Ichiki, A.T., Langenberg, M., Baker, E.J., Hodge, J.W., Bamberger, E.G., Gerard, D.A., and Lozzio, C.B. Differential regulation of IL-1α and IL-1β in K-562 cells. Journal of Interferon and Cytokine Research 18:1045-1050, 1998.
School of Engineering
& Computer Science
One Bear Place #97356
Waco, TX 76798-7356
Computer Science
One Bear Place #97141
Waco, TX 76798-7141