BINF 3350: Introduction to Genomics and Bioinformatics
BINF 43C9: Capstone
BINF 3360: Introduction to Computational Biology
CSI 3335: Introduction to Databases and Applications
Publications
Journal 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.
Conference Proceedings and Posters
Reynolds, T., Bubier, J. A., Agrawal, A., Baker, E. J., & Chesler, E. J. Integrative cross-species analysis uncovers convergent genomic regulatory features associated with complex disease. NIDA Genetics and Epigenetics Cross-Cutting Research Team Meeting, Rockville, MD. January, 2019.
Reynolds, T., Emerson, J., Berger, A., Bubier, J., Baker, E. J., & Chesler, E. J., GeneWeaver.org: A RESTful service for multi-species data integration in functional ge‐ nomics. Intelligent Systems for Molecular Biology, Basel, Switzerland. August, 2019.
S. Moore, A. Radunskaya, E. Zollinger, N. Walter, K. Grant, E.Baker. A mathematical model of blood ethanol concentration levels in rhesus macaques. 42nd Annual RSA Scientific Meeting, Minneapolis, MN. ACER 2019.43.issue-s1. doi.org/10.1111/acer.14056.
Pablo Rivas, Sharon Moore, Urszula Iwaniec, Russell Turner, Kathy Grant, and Erich baker. Optimizing Support Vector Machine Analysis in Low Density Biological Data Sets. IEEE, 2018 International Conference on Computational Science and Computational Intelligence (CSCI). Pre-print: https://www.rivas.ai/pdfs/rivas2018optimizing.pdf DOI 10.1109/CSCI.2018.00262.
E.J. Chesler, T. Reynolds, J.A. Bubier, C.A. Phillips,M.A. Langston, E.J. Baker. Finding convergent behavioral features of alcohol use disorder through functional genomic comparison across species. 41st Annual RSA Scientific Meeting, San Diego, CA. ACER 2018.65.issue-s1.
EJ Baker, SE Moore, Waltern N, Gonzalas S, Grant K. Distinctive Ethanol Consumption Patterns in the Monkey Schedule-Induced Polydipsia Model. 41st Annual RSA Scientific Meeting, San Diego, CA. ACER 2018.330.issue-s1.
Moore S.E., Radunskaya A., Zollinger E., Walter N., Grant K., and Baker, E. Simulation of Non-Human Primate Alcohol Consumption. 41st Annual RSA Scientific Meeting, San Diego, CA. ACER 2018.755.issue-s1.
SM Ashiqul Islam, Christopher Michel Kearney, Ankan Choudhury, and Erich J. Baker. 2017. Protein Classification using Modified N-Gram and Skip-Gram Models: Extended Abstract. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics (ACM-BCB ’17). ACM, New York, NY, USA, 586-586. DOI: https://doi.org/10.1145/3107411.3108193
Moore S.E., Radunskaya A., Zollinger E., Walter N., Grant K., and Baker, E. Modeling non-human primate alcohol self-administration studies. 40th Annual RSA Scientific Meeting, Denver, CO. ACER 2017.41.issue-S1.
Yang, Qi, Greg Speegle, Erich Baker. On Using Cached Results to Enumerate Maximal k-Cliques in GeneWeaver. IEEE ICNC-FSKD. Proceedings of the 13th International Conference on Natural Computation, Fuzzy Systems, and Knowledge Discovery. 2017. https://doi.org/10.1109/FSKD.2017.8393097.
Reynolds T., Baker E., and Chesler E. Grading ontology hierarchies: automated model checking using genomic data. 25th Conference for Molecular Biology. Prague, Czech Republic, July, 2017.
EJ Baker, C Phillips, J Bubier, M Langston and EJ Chesler. Efficient hierarchical biological network comparison in GeneWeaver using a bipartite edge list store. ISMB Conference. Dublin, IRE, July, 2015.
Charles A Phillips, Kai Wang, Jason Bubier, Erich J Baker, Elissa J Chesler, Michael A Langston: Scalable Multipartite Subgraph Enumeration for Integrative Analysis of Heterogeneous Experimental Functional Genomics Data. Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, Atlanta, Georgia; 01/2015
Aleksandr Salo, Steven Gonzales, Kathy Grant and Erich J Baker. Automated prediction of drinking categories in monkeys undergoing chronic alcohol self-administration. RECOMB. Warsaw, PLD, April, 2015.
J. Bubier, C. Phillips, M. Langston, E. Baker, E. Chesler: Application and validation of cross species integration of functional genomics studies in Geneweaver. 37th Annual Scientific Meeting of the Research-Society-on-Alcoholism; 06/2014
J. A. Bubier, J. Jay, M. A. Langston, E. J. Baker, E. J. Chesler. Cross-species integrative functional genomics using Geneweaver reveals a role for pafah1b1 in alcohol response preference. 37th Annual Scientific Meeting of the Research-Society-on-Alcoholism; 06/2014
E. Baker, J. Farro, S. Gonzales, J. Daunais, K. Grant. The Monkey Alcohol Tissue Research Resource (MATRR). 37th Annual Scientific Meeting of the Research-Society-on-Alcoholism; 06/2014
True J. Price, Kathy A. Grant and Erich J. Baker. Analysis of resting-state fMRI using pearson-VII mixture modeling. International ISMB/ECCB Conference. Berlin, DE, July, 2013.
Erich Baker, Jason Bubier, Jeremy Jay and Elissa Chesler. GeneWeaver: Building context-driven similarity on empirically-defined functional genomics relationships. International ISMB Conference, Berlin, DE, July, 2013.
E. J. Chesler, J. J. Jay, M. A. Langston, E. J. Baker, J. A. Bubier. Cross species integrative functional genomics of alcohol related behaviors in the Geneweaver web based software system. 16th World Congress of the; 09/2012
Nusser KD, Helms CM, Wakeling VA, Stull CA, Woodall AL, Daunais JB, Baker EJ, Davenport AT, Soltau N, Gonzales SW, Ferguson B, Hemby SE, Friedman DP, Grant KA. A Monkey Alcohol Tissue Research Resource (MATRR). International Society on the Biomedical Research on Alcohol (ISBRA). Sapporo, Japan, 2012.
Jeremy Jay, Erich Baker, Jason Bubier, Elissa Chesler. GeneWeaver.org: a platform for the analysis of gene set associations. International ISMB Conference, Long Beach, CA, July, 2012.
Charles Philips, Jeremy Jay, Erich Baker, Elissa Chesler, and Michael Langston. Bipartite graph decomposition in the presence of noise, with applications to biological data clustering. Cologne-Twente Workshop on Graphs and Combinatorial Optimization 2012.
Jeremy Jay, Erich Baker, Elissa Chesler. Extracting relationships from integrated functional genomics data with the Ontological Discovery Environment. International ISMB Conference, Vienna, Austria, July, 2011.
Daunais JB, Baker EJ, Davenport AT, Farro J, Gonzales SW3, Ferguson B, Hemby SE, Friedman DP, Grant KA. Monkey Alcohol Tissue Research Resource, 34th Annual RSA Research Meeting, Atlanta, GA, 2011.
V.M. Philip, J.J. Jay, M.A. Langston, E.J. Baker, E.J. Chesler. Integrating convergent evidence across species to find QTL candidate genes using the Ontological Discovery Environment. Society of Neuroscience, San Diego, CA, 2010, B4, 478.8.
Jeremy J. Jay, Michael A. Langston, Erich J. Baker, Elissa J. Chesler. High and Dry in a sea of genes: highlighting drug abuse and alcoholism relationships with the Ontological Discovery Environment. Society of Neuroscience, San Diego, CA, 2010, B4, 478.7.
Daunais JB, Chesler EJ, Davenport AT, Baker EJ, Hemby SE, Friedman DP, Grant KA. What’s a MATRR?. MMM Meetings, Ann Arbor, MI, 2010
Jeremy J Jay, Vivek Philip, Zuopan Li, Yun Zhang, Roumyana Kirova, Michael A Langston, Erich J Baker, Elissa J Chesler. The Ontological Discovery Environment: Integrating gene-centered data across diverse experiments. UT-ORNL-KBRIN Bioinformatics Summit, March, 2009.
Jeremy J Jay, Vivek Philip, Zuopan Li, Yun Zhang, Roumyana Kirova, Erich J Baker, Michael A Langston, Elissa J Chesler. The Phenome Interdependency and Similarity Hierarchy: A tool for genome-scale phenotypic analysis. 22nd International Mammalian Genome Conference, Prague, Czech Republic. Nov 2-5, 2008.
JJ Jay, Z Li, V Philip, Y Zhang, A Perkins, R Kirova, EJ Baker, MA Langston, EJ Chesler. Ontological Discovery Environment Web Tools. UT-ORNL-KBRIN Bioinformatics Summit, April, 2007.
Erich J. Baker, Zuopan Li, Jeremy Jay, Vivek Philip, Yun Zhang, Michael A. Langston, Elissa J. Chesler. OntologicalDiscovery.org: A web resource for the empirical discovery of phenotypic relations across species and experimental systems. Proceedings from the 21st International Mammalian Genome Conference, Kyoto, Japan, 2007.
E.J. Chesler, J.P. Hulvey, R. Kirova, J. Jay, Z. Li, V. Philip, Y. Zhang, H.R. Glenn, D.J. Swanson, M.A. Langston, D.A. Goldowitz, E.J. Baker. The Ontological Discovery Environment: An internet resource for integration of phenomic information through gene-centric analyses. Proceedings from the Society of Neuroscience, San Diego, CA, 2007. 100.3(23).
Batra S, Lee M, and Baker, E. Identification of RNAi-associated phenotypes in caenorhabditis elegans. Proceedings from the 16th International C. elegans Meeting, UCLA, CA, 2007 S(54).
Li, Z., Kirova, R., Perkins, A., Baker, E., Langston, M.A., Chesler, E. Mapping the phenome space using combinatorial analysis of the empirical associations of gene and phenotypes. Proceedings from the International Mouse Genome Conference, Charleston, SC, 2006.
Kirova, R., Perkins, A., Li, Z., Pitts, S.M., Baker, E., Langston, M.A., Chesler, E. J. Mapping of ethanol related phenome space using gene-centric combinatorial methods. Research Society on Alcoholism. Baltimore, Maryland, 2006.
Sushil, B., Myeongwoo, L., and Baker, E. RNAi phenotypes in C. elegans on the basis of sequence similarity. Development and Evolution, University of Wisconsin-Madison, WI, June, 2006, S(74).
Chessler, E., Kirova, R., Li, Z., Perkins A., Baker, E., Langston, M. Gene-centric combinatorial approaches for discovery of phenotype ontology. Eumorphia 3rd Annual Meeting, 23-24 February, 2006.
Ravi Kosuri, Jay Snoddy, Stefan Kirov and Erich Baker. IBP-BLAST: using logistical networking to distribute BLAST databases over a wide are network. Proceedings from the 12th International Conference on Intelligent Systems in Molecular Biology and the 3rd European Conference on Computational Biology. Glasgow, Scotland, July 34-Aug 4, 2004.
Baker, L.E. and Baker, E.J. Reuniting Families: using phenotypic and genotypic forensic evidence to identify unknown immigrant remains. Journal of Forensic Science Proceedings. p. 297, 2004.
Baker, E.J. and Baker, L.E. The creation of an anthropometric and DNA database to aid in the identification of illegal immigrant remains. American Journal of Physical Anthropology. Supplement 36:58, 2004.
Baker, E.J. and Baker, L.E. Reuniting Families: an on-line genetic database for identification and repatriation of forensic remains. American Association of Forensic Scientists, Dallas, TX, Feb, 2004.
J. Snoddy, S. Kirov, B. Zhang, S. Wang, X. Peng, A. Tebbe, B. Jackson, L. Galloway, D. Schmoyer, F. Bares, M. Galloway, E. Uberbacher, M. Leuze, B. Jones, F. Larimer, R. Williams, K. Grant, D. Goldowtiz, B. Whitehead and Erich Baker. Comparative and collaborative bioinformation systems required to study complex regulatory networks: sets of genes and sets of researchers. Cold Spring Harbor, Systems Biology. May, 2003. Supplement.
S. Kirov, B. Zhang, H-N. Wang, X. Peng, A. Tebbe, B. Jackson, L. Galloway, D. Schmoyer, F. Baes, M. Galloway, E. Uberbacher, M. Leuze, B. Jones, F. Larimer, Erich Baker, B. Whitehead and J. Snoddy. GeneKeyDB and BioTutos: comparative and collaborative bioinformation systems to study complex regulatory networks. Cold Spring Harbor, Systems Biology. May 2003. Supplement.
Stefan Kirov, Baker, E.J., Denise Schmoyer and Bing Zhang. High throughput gene and sequence analysis based on GeneKeyDB relational data mining. Tennessee Mouse Genome Consortium, Nashville, Tennessee, Jan, 2003.
Lelslie Galloway, Barbara Jackson, Denise Schmoyer, Baker, E.J., Fred Baas and Jay Snoddy. The TMGC Web Site and Mutrack. Tennessee Mouse Genome Consortium Meeting, Nashville, Tennessee, Jan, 2003.
Erich Baker, Brynn Jones, Doug Hyatt, et al. Integrating Computational Analysis of Orthologous Gene Sequences and RNA Expression Analysis in the Mouse Skin. Cold Spring Harbor, Genome Sequencing and Biology. May, 2002. Supplement.
Erich Baker, Doug Hyatt, Barbara Jackson, et al. Comparative and Collaborative Bioinformatics Required to Study the Gene Regulatory Networks that Create Phenotypes. Cold Spring Harbor, Genome Sequencing and Biology. May, 2002. Supplement.
Philip LoCascio, Norman Doggett, Erich Baker, et al. U.S. Department of Energy National Laboratories Collaborative High Throughput Genome Analysis Framework. Cold Spring Harbor, Genome Sequencing and Biology. May, 2002. Supplement.
Philip LoCascio, Erich Baker, Doug Hyatt, et al. An Ontological Framework for Terascale Biological Computing. Cold Spring Harbor, Genome Sequencing and Biology. May, 2002. Supplement.
Erich Baker, Doug Hyatt, Barbara Jackson, et al. Comparative and Collaborative Bioinformatics Systems to Promote Mammalian Phenotype Analysis and the Elucidation of Regulatory Networks. DOE Genome Contractor-Grantee Workshop IX. pp 65-67. January, 2002.
E. J. Michaud, J. R. Snoddy, E. J. Baker, et al. Genome-Wide, Gene-Driven Chemical Mutagenesis for Functional Genomics: The ORNL Cryopreserved Mutant Mouse Bank. DOE Genome Contractor-Grantee Workshop IX. pp 45-46. January, 2002.
Brynn H. Jones, Jay R. Snoddy, Cymbeline T. Culiat, Mitchel J. Doktycz, Peter R. Hoyt, Denise D. Schmoyer, Erich J. Baker, et al. Functional Analysis of Gene Regulatory Networks Underlying Skin Biology and Environmental Susceptibility. DOE Genome Contractor-Grantee Workshop IX. p 39. January, 2002.
Baker, E.J., Jackson, B., Chen G.L., Schmoyer D., Miller D., Snoddy J., and the Tennessee Mouse Genome Consortium. TMGC: MuTrack, A Collaborative Database for Integrated Computational and Experimental Research in the Tennessee Mouse Genome Consortium. Proceedings of the 15th Annual Mouse Genome Consortium. Edinburgh, Scotland, October, 2001.
Baker, E.J., Barbara Jackson, et al. TMGC:Mutrack, A Collaborative Database for Phenotype Screening in the Tennessee Mouse Genome Consortium. Cold Spring Harbor, Genome Sequencing and Biology. May, 2001. Supplement.
Baker, E.J., Barbara Jackson, Denise Schmoyer, et al. Large-Scale Mammalian Phenotype and Genotype Analysis: Towards Integrated Computational and Experimental Research. Cold Spring Harbor, Genome Sequencing and Biology. May, 2001. Supplement.
Schimmel, S., Baker, E.J., Gerrard, D.A., Day, N.E., and Ichiki, A.T. Induction of K-562 cells to elongate and adhere. American Association of Cancer Research, New Orleans, LA, 2001. Supplement.
Baker, E.J., Day, N.E., and Ichiki A.T. Type 2 immune response mediated by PHA-treated K-562 leukemia cells. American Association of Cancer Research Annual Meeting, San Francisco, CA, 2000.
Baker, E.J. and Ichiki, A.T. K-562 cells require treatment with phorbol 12-myristate 13-acetate to function as antigen presenting cells. Proceedings of the 16th Annual South-Central Flow Cytometry Association Meeting, May 1-2, 1998.
Baker, E.J. and Ichiki, A.T. K-562 cells treated with PMA can stimulate T cells to produce cytokines. The 1998 Macrophage Conference, Paris, Supplement, p26, 1998.
Brooke Morris. TITLE FORTHCOMING. Department of Biology, 2018 - present, co-mentor.
Timothy Reynolds. Information condensation in Gene Set relationships, Ph.D. Candidate, Institute for Biomedical Studies, Baylor University, 2015 - present, mentor.
Mishu Islam, Automated Discovery of Knottins, Ph.D. Candidate, Institute for Biomedical Studies, Baylor University, 2014 - 2018. co-mentor.
Timothy Zumwalt, Type I helper and cytotoxic T cell activity in microsatellite instable colorectal cancer, Ph.D. Candidate, Institute for Biomedical Studies, Baylor University, committee member.
Jeremy Jay, Graph theory applications in functional genomics, Ph.D., 2014, Department of Computer Science, University of Maine, committee member.
Sharath Rongali, Identification of germline and somatic cell specific genes essential for ovulation in Caenorhabditis elegans, Ph.D., 2011, Institute for Biomedical Studies, Baylor University, committee member.
Baoqing Ding, On the Origin of Lake Malawi Cichlid Species and Mechanisms of their Maintenance, Ph.D., 2011, Department of Biology, Baylor University, committee member.
Zun Liu, Determining the functionality of retroviral elements in nuclear export in plants for the improvement of a plant RNA virus vector. Ph.D., 2010, Institute for Biomedical Studies, Baylor University, committee member.
Sushil Batra, Identification of phenotype in caenorabhditis elegans on the basis of sequence similarity. Ph.D., 2007, Institute for Biomedical Studies, Baylor University, co-mentor.
Masters Students
Kelechi Fletcher, Identifying Phylogenetic Hierarchies and Functional Modules In Biological Networks Through Hierarchical Similarity Decomposition, M.S. Department of Computer Science, Baylor University, 2016 - 2018, mentor
Alex Salo, Automated discovery of drinking categories in monkeys in a self-induced alcohol drinking protocol, M.S. Department of Computer Science, Baylor University, 2015 - 2016, mentor.
Alvin Jude, Giving the users a hand: towards touchless hand gestures for the desktop, M.S., 2015, Department of Computer Science, committee member.
Ryan Hennings, Automated Detection of Leukocoria, M.S. Computer Science, 2014, committee member.
David Morillo, Bootstrapping bipartite graphs consisting of edges based on ontology terms occurring in scientific abstracts. M.S., Computer Science, 2010, mentor.
Kristi DeLeon, Dynamics and interaction studies of angiotensin I and II: experiment and molecular modeling, M.S., Biomedical Studies, 2009, committee member.
Stephen Bush, Automated sequence homology: using empirical correlations to create graph-based networks for the elucidation of protein relationships. M.S., Bioinformatics, 2008, mentor.
Kevin Kastner, GeneKeyAPI: a set of tools for dynamically updating and accessing GeneKeyDB. M.S., Computer Science, 2008, mentor.
Garvin Lee Chandler, Influenza hemagglutinin expression in Nicotiana tabacum and Nicotiana benthamiana. M.S., Biomedical Studies, 2007, committee member.
Nick Lin, Distributing sequence similarity algorithms on scale-free networks, M.S., 2006, mentor.
Ravi Kosuri, NFU-enabled FASTA. M.S., Computer Science, 2005, mentor.
Undergraduate Honors Thesis
Natasha Lie, Predication of novel genes involved in retinitis pigmentosa from GeneWeaver, B.S. Biochemistry, expected graduate – May, 2016, mentor.
True Price, Analysis of resting state fMRI using Pearson-VII mixture modeling, B.S. Bioinformatics, 2013, mentor.
Ali Beck, The semantic web: an alternative approach to dynamic data definition and integration in medical informatics systems, B.S., Computer Science, 2006, mentor.Top