Dr. Erich Baker

Dr. Erich Baker
Interim Dean, School of Engineering and Computer Science; Professor, Bioinformatics
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Interim Dean, School of Engineering and 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

  • Nowak, Hendderson, Gassen, Weaver, Baker, Muehlenbein. Is political affiliation a health risk factor during the COVID-19 pandemic? Attitudes toward vaccines, unapproved treatments, health recommendations, government response, and information sources. Journal of Health Politics, Policy, and Law. submitted for publication.
  • Nowak, Hendderson, Gassen, Weaver, Baker, Muehlenbein. Political affiliation during the COVID-19 pandemic: Attitudes toward vaccines, unapproved treatments, health recommendations, government response, and information sources. Health, Risk, and Society. submitted for publication.
  • Gassen, Nowak, Henderson, Alexandria, Weaver, Baker, Muehlenbein. Individual Differences in COVID-19 Pandemic Fatigue and Travel Behavior. (2022) Stress and Health. submitted for publication.
  • Huang, Jun and Duan, Qiang and Xing, Cong-Cong and Gu, Bo and Wang, Guodong and Zeadally, Sherali and Baker, Erich. A Fine-grained Video Traffic Control Mechanism in Software-Defined Networks. (2022) IEEE Transactions on Network and Service Management. doi: 10.1109/TNSM.2022.3164335.
  • Sharon Moore, Ami Radunskaya, Elizabeth Zollinger, Kathleen A. Grant, Steven Gonzales, Nicole A. R. Walter, Erich J. Baker. (2022) Pairing Food and Drink: a physiological model of blood ethanol levels for a variety of drinking behaviors. Mathematical Biosciences. doi.org/10.1016/j.mbs.2022.108778
  • Mary Lauren Benton, Vanessa A. Jimenez, Natali Newman, Steven W. Gonzales, Kathleen A. Grant, Russell T. Turner, Urszula T. Iwaniec, and Erich J. Baker. (2022) Dose-response effects of alcohol on biochemical markers of bone turnover in non-human primates: effects of species, sex and age of onset of drinking. Bone Reports. vol. 66. doi.org/10.1016/j.bonr.2021.101159
  • Samuel J. Shenoi and Erich J Baker. (2021) Using hierarchical similarity to examine the genetics of Behçet’s disease. BMC Research Notes 14(1). DOI: 10.1186/s13104-021-05767-6.
  • Gassen Jeffrey, Nowak Tomasz J., Henderson Alexandria D., Weaver Sally P., Baker Erich J., Muehlenbein Michael P. (2021) Unrealistic Optimism and Risk for COVID-19 Disease. Front. Psychol (12). doi.org/10.3389/fpsyg.2021.647461.
  • Palmer RHC, Johnson EC, Won H, Polimanti R, Kapoor M, Chitre A, Bogue MA, Benca-Bachman CE, Parker CC, Ursu O, Verma A, Reynolds T, Ernst J, Bray M, Kwon SB, Lai D, Quach BC, Gaddis NC, Saba L, Chen H, Hawrylycz M, Zhang S, Zhou Y, Mahaffey S, Fischer C, Sanchez-Roige S, Bandrowski A, Qing L, Shen L, Philip V, Gelernter J, Bierut LJ, Hancock DB, Edenberg HJ, Johnson EO, Nestler EJ, Barr PB, Prins P, Smith DJ, Akbarian S, Thorgeirsson T, Walton D, Baker E, Jacobson D, Palmer AA, Miles M, Chesler EJ, Emerson J, Agrawal A, Martone M, Williams RW. Integration of Evidence across Human and Model Organism Studies: A Meeting Report. Genes Brain Behav. 2021 Apr 23:e12738. doi: 10.1111/gbb.12738. Epub ahead of print. PMID: 33893716.
  • Reynolds, Timothy, Johnson, Emma C., Huggett, Spencer B., Bubier, Jason A., Palmer, Rohan H. C., Agrawal, Arpana, Baker, Erich J., Chesler, Elissa J. Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration. Neuropsychopharmacology (2020) 0:1–12; https://doi.org/10.1038/s41386-020-00795-5.
  • 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.
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