BINF 3350: Introduction to Genomics and Bioinformatics
BINF 43C9: Capstone
BINF 3360: Introduction to Computational Biology
CSI 3335: Introduction to Databases and Applications
CSI 2300: Introduction to Datascience
DSC 3310: Cloud Computing
Publications
Journal 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.
Gassen, Nowak, Henderson, Alexandria, Weaver, Baker, Muehlenbein.
Individual Differences in COVID-19 Pandemic Fatigue and Travel Behavior.
(2022) Stress and Health. submitted for publication.
Gassen, Nowak, Henderson, Alexandria, Weaver, Baker, Muehlenbein.
Exploring links between pathogen avoidance motivation, COVID-19 case
counts, and immune function. (2022) American Journal of Human Biology.
doi.org/10.1002/ajhb.23833 in print.
Muehlenbein, Gassen, Nowak, Henderson, Weaver, Baker. Waco COVID
Survey: A Community-Based SARS-CoV-2 Serological Surveillance Study in
Central Texas. (2022) Journal of Community Health.
doi.org/10.1007/s10900-022-01143-y.
Sattgast, Lara, Branscum, Adam, Newman, Natali, Gonzales, Steven,
Benton, Mary Lauren, Baker, Erich, Grant, Kathleen, Turner, Russell, and
Iwaniec, Urszula. Ethanol Alters the Relationship Between IGF-1 and Bone
Turnover in Male Macaques. (2022) Journal of Endocrinology.
doi.org/10.1530/JOE-22-0075.
Jeffrey Gassen, Tomasz J Nowak, Alexandria D Henderson, Sally P
Weaver, Erich J Baker, Michael P Muehlenbein. Longitudinal changes in
COVID-19 concern and stress: Pandemic fatigue overrides individual
differences in caution. (2022) Journal of Public Health Research.
doi.org/10.1177/22799036221119011.
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.
Conference Proceedings and
Posters
Javier Orduz-Ducuara*, Pablo Rivas, Erich Baker. Quantum Machine
Learning Foundations and Applications: A Succinct Literature Review.
(2021). Transactions on Computational Science & Computational
Intelligence. Accepted for publication.
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