Eddy Johana Bautista, PhD. 10 Discovery Drive Farmigton, CT-06032 [email protected] (860) 837-2908

EDUCATION

UNIVERSITY OF CONNECTICUT – Storrs, CT Ph., Chemical Engineering May 2014 GPA: 3.78/4.00 Honors: • Doctoral Dissertation, Fellowship Fall-2012

UNIVERSITY OF CONNECTICUT – Storrs, CT Master of Sciences, Chemical Engineering December-2012 GPA: 3.78/4.00

UNIVERSIDAD INDUSTRIAL DE SANTANDER (UIS)– Bucaramanga, Colombia B.S, Chemical Engineering September-2007 GPA: 4.34/5.00 Honors: • Honor Student 2002-2005 • Cum Laude • Exchange research student at Texas A&M University, August 2006-March 2007

RESEARCH INTERESTS

• Metabolic and gene regulatory networks • Bioinformatics reconstruction and analysis • Design and optimization of biochemical • Functional analysis of metagenomes and processes metatrascriptomes • Re-engineering of microbial strains • Computational biology tool development

RESEARCH EXPERIENCE

Postdoctoral associate, The Jackson Laboratory for Genomic Medicine. Farmington-CT (2014- present) Advisor: Dr. George Weinstock, The Jackson Laboratory for Genomic Medicine

Functional analysis of metagenomes and metatrasncriptomes (July 2014- present) • Design and code the pipelines for the functional analysis of metagenomes (16S and WGS), and metatrascriptomes. • Perform functional analysis on metagenomes samples (16S and mWGS) of prediabetic subjects with the goal of evaluating immunological triggers for diabetes as a part of the Human Microbiome Project • Formulate a model for the study of the metabolic interactions between bacteria related with periodontal disease such as Veillonella Parvula and Porphyromonas gingivalis • Conducte microbial whole-genome sequencing of a synthetic mock community of known organisms included a variety of genera commonly found on or within the human body

Eddy Johana Bautista, PhD.

Graduate Research Assistant, University of Connecticut-Chemical, Materials and Biomolecular Engineering Department. Storrs-CT (2008-2014) Advisor: Dr. Ranjan Srivastava, University of Connecticut. Title: Understanding the impact of iron availability on Bacillus anthracis metabolism

Metabolic Engineering August 2008-May 2014 • Developed and coded a methodology for understanding of metabolic insights and curation of metabolic networks, based on a genetic algorithm and flux balance analysis (GAFBA) • Generated a genome-scale metabolic model for Mycoplasma gallisepticum • Formulated a genome-scale metabolic model for Bacillus anthracis Sterne • Characterized the metabolism of Bacillus anthracis Sterne under iron poor/ iron rich conditions using a genome scale metabolic model • Evaluated possible mutations to Escherichia coli to enhance biohydrogen production using a heuristic approach. • Designed a graphic user interface in Lispworks for GAFBA

Fermentation Processes August 2008-May 2014 • Assayed the metabolism of Clostridium acetobutylicum ATCC 824 under different chemostat conditions with a constant pH of 4.5 • Executed Clostridium acetobutylicum ATCC 824 fermentation process for biobutanol production • Designed and performed fermentation process of Bacillus anthracis Sterne to measure different metabolites using bioanalyzer and colorimetric techniques • Verified the production of toxins in Bacillus anthracis Sterne' fermentation broth through Western blot analysis • Guided and trained graduate and undergraduate students for the batch production of 1,3-propanediol from pure glycerol using soil based bacterial consortium under anaerobic conditions • Designed the fermentation process for production of D-mannitol and D-fructose from glycerol using a combination of two sequential steps of yeast and Acetobacter and trained students to carry out experiments

Research Assistant, Texas A&M University-Chemical Engineering Dept. College Station-TX (2006-2007) Advisor: Dr. Jorge M. Seminario, Texas A&M University Title: Ab initio analysis of electron transport through oligoglycines.

Modeling Electron Transport August 2006-March 2007 • Studied the electron transport in molecules of benzene, naphthalene, antracene and glycine oligopeptides (1-, 3-, 6-, 9-mers) attached to gold nanoelectrodes using ab initio methods • Computed the conductance of molecular junctions composed of an oligo phenylene ethynylene (OPE) molecule sandwiched between a metallic gold or nanotube on one end and a semiconducting silicon contact on the other end • Calculated the harmonic force constant parameter for glycine oligopeptides using the FUERZA approach

TEACHING EXPERIENCE

University of Connecticut- Chemical and Biomolecular Engineering Department. Storrs-CT Teaching assistant January 2014-May 2014 Grader and proctor exams for Process dynamics and control. Conduct office hours for students.

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Chemical Engineering Senior Laboratory-University of Connecticut-Chemical and Biomolecular Engineering Department. Storrs-CT Mentor July 2012- May 2013 Set up and planned the experiment on cell culture and scale-up of a bioreactor for the senior students in the Chemical Engineering Program. Advise the students during the data analysis.

University of Connecticut- Chemical and Biomolecular Engineering Department. Storrs-CT Teaching assistant August 2008-May 2009 Graded and proctored exams for Thermodynamics II, Air Pollution and Transfer Operations II.

RELEVANT SKILLS

Spoken and Written Languages: English (fluent), Spanish (Native). Computer Knowledge: Python, , Matlab, /, Bash, R, Fortran, Gaussian, Gauss View,Visual Basic, Flash and Hysis. Laboratory Expertise: Western Blotting, Gel Electrophoresis, SDS-PAGE, whole shotgun sequencing, Incubator, Fermentor and Bioreactor System (New Brunswick BioFlo® 3000), Biochemistry Analyzer (YSI 2700 Biochemistry analyzer), HPLC, GC, Spectrophotometer, Sterilization Equipment, Carbon Dioxide and Dissolve Oxygen Concentration Probes.

PEER-REVIEWED PUBLICATIONS • B. Kanjilal, I. Noshadi, E. J. Bautista, N. Intoci, J. Helble, R. Srivastava, and R. Parnas, “Batch, Design Optimization and DNA Sequencing Study for Continuous Production of 1,3-propanediol from Waste Glycerol by a Soil Based Inoculum”. Accepted in Applied Microbiology and Biotechnology • E. J. Bautista and R. Srivastava, “Enhancing Genetic Algorithm-Based Genome-Scale Metabolic Network Curation Efficiency.” Proceeding Of The 2014 Annual Conference Companion On Genetic And Evolutionary Computation Conference (GECCO 2014). ACM, New York, NY, USA, 257-264 • E. J. Bautista, “Understanding the impact of iron availability on Bacillus anthracis metabolism”. Doctoral Dissertations. Paper 336. University of Connecticut- Digital Commons • E. J. Bautista, J. Zinski, S. Szczepanek, E. Johnson, E. Tulman, W.M. Ching S. Geary and R. Srivastava, “Curating a metabolic network via flux balance analysis: a case study with Mycoplasma gallisepticum.” PLoS Comp Bio. 9(9): e1003208 (2013) • E. J. Bautista, and R. Srivastava, “Leveraging Ensemble Information of Evolving Populations in Genetic Algorithms to Identify Incomplete Metabolic Pathways”, in ACM Proceeding Of The Fifteenth Annual Conference Companion On Genetic And Evolutionary Computation Conference Companion-GECCO 2013. July 06-10, 2013, Amsterdam, The Netherlands. • E. J. Bautista and J.M. Seminario, “Harmonic force field for glycine oligopeptides”, International Journal of Quantum Chemistry. 108 (1) (2008)180-188. • L. A. Agapito, E. J. Bautista, and J. M. Seminario, “Conductance model of gold-molecule-silicon and carbon nanotube-molecule-silicon junctions”, Physical Review B 76 (2007) 115316 1-12. • E. J. Bautista, L. Yan, and J. M. Seminario, “Ab initio analysis of electron transport in oligoglycines”, Journal Physical Chemistry 111 (39) (2007) 14552-14559 • L. Yan, E. J. Bautista, and J. M. Seminario, “Ab initio analysis of electron currents through benzene, naphthalene and anthracene nanojunctions” Nanotechnology 18 (2007) 485701 (8pp). PUBLICATIONS SUBMITTED OR IN PREPARATION • E. J. Bautista and R. Srivastava, “Impact of iron scarcity on Bacillus anthracis metabolism.” [SUBMITTED]. • E. J. Bautista and R. Srivastava, “Link between iron metabolism and quorum sensing circuit predicted in Bacillus anthracis through genome-scale metabolic reconstruction.” [MANUSCRIPT IN PROGRESS].

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• E. J. Bautista and R. Srivastava, “A tool for semi-automated curation (SeACur) of genome-scale metabolic reconstruction.” [MANUSCRIPT IN PROGRESS].

CONFERENCE ABSTRACTS AND PRESENTATIONS • C. Endicott, E. J. Bautista, K. Noll, . Wood, and R. Srivastava, “Analysis of the Metabolic Impact of (5Z)-4- Bromo-5-(Bromomethylene)-3-Butyl-2-(5H)-Furanone on Bacillus anthracis Physiology During Quorum Sensing Interference”. ASM Biodefense and Emerging Diseases Research Meeting, Oral Paper, February 2015, Washington, DC. (in review). • E. J. Bautista and R. Srivastava, “In silico analysis of Bacillus anthracis predicts link between quorum sensing circuit and iron metabolism” BMES National Meeting, Oral Paper, October 2014, San Antonio, TX • E. J. Bautista, A. M. DiVenere, and R. Srivastava, “Comparative analysis of Bacillus anthracis metabolic response in iron-rich vs. iron-poor environments” ACS National Meeting and Exposition, Oral Paper, March 2014, Dallas, TX. • E. J. Bautista and R. Srivastava, “Genome-scale metabolic analysis of the iron acquisition system of Bacillus anthracis” ACS National Meeting and Exposition, Oral Paper, March 2014, Dallas, TX. • E. J. Bautista and R. Srivastava, “Impact of iron availability on Bacillus anthracis metabolism” MIT Sloan’s BioInnovations Conference, Poster Session, February 2014, Boston, MA. • B.Kanjilal, I. Noshadi, E. J. Bautista, N. Intoci, J. Helble, R. Srivastava, R. Parnas. 1,3-propanediol batch production from pure and industrial glycerol using soil based innoculum. 35th Symposium on Biotechnology for Fuels and Chemicals. Poster session, April 2013, Portland, OR. • E. J. Bautista, A. M. DiVenere, and R. Srivastava, “Comparative analysis of the growth of Bacillus anthracis Sterne under iron replete and iron reduced condition.” ACS National Meeting and Exposition, Oral Paper, April 2013, New Orleans, LA. • E. J. Bautista, A. M. DiVenere, and R. Srivastava, “Developing a Genome-Scale Metabolic Model of Bacillus anthracis Via a Semi-Automated Curation Approach” ACS National Meeting and Exposition, Oral Paper, April 2013, New Orleans, LA. • E. J. Bautista, J. Zinski, E. Johnson, and R. Srivastava, “Use of a hybrid genetic algorithm/flux balance analysis approach to identify metabolic pathways not prediced by genome annotation”, ACS National Meeting and Exposition, Oral Paper 171, March 2012, San Diego, CA. • E. J. Bautista, J. Zinski, E. Johnson, and R. Srivastava, “Curating a genome-scale metabolic model of Mycoplasma gallisepticum via an evolutionary algorithm”, SIM Annual Meeting and Exhibition, Invited Oral Paper S90, July 2011, New Orleans, LA. • E. J. Bautista, J. Zinski, E. Johnson, R. Srivastava, “Curating a genome-scale metabolic model of Mycoplasma gallisepticum using an evolutionary algorithm.” Biochemical and Molecular Engineering XVII, Poster Session, June 2011, Seattle, WA. • E. J. Bautista, J. Zinski, E. Johnson, and R. Srivastava, “Curating A Genome-Scale Metabolic Model of Mycoplasma Gallisepticum Using An Evolutionary Algorithm” , AIChE – Society for Biological Engineering 3rd International Conference on Biomolecular Engineering,Poster Session, January 2011, San Francisco, CA.

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