Jeffrey O'Brien is seeking a computational biology internship utilizing his strong skills in written and verbal communication, analysis, and problem solving developed through his undergraduate research studying bioinformatics and molecular evolution. He has a bachelor's degree in molecular and cell biology from the University of Connecticut with honors and minors in bioinformatics. His qualifications include proficiency with bioinformatics tools and programming languages. He has research experience analyzing genetic sequences and testing evolutionary hypotheses.

1. Jeffrey O’Brien
115 Hickory Ln. w Naugatuck, CT 06770 w (203) 598-8052 w OBrien.JeffreyM@gmail.com
Objective: Seeking a computational biology internship utilizing high-level written and verbal communication,
analytical, and problem solving skills developed from attention to procedure over three years of undergraduate
research in the fields of Bioinformatics and Molecular Evolution
Education:
UNIVERSITY OF CONNECTICUT, Storrs, CT
Bachelor of Science, Molecular and Cell Biology, August 2015
Minor in Bioinformatics, GPA: 3.87/4.00, Honors Scholar, Magna cum Laude,
Deans List (7 semesters), University Grant - Spring 2013 and Fall 2014 (merit scholarship)
Publication:
O’Brien, Jeffrey M., “An Exploration of the Phylogenetic Position of Recently Discovered Ultrasmall Archaeal
Lineages” (2015). Honors Scholar Theses. Paper 462. http://digitalcommons.uconn.edu/srhonors_theses/462
Qualifications:
• Proficiency working and submitting jobs on a Dell/LINUX bioinformatics computing cluster
• Well-versed in PERL and UNIX, including scripting, program execution, and troubleshooting
• Independent study and use of R/Biocunductor and R software environment, familiarity with Python
• Experience running command line procedures for: PERL, R, RAxML, PhyML, Muscle, Fastqc, cutadapt
• Worked with UConn Bioservices Center in assembly of hypersaline metagenome data using Velvet
• Developed computational and graphic representation pipelines for phylogenetic analysis of “omics” data
• Can navigate NIH and NCBI databases and download data from command line interface
• Recently started a project exploring evolution of crassphage, a ubiquitous phage found in human
microbiome samples. This will be continued and developed in my graduate studies
Relevant Experience:
Gogarten Lab: Storrs CT – Undergraduate Researcher January 2013 –
September
2015
• Collaborated productively over three years with a team of graduate students, post-docs and professors
examining contemporary questions in Molecular Evolution in J. Peter Gogarten’s lab utilizing advanced
computational skills, culminating in an honors thesis
• Explored genetic diversity of archaeal bacteriorhopsin sequences from publicly available metagenomic
samples utilizing UNIX, BLAST, and FastTree to curate, organize, and search databases and to create
phylogenetic graphs. Presented data processing outcomes in descriptive tables and evolutionary trees
• Tested numerous evolutionary hypotheses for several recently discovered ultrasmall uncultivable archaea
through the development of a phylogenetic analysis pipeline; incorporating UNIX, PERL scripting,
Muscle, Seq-Gen, PhyML, RAxML, Phylip, Seaview, FigTree, and R.
• Presented written and graphic support for multiple scenarios and explored the effects of phylogenetic
reconstruction artifacts in thesis
Genetic Engineering Team: Storrs CT –
President January 2013 –
May 2015
• Organized and directed a group of motivated undergraduates using guided discussion and coordination
with faculty to develop project submission ideas in Synthetic Biology for the iGEM competition
• Arranged for our team to attend iGEM competition as volunteers using organization and delegation to
learn more about the competition and gain insight on how to be competitive in future years

2. Advanced and Graduate Coursework:
• Bioinformatics related: Introduction to Molecular Evolution and Bioinformatics (MCB 3421),
Computational Methods in Molecular Evolution (MCB 5472), Seminar in Phylogenetic Systematic Error
(EEB 6486), Current Topics in Molecular Evolution (MCB 5471)
• Systems Biology related: Genetic Engineering and Functional Genomics (MCB 3412), Statistics for
Engineering and Research (STAT 3025Q)
• Further pursuit of interests in online learning (Coursera): R, R/Bioconductor, UNIX for Genomics,
Statistical Genomics, Systems Biology
Work Experience:
Naugatuck Board of Education– Long Term Substitute Teacher December 2015 –
Present
• Coordinate with a team of professionals including administrators and teachers using communication and
interpersonal skills to plan lessons and report progress of a cohort of 120 eighth grade science students
• Instruct students in Biology (Central Dogma, Mutation, Evolution) using written and verbal
communication to ensure thorough comprehension of material and to ignite passion for science
Quassy Amusement Park: Middlebury CT –
Beach and Lifeguard Manager May 2009 –
Present
• Directed a team of lifeguards and water park attendants using interpersonal, management, and
organizational skills to effectively monitor the safety of hundreds of patrons daily
• Supervised care of ailing patrons in first aid room utilizing knowledge from lifeguard training course and
past experience to treat wounds, syncope, heat exhaustion etc. and to create a calm healing environment
Griffin Hospital: Derby, CT –
Patient Transport July 2014 –
Present
• Coordinated with a team of clinicians, nurses and medical technicians using excellent oral
communication to ensure the top priority of patient safety was met during transport
• Rapidly learned how to monitor and manage the data output of health technology in order to maintain
continuity of treatment throughout transport and report any changes to receiving staff
Activities:
UConn Chamber Singers: Storrs CT
–
Singer
August 2013 –
January 2015
• Senior member of UConn’s most select vocal ensemble
• Used prior choral technique and attention to precise instruction to cultivate a unique, professional sound
A Completely Different Note: Storrs CT –
Assistant Music Director August 2011 –
May 2015
• Led warm ups and directed rehearsals when necessary for UConn’s oldest all male a capella group
Volunteer and Community Service:
Science Olympiads: Naugatuck CT –
Mentor February 2016 – Present
• Attend after school meetings twice a week using instructional skills and oral communication to teach a
focused group of high school students how to use the JMOL protein modeling software
St. Vincent’s SWIM Across the Sound: Bridgeport CT Summers 2009 and 2013
• Swam across the Long Island Sound, a 15.5 mile stretch, on a relay team of five individuals
• Gathered $7,500 in donations for the SWIM, a charitable grassroots organization for cancer support

3. References: (Name: Relationship to Applicant)
Johann Peter Gogarten, PhD: Honors Advisor, Thesis Advisor, and Professor
• 860-486-4061
• gogarten@uconn.edu
Jonathan Klassen, PhD: Thesis Advisor and Professor
• 860-486-6890
• jonathan.klassen@uconn.edu
Rachel O’Neill, PhD: Genetic Engineering Team Advisor and Professor
• 860-486-6031
• Rachel.oneill@uconn.edu
Abhay Vaze, PhD: Professor
• 860-486-6719
• abhay.vaze@uconn.edu