289-C Perkins Green |Rochester, NY 14623| (575)-644-9356| Email: jnf3769@rit.edu
Education: Rochester Institute of Technology Rochester, NY June 2016 (expected)
Major(s): BS in Biotechnology and Molecular Bioscience, BS in Bioinformatics, Combined MS in Bioinformatics| Minor: Spanish | Undergraduate/Graduate GPA: 3.84/3.97 on 4.0 scale
Research: Masters Thesis (2015): Mitogenomic Construction of the Phylogeny of Major Iguana
Taxa from High-throughput Sequencing Data .
Performing targeted PCR and Illumia MiSeq sequencing to close several iguana mitogenomes.
Mitogenomes are then to be annotated and published. Ultimately, phylogenetic relationships will be drawn from the results. Primary Advisor: Dr. Larry Buckley | Committee: Dr. Larry Buckley,
Dr. Michael Osier, Dr. Gregory Babbitt. (ongoing)
Nucleosome Positioning (2015): Development of a Nucleosome Positioning Pipeline for use in Comparative Studies in Cancer Cell Lines.
Continued development of a nucleosome positioning pipeline in R and Perl as the head developer for use in Dr. Feng Cui's nucleosome positioning wo rk. Mentor: Dr. Feng Cui
(ongoing)
USC Wrigley Institute NSF Summer REU Fellow (2014): The Identification and
Quantification of deep bacterial and archaeal communities at the San Pedro Ocean
Time-series (SPOT) station using metagenomic and metatranscriptomic analyses
Performed marine microbiology research under Dr. John Heidelberg and USC Graduate student
Rohan Sachdeva. Identified and quantified bacterial and archaeal communities and their activity at 885meters below sea level. QIIME, mothur, Geneious, Bio-python, and R programs used.
Cancer Informatics (2014-present): Searching for Oncogene targets for miRNA therapies
Using TGDB, COSMIC, and miRBase, I have begun computationally looking for potential targets for synthetic microRNA therapies that present heightened specificity to the oncogenic form of the proto-oncogene. Note: This project is without mentorship.
Bioinformatics Research (2013-present): A SNP-Dense Exon Approach to Identifying
Paralogs in Humans.
An extension of a unique project from my Bioinformatics course. Using Galaxy,
NCBI, DGD, and USC Genome Browser, I have constructed a protocol for identifying potential paralogs in humans via gene functionality. Instructor: Dr. Feng Cui
Evolutionary Biology (2012): Geographic Reservoir Prediction and Phylogeny of
Filoviruses
Using NCBI, CodonCodeAligner, and a phylogenetic tree construction software, I reconstructed the evolutionary history of the filovirus family using bootstrap computational methods. After, I used the natural history of the virus and phylogenetic trees to make a prediction of the geographical origin of the common ancestor and a potential animal reservoir. Mentor: Dr. Larry
Buckley
Education/
Outreach: Biology Education Research (2012-present) : Central Dogma Misconceptions and Their
Origins

Conducted education research aimed at identifying student misconceptions in the Central
Dogma of Molecular Biology, recognizing potential sources thereof, and designing instructional tools and models for correcting them. DNA→RNA: What Do Students Think the Arrow Means?
Published in CBE—Life Sciences Education Vol. 13, 338–348, Summer 2014
Phylogenetics and Cladistics Education (2013-present): Pokémon Phylogenetics: A educational exercise in cladistics
Constructed a cladogram of over 300 of the fictional creatures Pokémon using categorical characters for instructional use. MEGA and Mesquite were used to develop the cladogram.
Subsequently, the results were developed into a hands-on educational activity presented at
ImagineRIT 2014.
ImagineRIT Creativity and Innovation Festival Exhibitor (2012, 2013, 2014, 2015):
2012 How Genetics Works : Preformed a hands-on presentation about genetics and population genetics to layman community.
2013 CSI Debunked: The Truth about Forensics : Preformed a hands-on forensics presentation, including a simple HTML game, aimed at debunking common misconceptions about forensics.
Was lead exhibitor and coordinator.
2014 CSI Debunked: The Truth about Fingerprints: Presented a hands-on activity about forensics, focusing on how fingerprinting and DNA fingerprinting work. Was lead exhibitor and coordinator.
2014
Pokémon Phylogenetics:
Designed and presented a cladistics exercise geared towards teaching systematics to children. Was lead exhibitor and coordinator
2015 The Science of Superheroes: Designed and presented a series of interactive modules to engage people in scientific learning, using superheroes as case studies. Stress was put on communication in the scientific community. Was lead exhibitor and coordinator
Celebrate Science and Mathematics (2014): Rochester Institute of Technology COS
Presented an adapted version of the Pokémon Phylogenetics exhibit described above.
Goodbye-Goodbuy (2015): Rochester Institute of Technology
Volunteered for a student organized attempt at reducing the waste of usable materials often discarded at the end of the year. Recovery of furniture, non-perishable food, and other materials was the focus. The recovered materials will be made available to incoming students in the fall.
My contribution was limited to aiding in the collection and moving of reusable materials. In particular, I was used to move larger objects.
Skills: Computational: Python, Java, MySQL, Terminal (Bash), R, C
Bioinformatic: Galaxy, UCSC Genome Browser, Chimera, CodonCodeAlginer, NCBI,
MEGA, Mesquite, mothur, QIIME, Bio-Python, Bio-Java, AutoDockVina, Geneious, FastQC,
Tuxedo Package, Bioconductor
Biotechnology: Blotting, Gel-Electrophoresis, Recombinant DNA techniques, Isolation of
Microbes, PCR, RT-PCR, qPCR, Cell culture (CHO, HeLa, ect), hybridization techniques,
Barcoding and Indexing for Multiplex Sequencing
Awards: Dean's List (Fall 2011-Fall 2015); Baldwin Wallace Memorial Scholarship (2013); Nathaniel
Rochester Scholarship (2012, 2013), MG James Ursano Scholarship (2013, 2014), ThanksUSA
Scholar (2014)
Coursework: General Chemistry I-III, Organic Chemistry I-III, Biochemistry I&II, Genetics, Genetic
Engineering, Bioinformatic Analysis of Macromolecules, Bioinformatics, Computer
Science I&II, Molecular Modeling and Proteomics, Evolutionary Biology, Tissue

Culture, Human Genetics, Microbiology, Databases and Data Modeling, Cell Biology,
Molecular Biology, Cancer Biology, Mechanics of Programming (C), Bioinformatics Algorithms
High-throughput Sequence Analysis, Genomics, Scientific Paper Writing, Bioinformatics
Seminar, Bioinformatics Languages, Biological Separations, Genetic Diseases and Disorders,
Concepts of Parallel and Distributed Systems, Statistical Models for Bioinformatics, Graduate
Ornithology, Seminar in Molecular Evolution and Genomics, TA for Database Management
Sciences, Intermediate Spanish I-III, Medical Informatics Seminar, Ethics in Bioinformatics,
Discrete Mathematics, Physics I&II, Data Analysis
Experience: Graduate Teaching Assistant: College of Science, Rochester Institute of Technology
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Fall 2014: Cell and Molecular Biology for Engineers I: Lab Instructor o Transformation, PCR, Electrophoresis, and other molecular biology techniques o Contact: Dr. Sarah McConnel, Dr. Greggory Babbitt
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Spring 2015: Cell and Molecular Biology for Engineers II: Lab Instructor o Tissue Culture of Eukaryotic Cells o Contact: Dr. Beth Van Winkle, Dr. Greggory Babbitt
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Fall 2015: Bioinformatic Analysis of Macromolecules o Introduction to Bioinformatics Tools and Algorithms for Biotechnology majors o Contact: Dr. David Lawlor, Dr. Gary Skuse
Bioprep Technician :Bio-preparatory Lab at Rochester Institute of Technology: 2012-2015
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Producing and maintaining cell cultures aseptically (HeLa, CHO, ect) for use in course laboratories and research. Duty includes training successor.
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Preparing media and reagents using sterile technique for laboratory use
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Biological and chemical waste manifestation and disposal
Interaction and communication with faculty concerning laboratory needs
Contact: Michelle Ubowski, Gabrielle Crandall, Allison Healy, Dr. Larry Buckley (RIT)
Publications: DNA→RNA: What Do Students Think the Arrow Means? L.Kate Wright, J. Nick Fisk , Dina
Newman CBE—Life Sciences Education Vol. 13, 338–348, Summer 2014
Posters: 2015 RIT WiSe (Women in Science) Annual Poster Symposium: “ The Identification and
Quantification of deep bacterial and archaeal communities at the San Pedro Ocean
Time-series (SPOT) station using metagenomic and metatranscriptomic analyses” Nick
Fisk , Rohan Sachdeva, Dr. John Heidelberg
2014 USC Wrigley Institute for Environmental Studies NSF REU Research Symposium:
“
The Identification and Quantification of deep bacterial and archaeal communities at the San Pedro Ocean Time-series (SPOT) station using metagenomic and metatranscriptomic analyses”
Nick Fisk , Rohan Sachdeva, Dr. John Heidelberg
SABER 2014
“Development of a Central Dogma Concept Inventory (CDCI) for Use at
All Levels of Undergraduate Biology” Dina L. Newman, J. Nick Fisk , Christopher Snyder,
L. Kate Wright
PKAL 2014
“Development of a Central Dogma Concept Inventory (CDCI) for Use at All
Levels of Undergraduate Biology”
Dina L. Newman, J. Nick Fisk , Christopher Snyder, L.
Kate Wright
Workshops: Bioinformatics Workshop on Next Generation Sequencing. Presented by Dr. Han Ming
Gan and Ms. Mun Hua Tan (MONASH UNIVERSITY) | May 26-May 28, 2015

Topics covered included NGS technologies, BioLinux, Local Blast, HMMsearch, Microbial
Genome Assembly and Annotation, Microbiome analysis (QIIME), Mitogenome Assembly and
Annotation, and Mitogenomic phylogenitcs (MitoPhAST).
Professional Development in the Sciences. Presented by Dr. Diane Kim and Dr. Karla
Heidelberg| July 29-30, 2014
Topics covered include scientific presentation, networking, CV and resume development, graduate school application, communication with potential collaborators, and investigation of graduate programs.
Professional
Memberships:
International Society for Computational Biology (2014-present)
Systematics Association (2014-present)
Activities: RIT Men's Division III Wrestling Team: (2011-Present):
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3 Time Academic All-Conference Team
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Volunteer tutor at organized, weekly study sessions.
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Interim Captain
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3 Time NCAA Regional Qualifier
Bioinformatics Journal Club: Public Relations Officer (2013-Present)
Biology Education Research Group (2012-Present): Peer evaluation and Journal Studies
Research Scholars (Biology) at RIT (2013-Present)
Pokémon League at RIT (2014-Present)
RIT College of Science Student Ambassador (2014-Present)