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Jeffrey Nicholas Fisk

52 Alverstone Way| Rochester, NY 14586| (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: 3.84/3.94 on 4.0 scale

Research:

Masters Thesis (2015): Killing Two Birds with One Stone: The Concurrent
Development of the Novel Alignment Free Tree Building Method, Scrawkov-Phy, and the
Extensible Phyloinformatics Utility, EMU-Phy
Available at http://scholarworks.rit.edu/theses/9000/
Primary Advisor: Dr. Larry Buckley | Committee: Dr. Larry Buckley, Dr. Michael Osier, Dr.
Gregory Babbitt.

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 work. Analysis of nucleosome

occupancy, modification, MeDIP, dnase positions, and other nucleosome related


information was performed. Original and ENCODE data were both used. Computation
was performed on RIT's research cluster. Mentor: Dr. Feng Cui (ongoing) | Original
Developer: Peter LoVerso (M.S.)

Directed Research in Bioinformatics (Fall 2015): Construction of a Support Vector


Machine Using a Phylogenetic-Distance Kernel to Predict Disease State from
Microbiome Data.
An individual project as part of a small directed research course focused on machine
learning in bioinformatics, I am developed a SVM that takes advantage of phylogentic
distances of OTUs as part of its kernel to predict disease state from a microbiome
dataset. The data being used was pulled from the Personal Genome Project (PGP).
Mentor: Dr. Michael Osier
Discipline Based Education Research (2015): Construction of a Web-application for
the Analysis and Visualization of the Central Dogma Concept Inventory (CDCI) Results
for use in External Institutions.
Developing a RShiny based web application that will allow adopters of the CDCI at
other institutions to analyze their results, both for internal trends and with regards to the
current data and statistics for the present version of the CDCI. As of Fall 2015, there
have been over 1,400 student participants. Mentors: Dr. L. Kate Wright and Dr. Dina
Newman
Differential Expression Analysis (2014): Investigation of the Effects of Different
Experimental Treatments, including Powdery Mildew Fungal Infection, in the
Differential Expression profile of Vitis vitis.
Using a variety of standard packages, including the Tuxedo suite and various quality
control softwares, preformed extensive quality control and differential expression
analysis on commercially important grapevine species. Special attention was paid to
how powdery mildew infection, a common vineyard aliment, affects the differential

expression profile of Vitis. Research was performed in a group including two other
individuals. Mentor: Dr. Michael Osier
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.
Mentors: Dr. John Heidelberg, Rohan Sachdeva, Dr. Diane Kim

Cancer Informatics (2014-present): Searching for Oncogene targets for Novel 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. Responsibilities range from student interviews to
statistical analysis of data. Related publications: DNARNA: What Do Students Think the
Arrow Means? Published in CBELife Sciences Education Vol. 13, 338348, Summer 2014 ;
Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool. Accepted with
revisions in CBE Life Sciences Education, Summer 2015.

Phylogenetics and Cladistics Education (2013-present): Pokmon Phylogenetics: A


educational exercise in cladistics
Constructed a cladogram of over 300 of the fictional creatures Pokmon 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.

Guest Lecturer/Bioinformatics Consultant (Fall 2015): Cell Physiology at R.I.T.

Spoke about the role of bioinformatics in the field of cell physiology and the potential
for incorporating bioinformatic methodologies to supplement and guide wet-bench cell
physiology research. Continued support, consultation, and guidance on the course
projects was provided. Contact/Instructor: Dr. Beth VanWinkle
Guest Lecturer/Scientific Outreach (Summer 2015): Science, Biology, and You
Gave guest lectures at New Americas Charter School in Las Cruces, NM about everyday
science, the nature of living things, and how design experiments. New Americas Charter
School aims to empower new immigrants, English language learners, and academically
underserved students. See: http://newamericaschool.org/newmexico/campuses-lascruces/
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 Pokmon 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
2015: Presented an adapted version of the Science of Superheroes exhibit described above.
2014: Presented an adapted version of the Pokmon 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.

Skills:

Computational: Java, R, Python, MySQL, Terminal (Bash), Perl, C, Octave/Matlab


Bioinformatic: Bioconductor, Tuxedo Package,Galaxy, UCSC Genome Browser, Chimera,
CodonCodeAlginer, NCBI, MEGA, Mesquite, mothur, QIIME, Bio-Python, Bio-Java,
AutoDockVina, Geneious, FastQC,
Biotechnology: ABI-Sanger Sequencing, 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:

2016 RIT College of Science Outstanding Research Scholar Award Recpient


Alpha Sigma Lambda Leadership Award and Honorary Society Inductee
RIT Criminal Justice Department Social and Justice Issue Haiku Contest Winner
3 Time NCAA D3 Wrestling Academic All-Conference Team
Baldwin Wallace Memorial Scholarship, RIT School of Life Sciences (2013)
Dean's List (Fall 2011-Spring 2015)
Nathaniel Rochester Scholarship (2012, 2013)
MG James Ursano Scholarship (2013, 2014, 2015),

ThanksUSA Scholar (2014,2015)

Coursework
(by Major):
Bioinformatics:
Molecular Modeling and Proteomics, Mechanics of Programming, Bioinformatics,
Computer Science I&II, Bioinformatics Seminar, Bioinformatics Languages, Databases
and Data Modeling, Bioinformatics Algorithms, Statistical Models for Bioinformatics,
Genetic Diseases and Disorders, Concepts of Parallel and Distributed Systems, Highthroughput Sequence Analysis, Pedagogy of Bioinformatics Databases, Directed
Research in Bioinformatics: Machine Learning, Ethics in Bioinformatics
Biotechnology:
Genetic Engineering, Cancer Biology, Genomics, Genetics, Bioinformatic Analysis of
Macromolecules, Tissue Culture, Biological Separations, Evolutionary Biology,
Microbiology, Cell Biology, Molecular Biology, Ornithology, Human Genetics
Special Topics in Molecular Evolution and Genomics
Other:
Intermediate Spanish I-III, Medical Informatics Seminar, Scientific Paper Writing,
General Chemistry I-III, Organic Chemistry I-III, Biochemistry I&II, Discrete
Mathematics, Physics I&II, Data Analysis, Calculus I&II.

Experience: Adjunct Faculty: College of Science, Rochester Institute of Technology

Summer 2016: Cellular and Molecular Biology: Lecture instructor


o Taught foundational cellular and molecular biology in this 2nd year course
o Contact: Dr. Larry Buckley
Graduate Teaching Assistant: College of Science, Rochester Institute of Technology
Spring 2016: Bioinformatics Languages: Lab instructor
o Teaching and designing programming assignments for the R and Perl languages
for Bioinformatics student use
o Contact: Dr. Feng Cui, Dr. Larry Buckley
Spring 2016: Genomics: Lab Coordinator/Lab Instructor
o Coordinated the lab course (planning each weeks lab, submitting requests to
support staff and ordering materials)
o Teaching the 1st lab of the week, dealing with library prep and sequencing
Fall 2015: Bioinformatic Analysis of Macromolecules: Lab Instructor
o Introduction to Bioinformatics Tools and Algorithms for Biotechnology majors
o Contact: Dr. David Lawlor, Dr. Gary Skuse, Dr Larry Buckley
Fall 2015: Tissue Culture: Lab Instructor
o Tissue Cultue of Eukaryotic Cells for Life Science majors. Includes instruction
of biotechnological techniques applied to mammalian cell lines
o Contact: Dr. Larry Buckley, Dr. Irene Evans
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
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
Contract Big Data Consultant: Medumail Inc, Mendon, NY 14506

Data scrubbed large database of medically relevant information and reformatted it for
local application to expand medical literature search and potential user list.
Performed database unions on local database with new large database
Summarized data into a human readable format.
Fall 2015
Contact: info@medumail.com

Contract Software Developer: Vaccinex Inc, 1895 Mt. Hope Ave Rochester,NY 14620

Constructed proprietary software to automate the analysis of immunological data.


Main components written in R and made use of Bioconductor packages.
Summer 2015
Contact: Mark Paris, Ph.D, Director of Bioinformatics and Molecular Biology. Phone:
585-271-2700. Website: www.vaccinex.com

Graduate Research Assistant: College of Science, Rochester Institute of Technology

Continued development of a previous student's nucleosome positioning pipeline (Perl


and R)
Responsibilities included incorporating new modules into the pipeline, running the
pipeline on a research computing cluster, optimizing code, and documentation of code.
Summer 2015
Contact: Dr. Feng Cui, RIT College of Science

Bioprep Technician:Bio-preparatory Lab at Rochester Institute of Technology: 2012-2015


Producing and maintaining cell cultures aseptically (HeLa, CHO, ect) for use in course
laboratories and research. Duty includes training successor.
Preparing media and reagents using sterile technique for laboratory use
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: DNARNA: What Do Students Think the Arrow Means? L.Kate Wright, J. Nick Fisk, Dina
Newman CBELife Sciences Education Vol. 13, 338348, Summer 2014
Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool. Dina Newman,
Christopher Snyder, J. Nick Fisk, L. Kate Wright CBELife Sciences Education Vol. 15, 114,
Summer 2016

Unique chromatin organization associated with in vivo DNA binding of the tumor
suppressor p53. Feng Cui, Peter LoVerso, Feifei Bao, J. Nick Fisk (Pending revisions)
Posters/Presentations:
2016 RIT CASTLE (Center For Adavncing STEM Teaching, Learning, and Evaluation)
Annual Spring Poster Symposium Development of CDCI-SHiNE, an R-based Web
Application for the Analysis of Results from the Central Dogma Concept Inventory
(CDCI)" J. Nick Fisk, Chistopher Snyder, Dina Newman, L. Kate Wright

2015 Rochester Academy of Science (RAS) Annual Fall Poster Symposium:


Development of CDCI-SHiNE, an R-based Web Application for the Analysis of Results
from the Central Dogma Concept Inventory (CDCI)" J. Nick Fisk, Chistopher Snyder,
Dina Newman, L. Kate Wright
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

2015 RIT Gosnell School of Life Sciences SlideSlam: What do Iguanas, Cancer,
Students, Microbes, and Pokmon have in Common? | Gave a presentation of my
research experiences as an undergraduate and graduate student at RIT, with particular
focus on encouraging undergraduates to seek out a diverse range of research experiences
both at RIT and through the vaious REU and SURF programs around the county. The
presentation was part of a seminar series where faculty and researchers present short
slides about their research in GSOLS. Nick Fisk, Dr. Dina Newman
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 2014Development 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 included scientific presentation, networking, CV and resume development,
graduate school application, communication with potential collaborators, and investigation of
graduate programs.
NSF Graduate Research Fellowship Program Application Preparation for 2016 GRFP.
Presented by Dr. Hector Flores, Dr. Raymond Ptucha, and Dr. Christy Tyler | September
2015
Topics covered included scientific writing, specifically for grants; the requirements for the
GRFP; and the discussion of potential, qualifying graduate projects for the GRFP.

Graduate Workshop in Public Speaking. Presented by the Tiger Tales Toastmasters Club
at RIT | October 2015
Topics covered included technical and casual speaking for Graduate students and professionals.
Tips on speaking to engage an audience and reduce presentation anxiety were discussed. The
seminar concluded with a series of mock-speeches on a variety of professional and nonprofessional topics with feedback from both the other participants and a panel of experts.
Field Ornithology Seminar Series and Birdwalk. Presented by Dr. Jed Burtt (Ohio
Wesleyan University) | April 2-April 3, 2015
Topics covered included the Evolution of Color in Avian Species, the founding of American
ornithology, and the role of undergraduates in research endeavors. The seminar series concluded
with a birding excursion lead by Dr. Jed Burtt.

Professional
Memberships:
Society for the Study of Evolution (2016-present)
International Society for Computational Biology (2014-present)
Systematics Association (2014-present)
ONSA: American Ornithologists Union (2015-present)

Activities:
RIT Men's Division III Wrestling Volunteer Coach (2015-Present)
Volunteer Coach
Volunteer Tutor and held office hours in addition to study sessions.
RIT Men's Division III Wrestling Team: (2011-2015):
3 Time Academic All-Conference Team
Volunteer tutor and leader at organized, weekly study sessions.
Interim Captain
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)
Pokmon League at RIT (2014-Present)
RIT College of Science Student Ambassador (2014-Present)
RIT GSOLS Student Representative (2013-Present)