Education

PhD

Deakin University: September 2016 to present
Currently pursuing a Doctor of Philosophy with a concentration in bioinformatics and medical genomics

MD

SUNY Upstate Medical University: August 2011 to May 2016
Graduated with a Medicinae Doctor, devoting credited hours to research in bioinformatics and medical genomics

BS

SUNY New Paltz: August 2009 to May 2011
Graduated summa cum laude, obtaining a Bachelor’s Degree in Biology with a concentration in biotechnology

AS

SUNY Orange: January 2007 to May 2009
Graduated summa cum laude, obtaining an Associate’s Degree in Science with a concentration in biology


Open source software

R packages which I designed and maintain,

exprso | CRAN
Supervised machine learning has an increasingly important role in data analysis. This package introduces a framework for rapidly building and deploying supervised machine learning in a high-throughput manner. This package provides a user-friendly interface that empowers investigators to execute state-of-the-art binary and multi-class classification, as well as regression, with minimal programming experience necessary.
peakRAM | CRAN
When working with big data sets, RAM conservation is critically important. However, it is not always enough to just monitor the size of the objects created. So-called “copy-on-modify” behavior, characteristic of R, means that some expressions or functions may require an unexpectedly large amount of RAM overhead. For example, replacing a single value in a matrix duplicates that matrix in the back-end, making this task require twice as much RAM as that used by the matrix itself. This package makes it easy to monitor the total and peak RAM used so that developers can quickly identify and eliminate RAM hungry code.
propr | CRAN
The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, correlation lacks validity when applied to relative data, including count data generated by next-generation sequencing. This package implements several metrics for proportionality, including phi [Lovell et al (2015)] and rho [Erb and Notredame (2016)]. This package also implements several metrics for differential proportionality. Unlike correlation, these measures give the same result for both relative and absolute data.

R packages to which I contributed,

ALDEx2 | Bioconductor
This package performs a differential abundance analysis of biological count data using log-ratio transformations.
catmap | CRAN
This package conducts a meta-analysis on combined case-control and family-based (TDT) genetic data.


Professional experience

In industry,

Adveq Management: April 2016 to August 2017
Employed as a Data Scientist to develop an object-oriented back-end in R for organizing, modeling, and analyzing transactions between financial institutions. Position held as a short-term, free-lance contract.

In research,

Deakin University: January 2018 to present
Employed as a Casual Research Fellow in the Pattern Recognition and Data Analysis (PRaDA) lab under Dr. Svetha Venkatesh to study autism spectrum disorder. This role involved pre-processing genomic data, building and deploying classifiers based on gene expression signatures, and supervising a research assistant.
SUNY Upstate Medical University: August 2012 to May 2016
Employed as a Student Research Assistant in the Psychiatric Genetic Epidemiology and Neurobiology (PsychGENe) lab under Dr. Stephen Glatt to study the molecular underpinnings of psychiatric disorders. This role involved the development of bioinformatic tools for the analysis of single nucleotide polymorphisms and microarray-based gene expression data. Extensive time devoted to the implementation machine learning for the classification of autism spectrum disorder.
SUNY New Paltz: September 2009 to August 2010
Employed as a Student Research Assistant in an organic chemistry lab under Dr. Frantz Folmer-Andersen to study synthetic diamine macrocycles which have the capability to distinguish between mirror image molecules.
SUNY Purchase: May 2009 to July 2009
Employed as a Student Research Assistant in an environmental science lab under Dr. Kristopher Baker to study the impact of anthropogenic input on the biodiversity of the Hudson River estuary.

In education,

Deakin University: March 2017 to present
Employed as a Graduate Assistant for two courses titled, Principles of Pharmacology and Therapeutic Development.
Coursera: September 2016 to October 2016
Employed as a Graduate Assistant for an online course titled, Big Data, Genes, and Medicine.
SUNY New Paltz: September 2009 to May 2011
Employed as a Teaching Assistant for an undergraduate organic chemistry laboratory class.
SUNY Orange: September 2008 to August 2009
Employed as a Tutor in a university math learning center.


Community engagement

Geelong Hacky Hour: October 2017 to present
Co-founder of the Geelong Hacky Hour chapter where researchers help other researchers learn to program.


Awards and scholarships

2017 Travel Award to Winter School in Mathematical & Computational Biology

2016 Travel Award to 2nd Bioconductor Asia-Pacific Developers’ Meeting

2014 Student Research Celebration Presenter Research Project Award

2010 New Paltz Student Undergraduate Research Experience (SURE) stipend

2009 Purchase Bridges to Baccalaureate Program stipend

2009 Outgoing Faculty Annual Scholarship awarded by SUNY Orange

2009 Outgoing William F. Ehlers Jr. Memorial Scholarship for excellence in anthropology awarded by SUNY Orange

2009 Outgoing Dr. Cortland R. Mapes Scholarship for excellence in biology awarded by SUNY Orange

2008 American Chemical Society award for excellence in chemistry

2007-2009 Recipient of President’s Scholarship for Outstanding Academic Achievement at SUNY Orange


Presentations

Quinn TP. October 2017. A compositionally valid pipeline for any-omics data. Invited abstract presented at Australasian Genomic Technologies Association in Hobart, Tasmania.


Peer-review contributions

Wellcome Trust

Statistical Methods in Medical Research


Publications

Quinn TP+, Lee SC+, Venkatesh S, & Nguyen T. 2018. Improving the classification of neuropsychiatric conditions using gene ontology terms as features. bioRxiv 393082. http://doi.org/10.1101/393082.

Quinn TP. 2018. Visualizing Balances of Compositional Data: A New Alternative to Balance Dendrograms [version 1; referees: 2 approved]. F1000Research 7:1278. http://doi.org/10.12688/f1000research.15858.1.

Quinn TP, Crowley TM, & Richardson MF. 2018. Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods. BMC Bioinformatics 19(1). http://doi.org/10.1186/s12859-018-2261-8.

Allnutt TR, Wade B, Quinn TP, Richardson MF, & Crowley TM. 2018. Shortlisting Aptamer Candidates from HT-SELEX data. Aptamers 2. http://japtamers.co.uk/shortlisting-aptamer-candidates-from-ht-selex-data.

Lee SC+, Quinn TP+, et al., & Nguyen T. 2018. Solving for X: evidence for sex-specific autism biomarkers across multiple transcriptomic studies. bioRxiv 309518. http://doi.org/10.1101/309518.

Quinn TP, Erb I, Richardson MF, & Crowley TM. 2018. Understanding sequencing data as compositions: an outlook and review. Bioinformatics 34(16). http://doi.org/10.1093/bioinformatics/bty175.

Erb I, Quinn T, Lovell D, & Notredame C. 2017. Differential Proportionality - A Normalization-Free Approach To Differential Gene Expression. Proceedings of CoDaWork 2017, The 7th Compositional Data Analysis Workshop; available under bioRxiv 134536. http://dx.doi.org/10.1101/134536.

Tylee DS, Kikinis Z, Quinn TP, et al., & Makris N. 2017. Machine-learning classification of 22q11.2 deletion syndrome: A diffusion tensor imaging study. NeuroImage: Clinical 15(1):832-42. http://dx.doi.org/10.1016/j.nicl.2017.04.029.

Quinn T, Richardson MF, Lovell D, & Crowley T. 2017. propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis. Scientific Reports 7:16252. http://dx.doi.org/10.1038/s41598-017-16520-0.

Englebert C, Quinn T, & Bichindaritz I. 2017. Feature selection for survival analysis in bioinformatics. CEUR Workshop Proceedings 1942:30-35. http://ceur-ws.org/Vol-1942/paper5.pdf.

Quinn T, Tylee D, & Glatt S. 2017. exprso: an R-package for the rapid implementation of machine learning algorithms [version 2; referees: 2 approved]. F1000Research 5:2588. http://dx.doi.org/10.12688/f1000research.9893.1.

Tylee DS, Hess JL, Quinn TP, et al., & Glatt SJ. 2016. Blood transcriptomic comparison of individuals with and without autism spectrum disorder: A combined-samples mega-analysis. American Journal of Medical Genetics B Neuropsychiatric Genetics. Rapid Publication. http://dx.doi.org/10.1002/ajmg.b.32511.

Bichindaritz IB, Cole E, et al., & Quinn TP. 2016. Machine Learning Based Automatic Multilevel Stress Detection from ECG Signals. IJCAI 2016: Workshop on Knowledge Discovery in Healthcare Data. http://sites.google.com/site/ijcai2016kdhealth/accepted-papers.

Hess JL, Quinn TP, Akbarian S, & Glatt SJ. 2015. Bioinformatic analyses and conceptual synthesis of evidence linking ZNF804A to risk for schizophrenia and bipolar disorder. American Journal of Medical Genetics B Neuropsychiatric Genetics 168(1):14-35. http://dx.doi.org/10.1002/ajmg.b.32284.

Quinn TP, Atwood PD, Tanski JM, Moore TF, & Folmer-Andersen J. 2011. Aza-crown macrocycles as chiral solvating agents for mandelic acid derivatives. Journal of Organic Chemistry 76(24):10020-30. http://dx.doi.org/10.1021/jo2018203.


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