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Curriculum Vitae

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David C. Molik

Computational Ecology and Evolution PhD

EDUCATION

University of Notre Dame, Notre Dame, IN
Phd. Integrated BioMedical Sciences
Concentration in Computational Biology
Advisor: Michael Pfrender
Aug/2016 – May/2021

Rensselaer Polytechnic Institute, Troy, NY
BS. Information Technology and Web Science
Concentration in Communications
Aug/2009 – Dec/2012

EMPLOYMENT

United States Department of Agriculture

Phd. Student Positions at the University of Notre Dame – Notre Dame, IN

Positions held prior to University of Notre Dame Phd. studentship

  • Scientific Informatics Developer, Cold Spring Harbor Labratory – Cold Spring Harbor, NY
    • Dec/2014 – Aug/2016
  • Software Engineer; Network Operations Center Manager, Synacor – Buffalo, NY
    • July/2013 – Nov/2014

Positions held during BS. studentship at Rensselaer Polytechnic Institute – Troy, NY

ARTICLES

[2024]

[Submitted] [editorial] Cannon, E., D.C. Molik, A. Wright, H. Zhang, L. Honaas, K. Chougule, and S. Dyer. “Guidelines for Gene and Genome Assembly Nomenclature”

[Submitted] Drolet, B., L. Reister-Hendricks, C. Mayo, C. Rodgers, D. Molik, D. McVey “Increased virulence of Culicoides midge cell-derived blue-tongue virus in IFNAR mice”

Wright, A., M. D. Wilkinson, C. Mungall, S. Cain, S. Richards, P. Sternberg, E. Provin, J. Jonathan, S. Geib, R. Daniela, K. Yook, L. Stein, D. Molik. “FAIR Header Reference genome: A TRUSTworthy standard.” Briefings in Bioinformatics, 2024. doi:10.1093/bib/bbae122

[In Press] Molik, David, Amanda R. Stahlke, Sharu P. Sharma, Tyler J. Simmonds, Renee L. Corpuz, Angela N. Kauwe, Jeremy E. Schrader, Charles J. Mason, Sheina B. Sim, and Scott M. Geib. “otb: Creating a HiC/HiFi Pipeline to Assemble the Prosapia bicincta Genome.” G3: Genes, Genomes, Genetics, 2024. doi:10.1093/g3journal/jkae129

[2023]

Scroggs SLP, Bird EJ, Molik DC, Nayduch D. “Vesicular Stomatitis Virus Elicits Early Transcriptome Response in Culicoides sonorensis Cells” Viruses. 2023, doi:10.3390/v15102108

[2022]

[forum] David C. Molik. “An Outsider’s Perspective on Why We Climb Mountains and Why Projects Like the i5k Matter” Journal of Insect Science, 2022. doi:10.1093/jisesa/ieac038

David C. Molik. “𝚖𝚎𝚝 𝚟𝟷: expanding on old estimations of biodiversity from eDNA with a new database framework” Database, 2022. doi:10.1093/database/baac032

[2021]

David C. Molik, DeAndre Tomlinson, Shane Davitt, Eric L. Morgan, Matt Sisk, Benjamin Roche, Natalie Meyers, Michael E. Pfrender. “Combining Natural Language Processing and Metabarcoding to Reveal Pathogen-Environment Associations” PLoS Negl Trop Dis, 2021. doi:10.1371/journal.pntd.0008755, Kudos Website

Ong Joseph Y., Julia T Pence, David C Molik, Holly V Goodson. “Yeast grown in continuous culture systems can detect mutagens with improved sensitivity relative to the Ames test” PLoS ONE, 2021. doi:10.1371/journal.pone.0235303

[2020]

Molik, David C., Michael Pfrender, Scott Emrich. “Uncovering Effects from the Structure of MetabarcodeSequences for Metagenetic and Microbiome Analysis” Methods and Protocols, 2020. doi:10.3390/mps3010022

[2019]

李诣远 (Yiyuan Li), David Molik, Michael Pfrender. 基于Nextflow构建的宏条形码自动化分析流程EPPS（基因组多样性专刊）(EPPS, a metabarcoding bioinformatics pipeline using Nextflow) . Biodiversity Science, 2019. doi:10.17520/biods.2018211.

[2018]

Ho, Yu-Jui, Naishitha Anaparthy, David Molik, Grinu Mathew, Toby Aicher, Ami Patel, James Hicks, and Molly Gale Hammell. “Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations.” Genome research, 2018, 1353-1363. doi:10.1101/gr.234062.117.

[2016]

Cumming, Grant P., Edward Morris, Paul Simpson, Tara French, Eva Kahana, Joanne S. Luciano, and David Molik. “The future of post-reproductive health–The role of the Internet, the Web, information provision and access.” Post Reproductive Health, 2016, 123-130. doi:10.1177/2053369116647858.

Conference Papers and Reports

[2022]

Walker, Kimberly. Divya Kalra, Rebecca Lowdon, Guangyi Chen, David Molik, Daniela C. Soto, Fawaz Dabbaghie, et al. “The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms” F1000Research, 2022. doi:10.12688/f1000research.110194.1

[2018]

Molik, David C., Michael Pfrender, Scott Emrich. “Effects from structure of Metabarcode Sequences on Lossy Analysis of Microbiome Data” IEEE International Conference on Bioinformatics and Biomedicine, Data Analytics in Metagenomics, 2018. doi:10.1109/BIBM.2018.8621143.

[short] Tomlinson, DeAndre. David Molik, Michael Pfrender, Scott Emrich. “The Effects of Normalization, Transformation, and Rarefaction on Clustering of OTU Abundance” IEEE International Conference on Bioinformatics and Biomedicine, 2018. 10.1109/BIBM.2018.8621347.

[2012]

[short] Molik, David, and Michelle Sharer. “The Use of Recursive Bisection in the Mapping of Sample New York State Electoral Districts.” Proceedings of the 6th International Conference on Electronic Governance, 2012, 520–21. doi:10.1145/2463728.2463844.

Chapters and Whitepapers

[2020]

RDA COVID-19 Working Group. recommendations and guidelines. Research Data Alliance. 2020. doi:10.15497/rda00046.

[2017]

Cumming, Grant P., Tara French, Jamie Hogg, Douglas McKendrick, Heidi Gilstad, David Molik, and Joanne S. Luciano. “Trust and Provenance in Communication to eHealth Consumers.” In The Digitization of Healthcare, pp. 189-203. Palgrave Macmillan, London, 2017. doi:10.1057/978-1-349-95173-4_11.

Cumming, Grant P., Douglas McKendrick, Jamie Hogg, Tara French, Eva Kahana, David Molik, and Joanne S. Luciano. “Formulating eHealth Utilizing an Ecological Understanding.” In The Digitization of Healthcare, pp. 81-98. Palgrave Macmillan, London, 2017. doi:10.1057/978-1-349-95173-4_5.

ABSTRACTS - TALKS

Only Talks and Posters in which I am the First or Last Author

[2024]

[invited panel] “Data Science and Analytics Seminar Series - ‘Computational Genomics, Data Science and AI Panel’.” SUNY Buffalo State University Data Science and Analytics Seminar Spring 2024 Series. Buffalo, 2024. dataanalytics.buffalostate.edu/dsa-seminar-series

[talk] Molik, David, Katheryn Buble, Leyla Cabugos, Jaqueline Campbell, Jenna Daenzer, Daniela Raciti, Leonore Reiser, Sook Jung, Adam Wright, Karen Yook. “FAIR Scientific Literature Is Not What You Think: How to Know Where Data Goes.” Plant and Animal Genomes 31, San Diego, 2024. plan.core-apps.com/pag_2024/event/b44b10371958e4ecc7a77988eb6d15b7

[talk] Molik, David, Joaquin Carbonara, Scott Geib, Marc Halfon, Olga S. Novikova, Jimmy Pitzer, Brian E. Scheffler, Phillip Shults, Tyler J. Simmonds, Caitlin Taylor. “Making Culicoides sonorensis a Blueprint for Pest Management Model Systems” Plant and Animal Genomes 31, San Diego, 2024. plan.core-apps.com/pag_2024/abstract/0576097b-5f81-45e2-bce6-df69d943ca9c

[2023]

[poster] Wright, Adam, David Molik. “Expanding FAIR-BioHeaders for Comprehensive Data Management.” Genome Informatics, Cold Spring Harbor, 2023. meetings.cshl.edu/meetings.aspx?meet=info&year=23

[poster] Molik, David, Amanda Stahlke. “OTB (Only The Best genome assembly tools)—A phased genome assembly nextflow pipeline.” Genome Informatics. Cold Spring Harbor, 2023. meetings.cshl.edu/meetings.aspx?meet=info&year=23

[invited panel] “AI Across Academia, Industry, Government, and Society” SUNY Buffalo State University Data Science and Analytics Seminar Fall 2023 Series. Buffalo, 2023. dataanalytics. buffalostate.edu/fall-2023-seminar-series

[2022]

[poster] Molik, David. “OTB: (Only The Best Genome Assembly Tools) Overcoming Scientific IT Infrastructure Problems for the Creation, Storage, and Use of a Large Number of Phased Insect Genomes: A Case Study Using The Two-Lined Spittlebug” Arthropod Genomics Symposium. Notre Dame, 2022. web.cvent.com/event/c19bd7ed-9ebc-47f4-9876-a524061871ed/summary

[2020]

[poster] Molik, David, DeAndre Tomlinson, Shane Davitt, Eric L. Morgan, Benjamin Roche, Natalie Meyers, Michael E. Pfrender. “Automated text categorization and metabarcoding reinforces Cryptococcus neoformans–woody decomposition association.” Biological Data Science (Virtual). Cold Spring Harbor, 2020. meetings.cshl.edu/meetings.aspx?meet=data&year=20

[2019]

[invited/talk] Molik, David, Stephen Richards, Michael Pfrender. “Data mining for the prioritization of American insecta genomes.” Entomology 2019. Entomological Society of America, 2019. esa.confex.com/esa/2019/meetingapp.cgi/Paper/143297.

[lightning talk/poster] Molik, David. “𝗆𝖾𝗍—A web application tool and framework for the extensive comparison of metagenetic datasets.” In Proceedings of Genome Informatics 2019. Cold Spring Harbor, 2019. doi:10.7490/f1000research.1117645.1.

[2017]

[talk] Molik, David, Michael Pfrender, Scott Emrich. “K-mer comparison methods in metagenomics, applications at the community level.” In Proceedings of Genome Informatics 2017. Cold Spring Harbor, 2017. meetings.cshl.edu/abstracts.aspx?meet=INFO&year=17.

[2016]

[poster] Molik, David, Yu-Jui Ho, Ying Jin, and Molly Hammell. “Deployment of a Bioinformatics Analytics Platform in the Cloud.” Proceedings of The Biological Data Science 2016 Cold Spring Harbor, 2016. meetings.cshl.edu/abstracts.aspx?meet=DATA&year=16.

[talk] Molik, David. “Implementing Best Practices in Bioinformatics, Issues of Data And Computational Tool Access That Will Affect Data Science in the Near Future.” In Data Analytics Across Disciplines: Academic Advancement And Business Competitiveness. National Professional Science Master’s Association, 2016. www.dataanalyticsacrossdisciplines.org.

[poster] Molik, David, Ying Jin, and Molly Hammell. “EDGY—Export of Data from Galaxy to Yabi, Automated Workflow Transfer to Command Line Tool” Proceedings of The Biology of Genomes, 2016. meetings.cshl.edu/abstracts.aspx?meet=genome&year=16.

[2015]

[poster] Molik, David, Ying Jin, and Molly Hammell. “Automated Transfer of Workflows from Galaxy to Yabi and Command Line Tools.” In Proceedings of Genome Informatics 2015, 151. Cold Spring Harbor, 2015. meetings.cshl.edu/abstracts.aspx?meet=info&year=15.

[talk] Luciano, Joanne, Grant Cumming, Eva Kahana, Tara French, and David Molik. “Health Web Science: Health Science, the Web and Web Observatories.” Proceedings of Informs Healthcare – 2015. meetings2.informs.org/wordpress/healthcare2015/.

TEACHING

Certified carpentries.org instructor, taught bioinformatics carpentries lessons for USDA ARS, three workshops in 2023, one workshop in 2024

Designed and Taught University of Notre Dame’s first Computational Genomics course, “BIOS 60132 - Introduction to Computational Genomics” a graduate level, three credit course teaching commonly used algorithms in Computational Genomics in Fall of 2020

Organized and led in teaching “Bioinformatics Introductory Program (BIP) Week 2020” a introductory bioinformatics program for incoming Life Sciences graduate students at the University of Notre Dame. Based on carpentries.org curriculum, the workshop spanned four days and had over 20 volunteers in Summer 2020, for Center for Digital Scholarship. Taught as a Lecturer in BIP Week 2021.

Taught Data Carpentries Genomics curriculum as a series of workshops over the course of Spring 2020, for Center for Digtial Scholarship. First in-person, and then online in Spring 2020, for Center for Digital Scholarship.

Taught Data Carpentries Genomics curriculm as a series of workshops over the course of Spring 2020, for Center for Digtial Scholarship. First in-person, and then online in Spring 2020, for Center for Digital Scholarship.

Lecture Teaching assistant for “BIOS 10172 - Biology II: Molecules to Ecosystems” in Spring of 2019, for Joesph O’Tousa.

Lab Teaching assistant for “BIOS 31312 - General Ecology Laboratory” in Fall 2018, for Dominic Chaloner.

Lab Teaching assistant for “BIOS 21202 - General Biology B Laboratory” in Spring 2018, for Dominic Chaloner.

ACHIEVEMENTS

Undergraduate Thesis, titled: “Oat: Comparing Ontologies and Text” Focused on Semantic Web Technologies and Distance Measures, Advisor: Deborah McGuinness, Fall 2012

Eagle Scout, Achieved the Rank of Eagle in the Boy Scouts of America

Funding

$150000, Co-PI, DoD Global Emering Infections Surveillance Grant. “Using house flies as xenosurveillance tools to monitor existing, emerging and cryptic microbial threats to US military”

Awarded 90000 in Oracle Cloud Credits for the build out of a scientific cloud application in 2021

AWS Grants -

  • Received 10000 in AWS Could Credits for Research for exploring alternative bioinformatics research systems in the Amazon Cloud in 2016 Development of Open Source Software
  • Received 30000 in AWS Could Credits for Research for exploring alternative bioinformatics research systems in the Amazon Cloud for as co-investigator in 2017 with
  • Received 20000 in AWS Could Credits for Research for building metagenomic enrichment databases pipelines in 2018, Development of a Cloud Service

Awarded “Rapid Exposure to Advanced Computational Training” (REACT) Program Grant, received $1500 in funding for attendance to Computational Short Course - Summer 2017

Awarded “Graduate Student Union Conference Presentation Grant” (GSU CPG) to attend CSHL Genome Informatics 2017

Awarded “Graduate School Professional Development Award” (ND Graduate School Professional Development) Notebaert grant in the amount of $1000 to attend IEEE BIBM 2018

Awarded $1176.43 from University of Notre Dame Professional Development Zahm Research Travel Grant Fund for travel to CSHL Genome Informatics 2019

Awarded “Graduate Student Union Conference Presentation Grant” (GSU CPG) to attend Entomology 2019

Awarded University of Notre Dame Professional Development Zahm Research Travel Grant Fund for attendance to CSHL Biological Data Science 2020

Society Memberships

  • Society of Systematic Biologists
  • Sigma Xi