Colin Small
Sc.M. Student in Biotechology, Brown University
Biotechnology Graduate Program and Brown Center for Computational & Molecular Biology
Lorin Crawford Lab
colin_small at brown.edu

I am a current master's student in the Biotechnology Graduate Program at Brown University under the supervision of Lorin Crawford through the Brown Center for Computational & Molecular Biology. During my undergraduate degree at the University of New Hampshire, I worked with Marek Petrik and Matthew Argall. My current research at Brown revolves around the use of graph neural networks to predict antibiotic synergy, but I am more broadly interested in computational small-molecule pharmacology, health informatics networks, and ethnopharmacology.

News

• Fall 2022: I co-founded Industry and Innovation in Biotechology (I2B) at Brown University, a student organization for professional development in biotechnology careers and entrepreneurship.
• Summer 2022: I interned with Harmonic Discovery developing virtual screening libraries and cheminformatics tools for the structural analysis of kinase inhibitors.
• Summer 2021: I was a summer researcher at UCLA working with Xianghong Jasmine Zhou and Wenyuan Li developing software calling tumor-derived single nucleotide variants in cell-free DNA from patient blood plasma samples.
• Spring 2021: I graduated from the University of New Hampshire with a B.S. in Computer Science, Magna Cum Laude

Publications

• cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA
  Shuo Li , Ran Hu , Colin Small , Ting-Yu Kang , Chun-Chi Liu , Wenyuan Li
  In review, 2022.
  Nature protocols.
  [coming soon]
  
  
• Automated Detection of Magnetopause Crossings
  Colin R Small, Matthew R Argall
  Machine Learning, Statistics, and Data Mining for Heliophysics.
  [paper]
  
  
• MMS SITL ground loop: Automating the burst data selection process
  Matthew R Argall, Colin R Small, Samantha Piatt, Liam Breen, Marek Petrik, Kim Kokkonen, Julie Barnum, Kristopher Larsen, Frederick D Wilder, Mitsuo Oka, William R Paterson, Roy B Torbert, Robert E Ergun, Tai Phan, Barbara L Giles, James L Burch
  Frontiers in astronomy and space sciences, 2020.
  [paper][code]
  
  

Conference Presentations and Posters

• Incorporating Machine Learning into Mission Operations
  Matthew R Argall, Colin R Small, Samantha Piatt, Marek Petrik, Kim Kokkonen, Julie Barnum, Kristopher William Larsen, Frederick D Wilder, Mitsuo Oka, William R Paterson, Roy B Torbert, Robert Ergun, Tai D Phan, Barbara L Giles, James Burch
  AGU Fall Meeting Abstracts, 2020.
  [abstract]
  
  
• Understanding patient-reported barriers to colorectal cancer screening: A literature review
  Colin Small, Victoria Raymond, Mark Jacobstein, Kathryn Lang
  AACR Cancer Epidemiology, Biomarkers & Prevention, 2020.
  [abstract]
  
  
• MMS SITL ground loop: Automating the burst data selection process
  Matthew R Argall, Colin R Small, Samantha Piatt, Liam Breen, Marek Petrik, Kim Kokkonen, Julie Barnum, Kristopher Larsen, Frederick D Wilder, Mitsuo Oka, William R Paterson, Roy B Torbert, Robert E Ergun, Tai Phan, Barbara L Giles, James L Burch
  Frontiers in astronomy and space sciences, 2020.
  [paper][code]
  
  

Contributions to Open Source Projects

I am a contributer to chemprop, a Python package for developing message passing neural networks (MPNNs) for molecular property prediction. See Analyzing Learned Molecular Representations for Property Prediction and chemprop's usage in A Deep Learning Approach to Antibiotic Discovery.

Extracurricular Activities

Industry and Innovation in Biotechology (I2B)

Co-founded Industry and Innovation in Biotechnology (I2B) at Brown University. I2B is a student organization offering members of the Brown Community education and opportunities in non-bench careers from corporate strategy to consulting and venture capital to entrepreneurship.

Rines Angel Fund

I spent three years working with the Rines Angel Fund, an undergraduate-run angle investment group at the University of New Hampshire, serving as an associate, principal, and head principal. In that time, I screened was pitched to by over 20 startups in-depth, played a key role in the fund’s three investments, and lead due-diligence research teams.