Logan Blaine

Logan Blaine

PhD Student

Harvard Medical School

Hello world!

My name is Logan (he/him) and I am a third-year graduate student in the Bioinformatics and Integrative Genomics PhD Program at Harvard Medical School. For my thesis research, I am working in the Pinello Lab to build computational tools for functional genomics and single-cell assays. I want to accelerate biomedical discoveries by developing statistical and machine learning approaches to analyze high-throughput, high-content biology experiments.

Outside of lab, I love getting together for food, games, and outdoor adventures.

Interests
  • CRISPR screens
  • Lineage tracing
  • Single-cell & spatial -omics
  • Probabilistic programming
  • Bayesian statistics
  • Deep learning
Education

  • PhD Student in Bioinformatics and Integrative Genomics, 2026 (Expected)

    Harvard Medical School

  • A.B. in Molecular Biology with High Honors, 2018

    Princeton University

  • High School, 2014

    Phillips Academy Andover

Experience

 
 
 
 
 
Harvard Medical School
PhD Student
Harvard Medical School
Aug 2020 – Present Boston, MA

I completed research rotations with Shamil Sunyaev, Jason Buenrostro, and Luca Pinello. I also took rigorous graduate-level courses in probabilistic modeling, statistical inference, and machine learning including:

  • Probability I (STAT 210)
  • Algorithms for Inference (MIT 6.438)
  • Bayesian Modeling and Inference (MIT 6.435)
 
 
 
 
 
Dana-Farber Cancer Institute
Associate Computational Biologist
Dana-Farber Cancer Institute
Jun 2018 – Jul 2020 Boston, MA
I analyzed single-cell genomics data for cancer biology research as a part of the Pellman Lab. With co-mentorship from Cheng-Zhong Zhang, I helped show how errors in cell division can cause genomic catastrophes frequently occurring in cancer and less commonly seen after CRISPR-Cas9 genome editing.
 
 
 
 
 
Princeton University
Undergraduate Student
Princeton University
Aug 2014 – Jun 2018 Princeton, NJ
I majored in Molecular Biology and earned certificates in Applications of Computing and Quantitative and Computational Biology. For my senior thesis, I worked with Peter Andolfatto on in silico modeling of protein evolution. I also served as the president of the Princeton University Cycling Club.

Recent Publications

Stamatis Papathanasiou, Styliani Markoulaki, Logan J. Blaine, Mitchell L. Leibowitz, Cheng-Zhong Zhang, Rudolf Jaenisch, David Pellman (2021). Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing. Nature Communications.

PDF Cite DOI URL

Mitchell L Leibowitz, Stamatis Papathanasiou, Phillip A Doerfler, Logan J Blaine, Lili Sun, Yu Yao, Cheng-Zhong Zhang, Mitchell J Weiss, David Pellman (2021). Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing. Nat. Genet..

PDF Cite DOI URL

Andrew M. Taverner, Logan J. Blaine, Peter Andolfatto (2020). Epistasis and physico-chemical constraints contribute to spatial clustering of amino acid substitutions in protein evolution. bioRxiv.

PDF Cite DOI URL

Neil T Umbreit, Cheng-Zhong Zhang, Luke D Lynch, Logan J Blaine, Anna M Cheng, Richard Tourdot, Lili Sun, Hannah F Almubarak, Kim Judge, Thomas J Mitchell, Alexander Spektor, David Pellman (2020). Mechanisms generating cancer genome complexity from a single cell division error. Science.

PDF Cite DOI URL

Projects

Estimating Player Skills in Real-World Communities using Variational Inference
Course project for MIT 6.435 “Bayesian Modeling and Inference”.
Slides
Estimating Player Skills in Real-World Communities using Variational Inference

Contact

Feel free to message me on social media, or email me here: