Alex Hernsdorf

About me

I'm a second year PhD student in the Plant and Microbiology department at UC Berkeley. I have extensive experience in next-generation sequence analysis and bioinformatics. I enjoy building useful tools for my research, and am passionate about creating flexible and extensible programs that evolve with my work. I find myself constantly reaching to explore new areas both in my research and in my side projects.

Education

UC Berkeley

Aug 2014 - Present

Graduate Student - Microbiology
  • NSF Graduate Research Fellow
  • Berkeley University Fellow
  • GPA: 3.9

Cornell University

Aug 2010 - May 2014

Bachelors of Science - Environmental Engineering
  • Tau Beta Pi Engineering Honor Society
  • GPA: 3.9

Skills

  • Bioinformatics
  • Data mining
  • Web development
  • Mathematical modeling
  • Data visualization

Languages

  • Python
  • Bash
  • HTML/CSS
  • C
  • SQL

Projects

Sciral: A web application for finding viral science papers
  • Envisioned, designed, and implemented a web app for discovering the most talked-about research papers in any field
  • Built app with Python/Flask and deployed in cloud using Heroku
  • Developed pipeline to auto-update SQL databases and process data from public APIs
cmd48: Python extensions to the curses library for rapid TUI development
  • Implemented a terminal-based version of the tile-shifting game 2048
  • Designed extensions to the curses library for quickly building menus, alerts, and grids
simply-python: Data structures and algorithms in pure Python
  • Developed a library of data structures and algorithms in Python
  • Data structures include lists, buffers, queues, heaps, graphs and hash tables
  • Algorithms include sorts, graph traversal and path-finding, random graph models

Experience

Metagenomics

Mar 2015 - Present

Environmental genomics in the Japanese Deep Subsurface
  • Designed sequencing studies of environmental DNA with team of Japanese scientists
  • Mined terabytes of data on computing cluster using custom Python and shell scripts
  • Built utilities for automated retrieval of data from public APIs
  • Optimized genome clustering tool to utilize multi-threading and reduce time complexity from quadratic to linear (speed-up of 500x on metagenome data)
UC Berkeley, CA

Undergraduate research

Aug 2013 - Dec 2013

Web applications for integration of "multi-omics" data
  • Constructed a locally hosted analysis pipeline for integrating multiple soruces of biological data
Cornell University, NY

TRC Solutions

Summer 2011 & Summer 2012

Environmental Consulting Intern
  • Negotiated meetings with clients, planned and executed site reconnaissance, and provided writing for over 100 pages of a technical report on the environmental history of an airport
Windsor, CT

Contact