Dan Knights

Dan Knights

Associate Professor, Computer Science and Engineering / Biotechnology Institute, University of Minnesota

People

Dr. Dan Knights, Principal Investigator​

Dan Knights

I am a data scientist, a teacher, a puzzle solver, and an Associate Professor in the Department of Computer Science and Engineering and the Biotechnology Institute at the University of Minnesota. I received my B.A. from Middlebury College, and my Ph.D. from the University of Colorado, both in Computer Science, followed by a post-doctoral fellowship at Harvard. My research uses data mining and machine learning to better understand the natural world and the place of humans in it. My primary research focus has been studying the role of the microbiome in human disease, and developing software for analyzing metagenomics data. I have also done some analysis of the sustainability of various activities in modern civilization. In 2015, I was named a McKnight Land-Grant Professor by the University of Minnesota. From 2016-2020, I was co-founder and CEO of CoreBiome, a genomics company that was acquired by OraSure, Inc. I received the 2019 Innovation Award from the University of Minnesota’s Office of the Vice President for Research together with Kenny Beckman and Daryl Gohl. In 2023, I received the Bowers Faculty Teaching Award from the University of Minnesota College of Science and Engineering.

Note: My lab is currently closed to new students and new research projects while I explore shifting my focus to teaching.


Suzie Hoops, Ph.D. Student

Suzie Hoops

Suzie is a Computer Science Ph.D. student, studying new methods in dimensionality reduction and longitudinal analysis, applying these and other machine learning methods to the human gut microbiome. Suzie assists with various projects, including the MAGIC study, where she explores the maturation of the infant gut microbiome. Suzie started with Knights Lab as a staff researcher for two years before beginning her Ph.D. Prior to joining the lab, Suzie conducted data visualization research and taught English in Linz, Austria as part of a Fulbright Award. Suzie received her B.A. in Mathematics from St. Olaf College.


Past members

Postdoctoral Associates

  • Dr. ABBY JOHNSON - Abby is Assistant Professor at the University of Minnesota School of Public Health.
  • Dr. JONATHAN CLAYTON - Jonathan is Assistant Professor at the University of Nebraska.
  • Dr. CHRISTOPHER McKINLAY - Chris is Team Lead at Helm.ai.
  • Dr. EMMANUEL MONTASSIER - Emmanuel is Professor of Medicine at the University of Nantes, France.
  • Dr. ROBIN SHIELDS-CUTLER - Robin is a Associate Professor of Biology at Macalester College.
  • Dr. TONYA WARD - Tonya is Senior Director of Microbiome Data Science at Rebiotix (a Ferring Company).

Doctoral Students

  • Dr. GABRIEL AL-GHALITH - Gabe is Vice President of Computational Biology at Holobiome
  • Dr. PAJAU (PJ) VANGAY - Pajau is Senior Director, Scientific Network, Hypothesis Fund.
  • Dr. BENJAMIN HILLMANN - Ben is Senior Data Scientist at Shipt.

Staff Members

  • Cal Thoma
  • JESSICA KENNEDY
  • SHANNON ZHOU

Undergraduates

  • MAX ABRAMSON
  • RAWDA AHMAD
  • JORDAN AKERS
  • KAIWEI ANG
  • VANESSA BRADFISH
  • ERICA ELLINGSON
  • LUKE FEELEY
  • ANDREW GRUESEN
  • JESSICA HALVERSON
  • PATRICK JOHNSON
  • KAYLEE KANGAS
  • AUSTIN KIM
  • GRANT KIM
  • CARTER LINHARDT
  • VARUN MANGALICK
  • JEREMY MEULEMANS
  • NICK PERINOVIC
  • KELSEY PORTER
  • NURUL QURATULAINI ABD SALIM NAST
  • LUTFE-E-NOOR RAHMAN
  • GITANJALI RAMAN
  • TIMOTHY RENIER
  • DOMINIQUE SABAS
  • ANNA SABOE
  • DIMITRI SIDIROPOULOS
  • MADELINE SMITH
  • ARZENG SYED
  • SANGEITHA THAYALAN
  • GAVIN TURNER
  • DIMITRI TRIFUNAC