CONTACT

 

Knights Lab

MCB 6-124

420 Washington Ave SE

Minneapolis, MN 55455

(612) 5-MICROB (612-564-2762)

dknights@umn.edu

ABOUT

 

Dr. Dan Knights is an Assistant Professor in the Department of Computer Science and Engineering and the Biotechnology Institute at the University of Minnesota. The Knights lab models host-microbiome interactions in human disease, with labs in Minneapolis and Saint Paul. Knights is a PI with the Minnesota Supercomputing Institute.

© 2013-2014 Knights Lab, University of Minnesota

Volunteers
SA KONG, undergraduate
Sa is a second year student majoring in physiology and minoring in pharmacology. She's working the infant microbiome project with Dr. Ward, where she helps to assemble kits, and picks up and processes biological samples. She hopes to attend medical school one day and be involved in cancer research. 
GRANT KIM, undergraduate
Grant is a sophomore undergraduate majoring in Microbiology along with a minor in Computer Science. He is interested in pursuing his dream of becoming a pediatrician after college. Grant has been working with Pajau Vangay on the Immigrant Microbiome Project since the Summer of 2016, and has been responsible for managing and curating dietary recall data, but has also helped with assembling sample kits and processing samples. 
KAIWEI ANG, undergraduate

Kaiwei is a senior undergraduate majoring in Computer Science with a focus on big data at the University of Minnesota. His interest lies in the field of data science, especially in its application to computational biology. Currently, he helps Gabe to design and develop a bioinformatics pipeline called shi7en, which is an open-source software. Kaiwei has a plan to apply to Bioinformatics and Computational Biology graduate program in the future.

LAB MEMBERS.

Current members
Dr. DAN KNIGHTS (Curriculum vitae)

 

Dr. Dan Knights is a computational microbiologist. He is a professor in the Department of Computer Science and Engineering and the Biotechnology Institute at the University of Minnesota. Dan received his B.A. from Middlebury College, and his PhD from the University of Colorado, both in Computer Science and Computational Biology, followed by a post-doctoral fellowship at Harvard. His research uses data mining and machine learning to aggregate and mine multiple sources of microbial and human genomic data for patterns linking to environmental conditions and human disease. Dan has co-authored articles in top multidisciplinary journals. In 2015 he was named a McKnight Land-Grant Professor by the University of Minnesota.

Dr. PAJAU (PJ) VANGAY, Research Assistant

 

Pajau recently completed a Ph.D. in Biomedical Informatics and Computational Biology in the Knights Lab at the University of Minnesota. She is currently a science policy post-doc fellowship with the California Council on Science and Technology. Pajau received her B.S. and M.S. in Math and Computer Science from Colorado School of Mines, followed by an M.S. in Food Microbiology from Cornell University.

Dr. ABBY JOHNSON, Postdoctoral Associate

 

Abby is a postdoctoral associate in the Knights Lab at the University of Minnesota, where she is studying the relationship between diet and the microbime. She received her Ph.D. in Nutrition from the University of Minnesota, where she studied the impact of bariatric surgery on body composition. She trained as a registered dietitian nutritionist through Iowa State University. Prior to her Ph.D., Abby obtained a B.S. with majors in Nutrition Science and Biology at the University of Minnesota. Before joining the lab Abby worked in R&D in the food industry.

Dr. JONATHAN CLAYTON, Postdoctoral Associate
Jonathan Clayton is a postdoctoral associate in the Knights Lab, where he studies host-microbiome interactions in humans and nonhuman primates. He received his Doctor of Veterinary Medicine (D.V.M.) and his Ph.D. in Comparative and Molecular Biosciences from the University of Minnesota. For his Ph.D. thesis research, he used nonhuman primates as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. During his Ph.D., Jonathan and his collaborators started the Primate Microbiome Project (PMP) with the intended purpose to develop a systematic map of variation in microbiome structure and function across all primates and to relate this to primate health, evolution, behavior, and conservation.​ Prior to his D.V.M and Ph.D., Jonathan obtained a B.A in Religion & Philosophy and a B.S. in Biology at Barton College, and a Certificate of Primatology at Duke University. While at Duke, he studied slender loris (Loris tardigradus) feeding behavior at the Duke Lemur Center.​ He recently accepted a tenure-track faculty position at the University of Nebraska - Omaha.
JESSE KENNEDY,  Research Professional

 

Jesse is the research professional in Knights Lab. She has a degree in biology from the University of Minnesota. Prior to joining Knights Lab she worked in one of the University’s distance learning program, and before that she worked in an instructional teaching lab. She is excited to return to her roots in biology, learn more about bioinformatics, computational biology, and microbiome research. Her work in Knights Lab includes a mixture of lab management, project management, and a wide array of other tasks.

SUZIE HOOPS, Data Scientist

Suzie is a Data Scientist for Knights Lab, where she assists with various projects. Prior to joining the lab, Suzie conducted data visualization research and taught English in Linz, Austria as part of a Fulbright Award. She is interested in expanding her knowledge of bioinformatics and computational biology through the complex analyses involved in microbiome research. Suzie received her B.S. in Mathematics from St. Olaf College.

MO HOUTTI

 

Mo is a student in the University of Minnesota’s Computer Science Ph.D. program. Before joining the Knights Lab, he worked as a web developer for several years. He hopes to further hone his computational and research skills by branching out into the field of microbiome informatics. Mo received his B.A. in Computer Science and Philosophy from Middlebury College. He enjoys oatmeal raisin cookies that look like chocolate chip cookies.

BRIENNA HEROLD

 

Brienna is a student in the University of Minnesota’s Computer Science Ph.D. program. Before joining the Knights Lab, she worked at the University of Rochester Medical Center as a data scientist to examine immune responses to influenza, and Rochester Institute of Technology as a web developer.

RAWDA AHMAD, undergraduate
Rawda is an undergraduate at the College of Biological Sciences. She is currently majoring in Genetics, Cell biology, and Development(GCD), and double minoring in Spanish and Sociology. She is especially interested in research related to the microbiome because of its significant effect on human health and medicine. Currently, she is working with Abby and Jonathan on the MAGIC study by processing and analyzing infant stool samples. Using the skills she has gained from this lab, she hopes that in the future she can do her own research related to the microbiome. Rawda then plans to move forward with this experience to work towards becoming a Pediatrician.
VANESSA BRADFISH, undergraduate
Vanessa is an undergraduate student at the University of Minnesota College of Biological Sciences studying Neuroscience with a minor in German. She is working on the Microbiome, Antibiotics, and Growth Infant Cohort (MAGIC) study by processing samples and helping with data entry. She hopes to learn more about aspects of the human microbiome and its overall health implications as well as gain useful lab skills and experience in order to become involved in additional research endeavors in the future. She plans on pursuing a career in medicine as a physician in either ob/gyn or pediatrics.
ERICA ELLINGSON, undergraduate
Erica is an undergraduate at the University of Minnesota College of Biological Sciences studying Microbiology. She is currently working on the Microbiome, Antibiotics, and Growth Infant Cohort (MAGIC) study with Abby and Jonathan by processing incoming stool samples for the study and working on the analysis of the data from said samples. Erica has an interest in pursuing a health career post-graduation, most likely as a physician specializing in dermatology.
GITANJALI RAMAN, undergraduate
Gita an undergraduate at the University of Minnesota majoring in Genetics, Cell Biology, and Development and minoring in Spanish studies and Pharmacology. Her research interests include microbial genomics and medicine. In the Knights Lab she is conducting computational analysis, processing, and sorting with the Microbiome, Antibiotics, and Growth Infant Cohort (MAGIC) Project with Dr. Abby Johnson and Dr. Jonathan Clayton. She hopes the experience and knowledge gained from the lab will help her reach her goal of being a physician. Outside of the lab, she enjoys running, volunteering at HCMC, and dancing with the DOOM Dance Crew.  
MADELINE SMITH, undergraduate
Madeline is a senior studying microbiology and French. She is currently working with Dr. Abby Johnson on the Fiber Study and the Chemotherapy and Dysbiosis study by developing computational tools, data munging, and performing data analysis. She one day hopes to go to graduate school for infectious diseases and/or global medicine. She would like to connect her study of the microbiome with preventative treatments for diseases in the future. 
SANGEITHA THAYALAN, undergraduate
Sangeitha is a freshman at the University of Minnesota majoring in biology. She is working with Dr. Abby Johnson and Dr. Jonanthan Clayton in the Microbiome, Antibiotics, Gut Microbiome, and Infant Cohot (MAGIC) study in the Knights Lab. She hopes to gain the skills and experience in research that could aid her in her career as a physician. Sangeitha is the Vice President of Educate U, and enjoys running on her freetime.
GAVIN TURNER
Gavin is a BioMedical Engineering student, and is currently working on data analysis, data curation, and computational tool creation related to the Chemotherapy and Dysbiosis study. He is studying Graft vs Host Disease in bone marrow transplant patients.
ANNA SABOE
Anna is working with Dr. Abby Johnson on creating a pipeline for microbiome and food analysis.
ARZENG SYED
Arzeng is working with Dr. Abby Johnson on creating a pipeline for microbiome and food analysis.
You

Interested in joining the lab? Contact Dan at dknights@umn.edu.

Past members
Postdoctoral Associates
Dr. EMMANUEL MONTASSIER - Emmanuel is now Associate Professor of Medicine at the University of Nantes, France.
Dr. CHRISTOPHER McKINLAY - Chris is now Director of Engineering at Formation.
Dr. TONYA WARD - Tonya is now a Senior Research Scientist at CoreBiome.
Dr. ROBIN SHIELDS-CUTLER - Robin is a tenure-track faculty member at Macalester College.
Doctoral Students
BEN HILLMANN
Dr. GABRIEL AL-GHALITH  - Gabe is now straddling a fine line of working at Johnson and Johnson and completing a post-doc fellowship with Dan Knights' mentor, Rob Knight
Dr. PAJAU (PJ) VANGAY - Pajau is currently a science policy post-doc fellow with the California Council on Science and Technology.
 
Undergraduates
MAX ABRAMSON -  now in the Pathmaker Internship with Palomar Health and preparing to apply for medical school
KAIWEI ANG
LUKE FEELEY
JESSICA HALVERSON
KAYLEE KANGAS
AUSTIN KIM - now at NIH
GRANT KIM - performing research at HCMC
VARUN MANGALICK
JEREMY MEULEMANS
KELSEY PORTER - now working with EXPLO, doing Exploration-based learning with youth groups
DIMITRI SIDIROPOULOS - now in the Cellular and Molecular Medicine PhD Program at Johns Hopkins
NURUL QURATULAINI ABD SALIM NAST
PATRICK JOHNSON - now working in biotechnology at Takeda Pharmaceuticals
LUTFE-E-NOOR RAHMAN
JORDAN AKERS
TIMOTHY RENIER
CARTER LINHARDT
DOMINIQUE SABAS
Plants
CHLORO-FIGHTER, the spider plant - deceased

Join us!

 

Interested in joining the lab? Contact Dan at dknights@umn.edu.

Want to support our research? Please contact the University of Minnesota Foundation, or give now.