Bioinformatics and Computational Biology

Cells are more resilient to environmental changes than previously thought
Research from CS&E's Chad Myers and collaborators from the Donnelly Centre is featured in the May issue of Science Magazine.

Knights named 2020 Highly Cited Researcher
Associate Professor Knights is one of the most influential researchers in his fields, according to analysis of citation counts by Clarivate Analytics.

When two are better than one: Why some gene duplicates are retained while others perish
New study from the Myers Lab finds that gene “backups” more likely when encoded proteins have little room for change.

Immigration to the United States changes a person’s microbiome
The study of communities migrating from Southeast Asia to the United States could provide insight into some of the metabolic health issues affecting immigrants to the country.
Research in this area explores the use of computational methods to better categorize, visualize, and model biological data and systems. These problems often involve massive, high-dimensional datasets and their solutions draw from many disciplines of computer science including database management, data mining, machine learning, and algorithmic optimization. Research in this group includes algorithms for sequence and structure analysis, protein structure prediction, virtual screening and lead discovery, data modeling of scientific applications, DBMS (database management system) extensions in support of brain image and proteomics analyses, and building predictive models for effective disease diagnoses. The research group has increasing collaboration with the College of Biological Sciences, the Medical School, and the Mayo Clinic.
Faculty








Labs and selected projects
- Bioinformatics George Karypis
- Bioinformatics and Computational Biology Vipin Kumar
- Chemical Informatics George Karypis
- Computational Biology Rui Kuang
- Karypis Lab
- Knights Lab
- Principal Research Projects Daniel Boley
Latest research projects, publications, and talks

Identification and characterization of a fungal-selective glutaminyl tRNA synthetase inhibitor with potent activity against Candida albicans [journal]
Posted December 17, 2021
Alice Xue, Amanda Veri, Xiang Zhang, Ci Fu, Emma Lash, Kali Iyer, Nicole Revie, Nicole Robbins, Charles Boone, Chad Myers (professor), Leah Cowen
Access Microbiology

Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling [journal]
Posted December 8, 2021
Willow Coyote-Maestas, David Nedrud, Antonio Suma, Yungui He, Kenneth A Matreyek, Douglas M Fowler, Vincenzo Carnevale, Chad L Myers (professor), Daniel Schmidt
Nature Communications

Microbiome based systems, apparatus and methods for monitoring and controlling industrial processes and systems [patent]
Posted December 2, 2021
Rob Knight, Ajay Kshatriya, Chris Lauber, J Gregory Caporaso, Dan Knights (professor), Ryan Gill, Joel Moxley

Participatory Microbiome Research With Hmong and Karen Communities: Lessons Learned [journal]
Posted November 17, 2021
Pajau Vangay, Nancy Yang, Shannon Pergament, Mary Xiong, Bwei Paw, Rodolfo Batres, Dan Knights (professor), Kathleen A Culhane-Pera
Journal of Participatory Research Methods

Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets [journal]
Posted November 11, 2021
Ci Fu, Xiang Zhang (Ph.D. student), Amanda O Veri, Kali R Iyer, Emma Lash, Alice Xue, Huijuan Yan, Nicole M Revie, Cassandra Wong, Zhen-Yuan Lin, Elizabeth J Polvi, Sean D Liston, Benjamin VanderSluis (Ph.D. 2014), Jing Hou, Yoko Yashiroda, Anne-Claude Gingras, Charles Boone, Teresa R O’Meara, Matthew J O’Meara, Suzanne Noble, Nicole Robbins, Chad L Myers (professor), Leah E Cowen
Nature Communications

Multi-omics analyses show disease, diet, and transcriptome interactions with the virome [journal]
Posted October 1, 2021
Kathie A Mihindukulasuriya, Ruben AT Mars, Abigail J Johnson, Tonya Ward, Sambhawa Priya, Heather R Lekatz, Krishna R Kalari, Lindsay Droit, Tenghao Zheng, Ran Blekhman, Mauro D’Amato, Gianrico Farrugia, Dan Knights (professor), Scott A Handley, Purna C Kashyap
Gastroenterology

Heuristic and Hierarchical-Based Population Mining of Salmonella enterica Lineage I Pan-Genomes as a Platform to Enhance Food Safety [journal]
Posted October 1, 2021
Joao Carlos Gomes-Neto, Natasha Pavlovikj, Carmen Cano, Baha Abdalhamid, Gabriel Asad Al-Ghalith, John Dustin Loy, Dan Knights (professor), Peter C Iwen, Byron D Chaves, Andrew K Benson
Frontiers in Sustainable Food Systems

Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline [journal]
Posted September 10, 2021
Henry N Ward (Ph.D. student), Michael Aregger, Thomas Gonatopoulos-Pournatzis, Maximilian Billmann (postdoctoral associate), Toshiro K Ohsumi, Kevin R Brown, Benjamin J Blencowe, Jason Moffat, Chad L Myers (professor)
Nature Protocols

Improving Measures of Chemical Structural Similarity Using Machine Learning on Chemical–Genetic Interactions [journal]
Posted July 28, 2021
Hamid Safizadeh (Ph.D. student), Scott W Simpkins (Ph.D. 2018), Justin Nelson (Ph.D. 2019), Sheena C Li, Jeff S Piotrowski, Mami Yoshimura, Yoko Yashiroda, Hiroyuki Hirano, Hiroyuki Osada, Minoru Yoshida, Charles Boone, Chad L Myers (professor)
Journal of Chemical Information and Modeling

Association of BMI, comorbidities and all-cause mortality by using a baseline mortality risk model [journal]
Posted July 9, 2021
Jia Li (M.S. 2020), Gyorgy Simon, M Regina Castro, Vipin Kumar (professor), Michael S Steinbach (researcher), Pedro J Caraballo
PLOS ONE
More About Research areas
- Architectures, Compiler Optimization, and Embedded Systems
- Data Mining, Databases, and Geographical Information Systems
- Graphics and Immersive Computing
- High Performance Computing
- Human Computer Interaction (HCI)
- Networks, Distributed Systems, and Security
- Robotics and Artificial Intelligence
- Software Engineering and Programming Languages
- Theoretical Foundations