Systems Biology

Photo: Proteoforms underlie complex traits and molecular mechanisms in biology
Proteoforms underlie complex traits and molecular mechanisms in biology
Photo: Proteoform Family for 50S Ribosomal Protein L7/L12
Proteoform Family for 50S Ribosomal Protein L7/L12. Figures adapted from illustrations by Yunxiang Dai (UW-Madison), and Michael Mullowney (Northwestern University). 

Systems Biology

Systems Biology seeks to understand how a biological system operates as a whole by measuring, modeling, and probing interactions between components in the system (e.g., genes, proteins, metabolites) rather than studying the components in isolation. To gain such an understanding, systems biology studies follow an iterative approach of collecting quantitative experimental data, computational and statistical modeling of these data, and implementing these models to make predictions in new experimental conditions. These studies can guide the next set of experiments to better model and understand how a system functions via the interaction of its parts. Example biological systems analyzed by these methods include cellular signaling networks in microbial cells, dynamic processes during viral infection, and multi-cellular interactions in animal models and human patients; each system of study presents unique opportunities and challenges in collecting, analyzing and modeling the data.  The resulting understanding gained from these studies can impact disease therapy (e.g., identifying new drug targets or biomarkers), biotechnology applications (e.g., determining methods to optimize biofuel production), as well as our general understanding of how biological networks operate. Students working in the research groups within the Systems Biology focus group will have the unique opportunity to work in a highly collaborative environment and gain inter-disciplinary training in both biological and computational fields. Students interested in this group may also be interested in the new QBio doctoral minor in quantitative biology that was designed to be compatible with a PhD in CMB.


Focus Group Chair Megan McClean
Biomedical Engineering Department
Biological signal processing

Focus Group Members

Reid Alisch

Neurological Surgery Department

Neuroepigenetics of human behavior

Daniel Amador-Noguez

Bacteriology Department

Metabolic regulation in biofuel producing bacteria

Richard Anderson

Medical School Dean's Office

Molecular and cellular signaling and cancer

Alan Attie

Biochemistry Department

Molecular genetics of diabetes & insulin resistance; cell biology of lipoprotein assembly, cholesterol trafficking

Jason Cantor

Biochemistry Department

Influence of environmental factors on human cell metabolism

Silvia Cavagnero

Chemistry Department

Protein folding and aggregation in the cell, molecular chaperones, role of the ribosome in protein folding

Jing Fan

Nutritional Sciences Department

Mammalian cellular metabolism; metabolic regulation; tumor microenvironment

Audrey Gasch

Genetics Department

Genomic expression in response to stress

Ying Ge

Cell & Regenerative Biology Department

Systems biology, cardiac disease and regeneration

Chris Hittinger

Genetics Department

Molecular evolution of gene networks

Zhen Huang

Neurology Department

Cerebral cortex development, neuronel migration, dendrite development

Lindsay Kalan

Medical Microbiology Department

Skin microbiome and wound healing

Yoshihiro Kawaoka

Pathobiological Sciences Department

Molecular pathogenesis of influenza and Ebola viruses

Melissa Kinney

Biomedical Engineering Department

Stem cell systems biology

Pamela Kreeger

Biomedical Engineering Department

Systems biology experiments and modeling for human cancers

Mark Mandel

Medical Microbiology & Immunology Department

Genetic analysis of bacterial colonization

Phillip Newmark

Integrative Biology Department

Regeneration and germ cell development in flatworms

David Pagliarini

Biochemistry Department

Mitochondrial biogenesis and metabolism; cell signaling; proteomics

Srivatsan Raman

Biochemistry Department

Synthetic biology, protein design, metabolic engineering, allostery, directed evolution

Jennifer Reed

Chemical & Biological Engineering Department

Biological network modeling of microbial systems

Philip Romero

Biochemistry Department

Protein engineering

Krishanu Saha

Biomolecular Chemistry Department

Human stem cell engineering

David Schwartz

Chemistry Department

Structural variation in mammalian genomes

Nathaniel Sharp

Genetics Department

Spontaneous mutation rate and spectrum

Raunak Sinha

Neuroscience Department

Neural signaling in the retina

Lloyd Smith

Chemistry Department

Development and application of novel bioanalytical methods; new instrumentation and chemistries for biological mass spectrometry and biologically modified surfaces

Michael Sussman

Biochemistry Department

Genome technologies applied to the plasma membrane of eukaryotes: signal transduction and bioenergetics

Ophelia Venturelli

Biochemistry Department

Systems and synthetic biology of genetic regulatory networks and microbial ecosystems

Chad Vezina

Comparative Biosciences Department

Urinary dysfunction in aging men

Han Wang

Integrative Biology Department

Genetic and circuit dissection of sleep

Jade Wang

Stress and genome integrity in bacteria

Stress and genome integrity in bacteria

Marvin Wickens

Biochemistry Department

RNA and gene control; role of RNA regulation in development and the nervous system

John Yin

Chemical & Biological Engineering Department

Molecular virology, computational biology, biochemical engineering

John-Paul (JP) Yu

Radiology Department

Neuroimaging, neuropsychiatric disorders, autism spectrum disorder, schizophrenia, systems neuroscience

Xuehua Zhong

Genetics Department

Epigenetic regulation in plants