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.

Headshot

Focus Group Chair Megan McClean
Biomedical Engineering Department
Biological signal processing
mmcclean@wisc.edu

Focus Group Members

Reid Alisch

Credentials: Neurological Surgery Department

Position title: Neuroepigenetics of human behavior

Email: alisch@wisc.edu

Daniel Amador-Noguez

Credentials: Bacteriology Department

Position title: Metabolic regulation in biofuel producing bacteria

Email: amadornoguez@wisc.edu

Richard Anderson

Credentials: Medical School Dean's Office

Position title: Molecular and cellular signaling and cancer

Email: raanders@wisc.edu

Alan Attie

Credentials: Biochemistry Department

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

Email: adattie@wisc.edu

Jason Cantor

Credentials: Biochemistry Department

Position title: Influence of environmental factors on human cell metabolism

Email: jcantor@morgridge.org

Silvia Cavagnero

Credentials: Chemistry Department

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

Email: cavagnero@chem.wisc.edu

Scott Coyle

Credentials: Biochemistry Department

Position title: Understanding and engineering cell behavior.

Email: smcoyle@wisc.edu

Huy Dinh

Credentials: Oncology Department

Position title: Computational biology, Tumor microenvironment heterogeneity

Email: huy.dinh@wisc.edu

Jing Fan

Credentials: Nutritional Sciences Department

Position title: Mammalian cellular metabolism; metabolic regulation; tumor microenvironment

Email: jfan4@wisc.edu

Audrey Gasch

Credentials: Genetics Department

Position title: Genomic expression in response to stress

Email: agasch@wisc.edu

Ying Ge

Credentials: Cell & Regenerative Biology Department

Position title: Systems biology, cardiac disease and regeneration

Email: ge2@wisc.edu

Chris Hittinger

Credentials: Genetics Department

Position title: Molecular evolution of gene networks

Email: cthittinger@wisc.edu

Zhen Huang

Credentials: Neurology Department

Position title: Cerebral cortex development, neuronel migration, dendrite development

Email: z.huang@neurology.wisc.edu

Lindsay Kalan

Credentials: Medical Microbiology Department

Position title: Skin microbiome and wound healing

Email: lkalan@wisc.edu

Yoshihiro Kawaoka

Credentials: Pathobiological Sciences Department

Position title: Molecular pathogenesis of influenza and Ebola viruses

Email: kawaokay@svm.vetmed.wisc.edu

Melissa Kinney

Credentials: Biomedical Engineering Department

Position title: Stem cell systems biology

Email: melissa.kinney@wisc.edu

Pamela Kreeger

Credentials: Biomedical Engineering Department

Position title: Systems biology experiments and modeling for human cancers

Email: kreeger@wisc.edu

Mark Mandel

Credentials: Medical Microbiology & Immunology Department

Position title: Genetic analysis of bacterial colonization

Email: mmandel@wisc.edu

Phillip Newmark

Credentials: Integrative Biology Department

Position title: Regeneration and germ cell development in flatworms

Email: pnewmark@wisc.edu

David Pagliarini

Credentials: Biochemistry Department

Position title: Mitochondrial biogenesis and metabolism; cell signaling; proteomics

Email: pagliarini@wisc.edu

Srivatsan Raman

Credentials: Biochemistry Department

Position title: Synthetic biology, protein design, metabolic engineering, allostery, directed evolution

Email: sraman4@wisc.edu

Philip Romero

Credentials: Biochemistry Department

Position title: Protein engineering

Email: promero2@wisc.edu

Krishanu Saha

Credentials: Biomolecular Chemistry Department

Position title: Human stem cell engineering

Email: ksaha@wisc.edu

David Schwartz

Credentials: Chemistry Department

Position title: Structural variation in mammalian genomes

Email: dcschwartz@wisc.edu

Nathaniel Sharp

Credentials: Genetics Department

Position title: Spontaneous mutation rate and spectrum

Email: nathaniel.sharp@wisc.edu

Michael Sussman

Credentials: Biochemistry Department

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

Email: msussman@wisc.edu

Ophelia Venturelli

Credentials: Biochemistry Department

Position title: Systems and synthetic biology of genetic regulatory networks and microbial ecosystems

Email: venturelli@wisc.edu

Chad Vezina

Credentials: Comparative Biosciences Department

Position title: Urinary dysfunction in aging men

Email: cmvezina@wisc.edu

Han Wang

Credentials: Integrative Biology Department

Position title: Genetic and circuit dissection of sleep

Email: han.wang@wisc.edu

Jade Wang

Credentials: Stress and genome integrity in bacteria

Position title: Stress and genome integrity in bacteria

Email: wang@bact.wisc.edu

Marvin Wickens

Credentials: Biochemistry Department

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

Email: wickens@biochem.wisc.edu

Yongna Xing

Credentials: Oncology Department

Position title: Cell signaling related to caner, structural biology, biochemistry, proteomics

Email: xing@oncology.wisc.edu

Jerry Yin

Credentials: Genetics Department

Position title: Cellular/molecular mechanisms of memory formation and psychiatric dysfunction

Email: jcyin@wisc.edu

John Yin

Credentials: Chemical & Biological Engineering Department

Position title: Molecular virology, computational biology, biochemical engineering

Email: john.yin@wisc.edu

John-Paul (JP) Yu

Credentials: Radiology Department

Position title: Neuroimaging, neuropsychiatric disorders, autism spectrum disorder, schizophrenia, systems neuroscience

Email: jpyu@uwhealth.org