University of Wisconsin–Madison

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

Neurological Surgery Department

Neuroepigenetics of human behavior

alisch@wisc.edu

Daniel Amador-Noguez

Bacteriology Department

Metabolic regulation in biofuel producing bacteria

amadornoguez@wisc.edu

Richard Anderson

Medical School Dean's Office

Molecular and cellular signaling and cancer

raanders@wisc.edu

Aseem Ansari

Biochemistry Department

Designing Synthetic Transcription Factors (SynTFs) for precision medicine

azansari@wisc.edu

Alan Attie

Biochemistry Department

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

adattie@wisc.edu

Silvia Cavagnero

Chemistry Department

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

cavagnero@chem.wisc.edu

Jing Fan

Nutritional Sciences Department

Mammalian cellular metabolism; metabolic regulation; tumor microenvironment

jfan4@wisc.edu

Audrey Gasch

Genetics Department

Genomic expression in response to stress

agasch@wisc.edu

Ying Ge

Cell & Regenerative Biology Department

Systems biology, cardiac disease and regeneration

ge2@wisc.edu

Chris Hittinger

Genetics Department

Molecular evolution of gene networks

cthittinger@wisc.edu

Zhen Huang

Neurology Department

Cerebral cortex development, neuronel migration, dendrite development

z.huang@neurology.wisc.edu

Timothy Kamp

Medicine Department

Cardiac ion channels function and regulation; basic mechanisms of heart failure and arrhythmias; stem cells and cardiac regeneration

tjk@medicine.wisc.edu

Yoshihiro Kawaoka

Pathobiological Sciences Department

Molecular pathogenesis of influenza and Ebola viruses

kawaokay@svm.vetmed.wisc.edu

Pamela Kreeger

Biomedical Engineering Department

Systems biology experiments and modeling for human cancers

kreeger@wisc.edu

Mark Mandel

Medical Microbiology & Immunology Department

Genetic analysis of bacterial colonization

mmandel@wisc.edu

Phillip Newmark

Integrative Biology Department

Regeneration and germ cell development in flatworms

pnewmark@wisc.edu

David O'Connor

Pathology & Laboratory Medicine Department

Pathogenetics of SIV and HIV Infections

dhoconno@wisc.edu

Shelby O'Connor

Pathology & Laboratory Medicine Department

Host immunity to SIV/HIV and Mtb

slfeinberg@wisc.edu

David Pagliarini

Biochemistry Department

Mitochondrial biogenesis and metabolism; cell signaling; proteomics

pagliarini@wisc.edu

Brian Pfleger

Chemical & Biological Engineering Department

Sustainability through synthetic biology

pfleger@engr.wisc.edu

Srivatsan Raman

Biochemistry Department

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

sraman4@wisc.edu

Jennifer Reed

Chemical & Biological Engineering Department

Biological network modeling of microbial systems

reed@engr.wisc.edu

Philip Romero

Biochemistry Department

Protein engineering

promero2@wisc.edu

Lixin Rui

Medicine Department

Molecular pathogenesis of lymphoma

lrui@medicine.wisc.edu

Krishanu Saha

Biomolecular Chemistry Department

Human stem cell engineering

ksaha@wisc.edu

David Schwartz

Chemistry Department

Structural variation in mammalian genomes

dcschwartz@wisc.edu

Lloyd Smith

Chemistry Department

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

smith@chem.wisc.edu

Antony Stretton

Integrative Biology Department

Nematode neurobiology

aostrett@wisc.edu

Robert Striker

Medicine Department

Role of immune imbalance (CD4/CD8 ratio) in viral infections and disease

rtstriker@wisc.edu

Michael Sussman

Biochemistry Department

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

msussman@wisc.edu

Ophelia Venturelli

Biochemistry Department

Systems and synthetic biology of genetic regulatory networks and microbial ecosystems

venturelli@wisc.edu

Chad Vezina

Comparative Biosciences Department

Urinary dysfunction in aging men

cmvezina@wisc.edu

Jade Wang

Stress and genome integrity in bacteria

Stress and genome integrity in bacteria

wang@bact.wisc.edu

Marvin Wickens

Biochemistry Department

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

wickens@biochem.wisc.edu

John Yin

Chemical & Biological Engineering Department

Molecular virology, computational biology, biochemical engineering

john.yin@wisc.edu

John-Paul (JP) Yu

Radiology Department

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

jpyu@uwhealth.org

Xuehua Zhong

Genetics Department

Epigenetic regulation in plants

xzhong28@wisc.edu