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Systems & Synthetic Biology

Systems biology is the integration of experimental and modeling approaches to dissect complex cellular phenomena. Fundamentally, systems biology aims to better quantify and comprehend the highly multivariate and interactive networks of genes, proteins, and metabolites that regulate cellular function. The faculty in Cornell’s Meinig School Biomedical Engineering apply new experimental and computational approaches to understand how these gene, signal transduction, and metabolic networks are regulated in healthy tissues and dysregulated, resulting in aberrant cell fates, in pathological settings such as development, cancer and aging. Furthermore, our researchers use modeling efforts to better engineer both novel biomolecules and new combinatorial therapeutic strategies to treat these pathophysiologies. Increasingly, our efforts aim to marry experiment and modeling at the single-cell level so as to elucidate how cell-to-cell variability arises and underlies disease progression and response to therapy. These efforts rely on connections with Cornell’s Nanobiotechnology Center, NIH-funded Physical Sciences Oncology Center, and Stem Cell Program, as well as in collaborations with clinical and research scientists at Weill Cornell Medicine.

Faculty research summaries:

Prof. Ilana Brito’s lab pioneers systems-level methods to examine horizontal gene transfer within the human microbiome, the predominant mechanism by which pathogens acquire antibiotic resistance. The Brito Lab studies the transmission of commensal microbes between people and their environments. They employ a combination of microbial engineering, single-cell sequencing approaches, and novel computational algorithms applied to metagenomic data to better understand the relationship between human health and the microbiome.

Prof. Jonathan Butcher’s lab develops and utilizes multi-scale systems modeling to analyze molecular and cellular decisions necessary to grow and organize embryonic cardiovascular tissues. They incorporate finite-element-based growth mechanics simulation with population-based systems modeling to identify key signaling and emergent cellular decision bottlenecks that predict appropriate and malformed heart valves. These computational approaches inform bio-hybrid intervention strategies to repair congenital heart defects.

Prof. Ben Cosgrove’s lab studies how aging influences a decline in the ability of resident stem cells to regenerate adult tissues. His lab explores how alterations in both the tissue microenvironment and cell signal transduction pathways within the stem cells themselves are altered in aging. His research uses computational and experimental approaches to better understand multivariate interactions in these signaling networks and to target aberrant network functions to rejuvenate stem cells in aged tissues.

Prof. Iwijn De Vlamick leads an experimental physical genomics lab focused on the development and application of sensitive single-cell genome sequencing principles. Single-cell sequencing enables highly multivariate measurements of genomic and transcriptomic cell-to-cell variability. When combined with microscopy techniques, single cell sequencing will enable the study of the systems biology of cells in tissue microenvironments.

Prof. Mert Sabuncu’s research is focused on the image processing problems of establishing in clinical biomedical image analysis, in partcular applied to spatial correspondence across multiple clinical scans. Previously at MIT and Harvard Medical School, he is joining Cornell to build a lab that will develop cutting-edge machine-learning algorithms to analyze and exploit biomedical image data, together with other clinical data types such as genomics.

Prof. Michael Shuler’s lab has pioneered the development of biologically detailed computer models of whole cells, primarily based on models of E. coli. These models predict the dynamic response of such single cells or a population of cells using an ensemble of single cell models to changes in their environment (e.g., medium composition, temperature, dissolved oxygen, etc). Using this approach his group has built models of a “minimal cell” in which all the genes necessary to sustain life.

Research Area Faculty

  Name Department Contact
jfa79.jpg Antaki, James F.
Susan K. McAdam Professor of Heart Assist Technology
Biomedical Engineering Kimball Hall
ilb8.jpg Brito, Ilana Lauren
Assistant Professor, Mong Family Sesquicentennial Faculty Fellow in Biomedical Engineering
Biomedical Engineering 289 Kimball Hall
607 254-2938
jtb47.jpg Butcher, Jonathan T.
Associate Professor, Associate Director of BME, Director of Undergraduate Studies
Biomedical Engineering 304 Weill Hall
607 255-3575
bdc68.jpg Cosgrove, Benjamin David
Assistant Professor
Biomedical Engineering 159 Weill Hall
607 255-7271
id93.jpg De Vlaminck, Iwijn
Robert N. Noyce Assistant Professor in Life Science and Technology
Biomedical Engineering 301 Weill Hall
md255.jpg DeLisa, Matthew P.
William L. Lewis Professor of Engineering
Chemical and Biomolecular Engineering 254 Olin Hall
607 254-8560
jtl10_eng.jpg Lis, John
Professor
Molecular Biology and Genetics
dl79_eng.jpg Luo, Dan
Professor
Biological and Environmental Engineering
am699.jpg Molnar, Alyosha Christopher
Associate Professor
Electrical and Computer Engineering Room 423 Phillips Hall
ms3375.jpg Sabuncu, Mert
Assistant Professor
Electrical and Computer Engineering, Biomedical Engineering 300 Frank H. T. Rhodes Hall
mls50.jpg Shuler, Michael Louis
Samuel B. Eckert Professor of Engineering
Biomedical Engineering, Chemical and Biomolecular Engineering 350 Duffield Hall (secondarily 381 Kimball)
607 255-7577
ads10.jpg Stroock, Abraham Duncan
William C. Hooey Director and Gordon L. Dibble ’50 Professor of Chemical and Biomolecular Engineering
Chemical and Biomolecular Engineering 124 Olin Hall
607 255-4276
jdv23.jpg Victor, Jonathan
Professor
Neurology and Neuroscience, Weill Cornell
hy299_eng.jpg Yu, Haiyuan
Associate Professor
Biological Statistics & Computational Biology