Welcome to the home of network biology at Washington University in St. Louis

Our Mission: Model, predict and design functions of biological systems that result from integration of signals and responses of biomolecular and cellular networks.





Soranno joins CBSE

October, 2016

We welcomed Dr. Andrea Soranno, a freshly minted Assistant Professor in Biochemistry & Molecular Biophysics. The CBSE was an important attractor for recruiting Andrea from the University of Zurich. Andrea will set up his lab on the WUSM campus and participate regularly in CBSE activities and in our scientific collaborations.

Andrea's interests are in the physics of intracellular phase transitions and the functions of intrinsically disordered proteins. To further his research, Andrea has developed and will continue to develop innovative single molecule fluorescence based methods to study macromolecular conformations and dynamics within cells and in membranless organelles. We are thrilled to have succeeded in recruiting Andrea.





Bowman wins Packard Fellowship

October, 2016

Dr. Gregory Bowman, Assistant Professor of Biochemistry & Molecular Biophysics, who formally became a member of CBSE as of July 01, 2016, will be one of eighteen recipients of the David & Lucille Packard Fellowship in Science and Engineering. Packard Fellowships are highly competitive science fellowships which provide $875,000 over five years for early-career investigators to pursue their research. Read more about the announcement here.

Greg's work focuses on using molecular dynamics simulations and experiments to understand how conformational changes in proteins impact their function, with a view to developing novel approaches for drug discovery. For more information on the Bowman lab see here





Silva lab pulls in grants

October, 2016

Jon Silva, CBSE member since July 2013, recently received a grant from the American Heart Association titled "Molecular Pathology of Brugada Syndrome Mutations". Additionally, late last week, Jon learned that his NIH RO1 received a score of 8%, which places it well within the funding pay line. Jon's work epitomizes the type of multiscale thinking that was the motivation behind forming the CBSE.

For more information on the Silva lab, see here.





Swamidass lab receives additional NIH funding

August, 2016

Dr. Grover P. Miller Ph.D. and Dr. S. Joshua Swamidass M.D. Ph.D. are pleased to announce that their grant 'Computationally Modeling the Impact of Ontogeny on Drug Metabolic Fate' was funded by the National Library of Medicine (NLM) of the NIH after receiving an outstanding impact score of 20 (6th percentile) by the independent study section.

This grant extends the lab's other recently awarded grant into modeling drug metabolism into children. Dr. Swamidass’ group will use mathematical models to understand how children metabolize drugs differently than adults. Dr. Miller’s group will validate these models with prospect experiments. The lab hopes that understanding these differences will help researchers develop safer and more effective medicines for children.

For more information on this project see here.





CBSE productivity reaches new highs

June 2016

In the first six months of 2016 labs associated with the Center for Biological Systems Engineering published 22 papers across a wide variety of journals in many different topics, from detailed technical reports to paradigm changing discoveries. The range of research performed and this exceptional productivity is testament to the environment and the quality of the researchers associated with the CBSE. Congratulations to all!




Raman lab develops cyborg super-sniffer locust

The Raman lab is pioneering the development of remote-control locusts in an effort to develop tools to rapidly and accurate search large areas for explosive material. By taking advantage of the locust's keen olfactory system, the lab is using electrodes connected directly to the insect's neural circuit to obtain a direct readout on the detected smells, which are then transmitted back to a central analysis unit via a low-power wireless transmission system. The work is being funded by the Office of Naval Research.

For more information see the press coverage from Popular Science and the BBC.




Naegle lab highlighted on Science homepage

A review paper by the Naegle lab was highlighted on the Science homepage as one of the top five most accessed articles across all Science journals. The review by first author Tom Ronan, a previous CBSE scholar, examines common pitfalls and challenges associated with the clustering of biological data, and provides a best-practices guide.

Read more about the work by clicking on the image below.




2016 - 2017 CBSE Scholars

The new CBSE scholarships for 2016-2017 have been announced! The CBSE scholarships reflect the academic excellence of doctoral students in the center. This year's recipients are listed below;


  • Tyler Harmon - Physics student in the Pappu Lab
  • Alex Holehouse (Kent and Bonnie Lattig Scholar) - Biophysics student in the Pappu Lab
  • Thomas Matthews - BME student in the Anastasio Lab
  • Wandi Zhu - BME student in the Silva Lab
  • Maxwell Zimmerman - Biophysics Student in the Bowman Lab

For more information on the scholars' research, check out the scholars page on the CBSE website.

Congratulations to all!




Pappu lab uncovers secrets of nucleolar organization

Work by the Pappu lab in collaboration with Cliff Brangwynne at Princeton University has helped uncover how the nucleolus (the ribosome factory found inside Eukaryotic nuclei) can simultaneously display liquid-like properties while maintaining a well defined substructure.

Specific protein-protein interactions facilitate the multi-phase behaviour observed in the nucleolus, a phenomenon which Pappu lab graduate student Tyler Harmon was able to explain using coarse-grained simulations. Tyler's work suggests that multi-phase behavior might be an expected feature of complex multi-component systems, implying a general mechanism for subcellular organization.

The work was published in Cell in May. For more information see the Princeton University press release.




Swamidass lab receives NIH funding

Dr. Grover P. Miller Ph.D. and Dr. S. Joshua Swamidass M.D. Ph.D. are pleased to announce that their grant “Data and Tools for Modeling Metabolism and Reactivity” was funded by the National Library of Medicine (NLM) of the NIH after receiving an outstanding impact score of 21 (5th percentile) by the independent study section.

This grant will fund research in their collaboration over the next several years. Dr. Swamidass’ group will use mathematical models to understand how and when “reactive metabolites” are formed, and validate this models with prospective experiments in Dr. Miller’s group. Reactive metabolites are the root cause of some of the most difficult to predict adverse drug reactions.

For more information on the Swamidass Lab's work, see here.





2016 CBSE Scholars Seminar Series:

Mondays at 4 PM


Sept 19th: Tyler Harmon
Pappu Lab
Brauer Hall, Room 012

Oct 10th: Thomas Matthews
Anastasio Lab
Brauer Hall, Room 012

Nov 14th: Maxwell Zimmerman
Bowman Lab
Brauer Hall, Room 012

Dec 12th: Dr. Phillip Payne
Institute for Informatics, WUSM
Brauer Hall, Room 3015

May 10th: Wandi Zhu
Silva Lab
Brauer Hall, Room 3015

Feb 20th: Alex Holehouse
Pappu Lab
Brauer Hall, Room 3015


Pak, CW., Kosno, M., Holehouse, AS., Padrick, SB., Mittal, A., Ali, R., Yunus, AA., Liu, DR., Pappu, RV., & Rosen, MK. (2016)

Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein - Molecular Cell, 63: pp 72 - 75


Dang, LN., Hughes, TB., Krishnamurthy, V., & Swamidass, SJ. (2016)

A Simple Model Predicts UGT-Mediated Metabolism - Bioinformatics, btw350 (ePub ahead of print)


Ronan, T., Zhijie, Q., & Naegle, KM. (2016)

Avoiding Common Pitfalls When Clustering Biological Data - Science Signalling, 9: 432


Katta, N., Meier, DC., Benkstein, KD., Semancik, S. & Raman, B. (2016)

The I/O transform of a chemical sensor - Sensors and Actuators B: Chemical, 232: pp 357 - 368


Feric, M., Vaidya, N., Harmon, TS., Mitrea, DM., Zhu, L., Richardson, TM., Kriwacki, RW., Pappu, RV., Brangwynne, CP. (2016)

Coexisting Liquid Phases Underlie Nucleolar Subcompartments - Cell, 165: pp 1-12


Huang, C., Wang, K., Schoonover, RW., Wang, LV., Anastasio, MA. (2016)

Joint Reconstruction of Absorbed Optical Energy Density and Sound Speed Distributions in Photoacoustic Computed Tomography: A Numerical Investigation - IEEE Transactions on Computational Imaging 2, 2: pp 136 - 149


Lin, CC., Bradstreet, TR., Schwarzkopf, EA., Jarjour, NN., Chou, C., Archambault, AS., Sim, J., Zinselmeyer, BH., Carrero, JA., Wu, GF., Taneja, R., Artyomov, MN., Russell, JH. & Edelson, BT. (2016)

IL-1 Induced Bhlhe40 Identifies Pathogenic T Helper Cells in a Model of Autoimmune Neuroinflammation - Journal of Experimental Medicine, 213(2): pp 251 - 271


Ronan, T., Jennifer, LMO., Huelsmann, L., Bessman, NJ., Naegle, KM., Pike, LJ. (2016)

Different Ligands and Concentrations Cause Different Downstream Signaling Molecules to Be Recruited to the Epidermal Growth Factor Receptor - Journal of Biological Chemistry, 291, pp 5528 - 5540


Ermilov, SA., Su R., Conjusteau A., Anis F., Nadvoretskiy V., Anastasio MA, Oraevsky, AA. (2016)

Three-Dimensional Optoacoustic and Laser-Induced Ultrasound Tomography System for Preclinical Research in Mice Design and Phantom Validation - Ultrasonic Imaging, 38: pp 77 - 95


Lam, HT., Graber, MC., Gentry, KA., Bieschke, J. (2016)

Stabilization of α-Synuclein Fibril Clusters Prevents Fragmentation and Reduces Seeding Activity and Toxicity - Biochemistry, 55, pp 675 - 685


Li, J., Zheng, S., Chen, B., Butte, AJ., Swamidass, SJ., Lu, Z. (2016)

A Survey of Current Trends in Computational Drug Repositioning - Briefings in Bioinformatics , 17(1), pp 2 - 12


Zhu, W., Varga, Z. & Silva, JR. (2016)

Molecular Motions that Shape the Cardiac Action Potential: Insights from Voltage Clamp Fluorometry. - Progress in Biophysics and Molecular Biology, 120, pp 3 - 17