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.

Spotlight on the Raman Lab and 2017 CBSE Summer Scholar Minerva Pappu on Automating Neural Recordings

February, 2018

The CBSE Summer Scholars program provides a way for high school students to directly engage in active research projects with CSBE labs. In the video below, 2017 CBSE Summer Scholar Minerva Pappu discusses her work in the Raman lab designing and building a micromanipulator for automated electrode positioning.

For more information on the Raman lab, see here.

Cryo-EM structure of Ebola nucleoprotein

February 2018

CBSE member Greg Bowman and our close colleagues Daisy Leung and Gaya Amarasinghe published a cryo-EM structure of the Ebola virus nucleoprotein. The paper was published in the February 22, 2018 issue of Cell.

For more information on the Bowman lab see here

Farwell to Jan Bieschke

February 2018

We bid goodbye to our friend and colleague Dr. Jan Bieschke. Jan recently moved to the UK to join the MRC’s Prion Institute at University College London as an Associate Professor. Congratulations to Jan and we wish him the very best in his pursuits!

Naegle lab makes advances in understanding tyrosine phosphorylation

October, 2017

The Naegle lab has received a $610,000 grant from the NIH to develop computational tools to better understand the consequences of tyrosine phosphorylation. Using extant data from cancer patients, the lab will develop a framework to understand cancer progression and response therapies.

For more information on the Naegle lab, see here


Raman lab to study relationship between neural circuits, behaviour, and genetics

August 2017

The Raman lab has received a $2.6 million grant from the National Science Foundation as part of their Next Generation Networks for Neuroscience (NeuroNex) award scheme. This collaborative grant will allow the Raman lab - along with colleagues in biology at Washington University and at the University of Illinois at Urbana-Champaign - to develop a genetic toolkit to explore and understand the relationship between animal behaviour and the organisms neural underpinnings.

In addition to recent funding success, this summer, the Raman lab also hosted Minerva Pappu, a 2017 CBSE summer scholar and rising high school senior from John Burroughs School. Minerva developed a semi-automated software and hardware toolkit to obtain extracellular neural recordings associated with the locust olfactory system.

For more information on the Raman lab, see here.

Pappu lab receives grant to engineer future materials

August 2017

The Pappu lab has received a $1.4 million grant to develop novel biomaterials using design principles elucidated from Nature. This work will be in collaboration with colleagues at Duke University, and will involve using lab's expertise in biological self-assembly and protein disorder to construct materials with specific environmental-stimuli sensitive behaviors.

For more information on the lab, see here.

Silva uncovers unexpected function in cardiac sodium channels

July 2017

The Silva lab has made an important finding regarding the molecular underpinnings of cardiac sodium channels. These channels are strongly implicated in cardiac arrhythmia, yet how they respond to different drugs, and indeed how they are regulated, has remained poorly understood. In recent work Silva discovered the regulatory mechanism associated with these channels is more complicated than previously understood.

This summer, the Silva lab hosted a CBSE scholar, Alex Keeley, who helped developed the lab's augmented-reality toolkit for surgical interventions .

For more information on the Silva lab, see here.

Anastasio lab peeks inside lungs

June 2017

The Anastasio lab, a world authority on photo-acoustic imaging, has received a $1.7 million grant from the NIH to image ventilation in live-patient lungs using a single X-ray image. This approach would avoid many of the complications associated with CT and MRI scans. The lab will leverage their image-processing and machine learning expertise to further develop methods that facilitate high-resolution insight into a patient's pulmonary status.

For more information on the Anastasio lab, see here.

Work from Soranno lab provides an integrative view of internal friction in unfolded polypeptides

March 2017

Unfolded polypeptides experience 'friction' as they explore conformational space. This friction can be introduced by the solvent, but can also originate from interactions intrinsic to the polypeptide, which manifests itself as so called internal friction. An in-depth study from Andrea Soranno published in the Proceedings of the National Academy of Sciences provides direct insight into our understanding of this internal friction, combining single-molecule spectroscopy with analytical theory and numerical simulations.

For more information on the Soranno lab, see here.

Bieschke lab further uncovers mechanistic underpinnings of EGCG

February 2017

Polyphenol epigallocatechin-3-gallate (EGCG), a natural compound found in green tea, represents an emerging possible treatment option for various neurodegenerative and systematic aggregation-based diseases, including the devastating systemic light chain amyloidosis. In work from the Bieschke lab examining the mechanism of action associated with EGCG on patient-derived proteins, it was found that EGCG appears to offer a general purpose treatment option, despite the fact that patients show a wide range of different types of aggregation in systemic light chain amyloidosis. These represent an important step towards general treatments for aggregation-related diseases.

For more information on the Bieschke lab's work on EGCG, see the video below

For more information on the Bieshke lab, see here.

Swamidass lab dives into deep-learning

February 2017

The Swamidass lab recently published work demonstrating the use of deep-learning to make highly accurate predictions for drug metabolomics. As new machine learning approaches are developed and new data becomes available, the Swamidass lab continues to remain at the forefront of the chemical-informatics world, supported by multiple five-year NIH grants.

For more information on the Swamidass lab, see here.

CBSE Events:

Monday May 7th (10:00 AM)
Thesis Defense (Tyler Hughes, Swamidass lab)
Moore Auditorium (Medical Campus)
Modeling the Bioactivation and Subsequent Reactivation of Drugs

Monday February 26th (11:00 AM)
Special Seminar (Prof. Samrat Mukhopadhyay, IISER Mohali, India)
Brauer Hall (012)
Prying into prions: a tale of a disordered protein tail

Friday. Nov. 17th (2:00 pm)
Thesis Defense (Tom Ronan, Naegle lab)
Whitaker Hall (216)
Binding affinity and specificity of SH2 domain interactions in receptor tyrosine kinase signaling networks

Thurs. Nov. 16th (4:30 pm - 6:30 pm)
CBSE Advances
Open house showcasing CBSE research
Brauer Hall Atrium

Poudel, J., T.P. Matthews, L. Li, M.A. Anastasio, and L.V. Wang (2017)

Mitigation of artifacts due to isolated acoustic heterogeneities in photoacoustic computed tomography using a variable data truncation-based reconstruction method - J. Biomed. Opt., 22 : pp 41018

Wei, M.-T.*, S. Elbaum-Garfinkle*, A.S. Holehouse*, C.C.-H. Chen, M. Feric, C.B. Arnold, R.D. Priestley, R.V. Pappu*, and C.P. Brangwynne*. (2017)

Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles - Nat. Chem., DOI:10.1038/nchem.2803

Saha, D., W. Sun, C. Li, S. Nizampatnam, W. Padovano, Z. Chen, A. Chen, E. Altan, R. Lo, D.L. Barbour, and B. Raman (2017)

Engaging and disengaging recurrent inhibition coincides with sensing and unsensing of a sensory stimulus - Nat. Commun, 8: pp 15413

Singh, S., and G.R. Bowman (2017)

Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS - J. Chem. Theory Comput , 13 : pp 1509–1517

Andrich, K., U. Hegenbart, C. Kimmich, N. Kedia, H.R. Bergen, S. Schönland, E.E. Wanker, and J. Bieschke (2017)

Aggregation of Full Length Immunoglobulin Light Chains from AL Amyloidosis Patients Is Remodeled by Epigallocatechin-3-gallate - J. Biol. Chem., 292: pp 2328-2344

Mangold, K.E., B.D. Brumback, P. Angsutararux, T.L. Voelker, W. Zhu, P.W. Kang, J.D. Moreno, and J.R. Silva (2017)

Mechanisms and models of cardiac sodium channel inactivation - Channels, pp 1–17

Hughes, T.B., and S.J. Swamidass (2017)

Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism - Chem. Res. Toxicol., 30: pp 642-656

Soranno, A., A. Holla, F. Dingfelder, D. Nettels, D.E. Makarov, and B. Schuler (2017)

Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations - Proc. Natl. Acad. Sci. , 114 : pp E1833–E1839

Zhu, W., T.L. Voelker, Z. Varga, A.R. Schubert, J.M. Nerbonne, and J.R. Silva (2017)

Mechanisms of noncovalent β subunit regulation of NaV channel gating - J. Gen. Phys., 149: pp 813-831

Ronan, T., Z. Qi, and K.M. Naegle. (2016)

Avoiding common pitfalls when clustering biological data - Sci. Signal, 9 : re6 (One of the top 5 most accessed Science journal articles)