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.

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.

Rohit Pappu inducted into the AIMBE

On April 4th 2016, Rohit Pappu was inducted into the American Institute for Medical and Biological Engineering (AIMBE) college of fellows. Dr. Pappu was nominated, reviewed, and elected by peers and members of the College of Fellows for outstanding contributions to protein engineering and design and the molecular basis of neurodegeneration through advances in computational biology.

2015-2016 CBSE Scholars

The new CBSE scholarships for 2015-2016 have been announced! The CBSE scholarships reflect the academic excellence of doctoral students in the center. This years recipients are listed below;

Congratulations to all!

Raman lab in Nature Communications

Work by professor Barani Raman exploring how locust brains process neural stimuli has been published in Nature Communications. This work, spearheaded by co-first authors Debajit Saha and Chao Li (CBSE scholar), sets a paradigm for tracking neural responses and sheds light on how neurons process and filter complex information. The work has been made open access through generous support from the CBSE.

For more information, see the Washington University press release, or read the paper now online.

Rohit Pappu Named Endowed Professor

Rohit Pappu was named as the Edwin. H. Murty endowed Professor of Engineering, with an installation ceremony held on March 2nd 2015. He and his lab members have developed and used novel combinations of polymer physics theories, molecular simulations and biophysical experiments to provide definitive descriptors that relate information contained in these intrinsically disordered proteins sequences to their conformational characteristics and aggregation mechanisms.

Artyomov lab on cover of Immunity

Work by professor Maxim Artyomov examining metabolic determinants of macrophage polarization has been published in Immunity. Using a systems biology approach to analyze cellular metabolic status, lead author Jha and colleagues identified the key metabolites and metabolic processes which are required for specific states of macrophage polarization. For more information, the paper is available here.

Biophysical Society Student Award

Alex Holehouse, a graduate student in the Pappu Lab, was one of the winners of the Biophysical Society's Student Research Achievement Award (SRAA). Alex won for his work on developing tools to understand sequence-conformation relationships in intrinsically disordered proteins.

Kathrin Andrich wins travel award

Kathrin Andrich, a graduate student in the Bieschke lab, won a travel award to the 59th Annual Biophysical Society Meeting in Baltimore, MD.

CBSE researchers aid in the battle against Ebola

Work by Anu Mittal, post doc in the Pappu lab, has contributed towards a groundbreaking study by the Amarasinghe lab at Washington University School of Medicine on the mechanism by which Ebola blocks the immune system. For more information, please see the press release .

Spring 2016 CBSE seminar series:

Noon (12 PM)
Brauer Hall, Room 3015 ( upper level seminar room )

Feb 23rd: Amy Gladfelter, Dartmouth College

Mar 8th: Bruce Mayer, University of Connecticut

Mar 15th: Steven Smith, Stony Brook University

Mar 22nd: Greg Voth, University of Chicago

May 10th: Atul Butte, UCSF

S. A. Ermilov, R. Su, A. Conjusteau, F. Anis, V. Nadvoretskiy, M. A. Anastasio, A. A. Oraevsky (2016)

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

Zhu, W., Varga, Z., Silva, J.R. (2015)

Molecular Motions that Shape the Cardiac Action Potential: Insights from Voltage Clamp Fluorometry. - Progress in biophysics and molecular biology

Holehouse, A. S. & Naegle, K. M. (2015)

Reproducible Analysis of Post-Translational Modifications in Proteomes-Application to Human Mutations - PLoS One, 10: e0144692

Brangwynne, C.P., Tompa, P.S., Pappu, R.V. (2015)

Polymer Physics of Intracellular Phase Transitions - Nature Physics, 11, 899-904

Ruff, K.M., Harmon, T.S., Pappu, R.V. (2015)

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences - Journal of Chemical Physics, 143, 243123

Hughes, T.B., Miller, G.P., Swamidass, S.J. (2015)

Modeling epoxidation of drug-like molecules with a deep machine learning network - ACS Central Science, 1, 168-180

Saha, D., Li, C., Peterson, S., Padovano, W., Katta, N., & Raman, B (2015)

Behavioural correlates of combinatorial versus temporal features of odour codes - Nature Communications, 6, 6953

Jha, A. K., Huang, S. C.-C., Sergushichev, A., ... Artyomov, M. N. (2015)

Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization - Immunity, 42(3), 419 - 430

Andrich, K., & Bieschke, J. (2015)

The Effect of (-)-Epigallo-catechin-(3)-gallate on Amyloidogenic Proteins Suggests a Common Mechanism - Adv. in Exp. Med. and Biol., 863, 139 - 161

Naegle, K., Gough, N. R., & Yaffe, M. B. (2015)

Criteria for biological reproducibility: what does “n” mean? Science Signaling, 8(371), fs7.863

Guan, H., Xu, Q., Garson, A. B., 3rd, & Anastasio, M. A. (2015)

Boundary-enhancement in propagation-based x-ray phase-contrast tomosynthesis improves depth position characterization - Phys. in Med. and Biol., 60(8), N151 - 65

Hughes TB, Miller GP, and Swamidass SJ (2015)

Site of Reactivity Models Predict Molecular Reactivity of Diverse Chemicals with Glutathione - Chem. Res. Toxicol., 28(4), 797–809

Holehouse AS, Garai K, Lyle N, Vitalis A, Pappu RV (2015)

Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation. JACS, 137, 2984 - 2995