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Welcome to the Program in Systems Biology

Our program aims to explore the mechanisms and principles of biological complexity. This is an exciting time for systems biology, with rapid technological advances in many fields including genomics, computational biology, imaging, mass spectroscopy and bioinformatics. Research in the program develops and leverages technological breakthroughs in these areas to explore the biology of complex systems. Today’s scientific research in general, and systems biology in particular, is increasingly multi-disciplinary. Therefore, we aim to create an intellectually diverse environment where combining different fields is encouraged and where students, post-doctoral fellows and faculty from different backgrounds work together in a collegial and interactive atmosphere.

Please browse through our website to learn more about our ongoing research, find recent publications and news items, upcoming speakers in our seminar series, or visit us at the UMass, Worcester campus.

A.J. Marian Walhout, PhD & Job Dekker, PhD, Co-Directors

A Delicate Balance between Bacterial Iron and Reactive Oxygen Species Supports Optimal C. elegans Development. Zhang J, Li X, Olmedo M, Holdorf AD, Shang Y, Artal-Sanz M, Yilmaz LS, Walhout AJM. Cell Host Microbe. 2019 Sep 11;26(3):400-411.
A Chromosome Folding Intermediate at the Condensin-to-Cohesin Transition During Telophase. Abramo K, Valton A, Venev SV, Ozadam H, Fox AN, Dekker J. Nat Cell Biol. 2019 Nov;21(11):1393-1402.
A Dual-Species Biofilm with Emergent Mechanical and Protective Properties. Yannarell SM, Grandchamp GM, Chen SY, Daniels KE, Shank EA. J Bacteriol. 2019 Aug 22;201(18). pii: e00670-18.
Modeling of Cisplatin-Induced Signaling Dynamics in Triple-Negative Breast Cancer Cells Reveals Mediators of Sensitivity. Heijink AM, Everts M, Honeywell ME, Richards R, Kok YP, de Vries EGE, Lee MJ, van Vugt MATM. Cell Rep. 2019 Aug 27;28(9):2345–5.
Harnessing Robotic Automation and Web-Based Technologies to Modernize Scientific Outreach. Dahan O, Dorfman BS, Sayin S, Rosener B, Hua T, Yarden A, Mitchell A. PLoS Biol. 2019 Jun 26;17(6):e3000348.
A Persistence Detector for Metabolic Network Rewiring in an Animal. Bulcha JT, Giese GE, Ali MZ, Lee YU, Walker MD, Holdorf AD, Yilmaz LS, Brewster RC, Walhout AJM. Cell Rep. 2019 Jan 8;26(2):460-468.
Integrative Detection and Analysis of Structural Variation in Cancer Genomes. Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F. Nat Genet. 2018 Oct;50(10):1388-1398.
Tumor‐Stroma Interactions Differentially Alter Drug Sensitivity Based on the Origin of Stromal Cells. Landry BD, Leete T, Richards R, Cruz-Gordillo P, Schwartz HR, Honeywell ME, Ren G, Schwartz AD, Peyton SR, Lee MJ. Mol Syst Biol. 2018 Jun 28;14, e8322.
A Pathway for Mitotic Chromosome Formation Gibcus JH*, Samejima K*, Goloborodko A*, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J. Science. 2018 Feb 9;359(6376).
Pirated Siderophores Promote Sporulation in Bacillus subtilis. Grandchamp GM, Caro L, Shank EA. Appl Environ Microbiol. 2017 May 1;83(10). pii: e03293-16.
Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics. García-González AP, Ritter AD, Shrestha S, Andersen EC, Yilmaz LS, Walhout AJM. Cell. 2017 Apr 20;169(3):431-441.
Effect of Transcription Factor Resource Sharing on Gene Expression Noise. Das D, Dey S, Brewster RC, Choubey S. PLoS Comput Biol. 2017 Apr 17;13(4):e1005491.
Structural Organization of the Inactive X Chromosome in the Mouse. Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J. Nature. 2016 Jul 28;535(7613):575-9.
Oscillatory Stress Stimulation Uncovers an Achilles' Heel of the Yeast MAPK Signaling Network. Mitchell A, Wei P, Lim WA. Science. 2015 Dec 11;350(6266):1379-83.
The Transcription Factor Titration Effect Dictates Level of Gene Expression. Brewster RC, Weinert FM, Garcia HG, Song D, Rydenfelt M, Phillips R. Cell. 2014 Mar 13;156(6):1312-23.