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Department of Systems Biology

Featured Publications

Guharajan S, Chhabra S, Parisutham V, Brewster RC. (2021) Quantifying the regulatory role of individual transcription factors in Escherichia coli, Cell Rep 9;37(6):109952.

Ali MZ, Choubey S, Brewster RC. (2020). Probing mechanisms of transcription elongation through cell-to-cell variability of RNA polymerase, Biophys J. 118(7):1769-1781.

Bulcha JT, Giese G, Ali MZ, Lee YU, Walker MD, Holdorf AD. Yilmaz S, Brewster RC, Walhout AJM, (2019). A Persistence Detector for Metabolic Netowrk Reqiring in an Amimal. Cell Rep.  8;26(2):460-468.e4.

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Belaghzal H, Borrman T, Stephens A.D. et al. (2021) Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nat Genet 53, 367–378.

Volume 53 Issue 5

Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum 

Image: Eric Tambutté, Centre Scientifique de Monaco. Cover Design: Valentina Monaco.

Nand A, Zhan Y, Salazar O.R. et al. (2021) Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum. Nat Genet 53, 618–629 (2021).

Oomen ME, Hedger AK, Watts JK, Dekker J. (2020). Detecting chromatin interactions between and along sister chromatids with SisterC. Nat Methods 17, 1002-9.

Tavares-Cadete F, Norouzi D, Dekker B, Liu Y, Dekker J. (2020) Multi-contact 3C reveals that the human genome during interphase is largely not entangled. Nat Struct Mol Biol On line.

Abramo K, Valton A-L, Venev SV, Ozadam H, Fox AN, Dekker J. (2019). A Chromosome Folding Intermediate at the Condensin-to-Cohesin Transition During Telophase. Nat Cell Biol 21, 1393-1402.

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Cruz-Gordillo P, Honeywell ME, Harper NW, Leete T, Lee MJ. (2020) ELP-dependent expression of MCL1 promotes resistance to EGFR inhibition in triple-negative breast cancer cells. Science Signaling 13(658), eabb9820.

Schwartz HR*, Richards R*, Fontana RE, Joyce AJ, Honeywell ME, Lee MJ. (2020). Drug GRADE: an Integrated Analysis of Population Growth and Cell Death Reveals Drug-Specific and Cancer Subtype-Specific Response Profiles. Cell Rep 31, 107800.

Richards R, Schwartz HR, Honeywell ME, Stewart MS, Cruz-Gordillo P, Joyce AJ, Landry BD, Lee MJ. (2020) Drug Antagonism and Single Agent Dominance Result from Differences in Death Kinetics. Nature Chem Biol 16, 791-800.

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Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods

Khoshkenar P, Lowry E, Mitchell A. (2021). Rapid signaling reactivation after targeted BRAF inhibition predicts the proliferation of individual melanoma cells from an isogenic population. Sci Rep 11, 15473

Rosener B, Sayin S, Oluoch PO, Garcia Gonzalez AP, Mori H, Walhout AJM, Mitchell A. (2020). Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in the Caenorhabditis elegans host. eLife 2020;9:e59831.

 Xavier JB, et al. (2019). The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends in Cancer.

Dahan O, Dorfman BS, Sayin S, Rosener B, Hua T, Yarden A, Mitchell A. (2019). Harnessing robotic automation and web-based technologies to modernize scientific outreach. PLoS Biology.

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Expanding Molecular Coverage in Mass Spectrometry Imaging of Microbial Systems Using Metal-Assisted Laser Desorption/Ionization

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Lukowski JK, Bhattacharjee A, Yannarell SM, Schwarz K, Shor LM, Shank EA, Anderton CR. (2021). Expanding Molecular Coverage in Mass Spectrometry Imaging of Microbial Systems Using Metal-Assisted LaserDesorption/Ionization. Spectrum Vol 9, Number 1

A new study shows that transparent soil substitutes can be used to replicate the interactions of bacteria and fungi in soil, opening up a new approach to learning how soil microbes contribute to a healthy ecosystem. Elizabeth Shank, PhD, associate professor of microbiology & physiological systems and senior author on the study, describes how using two transparent soil substitutes allowed scientists to follow how soil bacteria rely on fungi to help them survive extended dry periods. 

Sharma K, Palatinszky M, Nikolov G, Berry D, Shank EA. (2020) Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. Elife 9:e56275

Yannarell SM, Grandchamp GM, Chen S-Y, Daniels KE, Shank EA. (2019) A dual-species biofilm with emergent mechanical and protective properties. J Bacteriology. pii: JB.00670-18. 

Grubbs KJ*, Bleich RM*, Santa Maria KC, Allen SE, AgBiome Team, Shank EA, and Bowers AA. (2017) Large-scale bioinformatics analysis of Bacillus genomes uncovers conserved roles of natural products in bacterial physiology. mSystems  2, pii:e00040-17. 

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Walker MD, Giese G, Holdorf AD, Bhattacharya S, Diot C, García-González AP, Horowitz B, Lee YU, Leland T, Li X, Mirza Z, Na H, Nanda S, Ponomarova O, Zhang H, Yilmaz LS, Walhout AJM. (2021). WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization, Genetics, iyab089, https://doi.org/10.1093/genetics/iyab089

Rosener B, Sayin S, Oluoch PO, Garcia Gonzalez AP, Mori H, Walhout AJM, Mitchell A. (2020). Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in the Caenorhabditis elegans host. eLife 2020;9:e59831.

Molecular Systems Biology CoverYilmaz LS, Li X, Nanda S, Fox B, Schroeder F, Walhout AJM. (2020). Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels. Mol Syst Biol 16:e9649.

Giese GE, Walker MD, Ponomarova O, Zhang H, Li X, Minevich G, Walhout AJM. (2020) C. elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor. eLife 9:e60259.

Na H, Zdraljevic S, Tanny RE, Walhout AJM, Andersen EC. (2020). Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model. PLoS Genet 16(8):e1008984.

Zhang J, Li X, Olmedo M, Holdorf AD, Shang Y, Artal-Sanz M, Yilmaz LS, Walhout AJM. (2019). A Delicate Balance between Bacterial Iron and Reactive Oxygen Species Supports Optimal C. elegans Development. Cell Host Microbe 26, 400-11.

Bulcha JT, Giese GE, Ali MZ, Lee Y-U, Walker MD, Holdorf AD, Yilmaz LS, Brewster RC, Walhout AJM. (2019). A Persistence Detector for Metabolic Network Rewiring in an Animal. Cell Rep 26, 460-68.

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Maire T, Allertz T, Betjes MA, Youk H. (2020) Dormancy-to-death transition in yeast spores occurs due to gradual loss of gene-expressing ability, Mol Syst Biol Mol Syst Biol 16:e9245.

Laman Trip DS, Youk H. (2020) Yeasts collectively extend the limits of habitable temperatures by secreting glutathione, Nature Microbiology 5:943-954.

Dang Y, Grundel DAJ, Youk H. (2020) Cellular dialogues: cell-cell communication through diffusible molecules yields dynamic spatial patterns, Cell Systems 10:1-17.