[Review] Thomas JL˜, Rowland-Chandler J˜, Shou WY* (2024). Artificial selection of microbial communities: what have we learnt and how can we improve? Current Opinion in Microbiology

https://doi.org/10.1016/j.mib.2023.102400

​

[Research] Sonal*, Yuan AE, Shou WY* (2023). Collective production of hydrogen sulfide gas enables budding yeast lacking MET17 to overcome their metabolic defect, PLoS Biology

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002439

​

[Voices] Segrè D, Mitri S, Shou WY, Süel GM, Mizrahi I, Kelly L, Rebolleda-Gómez M, Ratzke C, Ogbunugafor CB, Schwartzman JA, Kryazhimskiy S, Leventhal GE, Kost C, Bell T (2023). What do you most want to understand about how collective features emerge in microbial communities? Cell Press

https://www.cell.com/cell-systems/fulltext/S2405-4712(23)00027-3#%20

• View the article here

 

[Synthesis] Yuan AE*, Shou WY* (2022). Data-driven causal analysis of observational biological time series, eLife

https://elifesciences.org/articles/72518

• See Alex's video walkthrough of this paper: https://www.youtube.com/watchv=AlV0ttQrjK8&feature=youtu.be

​

[Research] Xie L*, Shou WY* (2021). Steering ecological-evolutionary dynamics during artificial selection of microbial communities. Nature Communications

https://www.nature.com/articles/s41467-021-26647-4

• See Li's video walkthrough of this paper: https://youtu.be/a4_xNn2ip84

• See Wenying's KITP talk: https://online.kitp.ucsb.edu/online/ecoevo21/shou2/

 

[Research] Hart SFM, Chen CC, Shou WY* (2021). Pleiotropic mutations can rapidly evolve to directly benefit self and cooperative partner despite unfavorable conditions. eLife 10:e57838.

https://elifesciences.org/articles/57838

 

[Research] Green R.*˜, Sonal˜, Wang L, Hart SFM, Lu W, Skelding D, Burton JC, Mi H, Capel A, Chen HA, Lin A, Subramaniam AR, Robinowitz JD, Shou WY* (2020). Metabolic excretion associated with nutrient–growth dysregulation promotes the rapid evolution of an overt metabolic defect. PLoS Biol 18(8): e3000757. https://doi.org/10.1371/journal.pbio.3000757

 

[Research] Xie L*, Yuan A, Shou WY* (2019). Simulations reveal challenges to artificial community selection and possible strategies for success. PLoS Biol, 17(6), e3000295

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000295

• This article was featured in:

  • "Artificially selecting microbial communities: If we can breed dogs, why not microbiomes?" by F.I. Arias-Sanchez, B. Vessman, & S. Mitri. eLife https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000356

• See Wenying's medium.com story about this paper: "Escaping a black hole"

 

[Research] Hart SFM˜, Pineda JMB˜, Chen CC, Green R, Shou WY* (2019). Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community. eLife 8: e44812.

https://elifesciences.org/articles/44812

• See Wenying's medium.com story about this paper: "Foresight, hindsight, insight, and the blur in-between"

 

[Research] Niehaus L., Boland I., Liu M., Chen K., Fu D., Henckel C., Chaung K., Miranda S.E., Dyckman S., Crum M., Dedrick S., Shou WY, Momeni B* (2019). Microbial coexistence through chemical-mediated interactions. Nat. Comm. 10 (1), 2052.

https://www.nature.com/articles/s41467-019-10062-x

 

[Research] Hart SFM, Mi H, Green R, Xie L, Pineda JMB, Momeni B, Shou WY* (2019). Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells. PLoS Biol, 17(2): e3000135. https://doi.org/10.1371

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000135

• See Wenying's medium.com story about this paper: "The devil in the closet"​​

 

[Methods] Hart SFM, Skelding D, Waite AJ, Burton J, Xie L, Shou WY* (2019). High-throughput quantification of microbial birth and death dynamics using fluorescence microscopy. Quant. Biol. 7, 69-81.

https://link.springer.com/article/10.1007/s40484-018-0160-7

 

[Methods] Skelding D*, Hart S,  Vidyasagar T, Pozhitkov AE, Shou WY* (2018). Developing a low-cost milliliter-scale chemostat array for precise control of cellular growth. Quant. Biol. 6, 129-141.

https://link.springer.com/article/10.1007/s40484-018-0143-8

 

[Research] Momeni B*, Xie L, Shou WY* (2017). Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions. eLife 6: e25051.

https://elifesciences.org/articles/25051

• This article was recommended by Faculty of 1000.

 

[Review] Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou WY, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groszkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H; Isaac Newton Institute Fellows, Soyer OS (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME J. doi: 10.1038/ismej.2016.45.

http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201645a.html

 

[Research] Shou WY* (2015). Acknowledging selection at sub-organismal levels resolves controversy on pro-cooperation mechanisms. eLife 4: e10106.

http://elifesciences.org/content/early/2015/12/29/eLife.10106

 

[Research] Waite AJ*, Cannistra C, Shou WY* (2015). Defectors can create conditions that rescue cooperation. PLoS Comput Biol 11: e1004645.

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004645

 

[Review] Beliaev A, Lindemann S, Bernstein H, Song H-S, Fredrickson J, Fields M, Shou WY, and Johnson D. (2016) Engineering Microbial Consortia for Controllable Outputs. ISME J. doi: 10.038/ismej.2016.26.

http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201626a.html

 

[Editorial] Shou WY, Bergstrom CT, Chakraborty AK, Skinner FK (2015).  Theory, models and biology. eLife: e07158

http://elifesciences.org/content/4/e07158

 

[Methods] Green R, Shou WY* (2014). Modeling community population dynamics with the open-source language R.  Methods Mol Biol. 1151:209-31. doi: 10.1007/978-1-4939-0554-6_15.

http://rd.springer.com/protocol/10.1007%2F978-1-4939-0554-6_15

 

[Methods] Waite AJ, Shou WY* (2014). Constructing synthetic microbial communities to explore the ecology and evolution of symbiosis.  Methods Mol Biol. 1151:27-38. doi: 10.1007/978-1-4939-0554-6_2.

http://rd.springer.com/protocol/10.1007%2F978-1-4939-0554-6_2

 

[Research] Momeni B*, Waite AJ, Shou WY* (2013).  Spatial self-organization favors heterotypic cooperation over cheating. eLife 2: e00960.

http://elife.elifesciences.org/content/2/e00960

 

[Research] Momeni B*, Brileya KA, Fields MW, Shou WY* (2013).  Strong inter-population cooperation leads to partner intermixing in microbial communities. eLife 2: e00230.

http://elife.elifesciences.org/content/2/e00230

 

[]Methods]  Momeni B*, Shou WY (2012).  Cryosectioning yeast communities for examining fluorescence patterns. J. Vis. Exp. (70), e50101, doi:10.3791/5010115.

http://www.jove.com/video/50101/cryosectioning-yeast-communities-for-examining-fluorescence-patterns

 

[Research] Waite AJ*, Shou WY* (2012).  Adaptation to a new environment allows cooperators to purge cheaters stochastically. PNAS 109:19079-19086. (Feature article).

http://www.pnas.org/content/109/47/19079.short

• This article was highlighted in:

  • “Ecological communities by design” by J.K. Fredrickson, Science 348:1425-1427 (2015).

  • “Mutually helping microbes can evolve by hitchhiking” by C.D. Nadell and K.R. Foster, PNAS 109:19037-8 (2012).

  • “Cheating yeast finish last”, Nature 491, 11-11 (2012).

  • “Cheaters, cooperators, and evolutionary theory” by P. Gwynne, Inside Science (2012).

 

[Review] Momeni B, Chen CC, Hillesland K, Waite A, Shou WY* (2011).  Using artificial systems to explore the ecology and evolution of symbioses.  Cellular and Molecular Life Sciences  68:1353–1368.

http://rd.springer.com/article/10.1007/s00018-011-0649-y

 

[Research]Shou WY*, Ram S, Vilar JMG (2007): Synthetic cooperation in engineered yeast populations.  PNAS 104: 1877-1882.

http://www.pnas.org/content/104/6/1877

• This article was highlighted in:

  • “Synthetic ecology: A model system for cooperation” by M.J. Dunham, PNAS 104:1741 (2007).

 

Papers from before the Shou Lab

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[Research] Azzam R, Chen SL, Shou WY, Mah AS, Alexandru G, Nasmyth K, Annan RS, Carr SA, Deshaies RJ (2004): Phosphorylation by cyclin B-Cdk underlies release of mitotic exit activator Cdc14 from the nucleolus.  Science 305:516-519.

http://www.sciencemag.org/content/305/5683/516.long

 

[Research] Park CJ, Song SG, Lee PR, Shou WY, Deshaies RJ, Lee KS (2003): Loss of CDC5 function in Saccharomyces cerevisiae leads to defects in Swe1p regulation and Bfa1p/Bub2p-independent cytokinesis.  Genetics 163:21-33.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462412/

 

[Research] Shou WY, Deshaies RJ (2002): Multiple telophase arrest bypassed (tab) mutants alleviate the essential requirement for Cdc15 in exit from mitosis in S.cerevisiae. BMC Genetics 3(1):4.

http://www.biomedcentral.com/1471-2156/3/4

 

[Research] Shou WY, Azzam R, Chen SL, Huddleston MJ, Baskerville C, Charbonneau H, Annan RS, Carr SA, Deshaies RJ (2002): Cdc5 influences phosphorylation of Net1 and disassembly of the RENT complex.  BMC Mol Biol 3(1):3.

http://www.biomedcentral.com/1471-2199/3/3

 

[Methods] Chen SL, Huddleston MJ, Shou WY, Deshaies RJ, Annan RS, Carr SA (2002): Mass spectrometry-based methods for phosphorylation site mapping of hyperphosphorylated proteins applied to Net1, a regulator of exit from mitosis in yeast. Mol Cell Proteomics 1:186-196.

http://www.mcponline.org/content/1/3/186.long

 

[Methods] Shou WY, Verma R, Annan RS, Huddleston MJ, Chen SL, Carr SA, Deshaies RJ (2002): Mapping phosphorylation sites in proteins by mass spectrometry. Methods Enzymol 351 (Guide to Yeast Genetics and Molecular and Cell Biology, Pt C):279-296.

http://dx.doi.org/10.1016/S0076-6879(02)51853-X

 

[Research] Traverso EE, Baskerville C, Liu Y, Shou WY, James P, Deshaies RJ, Charbonneau H (2001): Characterization of the Net1 cell cycle-dependent regulator of the Cdc14 phosphatase from budding yeast.  J Biol Chem 276:21924-21931.

http://www.jbc.org/content/276/24/21924.long

 

[Research] Shou WY, Sakamoto KM, Keener J, Morimoto KW, Traverso EE, Azzam R, Hoppe GJ, Feldman RMR, DeModena J, Moazed D, Charbonneau H, Nomura M, Deshaies RJ (2001): Net1 stimulates RNA polymerase I transcription and regulates nucleolar structure independently of controlling mitotic exit.  Mol Cell 8:45-55.

http://www.sciencedirect.com/science/article/pii/S109727650100291X

 

[Research] Lippincott J, Shannon KB, Shou WY, Deshaies J, Li R (2001): The Tem1 small GTPase controls actomyosin and septin dynamics during cytokinesis.  J Cell Sci 114:1379-1386.

http://jcs.biologists.org/content/114/7/1379.long

 

[Research] Straight AF, Shou WY, Dowd GJ, Turck CW, Deshaies RJ, Johnson AD, Moazed D (1999): Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity.  Cell 97:245-256.

http://www.cell.com/abstract/S0092-8674(00)80734-5

 

[Research] Shou WY, Seol JH, Shevchenko A, Baskerville C, Moazed D, Chen ZWS, Jang J, Shevchenko A, Charbonneau H, Deshaies RJ (1999): Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex.  Cell 97:233-244.

http://www.sciencedirect.com/science/article/pii/S0092867400807333

• This article was highlighted in:

  • “Net Results of Nucleolar Dynamics” by S.N. Garcia and L. Pillus, Cell 97:825-828 (1999).

  • “Cell cycle:  Mitotic treasures in the nucleolus” by J.B. Bachant and S.J. Elledge, Nature 398:757-758 (1999).

​

[Research] Shou WY, Dunphy WG (1996): Cell cycle control by Xenopus p28(Kix1), a developmentally regulated inhibitor of cyclin-dependent kinases.  Mol Biol Cell 7:457-469.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC275897/