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Center for Systems Biology Publications

Funded Publications by the Stanford Center for Systems Biology

Monday, April 17, 2017 -Last Updated

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245: Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.
Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM, Elias JE, Bhatt AS,
Huang KC, Sonnenburg JL.
Cell. 2018 Jun 14;173(7):1742-1754.e17. doi: 10.1016/j.cell.2018.05.008.
PubMed PMID: 29906449.

244: Lateral interactions between protofilaments of the bacterial tubulin homolog FtsZ are essential for cell division.
Guan F, Yu J, Yu J, Liu Y, Li Y, Feng XH, Huang KC, Chang Z, Ye S.
Elife. 2018 Jun 11;7. pii: e35578. doi: 10.7554/eLife.35578. [Epub ahead of print]
PubMed PMID: 29889022.

243: Cutting the Gordian Knot of the Microbiota.
Vasquez KS, Shiver AL, Huang KC.
Mol Cell. 2018 Jun 7;70(5):765-767. doi: 10.1016/j.molcel.2018.05.034. Epub 2018 Jun 7.
PubMed PMID: 29883604.

242: EMI1 switches from being a substrate to an inhibitor of APC/C(CDH1) to start the cell cycle.
Cappell SD, Mark KG, Garbett D, Pack LR, Rape M, Meyer T.
Nature. 2018 Jun 6. doi: 10.1038/s41586-018-0199-7. [Epub ahead of print]
PubMed PMID: 29875408.

241: Excitation wavelength optimization improves photostability of ASAP-family GEVIs.
Xu F, Shi DQ, Lau PM, Lin MZ, Bi GQ.
Mol Brain. 2018 Jun 4;11(1):32. doi: 10.1186/s13041-018-0374-7.
PubMed PMID: 29866136.

240:Stochastic Endogenous Replication Stress Causes ATR-Triggered Fluctuations in CDK2 Activity that Dynamically Adjust Global DNA Synthesis Rates.
Daigh LH, Liu C, Chung M, Cimprich KA, Meyer T.
Cell Syst. 2018 Jun 4. pii: S2405-4712(18)30229-1. doi: 10.1016/j.cels.2018.05.011.
[Epub ahead of print] PubMed PMID: 29909278.

239: Listeria monocytogenes InlP interacts with afadin and facilitates basement membrane crossing.
Faralla C, Bastounis EE, Ortega FE, Light SH, Rizzuto G, Nocadello S, Anderson WF, Robbins JR, Theriot JA, Bakardjiev AI.
PLoS Pathog. 2018 May 30;14(5):e1007094. doi: 10.1371/journal.ppat.1007094. [Epub ahead of print]
PubMed PMID: 29847585.

238: Surface Area to Volume Ratio: A Natural Variable for Bacterial Morphogenesis.
Harris LK, Theriot JA.
Trends Microbiol. 2018 May 26. pii: S0966-842X(18)30102-1. doi: 10.1016/j.tim.2018.04.008. [Epub ahead of print] Review.
PubMed PMID: 29843923.

237: Expression variation and covariation impair analog and enable binary signaling control.
Kovary KM, Taylor B, Zhao ML, Teruel MN.
Mol Syst Biol. 2018 May 14;14(5):e7997. doi: 10.15252/msb.20177997.
PubMed PMID: 29759982.

236: Matrix stiffness modulates infection of endothelial cells by Listeria monocytogenes via expression of cell surface vimentin.
Bastounis EE, Yeh YT, Theriot JA.
Mol Biol Cell. 2018 May 2:mbcE18040228. doi: 10.1091/mbc.E18-04-0228. [Epub ahead of print]
PubMed PMID: 29718765.

235: Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.
Bell JC, Jukam D, Teran NA, Risca VI, Smith OK, Johnson WL, Skotheim JM, Greenleaf WJ, Straight AF.
Elife. 2018 Apr 12;7. pii: e27024. doi: 10.7554/eLife.27024. [Epub ahead of print]
PubMed PMID: 29648534.

234: Robustly Cycling Xenopus laevis Cell-Free Extracts in Teflon Chambers.
Chang JB, Ferrell JE Jr.
Cold Spring Harb Protoc. 2018 Feb 23. doi: 10.1101/pdb.prot097212. [Epub ahead of print]
PubMed PMID: 29475997.

233: Acute modulation of mycobacterial cell envelope biogenesis by front-line TB drugs.
Rodriguez-Rivera FP, Zhou X, Theriot JA, Bertozzi CR.
Angew Chem Int Ed Engl. 2018 Feb 1. doi: 10.1002/anie.201712020. [Epub ahead of print]
PubMed PMID: 29392891.

232: Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements.
Gu B, Swigut T, Spencley A, Bauer MR, Chung M, Meyer T, Wysocka J.
Science. 2018 Jan 25. pii: eaao3136. doi: 10.1126/science.aao3136. [Epub ahead of print]
PubMed PMID: 29371426.

231: A Precise Cdk Activity Threshold Determines Passage through the Restriction Point.
Schwarz C, Johnson A, Kõivomägi M, Zatulovskiy E, Kravitz CJ, Doncic A, Skotheim JM.
Mol Cell. 2018 Jan 18;69(2):253-264.e5. doi: 10.1016/j.molcel.2017.12.017.
PubMed PMID: 29351845.

230: Live-cell measurements of kinase activity in single cells using translocation reporters.
Kudo T, Jeknić S, Macklin DN, Akhter S, Hughey JJ, Regot S, Covert MW.
Nat Protoc. 2018 Jan;13(1):155-169. doi: 10.1038/nprot.2017.128. Epub 2017 Dec 21.
PubMed PMID: 29266096.



229: Plasmon-actuated nano-assembled microshells.
Quint MT, Sarang S, Quint DA, Keshavarz A, Stokes BJ, Subramaniam AB, Huang KC, Gopinathan A, Hirst LS, Ghosh S.
Sci Rep. 2017 Dec 19;7(1):17788. doi: 10.1038/s41598-017-17691-6.
PubMed PMID: 29259223.

228: A novel missense variant in the GLI3 zinc finger domain in a family with digital anomalies.
Crapster JA, Hudgins L, Chen JK, Gomez-Ospina N.
Am J Med Genet A. 2017 Dec;173(12):3221-3225. doi: 10.1002/ajmg.a.38415. Epub 2017 Sep 8. PubMed PMID: 28884880;
PubMed Central PMCID: PMC5685880.

227: FijiWingsPolarity: an open source toolkit for semi-automated detection of cell polarity.
Dobens LL, Shipman A, Axelrod JD.
Fly (Austin). 2017 Nov 30:0. doi: 10.1080/19336934.2017.1409927. [Epub ahead of print]
PubMed PMID: 29189094.

226: Homeostatic Cell Growth Is Accomplished Mechanically through Membrane Tension Inhibition of Cell-Wall Synthesis.
Rojas ER, Huang KC, Theriot JA.
Cell Syst. 2017 Nov 30. pii: S2405-4712(17)30494-5. doi: 10.1016/j.cels.2017.11.005. [Epub ahead of print]
PubMed PMID: 29203279.

225: Regulation of microbial growth by turgor pressure.
Rojas ER, Huang KC.
Curr Opin Microbiol. 2017 Nov 7;42:62-70. doi: 10.1016/j.mib.2017.10.015. [Epub ahead of print] Review.
PubMed PMID: 29125939.

224: Cytoplasmic Flow and Mixing Due to Deformation of Motile Cells.
Koslover EF, Chan CK, Theriot JA.
Biophys J. 2017 Nov 7;113(9):2077-2087. doi: 10.1016/j.bpj.2017.09.009.
PubMed PMID: 29117530.

223: Ultrasensitive optical imaging with lanthanide lumiphores.
Cho U, Riordan DP, Ciepla P, Kocherlakota KS, Chen JK, Harbury PB.
Nat Chem Biol. 2017 Nov 6. doi: 10.1038/nchembio.2513. [Epub ahead of print]
PubMed PMID: 29106397.

222: Dash-and-Recruit Mechanism Drives Membrane Curvature Recognition by the Small Bacterial Protein SpoVM.
Kim EY, Tyndall ER, Huang KC, Tian F, Ramamurthi KS.
SpoVM. Cell Syst. 2017 Oct 31. pii: S2405-4712(17)30441-6. doi: 10.1016/j.cels.2017.10.004. [Epub ahead of print]
PubMed PMID: 29102609.

221: Deep Phenotypic Mapping of Bacterial Cytoskeletal Mutants Reveals Physiological Robustness to Cell Size.
Shi H, Colavin A, Bigos M, Tropini C, Monds RD, Huang KC.
Curr Biol. 2017 Oct 23. pii: S0960-9822(17)31265-4. doi: 10.1016/j.cub.2017.09.065. [Epub ahead of print]
PubMed PMID: 29103935.

220: Marine Mammal Microbiota Yields Novel Antibiotic with Potent Activity Against Clostridium difficile.
Ochoa JL, Sanchez LM, Koo BM, Doherty JS, Rajendram M, Huang KC, Gross CA, Linington RG.
ACS Infect Dis. 2017 Oct 18. doi:10.1021/acsinfecdis.7b00105. [Epub ahead of print]
PubMed PMID: 29043783.

219: Disruption of Core Planar Cell Polarity Signaling Regulates Renal Tubule Morphogenesis but Is Not Cystogenic.
Kunimoto K, Bayly RD, Vladar EK, Vonderfecht T, Gallagher AR, Axelrod JD.
Curr Biol. 2017 Oct 11. pii: S0960-9822(17)31175-2. doi: 10.1016/j.cub.2017.09.011. [Epubahead of print]
PubMed PMID: 29033332.

218: Desynchronizing Embryonic Cell Division Waves Reveals the Robustness of Xenopus laevis Development.
Anderson GA, Gelens L, Baker JC, Ferrell JE Jr.
Cell Rep. 2017 Oct 3;21(1):37-46. doi: 10.1016/j.celrep.2017.09.017.
PubMed PMID: 28978482.

217: Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology.
Tanouchi Y, Covert MW.
MBio. 2017 Sep 19;8(5). pii: e01038-17. doi: 10.1128/mBio.01038-17.
PubMed PMID: 28928209.

216: Understanding CRY2 interactions for optical control of intracellular signaling.
Duan L, Hope J, Ong Q, Lou HY, Kim N, McCarthy C, Acero V, Lin MZ, Cui B.
Nat Commun. 2017 Sep 15;8(1):547. doi: 10.1038/s41467-017-00648-8.
PubMed PMID: 28916751.

215: The Adder Phenomenon Emerges from Independent Control of Pre- and Post-Start Phases of the Budding Yeast Cell Cycle.
Chandler-Brown D, Schmoller KM, Winetraub Y, Skotheim JM.
Curr Biol. 2017 Sep 6. pii: S0960-9822(17)31024-2. doi: 10.1016/j.cub.2017.08.015. [Epub ahead of print]
PubMed PMID: 28889980.

214: Adhesion to the host cell surface is sufficient to mediate Listeria monocytogenes entry into epithelial cells.
Ortega FE, Rengarajan M, Chavez N, Radhakrishnan P, Gloerich M, Bianchini J, Siemers K, Luckett WS, Lauer P, Nelson WJ, Theriot JA.
Mol Biol Cell. 2017 Sep 6. pii: mbc.E16-12-0851. doi: 10.1091/mbc.E16-12-0851. [Epub ahead of print]
PubMed PMID: 28877987.

213: Competing memories of mitogen and p53 signalling control cell-cycle entry.
Yang HW, Chung M, Kudo T, Meyer T.
Nature. 2017 Sep 6. doi: 10.1038/nature23880. [Epub ahead of print]
PubMed PMID: 28869970.

212: Full color palette of fluorescent d-amino acids for in situ labeling of bacterial cell walls.
Hsu YP, Rittichier J, Kuru E, Yablonowski J, Pasciak E, Tekkam S, Hall E, Murphy B, Lee TK, Garner EC, Huang KC, Brun YV, VanNieuwenhze MS.
Chem Sci. 2017 Sep 1;8(9):6313-6321. doi: 10.1039/c7sc01800b. Epub 2017 Jul 7.
PubMed PMID: 28989665; PubMed Central PMCID: PMC5628581.

211: Zygotic Genome Activation in Vertebrates.
Jukam D, Shariati SAM, Skotheim JM.
Dev Cell. 2017 Aug 21;42(4):316-332. doi: 10.1016/j.devcel.2017.07.026. Review.
PubMed PMID: 28829942.

210: Sizing up the bacterial cell cycle.
Willis L, Huang KC.
Nat Rev Microbiol. 2017 Aug 14. doi: 10.1038/nrmicro.2017.79. [Epub ahead of print] Review.
PubMed PMID: 28804128.

209: Calcium Ion Induced Structural Changes Promote Dimerization of Secretagogin, Which Is Required for Its Insulin Secretory Function.
Lee JJ, Yang SY, Park J, Ferrell JE Jr, Shin DH, Lee KJ.
Sci Rep. 2017 Aug 1;7(1):6976. doi: 10.1038/s41598-017-07072-4.
PubMed PMID: 28765527.

208: Thinking big: the tunability of bacterial cell size.
Cesar S, Huang KC.
FEMS Microbiol Rev. 2017 Jul 28. doi: 10.1093/femsre/fux026. [Epub ahead of print]
PubMed PMID: 28961755.

207: Fast two-photon imaging of subcellular voltage dynamics in neuronal tissue with genetically encoded indicators.
Chamberland S, Yang HH, Pan MM, Evans SW, Guan S, Chavarha M, Yang Y, Salesse C, Wu H, Wu JC, Clandinin TR, Toth K, Lin MZ, St-Pierre F.
Elife. 2017 Jul 27;6. pii: e25690. doi: 10.7554/eLife.25690.
[Epub ahead of print]
PubMed PMID: 28749338.

206: E-cadherin and LGN align epithelial cell divisions with tissue tension independently of cell shape.
Hart KC, Tan J, Siemers KA, Sim JY, Pruitt BL, Nelson WJ, Gloerich M.
Proc Natl Acad Sci U S A. 2017 Jul 3. pii: 201701703. doi: 10.1073/pnas.1701703114. [Epub ahead of print]
PubMed PMID: 28674014.

205: Changes in E-cadherin rigidity sensing regulate cell adhesion.
Collins C, Denisin AK, Pruitt BL, Nelson WJ.
Proc Natl Acad Sci U S A. 2017 Jul 3. pii: 201618676. doi: 10.1073/pnas.1618676114. [Epub ahead of print]
PubMed PMID: 28674019.

204: Non-model model organisms.
Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A.
BMC Biol. 2017 Jun 29;15(1):55. doi: 10.1186/s12915-017-0391-5.
PubMed PMID: 28662661.

203: Cell Size: Fat Makes Cells Fat.
Willis L, Huang KC.
Curr Biol. 2017 Jun 19. doi: 10.1016/j.cub.2017.05.017.
Pubmed PMID: 28633027.

202: Cell-Cell Junctions Organize Structural and Signaling Networks.
Garcia MA, Nelson WJ, Chavez N.
Perspect Biol. 2017 Jun 9. pii: S1097-2765(17)30361-1.
Pubmed PMID: 28600395.

201: Heterogenous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide.
Shi Z, Fujii K, Kovary KM, Genuth NR, Rost HL, Teruel MN, Barna M.
Mol Cell. 2017 Jun 7. pii: S1097-2765(17)30361-1.
Pubmed PMID: 28625553.

200: Chemical structure-guided design of dynapyrazoles, cell-permeable dynein inhibitors with a unique mode of action.
Steinman JB, Santarossa CC, Miller RM, Yu LS, Serpinskaya AS, Furukawa H, Morimoto S, Tanaka Y, Nishitani M, Asano M, Zalyte R, Ondrus AE, Johnson AG, Ye F, Nachury MV, Fukase Y, Aso K, Foley MA, Gelfand VI, Chen JK, Carter AP, Kapoor TM.
ELife. 2017 May 19. pii: e25174.
Pubmed PMID: 28524820.

199: Illuminating developmental biology through photochemistry.
Kowalik L, Chen JK.
Nat Chem Biol. 2017 May 17. doi: 10.1038/nchembio.2369.
Pubmed PMID: 28514427.

198: The Gut Microbiome: Connecting Spatial Organization to Function.
Tropini C, Earle KA, Huang KC, Sonnenburg JL.
Cell Host Microbe. 2017 Apr 12.doi: 10.1016/j.chom.2017.03.010.
Pubmed PMID: 28407481.

197: Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κ B Activation.
Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW.
Cell Syst. 2017 Apr 4. pii: S2405-4712(17)30132-1.
Pubmed PMID: 28396000

196: Form and function of topologically associating genomic domains in budding yeast.
Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM.
Proc Natl Acad Sci U S A. 2017 Mar 27. pii: 201612256.
Pubmed PMID: 28348222.

195: Staying in Touch while on the Go.
Huang KC.
Cell. 2017 Mar 23. doi: 10.1016/j.cell.2017.03.015.
Pubmed PMID: 28340342.

194: Discovery of novel determinants of endothelial lineage using chimeric heterokaryons.
Wong WT, Matrone G, Tian X, Tomoiaga SA, Au KF, Meng S, Yamazoe S, Sieveking D, Chen K, Burns DM, Chen JK, Blau HM, Cooke JP.
Elife. 2017 Mar 21;6. pii: e23588. doi: 10.7554/eLife.23588.
Pubmed PMID: 28323620.

193: Structural and functional characterization of Caenorhabditis elegans α-catenin reveals constitutive binding to β -Catenin and F-actin.
Kang H, Bang I, Jin KS, Lee B, Lee J, Shao X, Heier JA, Kwiatkowski AV, Nelson WJ, Hardin J, Weis WI, Choi HJ.
J Biol Chem. 2017 Mar 15. pii: jbc.M116.769778.
Pubmed PMID: PMID: 28298447.

192: Coupling between Protein Stability and Catalytic Activity Determines Pathogenicity of G6PD Variants.
Cunningham AD, Colavin A, Huang KC, Mochly-Rosen D.
Cell. 2017 Mar 14. doi: 10.1016/j.celrep.2017.02.048.
Pubmed PMID: 28297664.

191: Emergent Phototactic Responses of Cyanobacteria under Complex Light Regimes.
Huang KC.
MBio. 2017 Mar 7. pii: e02330-16.
Pubmed PMID: 28270586.

190: Optical control of cell signaling by single-chain photoswitchable kinases.
Zhou XX, Fan LZ, Li P, Shen K, Lin MZ.
Science. 2017 Feb 24;355(6327):836-842.
Pubmed PMID: 28232577.

189: Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library.
Ursell T, Lee TK, Shiomi D, Shi H, Tropini C, Monds RD, Colavin A, Billings G, Bhaya-Grossman I, Broxton M, Huang BE, Niki H, Huang KC.
BMC Biol. 2017 Feb 21;15(1):17. doi: 10.1186/s12915-017-0348-8. PubMed
PMID: 28222723; PubMed Central PMCID: PMC5320674.

188: GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell wall synthesis.
Yang X, Lyu Z, Miguel A, McQuillen R, Huang KC, Xiao J.
Science. 2017 Feb 17;355(6326):744-747. doi: 10.1126/science.aak9995.
PubMed PMID: 28209899.

187: Hyaluronic acid synthesis is required for zebrafish tail fin regeneration.
Ouyang X, Panetta NJ, Talbott MD, Payumo AY, Halluin C, Longaker MT, Chen JK.
PLoS One. 2017 Feb 16;12(2):e0171898.
Pubmed PMID: 28207787; PubMed Central PMCID: PMC5313160.

186: Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing.
Yu FB, Willis L, Chau RM, Zambon A, Horowitz M, Bhaya D, Huang KC, Quake SR.
BMC Biol. 2017 Feb 14;15(1):11. doi: 10.1186/s12915-016-0344-4.
PubMed PMID: 28196492; PubMed Central PMCID: PMC5310064.

185: The Temporal Ordering of Cell-Cycle Phosphorylation.
Kamenz J, Ferrell JE Jr.
Mol Cell. 2017 Feb 2;65(3):371-373.
Pubmed PMID: 28157499.

184: Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates.
Shi H, Colavin A, Lee TK, Huang KC.
Nat Protoc. 2017 Feb 12(2):429-438. doi: 10.1038/nprot.2016.181. Epub 2017 Jan 26.
PubMed PMID: 28125106.

183: Wnt Signaling in Chronic Rhinosinusitis with Nasal Polyps.
Böscke R, Vladar EK, Könnecke M, Hüsing B, Linke R, Pries R, Reiling N, Axelrod JD, Nayak JV, Wollenberg B.
Am J Respir Cell Mol Biol. 2017 Jan 6.
Pubmed PMID: 28059551.

182: Cell division orientation is coupled to cell-cell adhesion by the E-cadherin/LGN complex.
Gloerich M, Bianchini JM, Siemers KA, Cohen DJ, Nelson WJ.
Nat Commun. 2017 Jan 3;8:13996.
Pubmed PMID: 28045117; PubMed Central PMCID: PMC5216124.

181: Spatial and temporal signal processing and decision making by MAPK pathways.
Atay O, Skotheim JM.
J Cell Biol. 2017 Jan 2. pii: jcb.201609124.
Pubmed PMID: 28043970; PubMed Central PMCID: PMC5294789.



180: Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche.
Willis L, Refahi Y, Wightman R, Landrein B, Teles J, Huang KC, Meyerowitz EM, Jönsson H.
Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):E8238-E8246. doi: 10.1073/pnas.1616768113.
Epub 2016 Dec 5.
PubMed PMID: 27930326; PubMed Central PMCID: PMC5187701.

179: Epithelial self-healing is recapitulated by a 3D biomimetic E-cadherin junction.
Cohen DJ, Gloerich M, Nelson WJ
Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):14698-14703.
Pubmed PMID: 27930308; PubMed Central PMCID: PMC5187740.

178: Adhesion-Dependent Wave Generation in Crawling Cells.
Barnhart EL, Allard J, Lou SS, Theriot JA, Mogilner A.
Curr Biol. 2016 Dec 1. pii: S0960-9822(16)31336-7.
Pubmed PMID: 27939309; PubMed Central PMCID: PMC5225140.

177: Cell-Type-Specific Optical Recording of Membrane Voltage Dynamics in Freely Moving Mice.
Marshall JD, Li JZ, Zhang Y, Gong Y, St-Pierre F, Lin MZ, Schnitzer MJ.
Cell. 2016 Dec 1;167(6):1650-1662.e15.
Pubmed PMID: PMID: 27912066.

176: Engulfed cadherin fingers are polarized junctional structures between collectively migrating endothelial cells.
Hayer A, Shao L, Chung M, Joubert LM, Yang HW, Tsai FC, Bisaria A, Betzig E, Meyer T.
Nat Cell Biol. 2016 Nov 14.
Pubmed PMID: PMID: 27846954.

175: Control of inflammation by stromal Hedgehog pathway activation restrains colitis.
Lee JJ, Rothenberg ME, Seeley ES, Zimdahl B, Kawano S, Lu WJ, Shin K, Sakata-Kato T, Chen JK, Diehn M, Clarke MF, Beachy PA.
Proc Natl Acad Sci U S A. 2016 Nov 4. pii: 201616447.
Pubmed PMID: 27815529; PubMed Central PMCID: PMC5127312.

174: Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.
Van Valen DA, Kudo T, Lane KM, Macklin DN, Quach NT, DeFelice MM, Maayan I, Tanouchi Y, Ashley EA, Covert MW.
PLoS Comput Biol. 2016 Nov 4;12(11):e1005177.
Pubmed PMID: 27814364; PubMed Central PMCID: PMC5096676.

173: The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins.
Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A, Palmer AE, Shu X, Zhang J, Tsien RY.
Trends Biochem Sci. 2016 Nov 1. pii: S0968-0004(16)30173-6.
Pubmed PMID: 27814948; PubMed Central PMCID: PMC5272834.

172: An inducible long noncoding RNA amplifies DNA damage signaling.
Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY.
Nat Genet. 2016 Nov;48(11):1370-1376.
Pubmed PMID: 27668660; PubMed Central PMCID: PMC5083181

171: Fluorescent indicators for simultaneous reporting of all four cell cycle phases.
Bajar BT, Lam AJ, Badiee RK, Oh YH, Chu J, Zhou XX, Kim N, Kim BB, Chung M, Yablonovitch AL, Cruz BF, Kulalert K, Tao JJ, Meyer T, Su XD, Lin MZ.
Nat Methods. 2016 Oct 31.
Pubmed PMID: 27798610.

170: Simultaneous dual-color fluorescence lifetime imaging with novel red-shifted fluorescent proteins.
Laviv T, Kim BB, Chu J, Lam AJ, Lin MZ, Yasuda R.
Nat Methods. 2016 Oct 31.
Pubmed PMID: 27798609.

169: Increasing β-catenin/Wnt3A activity levels drive mechanical strain-induced cell cycle progression through mitosis.
Benham-Pyle BW, Sim JY, Hart KC, Pruitt BL, Nelson WJ.
Elife. 2016 Oct 26;5. pii: e19799.
Pubmed PMID: 27782880; PubMed Central PMCID: PMC5104517.

168: Rickettsia Sca4 Reduces Vinculin-Mediated Intercellular Tension to Promote Spread.
Lamason RL, Bastounis E, Kafai NM, Serrano R, Del Álamo JC, Theriot JA, Welch MD.
Cell. 2016 Oct 20;167(3):670-683.e10.
Pubmed PMID: 27768890; PubMed Central PMCID: PMC5097866.

167: An inducible long noncoding RNA amplifies DNA damage signaling.
Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY.
Nat Genet. 2016 Sep 26.
Pubmed PMID: 27668660; PubMed Central PMCID: PMC5083181.

166: A Guide to Fluorescent Protein FRET Pairs.
Bajar BT, Wang ES, Zhang S, Lin MZ, Chu J.
Sensors (Basel). 2016 Sep 14;16(9). pii: E1488.
Pubmed PMID: 27649177; PubMed Central PMCID: PMC5038762.

165: FtsZ-Dependent Elongation of a Coccoid Bacterium.
Pereira AR, Hsin J, Król E, Tavares AC, Flores P, Hoiczyk E, Ng N, Dajkovic A,
Brun YV, VanNieuwenhze MS, Roemer T, Carballido-Lopez R, Scheffers DJ, Huang KC,
Pinho MG.
MBio. 2016 Sep 6;7(5). pii: e00908-16. doi: 10.1128/mBio.00908-16. PubMed PMID: 27601570; PubMed Central PMCID: PMC5013293.

164: Fast Mechanically Driven Daughter Cell Separation Is Widespread in Actinobacteria.
Zhou X, Halladin DK, Theriot JA.
MBio. 2016 Aug 30;7(4). pii: e00952-16.
Pubmed PMID: 27578753; PubMed Central PMCID: PMC4999543.

163: Genetically encoded indicators of neuronal activity.
Lin MZ, Schnitzer MJ.
Nat Neurosci. 2016 Aug 26;19(9):1142-53.
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162: PLEKHG3 enhances polarized cell migration by activating actin filaments at the cell front.
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161: Airway epithelial homeostasis and planar cell polarity signaling depend on multiciliated cell differentiation.
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JCI Insight. 2016 Aug 18;1(13). pii: e88027.
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160: The Phenotypic Effects of Royal Jelly on Wild-Type D. melanogaster Are Strain-Specific.
Morgan SL, Seggio JA, Nascimento NF, Huh DD, Hicks JA, Sharp KA, Axelrod JD, Wang KC.
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159: Structure-guided wavelength tuning in far-red fluorescent proteins.
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158: Switch-like Transitions Insulate Network Motifs to Modularize Biological Networks.
Atay O, Doncic A, Skotheim JM.
Cell Syst. 2016 Jul 20. pii: S2405-4712(16)30215-0.
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157: High-resolution imaging and computational analysis of haematopoietic cell dynamics in vivo.
Koechlein CS, Harris JR, Lee TK, Weeks J, Fox RG, Zimdahl B, Ito T, Blevins A, Jung SH, Chute JP, Chourasia A, Covert MW, Reya T.
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156: Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion.
Malmersjö S, Di Palma S, Diao J, Lai Y, Pfuetzner RA, Wang AL, McMahon MA, Hayer A, Porteus M, Bodenmiller B, Brunger AT, Meyer T.
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155: Tbx16 regulates hox gene activation in mesodermal progenitor cells.
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154: Irreversible APC(Cdh1) Inactivation Underlies the Point of No Return for Cell-Cycle Entry.
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153: Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.
Treutlein B, Lee QY, Camp JG, Mall M, Koh W, Shariati SA, Sim S, Neff NF, Skotheim JM, Wernig M, Quake SR.
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152: Relative Rates of Surface and Volume Synthesis Set Bacterial Cell Size.
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151: Subcellular Imaging of Voltage and Calcium Signals Reveals Neural Processing In Vivo.
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150: A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo.
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149: A method to rapidly create protein aggregates in living cells.
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148: Thresholds and ultrasensitivity from negative cooperativity.
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147: The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression.
Ewald JC, Kuehne A, Zamboni N, Skotheim JM.
Mol Cell. 2016 May 19;62(4):532-45.
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146: Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.
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145: Endothelial Cells Use a Formin-Dependent Phagocytosis-Like Process to Internalize the Bacterium Listeria monocytogenes.
Rengarajan M, Hayer A, Theriot JA
PLoS Pathog. 2016 May 6;12(5):e1005603.
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144: Characterization of the cadherin-catenin complex of the sea anemone Nematostella vectensis and implications for the evolution of metazoan cell-cell adhesion.
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Mol Biol Evol. 2016 Apr 28. pii: msw084.
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143: Disruption of lipid homeostasis in the Gram-negative cell envelope activates a novel cell death pathway.
Sutterlin HA, Shi H, May KL, Miguel A, Khare S, Huang KC, Silhavy TJ.
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142: Perfect and Near-Perfect Adaptation in Cell Signaling.
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Cell Syst. 2016 Feb 24;2(2):62-7. doi: 10.1016/j.cels.2016.02.006.
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141: Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments.
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Dev Cell. 2016 Feb 22;36(4):462-75.
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140: Prickle1 mutation causes planar cell polarity and directional cell migration defects associated with cardiac outflow tract anomalies and other structural birth defects.
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Biol Open. 2016 Feb 16. pii: bio.015750.
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139: Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting.
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138: Prickle isoforms control the direction of tissue polarity by microtubule independent and dependent mechanisms.
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Biol Open. 2016 Feb 10. pii: bio.016162.
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137: The Prozone Effect Accounts for the Paradoxical Function of the Cdk-Binding Protein Suc1/Cks.
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136: Disentangling Random Motion and Flow in a Complex Medium.
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Biophys J. 2016 Feb 2;110(3):700-9.
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135: Waves of actin and microtubule polymerization drive microtubule-based transport and neurite growth before single axon formation.
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134: I only have eye for ewe: the discovery of cyclopamine and development of Hedgehog pathway-targeting drugs.
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133: High-throughput, Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography.
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J Biol Chem. 2015 Dec 25;290(52):31090-100.
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132: Locally excitable Cdc42 signals steer cells during chemotaxis.
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131: Mitosis is swell.
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130: The effect of microbial colonization on the host proteome varies by gastrointestinal location.
Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE.
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129: Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time.
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PLoS One. 2015 Nov 13;10(11):e0142825.
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128: The Biosynthetic Basis of Cell Size Control.
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Trends Cell Biol. 2015 Nov 10. pii: S0962-8924(15)00193-2.
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127: Applications of imaging for bacterial systems biology.
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126: Quantitative Imaging of Gut Microbiota Spatial Organization.
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125: Why Build Whole-Cell Models?
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Trends Cell Biol. 2015 Oct 12. pii: S0962-8924(15)00170-1.
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124: Accelerating Submovement Decomposition With Search-Space Reduction Heuristics.
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IEEE Trans Biomed Eng. 2015 Oct;62(10):2508-15.
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123: Reevaluating αE-catenin monomer and homodimer functions by characterizing E-cadherin/αE-catenin chimeras.
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J Cell Biol. 2015 Sep 28;210(7):1065-1074.
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122: Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size.
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Nature. 2015 Sep 21.
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121: Replication-Competent Influenza and Respirtory Syncytial Virus Luciferase Reporter Strains Engineered for Co-Infections Identify Antiviral.
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Biochemistry. 2015 Sep 15;54(36):5589-604.
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120: Phosphodiesterase 4D acts downstream of Neuropilin to control Hedgehog signal transduction and the growth of medulloblastoma.
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119: Studying epithelial morphogenesis in Dictyostelium.
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118: Distinct transcriptional responses elicited by unfolded nuclear or cytoplasmic protein in mammalian cells.
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117: Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome.
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Cell Syst. 2015 Aug 26;1(2):106-15.
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116: Cell-Size Control.
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Cold Spring Harb Perspect Biol. 2015 Aug 7.
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115: Tunable and reversible drug control of protein production via a self-excising degron.
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Nat Chem Biol. 2015 Jul 27.
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114: How Does the Xenopus laevis Embryonic Cell Cycle Avoid Spatial Chaos?
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113: Investigating neuronal function with optically controllable proteins.
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Front Mol Neurosci. 2015 Jul 21;8:37.
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112: Running with neighbors: coordinating cell migration and cell-cell adhesion.
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Curr Opin Cell Biol. 2015 Jul 17;36:62-70.
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111: Spatial distribution of cell-cell and cell-ECM adhesions regulates force balance while main-taining E-cadherin molecular tension in cell pairs.
Sim JY, Moeller J, Hart KC, Ramallo D, Vogel V, Dunn AR, Nelson WJ, Pruitt BL.
Mol Biol Cell. 2015 Jul 1;26(13):2456-65.
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110: Designs and sensing mechanisms of genetically encoded fluorescent voltage indicators.
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Curr Opin Chem Biol. 2015 Jun 11;27:31-38.
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109: Cell adhesion. Mechanical strain induces E-cadherin-dependent Yap1 and β-catenin activation to drive cell cycle entry.
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108: Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.
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107: NetworkPainter: dynamic intracellular pathway animation in Cytobank.
Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW.
BMC Bioinformatics. 2015 May 25;16:172.
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106: Clustering and Negative Feedback by Endocytosis in Planar Cell Polarity Signaling Is Modulated by Ubiquitinylation of Prickle.
Cho B, Pierre-Louis G, Sagner A, Eaton S, Axelrod JD.
PLoS Genet. 2015 May 21;11(5):e1005259.
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105: The mechanotransduction machinery at work at adherens junctions.
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104: Bacterial division. Mechanical crack propagation drives millisecond daughter cell separation in Staphylococcus aureus.
Zhou X, Halladin DK, Rojas ER, Koslover EF, Lee TK, Huang KC, Theriot JA.
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103: Using SRM-MS to quantify nuclear protein abundance differences between adipose tissue depots of insulin-resistant mice.
Ota A, Kovary KM, Wu OH, Ahrends R, Shen WJ, Costa MJ, Feldman BJ, Kraemer FB, Teruel MN.
J Lipid Res. 2015 Apr 3.
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102: Myosin light chain kinase regulates cell polarization independently of membrane tension or Rho kinase. 
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J Cell Biol. 2015 Apr 27;209(2):275-88.
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101: Using light to shape chemical gradients for parallel and automated analysis of chemotaxis. 
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Mol Syst Biol. 2015 Apr 23;11(4):804. 
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100: Disentangling multidimensional spatio-temporal data into their common and aberrant responses.
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PLoS One. 2015 Apr 22;10(4):e0121607.
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99: Balance between cell-substrate adhesion and myosin contraction determines the frequency of motility initiation in fish keratocytes.
Barnhart E, Lee KC, Allen GM, Theriot JA, Mogilner A.
Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):5045-50.
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98: Structural basis for the geometry-driven localization of a small protein. 
Gill RL Jr, Castaing JP, Hsin J, Tan IS, Wang X, Huang KC, Tian F, Ramamurthi KS.
Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):E1908-15.
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97: Thinking big with small molecules. 
Mruk K, Chen JK.
J Cell Biol. 2015 Apr 13;209(1):7-9.
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96: Optical control of biological processes by light-switchable proteins.
Fan LZ, Lin MZ.
Wiley Interdiscip Rev Dev Biol. 2015 Apr 8. 
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95: Maintenance of motility bias during cyanobacterial phototaxis.
Chau RM, Ursell T, Wang S, Huang KC, Bhaya D.
Biophys J. 2015 Apr 7;108(7):1623-32.
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94: A dynamic picture of protein behavior in cells.
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Nat Biotechnol. 2015 Apr 7;33(4):356-7. 
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93: p53 suppresses muscle differentiation at the myogenin step in response to genotoxic stress.
Yang ZJ, Kenzelmann Broz D, Noderer WL, Ferreira JP, Overton KW, Spencer SL, Meyer T, Tapscott SJ, Attardi LD, Wang CL. 
Cell Death Differ. 2015 Apr;22(4):560-73. 
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92: A genetically encoded Förster resonance energy transfer sensor for monitoring in vivo trehalose-6-phosphate dynamics.
Peroza EA, Ewald JC, Parakkal G, Skotheim JM, Zamboni N. 
Anal Biochem. 2015 Apr 1;474:1-7.
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91: Optochemical Dissection of T-box Gene-Dependent Medial Floor Plate Development.
Payumo AY, Walker WJ, McQuade LE, Yamazoe S, Chen JK
ACS Chem Biol. 2015 Mar 17.
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90: Compartmentalization of a Bistable Switch Enables Memory to Cross a Feedback-Driven Transition.
Doncic A, Atay O, Valk E, Grande A, Bush A, Vasen G, Colman-Lerner A, Loog M, Skotheim JM.
Cell. 2015 Mar 12;160(6):1182-1195. 
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89: Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus midblastula transition.
Amodeo AA, Jukam D, Straight AF, Skotheim JM. 
Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1086-95. 
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88: Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species. 
Miguel A, Hsin J, Liu T, Tang G, Altman RB, Huang KC
PLoS Comput Biol. 2015 Mar 26;11(3):e1004117. 
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87: Systematic Discovery of Human Gene Function and Principles of Modular Organization through Phylogenetic Profiling.
Dey G, Jaimovich A, Collins SR, Seki A, Meyer T. 
Cell Rep. 2015 Feb 11. pii: S2211-1247(15)00050-9. 
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86: Single-cell variation leads to population invariance in NF-κ B signaling dynamics.
Hughey JJ, Gutschow MV, Bajar BT, Covert MW. 
Mol Biol Cell. 2015 Feb 1;26(3):583-90. 
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85: Observing planar cell polarity in multiciliated mouse airway epithelial cells.
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84: The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokinesis. 
Zhou Z, Munteanu EL, He J, Ursell T, Bathe M, Huang KC, Chang F.
Mol Biol Cell. 2015 Jan 1;26(1):78-90.
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83: Dynamic recruitment of the curvature-sensitive protein ArhGAP44 to nanoscale membrane deformations limits exploratory filopodia initiation in neurons.
Galic M, Tsai FC, Collins SR, Matis M, Bandara S, Meyer T.
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82: Exact reconstruction of gene regulatory networks using compressive sensing.
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BMC Bioinformatics. 2014 Dec 14;15(1):400.
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81: Ultrasensitivity part III: cascades, bistable switches, and oscillators.
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Trends Biochem Sci. 2014 Dec;39(12):612-618. 
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80: Principles of bacterial cell-size determination revealed by cell-wall synthesis perturbations.
Tropini C, Lee TK, Hsin J, Desmarais SM, Ursell T, Monds RD, Huang KC.
Cell Rep. 2014 Nov 20;9(4):1520-7.
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79: Systematic perturbation of cytoskeletal function reveals a linear scaling relationship between cell geometry and fitness.
Monds RD, Lee TK, Colavin A, Ursell T, Quan S, Cooper TF, Huang KC.
Cell Rep. 2014 Nov 20;9(4):1528-37.
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78: Modularity and predictability in cell signaling and decision making.
Atay O, Skotheim JM.
Mol Biol Cell. 2014 Nov 5;25(22):3445-50. 
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77: Spatial trigger waves: positive feedback gets you a long way.
Gelens L, Anderson GA, Ferrell JE Jr.
Mol Biol Cell. 2014 Nov 5;25(22):3486-93. 
PubMed PMID: 25368427; PubMed Central PMCID: PMC4230609.

76: Ultrasensitivity part II: multisite phosphorylation, stoichiometric inhibitors, and positive feedback.
Ferrell JE Jr, Ha SH. 
Trends Biochem Sci. 2014 Nov;39(11):556-569.
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75: Basal p21 controls population heterogeneity in cycling and quiescent cell cycle states.
Overton KW, Spencer SL, Noderer WL, Meyer T, Wang CL.
Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):E4386-93.
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74: Ultrasensitivity part I: Michaelian responses and zero-order ultrasensitivity.
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Trends Biochem Sci. 2014 Oct;39(10):496-503. 
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73: A Caulobacter MreB mutant with irregular cell shape exhibits compensatory widening to maintain a preferred surface area to volume ratio.
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Mol Microbiol. 2014 Sep 30.
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72: Nitroreductase-activatable morpholino oligonucleotides for in vivo gene silencing.
Yamazoe S, McQuade LE, Chen JK.
ACS Chem Biol. 2014 Sep 19;9(9):1985-90.
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71: Chemical Biology Strategies for Posttranslational Control of Protein Function.
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Chem Biol. 2014 Sep 18;21(9):1238-1252. 
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70: WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.
Karr JR, Phillips NC, Covert MW.
Database (Oxford). 2014 Sep 16;2014. pii: bau095. 
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69: Sequential gene silencing using wavelength-selective caged morpholino oligonucleotides. 
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Angew Chem Int Ed Engl. 2014 Sep 15;53(38):10114-8. 
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68: Nonlytic viral spread enhanced by autophagy components.
Bird SW, Maynard ND, Covert MW, Kirkegaard K.
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67: De novo morphogenesis in L-forms via geometric control of cell growth.
Billings G, Ouzounov N, Ursell T, Desmarais SM, Shaevitz J, Gitai Z, Huang KC.
Mol Microbiol. 2014 Sep;93(5):883-96.
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66: Coordinating cell polarity: heading in the right direction?
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65: Induced neuronal reprogramming.
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64: Microtubules provide directional information for core PCP function.
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63: The proteome of cholesteryl-ester-enriched versus triacylglycerol-enriched lipid droplets.
Khor VK, Ahrends R, Lin Y, Shen WJ, Adams CM, Roseman AN, Cortez Y, Teruel MN, Azhar S, Kraemer FB.
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62: How and why cells grow as rods.
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61: The future of whole-cell modeling.
Macklin DN, Ruggero NA, Covert MW.
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60: prickle modulates microtubule polarity and axonal transport to ameliorate seizures in flies.
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Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11187-92. 
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59: Stromal response to Hedgehog signaling restrains pancreatic cancer progression.
Lee JJ, Perera RM, Wang H, Wu DC, Liu XS, Han S, Fitamant J, Jones PD, Ghanta KS, Kawano S, Nagle JM, Deshpande V, Boucher Y, 
Kato T, Chen JK, Willmann JK, Bardeesy N, Beachy PA.
Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):E3091-100. 
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58: Arhgap36-dependent activation of Gli transcription factors.
Rack PG, Ni J, Payumo AY, Nguyen V, Crapster JA, Hovestadt V, Kool M, Jones DT, Mich JK, Firestone AJ, Pfister SM, Cho YJ, Chen JK
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57: In vivo imaging of hedgehog pathway activation with a nuclear fluorescent reporter.
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56: Docking interactions: cell-cycle regulation and beyond.
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55: Direct kinetochore-spindle pole connections are not required for chromosome segregation.
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54: Prickle/spiny-legs isoforms control the polarity of the apical microtubule network in planar cell polarity.
Olofsson J, Sharp KA, Matis M, Cho B, Axelrod JD
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53: Controlling low rates of cell differentiation through noise and ultrahigh feedback.
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52: High-sensitivity measurements of multiple kinase activities in live single cells.
Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW.
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51: High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor.
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50: Methods for studying planar cell polarity.
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49:The wing disc as a platform for studying Hedgehog signaling.
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48: Response of Escherichia coli growth rate to osmotic shock.
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47: Non-invasive intravital imaging of cellular differentiation with a bright red-excitable fluorescent protein.
Chu J, Haynes RD, Corbel SY, Li P, González-González E, Burg JS, Ataie NJ, Lam AJ, Cranfill PJ, Baird MA, Davidson MW, Ng HL, Garcia KC, Contag CH, Shen K, Blau HM, Lin MZ.
Nat Methods. 2014 May;11(5):572-8. 
PubMed PMID: 24633408; PubMed Central PMCID: PMC4008650.

46: Insight into insulin secretion from transcriptome and genetic analysis of insulin-producing cells of Drosophila.
Cao J, Ni J, Ma W, Shiu V, Milla LA, Park S, Spletter ML, Tang S, Zhang J, Wei X, Kim SK, Scott MP.
Genetics. 2014 May;197(1):175-92.
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45: Calcineurin signaling regulates neural induction through antagonizing the BMP pathway.
Cho A, Tang Y, Davila J, Deng S, Chen L, Miller E, Wernig M, Graef IA.
Neuron. 2014 Apr 2;82(1):109-24.
PubMed PMID: 24698271.

44: A dynamically assembled cell wall synthesis machinery buffers cell growth.
Lee TK, Tropini C, Hsin J, Desmarais SM, Ursell TS, Gong E, Gitai Z, Monds RD, Huang KC.
Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4554-9.
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43: Incorporation of flexible objectives and time-linked simulation with flux balance analysis. 
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J Theor Biol. 2014 Mar 21;345:12-21.
PubMed PMID: 24361328; PubMed Central PMCID: PMC3933926.

42: Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.
Ursell TS, Nguyen J, Monds RD, Colavin A, Billings G, Ouzounov N, Gitai Z, Shaevitz JW, Huang KC.
Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):E1025-34.
PubMed PMID: 24550515; PubMed Central PMCID: PMC3964057.

41: Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB.
Colavin A, Hsin J, Huang KC.
Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3585-90.
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40: Changes in Oscillatory Dynamics in the Cell Cycle of Early Xenopus laevis Embryos. 
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PLoS Biol. 2014 Feb 11;12(2):e1001788. 
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39: A polarized Ca2+, diacylglycerol and STIM1 signalling system regulates directed cell migration. 
Tsai FC, Seki A, Yang HW, Hayer A, Carrasco S, Malmersjö S, Meyer T.
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PubMed PMID: 24463606; PubMed Central PMCID: PMC3953390.

38: General method for regulating protein stability with light. 
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37: Gli protein activity is controlled by multisite phosphorylation in vertebrate Hedgehog signaling.
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Cell Rep. 2014 Jan 16;6(1):168-81. 
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36: Isolation and preparation of bacterial cell walls for compositional analysis by ultra performance liquid chromatography.
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35: Parallel measurement of dynamic changes in translation rates in single cells. 
Han K, Jaimovich A, Dey G, Ruggero D, Meyuhas O, Sonenberg N, Meyer T.
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34: Motility enhancement through surface modification is sufficient for cyanobacterial community organization during phototaxis.
Ursell T, Chau RM, Wisen S, Bhaya D, Huang KC.
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33: Harnessing the stem cell potential: a case for neural stem cell therapy.
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32: Why are bacteria different from eukaryotes?
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31: Constraints on the adult-offspring size relationship in protists.
Caval-Holme F, Payne J, Skotheim JM.
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30: Start and the restriction point.
Johnson A, Skotheim JM.
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29: Accelerated discovery via a whole-cell model.
Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B Jr, Covert MW.
Nat Methods. 2013 Dec;10(12):1192-5.
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28: The role of hydrolases in bacterial cell-wall growth.
Lee TK, Huang KC.
Curr Opin Microbiol. 2013 Dec;16(6):760-6.
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27: Dimer dynamics and filament organization of the bacterial cell division protein FtsA.
Hsin J, Fu R, Huang KC.
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PubMed PMID: 23871894; PubMed Central PMCID: PMC3818905.

26: Neuropilin-2 contributes to tumorigenicity in a mouse model of Hedgehog pathway medulloblastoma.
Hayden Gephart MG, Su YS, Bandara S, Tsai FC, Hong J, Conley N, Rayburn H, Milenkovic L, Meyer T, Scott MP.
J Neurooncol. 2013 Nov;115(2):161-8.
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25: The E3 ubiquitin ligase UBE3C enhances proteasome processivity by ubiquitinating partially proteolyzed substrates.
Chu BW, Kovary KM, Guillaume J, Chen LC, Teruel MN, Wandless TJ.
J Biol Chem. 2013 Nov 29;288(48):34575-87.
PubMed PMID: 24158444; PubMed Central PMCID: PMC3843071.

24: Distinct biophysical mechanisms of focal adhesion kinase mechanoactivation by different extracellular matrix proteins.
Seong J, Tajik A, Sun J, Guan JL, Humphries MJ, Craig SE, Shekaran A, García AJ, Lu S, Lin MZ, Wang N, Wang Y.
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23: Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons.
Wapinski OL, Vierbuchen T, Qu K, Lee QY, Chanda S, Fuentes DR, Giresi PG, Ng YH, Marro S, Neff NF, Drechsel D, Martynoga B, Castro DS, Webb AE, Südhof TC, Brunet A, Guillemot F, Chang HY, Wernig M.
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22: Regulation of PCP by the Fat signaling pathway.
Matis M, Axelrod JD.
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PubMed PMID: 24142873; PubMed Central PMCID: PMC3814641.

21: Dosage of Dyrk1a shifts cells within a p21-cyclin D1 signaling map to control the decision to enter the cell cycle.
Chen JY, Lin JR, Tsai FC, Meyer T.
Mol Cell. 2013 Oct 10;52(1):87-100.
PubMed PMID: 24119401.

20: The proliferation-quiescence decision is controlled by a bifurcation in CDK2 activity at mitotic exit.
Spencer SL, Cappell SD, Tsai FC, Overton KW, Wang CL, Meyer T.
Cell. 2013 Oct 10;155(2):369-83.
PubMed PMID: 24075009.

19: Myb promotes centriole amplification and later steps of the multiciliogenesis program.
Tan FE, Vladar EK, Ma L, Fuentealba LC, Hoh R, Espinoza FH, Axelrod JD, Alvarez-Buylla A, Stearns T, Kintner C, Krasnow MA.
Development. 2013 Oct;140(20):4277-86.
PubMed PMID: 24048590; PubMed Central PMCID: PMC3787764.

18: Neurons generated by direct conversion of fibroblasts reproduce synaptic phenotype caused by autism-associated neuroligin-3 mutation.
Chanda S, Marro S, Wernig M, Südhof TC.
Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):16622-7.
PubMed PMID: 24046374; PubMed Central PMCID: PMC3799342.

17: Optobiology: optical control of biological processes via protein engineering.
Kim B, Lin MZ.
Biochem Soc Trans. 2013 Oct;41(5):1183-8.
PubMed PMID: 24059506; PubMed Central PMCID: PMC4076147.

16: The Stanford Institute for Chemical Biology.
Chen JK, Du Bois J, Glenn J, Herschlag D, Khosla C.
ACS Chem Biol. 2013 Sep 20;8(9):1860-1.
PubMed PMID: 24053754.

15: Genetic dissection of a cell-autonomous neurodegenerative disorder: lessons learned from mouse models of Niemann-Pick disease type C.
Lopez ME, Scott MP.
Dis Model Mech. 2013 Sep;6(5):1089-100.
PubMed PMID: 23907005; PubMed Central PMCID: PMC3759329.

14: Engineered knottin peptide enables noninvasive optical imaging of intracranial medulloblastoma.
Moore SJ, Hayden Gephart MG, Bergen JM, Su YS, Rayburn H, Scott MP, Cochran JR.
Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14598-603.
PubMed PMID: 23950221; PubMed Central PMCID: PMC3767496.

13: Rapid and tunable control of protein stability in Caenorhabditis elegans using a small molecule.
Cho U, Zimmerman SM, Chen LC, Owen E, Kim JV, Kim SK, Wandless TJ.
PLoS One. 2013 Aug 22;8(8):e72393.
PubMed PMID: 23991108; PubMed Central PMCID: PMC3750007.

12: WholeCellViz: data visualization for whole-cell models.
Lee R, Karr JR, Covert MW.
BMC Bioinformatics. 2013 Aug 21;14:253.
PubMed PMID: 23964998; PubMed Central PMCID: PMC3765349.

11: Photoswitchable fluorescent proteins: ten years of colorful chemistry and exciting applications.
Zhou XX, Lin MZ.
Curr Opin Chem Biol. 2013 Aug;17(4):682-90.
PubMed PMID: 23876529; PubMed Central PMCID: PMC3771498.

10: FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis.
Webb AE, Pollina EA, Vierbuchen T, Urbán N, Ucar D, Leeman DS, Martynoga B, Sewak M, Rando TA, Guillemot F, Wernig M, Brunet A.
Cell Rep. 2013 Aug 15;4(3):477-91.
PubMed PMID: 23891001; PubMed Central PMCID: PMC3838667.

9: Single timepoint models of dynamic systems.
Sachs K, Itani S, Fitzgerald J, Schoeberl B, Nolan GP, Tomlin CJ.
2013 Aug 6;3(4):20130019.
PubMed PMID: 24511382; PubMed Central PMCID: PMC3915837.

8: FK506 activates BMPR2, rescues endothelial dysfunction, and reverses pulmonary hypertension.
Spiekerkoetter E, Tian X, Cai J, Hopper RK, Sudheendra D, Li CG, El-Bizri N, Sawada H, Haghighat R, Chan R, Haghighat L, de Jesus Perez V, Wang L, Reddy S, Zhao M, Bernstein D, Solow-Cordero DE, Beachy PA, Wandless TJ, Ten Dijke P, Rabinovitch M.
J Clin Invest. 2013 Aug 1;123(8):3600-13.
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7: Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle.
Chang JB, Ferrell JE Jr.
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PubMed PMID: 23863935; PubMed Central PMCID: PMC3758429.

6: Peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly.
Desmarais SM, De Pedro MA, Cava F, Huang KC.
Mol Microbiol. 2013 Jul;89(1):1-13
PubMed PMID: 23679048; PubMed Central PMCID: PMC3694805.

5: Regulators of calcium homeostasis identified by inference of kinetic model parameters from live single cells perturbed by siRNA.
Bandara S, Malmersjö S, Meyer T.
Sci Signal. 2013 Jul 9;6(283):ra56.
PubMed PMID: 23838183; PubMed Central PMCID: PMC3897207.

4: Inside-out connections: the ER meets the plasma membrane.
Malmersjö S, Meyer T.
Cell. 2013 Jun 20;153(7):1423-4.
PubMed PMID: 23791170.

3: Rapid single-step induction of functional neurons from human pluripotent stem cells.
Zhang Y, Pak C, Han Y, Ahlenius H, Zhang Z, Chanda S, Marro S, Patzke C, Acuna C, Covy J, Xu W, Yang N, Danko T, Chen L, Wernig M, Südhof TC.
Neuron. 2013 Jun 5;78(5):785-98.
PubMed PMID: 23764284; PubMed Central PMCID: PMC3751803.

2: Feedforward regulation ensures stability and rapid reversibility of a cellular state.
Doncic A, Skotheim JM.
Mol Cell. 2013 Jun 27;50(6):856-68.
PubMed PMID: 23685071.

1: Mechanical consequences of cell-wall turnover in the elongation of a Gram-positive bacterium.
Misra G, Rojas ER, Gopinathan A, Huang KC.
Biophys J. 2013 Jun 4;104(11):2342-52.
PubMed PMID:23746506; PubMed Central PMCID: PMC3672878.

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