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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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2017

218: 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.

217: 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.

216: 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.

215: 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.

214: 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.

213: 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.

212: 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.

211: 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.

210: 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.

209: 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.

208: 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.

207: 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.

206: 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.

205: 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.

204: 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.

203: 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.

202: 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.

201: 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.

200: 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.

199: 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.

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

197: 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.

196: Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB 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

195: 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.

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

193: 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.

192: 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.

191: 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.

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

189: 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.

188: Rapid, precisequantification 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.

187: 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.

186: 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.

185: Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robustcontrol 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.

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

183: 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.

182: 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.

181: 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.

180: 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.

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2016

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 Álamo 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.
Pubmed PMID: 27571193.

162: PLEKHG3 enhances polarized cell migration by activating actin filaments at the cell front.
Nguyen TT, Park WS, Park BO, Kim CY, Oh Y, Kim JM, Choi H, Kyung T, Kim CH, Lee G, Hahn KM, Meyer T, Heo WD.
Proc Natl Acad Sci U S A. 2016 Aug 23. pii: 201604720.
Pubmed PMID: 27555588; PubMed Central PMCID: PMC5018766.

161: Airway epithelial homeostasis and planar cell polarity signaling depend on multiciliated cell differentiation.
Vladar EK, Nayak JV, Milla CE, Axelrod JD.
JCI Insight. 2016 Aug 18;1(13). pii: e88027.
Pubmed PMID: 27570836; PubMed Central PMCID: PMC4996276.

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.
PLoS One. 2016 Aug 3;11(8):e0159456.
Pubmed PMID: 27486863; PubMed Central PMCID: PMC4972316.

159: Structure-guided wavelength tuning in far-red fluorescent proteins.
Ng HL, Lin MZ.
Curr Opin Struct Biol. 2016 Jul 25;39:124-133. doi: 10.1016/j.sbi.2016.07.010.
Pubmed PMID: 27468111.

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.
Pubmed PMID: 27453443; PubMed Central PMCID: PMC5001915.

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.
Nat Commun. 2016 Jul 18;7:12169.
Pubmed PMID: 27425143; PubMed Central PMCID: PMC4960315.

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.
EMBO J. 2016 Jul 11. pii: e201694071.
Pubmed PMID: 27402227; PubMed Central PMCID: PMC5010044.

155: Tbx16 regulates hox gene activation in mesodermal progenitor cells.
Payumo AY, McQuade LE, Walker WJ, Yamazoe S, Chen JK.
Nat Chem Biol. 2016 Jul 4.
Pubmed PMID: 27376691; PubMed Central PMCID: PMC4990471.

154: Irreversible APC(Cdh1) Inactivation Underlies the Point of No Return for Cell-Cycle Entry.
Cappell SD, Chung M, Jaimovich A, Spencer SL, Meyer T.
Cell. 2016 Jun 30;166(1):167-80.
Pubmed PMID: 27368103.

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.
Nature. 2016 Jun 8.
Pubmed PMID: 27281220; PubMed Central PMCID: PMC4928860.

152: Relative Rates of Surface and Volume Synthesis Set Bacterial Cell Size.
Harris LK, Theriot JA.
Cell. 2016 Jun 2;165(6):1479-92.
Pubmed PMID: 27259152; PubMed Central PMCID: PMC4933963.

151: Subcellular Imaging of Voltage and Calcium Signals Reveals Neural Processing In Vivo.
Yang HH, St-Pierre F, Sun X, Ding X, Lin MZ, Clandinin TR.
Cell. 2016 May 31. pii: S0092-8674(16)30582-7.
Pubmed PMID: 27264607.

150: A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo.
Chu J, Oh Y, Sens A, Ataie N, Dana H, Macklin JJ, Laviv T, Welf ES, Dean KM, Zhang F, Kim BB, Tang CT, Hu M, Baird MA, Davidson MW, Kay MA, Fiolka R, Yasuda R, Kim DS, Ng HL, Lin MZ.
Nat Biotechnol. 2016 May 30.
Pubmed PMID: 27240196; PubMed Central PMCID: PMC4942401.

149: A method to rapidly create protein aggregates in living cells.
Miyazaki Y, Mizumoto K, Dey G, Kudo T, Perrino J, Chen LC, Meyer T, Wandless TJ.
Nat Commun. 2016 May 27;7:11689.
Pubmed PMID: 27229621; PubMed Central PMCID: PMC4894968.

148: Thresholds and ultrasensitivity from negative cooperativity.
Ha SH, Ferrell JE Jr.
Science. 2016 May 20;352(6288):990-3.
Pubmed PMID: 27174675; PubMed Central PMCID: PMC5184821.

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.
Pubmed PMID: 27203178; PubMed Central PMCID: PMC4875507.

146: Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.
Medina EM, Turner JJ, Gordân R, Skotheim JM, Buchler NE.
Elife. 2016 May 10;5. pii: e09492
Pubmed PMID: 27162172; PubMed Central PMCID: PMC4862756.

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.
Pubmed PMID: 27152864; PubMed Central PMCID: PMC4859537.

144: Characterization of the cadherin-catenin complex of the sea anemone Nematostella vectensis and implications for the evolution of metazoan cell-cell adhesion.
Clarke DN, Miller PW, Lowe CJ, Weis WI, Nelson WJ.
Mol Biol Evol. 2016 Apr 28. pii: msw084.
Pubmed PMID: 27189570; PubMed Central PMCID: PMC4948710.

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.
Proc Natl Acad Sci U S A. 2016 Feb 29. pii: 201601375. 
Pubmed PMID: 26929379; PubMed Central PMCID: PMC4801249.

142: Perfect and Near-Perfect Adaptation in Cell Signaling.
Ferrell JE Jr.
Cell Syst. 2016 Feb 24;2(2):62-7. doi: 10.1016/j.cels.2016.02.006.
Pubmed PMID: 27135159.

141: Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments.
Welf ES, Driscoll MK, Dean KM, Schäfer C, Chu J, Davidson MW, Lin MZ, Danuser G, Fiolka R.
Dev Cell. 2016 Feb 22;36(4):462-75.
Pubmed PMID: 26906741; PubMed Central PMCID: PMC4784259.

140: Prickle1 mutation causes planar cell polarity and directional cell migration defects associated with cardiac outflow tract anomalies and other structural birth defects.
Gibbs BC, Rao Damerla R, Vladar EK, Chatterjee B, Wan Y, Liu X, Cui C, Gabriel GC, Zahid M, Yagi H, Szabo-Rogers HL, Suyama KL, Axelrod JD, Lo CW.
Biol Open. 2016 Feb 16. pii: bio.015750.
Pubmed PMID: 26883626; PubMed Central PMCID: PMC4810743.

139: Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting.
Bajar BT, Wang ES, Lam AJ, Kim BB, Jacobs CL, Howe ES, Davidson MW, Lin MZ, Chu J.
Sci Rep. 2016 Feb 16;6:20889.
Pubmed PMID: 26879144; PubMed Central PMCID: PMC4754705.

138: Prickle isoforms control the direction of tissue polarity by microtubule independent and dependent mechanisms.
Sharp KA, Axelrod JD.
Biol Open. 2016 Feb 10. pii: bio.016162.
Pubmed PMID: 26863941; PubMed Central PMCID: PMC4810745.

137: The Prozone Effect Accounts for the Paradoxical Function of the Cdk-Binding Protein Suc1/Cks.
Ha SH, Kim SY, Ferrell JE Jr.
Cell Rep. 2016 Feb 3. pii: S2211-1247(16)00054-1.
Pubmed PMID: 26854218; PubMed Central PMCID: PMC4928677.

136: Disentangling Random Motion and Flow in a Complex Medium.
Koslover EF, Chan CK, Theriot JA.
Biophys J. 2016 Feb 2;110(3):700-9.
Pubmed PMID: 26840734; PubMed Central PMCID: PMC4744162.

135: Waves of actin and microtubule polymerization drive microtubule-based transport and neurite growth before single axon formation.
Winans AM, Collins SR, Meyer T.
Elife. 2016 Feb 2;5. pii: e12387.
Pubmed PMID: 26836307; PubMed Central PMCID: PMC4805541.

134: I only have eye for ewe: the discovery of cyclopamine and development of Hedgehog pathway-targeting drugs.
Chen JK.
Nat Prod Rep. 2016 Jan 20.
Rheum Dis Clin North Am. 2016 Feb;42(1):103-18.
Pubmed PMID: 26787175; PubMed Central PMCID: PMC4856577.

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2015

133: High-throughput, Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography.
Desmarais SM, Tropini C, Miguel A, Cava F, Monds RD, de Pedro MA, Huang KC.
J Biol Chem. 2015 Dec 25;290(52):31090-100.
Pubmed PMID: 26468288; PubMed Central PMCID: PMC4692233.

132: Locally excitable Cdc42 signals steer cells during chemotaxis.
Yang HW, Collins SR, Meyer T.
Nat Cell Biol. 2015 Dec 21.
Pubmed PMID: 26689677; PubMed Central PMCID: PMC5015690.

131: Mitosis is swell.
Zatulovskiy E, Skotheim JM.
J Cell Biol. 2015 Nov 23;211(4):733-5.
Pubmed PMID: 26598610; PubMed Central PMCID: PMC4657178.

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.
ISME J. 2015 Nov 17.
Pubmed PMID: 26574685; PubMed Central PMCID: PMC5029216.

129: Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time.
Hoy YE, Bik EM, Lawley TD, Holmes SP, Monack DM, Theriot JA, Relman DA.
PLoS One. 2015 Nov 13;10(11):e0142825.
Pubmed PMID: 26565698; PubMed Central PMCID: PMC4643986.

128: The Biosynthetic Basis of Cell Size Control.
Schmoller KM, Skotheim JM.
Trends Cell Biol. 2015 Nov 10. pii: S0962-8924(15)00193-2.
Pubmed PMID: 26573465.

127: Applications of imaging for bacterial systems biology.
Huang KC
Curr Opin Microbiol. 2015 Oct;27:114-20.
Pubmed PMID: 26356259.

126: Quantitative Imaging of Gut Microbiota Spatial Organization.
Earle KA, Billings G, Sigal M, Lichtman JS, Hansson GC, Elias JE, Amieva MR, Huang KC, Sonnenburg JL.
Cell Host Microbe. 2015 Oct 14;18(4):478-88.
Pubmed PMID: 26439864; PubMed Central PMCID: PMC4628835.

125: Why Build Whole-Cell Models?
Carrera J, Covert MW.
Trends Cell Biol. 2015 Oct 12. pii: S0962-8924(15)00170-1.
Pubmed PMID: 26471224; PubMed Central PMCID: PMC4663153.

124: Accelerating Submovement Decomposition With Search-Space Reduction Heuristics.
Gowda S, Overduin SA, Chen M, Chang YH, Tomlin CJ, Carmena JM.
IEEE Trans Biomed Eng. 2015 Oct;62(10):2508-15.
Pubmed PMID: 26011861.

123: Reevaluating αE-catenin monomer and homodimer functions by characterizing E-cadherin/αE-catenin chimeras.
Bianchini JM, Kitt KN, Gloerich M, Pokutta S, Weis WI, Nelson WJ.
J Cell Biol. 2015 Sep 28;210(7):1065-1074.
Pubmed PMID: 26416960; PubMed Central PMCID: PMC4586751.

122: Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size.
Schmoller KM, Turner JJ, Kõivomägi M, Skotheim JM.
Nature. 2015 Sep 21.
Pubmed PMID: 26390151; PubMed Central PMCID: PMC4600446.

121: Replication-Competent Influenza and Respirtory Syncytial Virus Luciferase Reporter Strains Engineered for Co-Infections Identify Antiviral.
Yan D, Weisshaar M, Lamb K, Chung HK, Lin MZ, Plemper RK.
Biochemistry. 2015 Sep 15;54(36):5589-604.
Pubmed PMID: 26307636; PubMed Central PMCID: PMC4719150.

120: Phosphodiesterase 4D acts downstream of Neuropilin to control Hedgehog signal transduction and the growth of medulloblastoma.
Ge X, Milenkovic L, Suyama K, Hartl T, Purzner T, Winans A, Meyer T, Scott MP.
Elife. 2015 Sep 15;4.
Pubmed PMID: 26371509; PubMed Central PMCID: PMC4569902.

119: Studying epithelial morphogenesis in Dictyostelium.
Dickinson DJ, Nelson WJ, Weis WI.
Methods Mol Biol. 2015;1189:267-81.
Pubmed PMID: 25245700.

118: Distinct transcriptional responses elicited by unfolded nuclear or cytoplasmic protein in mammalian cells.
Miyazaki Y, Chen LC, Chu BW, Swigut T, Wandless TJ.
Elife. 2015 Aug 28;4.
Pubmed PMID: 26314864; PubMed Central PMCID: PMC4566031.

117: Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome.
Dey G, Meyer T.
Cell Syst. 2015 Aug 26;1(2):106-15.
Pubmed PMID: 27135799.

116: Cell-Size Control.
Amodeo AA, Skotheim JM.
Cold Spring Harb Perspect Biol. 2015 Aug 7.
Pubmed PMID: 26254313; PubMed Central PMCID: PMC4744813.

115: Tunable and reversible drug control of protein production via a self-excising degron.
Chung HK, Jacobs CL, Huo Y, Yang J, Krumm SA, Plemper RK, Tsien RY, Lin MZ.
Nat Chem Biol. 2015 Jul 27.
PubMed PMID: 26214256.

114: How Does the Xenopus laevis Embryonic Cell Cycle Avoid Spatial Chaos?
Gelens L, Huang KC, Ferrell JE Jr.
Cell Rep. 2015 Jul 22. pii: S2211-1247(15)00708-1.
PubMed PMID: 26212326; PubMed Central PMCID: PMC4531097.

113: Investigating neuronal function with optically controllable proteins.
Zhou XX, Pan M, Lin MZ.
Front Mol Neurosci. 2015 Jul 21;8:37.
PubMed PMID: 26257603; PubMed Central PMCID: PMC4508517.

112: Running with neighbors: coordinating cell migration and cell-cell adhesion.
Collins C, Nelson WJ.
Curr Opin Cell Biol. 2015 Jul 17;36:62-70.
PubMed PMID: 26201843; PubMed Central PMCID: PMC4639402.

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.
PubMed PMID: 25971797; PubMed Central PMCID: PMC4553077.

110: Designs and sensing mechanisms of genetically encoded fluorescent voltage indicators.
St-Pierre F, Chavarha M, Lin MZ.
Curr Opin Chem Biol. 2015 Jun 11;27:31-38.
PubMed PMID: 26079047.

109: Cell adhesion. Mechanical strain induces E-cadherin-dependent Yap1 and β-catenin activation to drive cell cycle entry.
Benham-Pyle BW, Pruitt BL, Nelson WJ.
Science. 2015 May 29;348(6238):1024-7.
PubMed PMID: 26023140.

108: Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.
Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P.
PLoS Comput Biol. 2015 May 28;11(5):e1004096.
PubMed PMID: 26020786; PubMed Central PMCID: PMC4447414.

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.
PubMed PMID: 26003204; PubMed Central PMCID: PMC4491883.

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.
PubMed PMID: 25996914; PubMed Central PMCID: PMC4440771.

105: The mechanotransduction machinery at work at adherens junctions.
Ladoux B, Nelson WJ, Yan J, Mège RM.
Integr Biol (Camb). 2015 May 13.
PubMed PMID: 25968913.

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.
Science. 2015 May 1;348(6234):574-8.
PubMed PMID: 25931560.

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.
PubMed PMID: 25840986; PubMed Central PMCID: PMC4409283.

102: Myosin light chain kinase regulates cell polarization independently of membrane tension or Rho kinase. 
Lou SS, Diz-Muñoz A, Weiner OD, Fletcher DA, Theriot JA
J Cell Biol. 2015 Apr 27;209(2):275-88.
PubMed PMID: 25918227; PubMed Central PMCID: PMC4411279.

101: Using light to shape chemical gradients for parallel and automated analysis of chemotaxis. 
Collins SR, Yang HW, Bonger KM, Guignet EG, Wandless TJMeyer T.
Mol Syst Biol. 2015 Apr 23;11(4):804. 
PubMed PMID: 25908733; PubMed Central PMCID: PMC4422560.

100: Disentangling multidimensional spatio-temporal data into their common and aberrant responses.
Chang YH, Korkola J, Amin DN, Moasser MM, Carmena JM, Gray JW, Tomlin CJ.
PLoS One. 2015 Apr 22;10(4):e0121607.
PubMed PMID: 25901353; PubMed Central PMCID: PMC4593723.

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.
PubMed PMID: 25848042; PubMed Central PMCID: PMC4413303.

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.
PubMed PMID: 25825747; PubMed Central PMCID: PMC4403194.

97: Thinking big with small molecules. 
Mruk K, Chen JK.
J Cell Biol. 2015 Apr 13;209(1):7-9.
PubMed PMID: 25869661; PubMed Central PMCID: PMC4395478.

96: Optical control of biological processes by light-switchable proteins.
Fan LZ, Lin MZ.
Wiley Interdiscip Rev Dev Biol. 2015 Apr 8. 
PubMed PMID: 25858669; PubMed Central PMCID: PMC4529752.

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.
PubMed PMID: 25863054; PubMed Central PMCID: PMC4390813.

94: A dynamic picture of protein behavior in cells.
Teruel MN, Gu B, Zhao ML.
Nat Biotechnol. 2015 Apr 7;33(4):356-7. 
PubMed PMID: 25850058.

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. 
PubMed PMID: 25501595; PubMed Central PMCID: PMC4356341.

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.
PubMed PMID: 25582303.

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.
PubMed PMID: 25781211.

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. 
PubMed PMID: 25768911; PubMed Central PMCID: PMC4377233.

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. 
 PubMed PMID: 25713373; PubMed Central PMCID: PMC4364222.

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. 
PubMed PMID: 25811761; PubMed Central PMCID: PMC4374959.

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. 
PubMed PMID: 25683721.

86: Single-cell variation leads to population invariance in NF-κB signaling dynamics.
Hughey JJ, Gutschow MV, Bajar BT, Covert MW. 
Mol Biol Cell. 2015 Feb 1;26(3):583-90. 
PubMed PMID: 25473117; PubMed Central PMCID: PMC4310747.

85: Observing planar cell polarity in multiciliated mouse airway epithelial cells.
Vladar EK, Lee YL, Stearns T, Axelrod JD.
Methods Cell Biol. 2015;127:37-54. 
PubMed PMID: 25837385; PubMed Central PMCID: PMC4423753.

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.
PubMed PMID: 25355954; PubMed Central PMCID: PMC4279231.

................................................................................................................................................................

2014

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.
Elife. 2014 Dec 15;3.
PubMed PMID: 25498153.

82: Exact reconstruction of gene regulatory networks using compressive sensing.
Chang Y, Gray JW, Tomlin CJ.
BMC Bioinformatics. 2014 Dec 14;15(1):400.
PubMed PMID: 25495633; PubMed Central PMCID: PMC4308013.

81: Ultrasensitivity part III: cascades, bistable switches, and oscillators.
Ferrell JE Jr, Ha SH.
Trends Biochem Sci. 2014 Dec;39(12):612-618. 
PubMed PMID: 25456048; PubMed Central PMCID: PMC4254632.

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.
PubMed PMID: 25456140; PubMed Central PMCID: PMC4254626.

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.
PubMed PMID: 25456141.

78: Modularity and predictability in cell signaling and decision making.
Atay O, Skotheim JM.
Mol Biol Cell. 2014 Nov 5;25(22):3445-50. 
PubMed PMID: 25368418.

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.
PubMed PMID: 25440716; PubMed Central PMCID: PMC4435807.

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.
PubMed PMID: 25267623; PubMed Central PMCID: PMC4205626.

74: Ultrasensitivity part I: Michaelian responses and zero-order ultrasensitivity.
Ferrell JE Jr, Ha SH.
Trends Biochem Sci. 2014 Oct;39(10):496-503. 
PubMed PMID: 25240485; PubMed Central PMCID: PMC4214216.

73: A Caulobacter MreB mutant with irregular cell shape exhibits compensatory widening to maintain a preferred surface area to volume ratio.
Harris LK, Dye NA, Theriot JA.
Mol Microbiol. 2014 Sep 30.
PubMed PMID: 25266768;  PubMed Central PMCID: PMC4379118.

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.
PubMed PMID: 25069083.

71: Chemical Biology Strategies for Posttranslational Control of Protein Function.
Rakhit R, Navarro R, Wandless TJ.
Chem Biol. 2014 Sep 18;21(9):1238-1252. 
PubMed PMID: 25237866; PubMed Central PMCID: PMC4174368.

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. 
PubMed PMID: 25231498; PubMed Central PMCID: PMC4165886.

69: Sequential gene silencing using wavelength-selective caged morpholino oligonucleotides. 
Yamazoe S, Liu Q, McQuade LE, Deiters A, Chen JK.
Angew Chem Int Ed Engl. 2014 Sep 15;53(38):10114-8. 
PubMed PMID: 25130695; PubMed Central PMCID: PMC4206551.

68: Nonlytic viral spread enhanced by autophagy components.
Bird SW, Maynard ND, Covert MW, Kirkegaard K.
Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13081-6. 
PubMed PMID: 25157142; PubMed Central PMCID: PMC4246951.

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.
PubMed PMID: 24995493; PubMed Central PMCID: PMC4459576.

66: Coordinating cell polarity: heading in the right direction?
Axelrod JD, Bergmann DC.
Development. 2014 Sep;141(17):3298-302. 
PubMed PMID: 25139852.

65: Induced neuronal reprogramming.
Ang CE, Wernig M.
J Comp Neurol. 2014 Aug 15;522(12):2877-86. 
PubMed PMID: 24771471; PubMed Central PMCID: PMC4099045.

64: Microtubules provide directional information for core PCP function.
Matis M, Russler-Germain DA, Hu Q, Tomlin CJAxelrod JD.
Elife. 2014 Aug 14;3:e02893. 
PubMed PMID: 24948735; PubMed Central PMCID: PMC4151085.

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.
PLoS One. 2014 Aug 11;9(8):e105047. 
PubMed PMID: 25111084; PubMed Central PMCID: PMC4128735.

62: How and why cells grow as rods.
Chang F, Huang KC.
BMC Biol. 2014 Aug 2;12(1):54.
PubMed PMID: 25185019; PubMed Central PMCID: PMC4243964.

61: The future of whole-cell modeling.
Macklin DN, Ruggero NA, Covert MW.
Curr Opin Biotechnol. 2014 Aug;28C:111-115.
PubMed PMID: 24556244; PubMed Central PMCID: PMC4111988.

60: prickle modulates microtubule polarity and axonal transport to ameliorate seizures in flies.
Ehaideb SN, Iyengar A, Ueda A, Iacobucci GJ, Cranston C, Bassuk AG, Gubb D, Axelrod JD, Gunawardena S, Wu CF, Manak JR.
Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11187-92. 
PubMed PMID: 25024231; PubMed Central PMCID: PMC4121842.

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. 
PubMed PMID: 25024225; PubMed Central PMCID: PMC4121834.

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
Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11061-6. 
PubMed PMID: 25024229; PubMed Central PMCID: PMC4121843.

57: In vivo imaging of hedgehog pathway activation with a nuclear fluorescent reporter.
Mich JK, Payumo AY, Rack PG, Chen JK.
PLoS One. 2014 Jul 28;9(7):e103661. 
PubMed PubMed PMID: 25068273; PubMed Central PMCID: PMC4113417.

56: Docking interactions: cell-cycle regulation and beyond.
Kõivomägi M, Skotheim JM. 
Curr Biol. 2014 Jul 21;24(14):R647-9. 
PubMed PubMed PMID: 25050961.

55: Direct kinetochore-spindle pole connections are not required for chromosome segregation.
Sikirzhytski V, Magidson V, Steinman JB, He J, Le Berre M, Tikhonenko I, Ault JG, McEwen BF, Chen JK, Sui H, Piel M, Kapoor TM, Khodjakov A.
J Cell Biol. 2014 Jul 21;206(2):231-43. 
PubMed PMID: 25023516; PubMed Central PMCID: PMC4107786.

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
Development. 2014 Jul;141(14):2866-74. 
PubMed PMID: 25005476; PubMed Central PMCID: PMC4197621.

53: Controlling low rates of cell differentiation through noise and ultrahigh feedback.
Ahrends R, Ota A, Kovary KM, Kudo T, Park BO, Teruel MN
Science. 2014 Jun 20;344(6190):1384-9. 
PubMed PMID: 24948735.

52: High-sensitivity measurements of multiple kinase activities in live single cells.
Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW.
Cell. 2014 Jun 19;157(7):1724-34.
PubMed PMID: 24949979; PubMed Central PMCID: PMC4097317.

51: High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor.
St-Pierre F, Marshall JD, Yang Y, Gong Y, Schnitzer MJ, Lin MZ.
Nat Neurosci. 2014 Jun;17(6):884-9.
PubMed PMID: 24755780.

50: Methods for studying planar cell polarity.
Olofsson J, Axelrod JD.
Methods.2014 Jun 15;68(1):97-104. 
PubMed PMID: 24680701; PubMed Central PMCID: PMC4048770.

49:The wing disc as a platform for studying Hedgehog signaling.
Hartl TA, Scott MP. Wing tips: 
Methods. 2014 Jun 15;68(1):199-206. 
PubMed PMID: 24556557.

48: Response of Escherichia coli growth rate to osmotic shock.
Rojas E, Theriot JAHuang KC.
Proc Natl Acad Sci U S A. 2014 May 27;111(21):7807-12. 
PubMed PMID: 24821776; PubMed Central PMCID: PMC4040581.

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.Â
PubMed PMID: 24558258.

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.
PubMed PMID: 24550500; PubMed Central PMCID: PMC3970539.

43: Incorporation of flexible objectives and time-linked simulation with flux balance analysis. 
Birch EW, Udell M, Covert MW
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.
PubMed PMID: PMID: 24550504; PubMed Central PMCID: PMC3948266.

40: Changes in Oscillatory Dynamics in the Cell Cycle of Early Xenopus laevis Embryos. 
Tsai TY, Theriot JAFerrell JE Jr. 
PLoS Biol. 2014 Feb 11;12(2):e1001788. 
PubMed PMID: 24523664; PubMed Central PMCID: PMC3921120.

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.
Nat Cell Biol. 2014 Feb;16(2):133-44. 
PubMed PMID: 24463606; PubMed Central PMCID: PMC3953390.

38: General method for regulating protein stability with light. 
Bonger KM, Rakhit R, Payumo AY, Chen JKWandless TJ
ACS Chem Biol. 2014 Jan 17;9(1):111-5.
PubMed PMID: 24180414; PubMed Central PMCID: PMC3906921.

37: Gli protein activity is controlled by multisite phosphorylation in vertebrate Hedgehog signaling.
Niewiadomski P, Kong JH, Ahrends R, Ma Y, Humke EW, Khan S, Teruel MN, Novitch BG, Rohatgi R. 
Cell Rep. 2014 Jan 16;6(1):168-81. 
PubMed PMID: 24373970; PubMed Central PMCID: PMC3915062.

36: Isolation and preparation of bacterial cell walls for compositional analysis by ultra performance liquid chromatography.
Desmarais SM, Cava F, de Pedro MA, Huang KC.
J Vis Exp. 2014 Jan 15;(83):e51183.
PubMed PMID: 24457605; PubMed Central PMCID: PMC3987682.

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.
Nat Methods. 2014 Jan;11(1):86-93.
PubMed PMID: 24213167.

................................................................................................................................................................

2013

34: Motility enhancement through surface modification is sufficient for cyanobacterial community organization during phototaxis.
Ursell T, Chau RM, Wisen S, Bhaya D, Huang KC.
PLoS Comput Biol. 2013;9(9):e1003205.
PubMed PMID: 24039562; PubMed Central PMCID: PMC3763999.

33: Harnessing the stem cell potential: a case for neural stem cell therapy.
Yang N, Wernig M.
Nat Med. 2013 Dec;19(12):1580-1.
PubMed PMID: 24309657.

32: Why are bacteria different from eukaryotes?
Theriot JA.
BMC Biol. 2013 Dec 13;11:119.
PubMed PMID: 24330667; PubMed Central PMCID: PMC3874686.

31: Constraints on the adult-offspring size relationship in protists.
Caval-Holme F, Payne J, Skotheim JM.
Evolution. 2013 Dec;67(12):3537-44.
PubMed PMID: 24299406.

30: Start and the restriction point.
Johnson A, Skotheim JM.
Curr Opin Cell Biol. 2013 Dec;25(6):717-23.
PubMed PMID: 23916770; PubMed Central PMCID: PMC3836907.

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.
PubMed PMID: 24185838; PubMed Central PMCID: PMC3856890.

28: The role of hydrolases in bacterial cell-wall growth.
Lee TK, Huang KC.
Curr Opin Microbiol. 2013 Dec;16(6):760-6.
PubMed PMID: 24035761; PubMed Central PMCID: PMC3986426.

27: Dimer dynamics and filament organization of the bacterial cell division protein FtsA.
Hsin J, Fu R, Huang KC.
J Mol Biol. 2013 Nov 15;425(22):4415-26.
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.
PubMed PMID: 24026530.

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.
Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19372-7. doi: 10.1073/pnas.1307405110. Epub 2013 Nov 12.
PubMed PMID: 24222685; PubMed Central PMCID: PMC3845171.

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.
Cell. 2013 Oct 24;155(3):621-35.
PubMed PMID: 24243019; PubMed Central PMCID: PMC3871197.

22: Regulation of PCP by the Fat signaling pathway.
Matis M, Axelrod JD.
Genes Dev. 2013 Oct 15;27(20):2207-20.
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.
PubMed PMID: 23867624; PubMed Central PMCID: PMC3726153.

7: Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle.
Chang JB, Ferrell JE Jr.
Nature. 2013 Aug 29;500(7464):603-7.
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.

Monday, April 17, 2017 -Last Updated