Publications

Ma R, Hendel NL, Marshall WF, Qin H. 2020. Speed and Diffusion of Kinesin-2 Are Competing Limiting Factors in Flagellar Length-Control Model. Biophys J. 2020 Jun 2;118(11):2790-2800. doi: 10.1016/j.bpj.2020.03.034. Epub 2020 Apr 22.

Bianco S, Chan YH, Marshall WF. 2020. Towards computer aided design of cellular structure. Phys. Biol. accepted manuscript online.

Wemmer K, Ludington W, Marshall WF. 2020. Testing the role of intraflagellar transport in flagellar length control using length-altering mutants of Chlamydomonas. Philos Trans R Soc Lond B Biol Sci 375(1792):20190159

Wan KY, Hürlimann SK, Fenix AM, McGillivary RM, Makushok T, Burns E, Sheung JY, Marshall WF. 2020. Reorganization of complex ciliary flows around regenerating Stentor coeruleus. Philos Trans R Soc Lond B Biol Sci 375, 20190167

Marshall WF. 2019. Cellular Cognition: sequential logic in a giant protist. Curr. Biol. 29, R1303-R1305.

Kimmel JC, Hwang A, Marshall WF, Brack A. 2019. Aging induces aberrant state transition kinetics in murine muscle stem cells. Submitted. preprint: bioRxiv https://doi.org/10.1101/739185

Ramirez-San Juan GR, Mathijssen AJTM, He M, Jan L, Marshall WF, Prakash M. 2019. Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays. Submitted preprint: bioRxiv https://doi.org/10.1101/665125

Diaz U, Bergman Z, Johnson B, Edington AR, de Cruz MA, Marshall WF, Riggs B. 2019. Microtubules are necessary for proper Reticulon localization during mitosis. PLoS One 14, e0226327

Chang AY, Marshall WF. 2019. Dynamics of living cells in a cytomorphological state space. Proc. Natl. Acad. Sci. U.S.A. 116, 21556-21562

Yu W, Marshall WF, Metzger RJ, Brakeman PR, Morsut L, Lim WA, Mostov KE. 2019. Design rules for kidney branching morphogenesis. Cell Systems. 9, P221-P227,

Kimmel JC, Brack A, Marshall WF. 2019. Deep convolutional and recurrent neural networks for cell motility discrimination and prediction. IEEE/ACM Trans. Comp. Biol. Bioinformatics doi: 10.1109/TCBB.2019.2919307

Ishikawa H, Yu JE, Tian J, Tang SKY, Qin H, Marshall WF. 2019. Cell-based biosynthesis of linear protein nanoarrays. Proc. SPIE 108930F

Marshall WF, Fung JC.  2019.  Modeling meiotic chromosome pairing: a tug of war between telomere forces and a pairing-based Brownian ratchet leads to increased pairing fidelity.  Phys Biol. 2019 May 7;16(4):046005

Li S, Fernandez JJ, Marshall WF, Agard DA  2019.  Electron cryo-tomography provides insight into procentriole architecture and assembly mechanism.  Elife. 2019 Feb 11;8. pii: e43434

Marshall WF.  2018.  A Dilution Model for Embryonic Scaling.  Dev Cell. 2018 Sep 10;46(5):529-530

Lin A, Makushok T, Diaz U, Marshall WF.  2018.  Methods for the Study of Regeneration in Stentor.  J Vis Exp. 2018 Jun 13;(136). doi: 10.3791/57759

Tang SKY, Marshall WF.  2018.  Cell learning.  Curr Biol. 2018 Oct 22;28(20):R1180-R1184.

Hendel N, Thomson M, Marshall WF. Diffusion as a ruler: modeling kinesin diffusion as a length sensor for intraflagellar transport. 
Biophysical Journal 2018 114: 663-674. doi: https://doi.org/10.1101/156760

Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance. Kimmel JC, Chang AY, Brack AS, Marshall WF.
PLoS Computational Biology 2018 14(1): e1005927. doi: https://doi.org/10.1371/journal.pcbi.1005927

Mechanical Forces Program the Orientation of Cell Division during Airway Tube Morphogenesis.  Tang Z, Hu Y, Wang Z, Jiang K, Zhan C, Marshall WF, Tang N.
Dev. Cell 2018 44: 313-325. doi: https://doi.org/10.1016/j.devcel.2017.12.013

Condon A, Kirchner H, Lariviere D, Marshall WF, Noireaux V, Tlusty T, Fourmentin E. 2018. Will biologists become computer scientists? EMBO Reports 19, E46628.

The Transcriptional Program of Regeneration in the Giant Single Cell, Stentor coeruleus. Sood P, McGillivary R, Marshall WF.
bioRxiv. 2017 doi: https://doi.org/10.1101/240788

The macronuclear genome of Stentor coeruleus reveals tiny introns in a giant cell.  Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM Jr, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P.
Curr Biol. 2017 27(4):569-575. doi: 10.1016/j.cub.2016.12.057

Testing the time-of-flight model for flagellar length sensing. Ishikawa H, Marshall WF.
Mol Biol Cell. 2017 28:3447-3456. doi: 10.1091/mbc.E17-06-0384

Microfluidic guillotine for single-cell wound repair studies. Blauch LR, Gai Y, Khor JW, Sood P, Marshall WF, Tang SKY.
Proc Natl Acad Sci U S A.. 2017 114(28):7283-7288. doi: 10.1073/pnas.1705059114

Self-repairing cells: How single cells heal membrane ruptures and restore lost structures. Tang SKY, Marshall WF.
Science. 2017 356(6342):1022-1025. doi: 10.1126/science.aam6496.

Deep convolutional neural networks allow analysis of cell motility during stem cell differentiation and neoplastic transformation. Kimmel JC, Brack A, Marshall WF.
bioRxiv. 2017 doi: https://doi.org/10.1101/159202

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 15:55. doi: 10.1186/s12915-017-0391-5

A large kinome in a large cell: Stentor coeruleus possesses highly expanded kinase families and novel domain architectures. Reiff SB, Marshall WF.
bioRxiv. 2017 doi: https://doi.org/10.1101/168187

Organelles - understanding noise and heterogeneity in cell biology at an intermediate scale. Chang AY, Marshall WF.
J Cell Sci. 2017 130(5):819-826. doi: 10.1242/jcs.181024

Ishikawa H, Marshall WF.  2017.  Intraflagellar Transport and Ciliary Dynamics.  Cold Spring Harb Perspect Biol. 2017 Mar 1;9(3). pii: a021998

Organelle size scaling of the budding yeast vacuole by relative growth and inheritance.  Chan YH, Reyes L, Sohail SM, Tran NK, Marshall WF.
Curr Biol. 2016 May 9;26(9):1221-8. doi: 10.1016/j.cub.2016.03.020.

Cell geometry:  how cells count and measure size.   Marshall WF.
Annu Rev Biophys. 2016 Jul 5;45:49-64. doi: 10.1146/annurev-biophys-062215-010905.

Modeling meiotic chromosome pairing:  nuclear envelope attachment, telomere-led active random motion. and anomalous diffusion.   Marshall WF, Fung JC.  
Phys Biol. 2016 Apr 5;13(2):026003. doi: 10.1088/1478-3975/13/2/026003

Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert LA, Ishikawa H, Leonetti MD, Marshall WF, Weissman JS, Huang B.  2016.  Versatile protein tagging in cells with split fluorescent protein.  Nat Commun. 2016 Mar 18;7:11046

A systematic comparison of mathematical models for inherent measurement of ciliary length:  how a cell can measure length and volume. Ludington WB, Ishikawa H, Serebrenik YV, Ritter A, Hernandez-Lopez RA, Gunzenhauser J, Kannegaard E, Marshall WF
Biophys J. 2015 Mar 24;108(6):1361-79. doi: 10.1016/j.bpj.2014.12.051.

Marshall WF.  2015.  How Cells Measure Length on Subcellular Scales.  Trends Cell Biol. 2015 Dec;25(12):760-768

Ishikawa H, Marshall WF  2015.  Efficient live fluorescence imaging of intraflagellar transport in mammalian primary cilia.  Methods Cell Biol. 2015;127:189-201

Marshall WF.  2015.  Subcellular size.  Cold Spring Harb Perspect Biol. 2015 May 8;7(6). pii: a019059.

Stentor coeruleus.      Slabodnick MM, Marshall WF
Curr Biol. 2014 Sep 8;24(17):R783-4. doi: 10.1016/j.cub.2014.06.044

Actin is required for IFT regulation in Chlamydomonas reinhardtii. Avasthi P, Onishi M, Karpiak J, Yamamoto R, Mackinder L, Jonikas MC, Sale WS, Shoichet B, Pringle JR, Marshall WF
Curr Biol. 2014 Sep 8;24(17):2025-32. doi: 10.1016/j.cub.2014.07.038.

Quantitative analysis and modeling of katanin function in flagellar length control. Kannegaard E, Rego EH, Schuck S, Feldman JL, Marshall WF.
Mol Biol Cell. 2014 Nov 5;25(22):3686-98. doi: 10.1091/mbc.E14-06-1116

The kinase regulator mob1 acts as a patterning protein for Stentor morphogenesis. Slabodnick MM, Ruby JG, Dunn JG, Feldman JL, DeRisi JL, Marshall WF
PLoS Biol. 2014 May 13;12(5):e1001861. doi: 10.1371/journal.pbio.1001861

Organelle size scaling of the budding yeast vacuole is tuned by membrane trafficking rates. Chan YH, Marshall WF.
Biophys J. 2014 May 6;106(9):1986-96. doi: 10.1016/j.bpj.2014.03.014

TTC26/DYF13 is an intraflagellar transport protein required for transport of motility-related proteins into flagella.     Ishikawa H, Ide T, Yagi T, Jiang X, Hirono M, Sasaki H, Yanagisawa H, Wemmer KA, Stainier DY, Qin H, Kamiya R, Marshall WF
Elife. 2014 Jan 1;3:e01566. doi: 10.7554/eLife.01566

FAP20 is an inner junction protein of doublet microtubules essential for both the planar asymmetrical waveform and stability of flagella in Chlamydomonas. Yanagisawa HA, Mathis G, Oda T, Hirono M, Richey EA, Ishikawa H, Marshall WF, Kikkawa M, Qin H.
Mol Biol Cell. 2014 May;25(9):1472-83. doi: 10.1091/mbc.E13-08-0464

Avalanche like behavior in ciliary import. Ludington WB, Wemmer KA, Lechtreck KF, Witman GB, Marshall WF.
PNAS 2013 110: 3925-30.

Centrosome positioning in vertebrate development. Tang N, Marshall WF.
J. Cell Sci. 2012 Nov 1;125(Pt 21):4951-61

What determines cell size? Marshall WF, Young KD, Swaffer M, Wood E, Nurse P, Kimura A, Frankel J, Wallingford J, Walbot V, Qu X, Roeder AH.
BMC Biol. 2012 Dec 14;10:101

Statistical method for comparing the level of intracellular organization between cells. Apte ZS, Marshall WF.
PNAS 2013 110: E1006-15

Cell biology 2.0. Lim WA, Alvania R, Marshall WF.
Trends in Cell Biology 2012 Dec;22(12):611-2

Mitochondrial network size scaling in budding yeast. Rafelski SM, Viana MP, Zhang Y, Chan YH, Thorn KS, Yam P, Fung JC, Li H, Costa Lda F, Marshall WF.
Science 2012 Nov 9;338(6108):822-4

Organelle size equalization by a constitutive process. Ludington WB, Shi LZ, Zhu Q, Berns MW, Marshall WF.
Curr. Biol. 2012 Nov 20;22(22):2173-9

The role of retrograde intraflagellar transport in flagellar assembly, maintenance, and function. Engel BD, Ishikawa H, Wemmer KA, Geimer S, Wakabayashi K, Hirono M, Craige B, Pazour GJ, Witman GB, Kamiya R, Marshall WF.
J. Cell Biol. 2012, 199(1):151-67

Centriole asymmetry determines algal cell geometry. Marshall WF.
Curr Opin Plant Biol. 2012, 15(6):632-7

How cells know the size of their organelles. Chan YH, Marshall WF.
Science 2012, 337(6099):1186-9

Organelle size control systems: From cell geometry to organelle-directed medicine Marshall WF
Bioessays 2012, 34:721-4

A chemical screen identifies class a g-protein coupled receptors as regulators of cilia. Avasthi P, Marley A, Lin H, Gregori-Puigjane E, Shoichet BK, von Zastrow M, Marshall WF.
ACS Chemical Biology 2012 7:911-9.

Proteomic analysis of mammalian primary cilia
Ishikawa H, Thompson J, Yates JR, Marshall WF.
Current Biology 2012 22:414-9.

Centrosome Loss in the Evolution of Planarians
Azimzadeh J, Wong ML, Downhour DM, Sanchez Alvarado A, Marshall WF.
Science 2012 335:461-3.

Stages of ciliogenesis and regulation of ciliary length
Avasthi P, Marshall WF.
Differentiation 2012 83:S30-42.

Three-dimensional structure of basal body triplet revealed by electron cryo-tomography
Li s, Fernandez JJ, Marshall WF, Agard DA.
EMBO J. 2011 31:552-62.

CLUMPED CHLOROPLASTS 1 is required for plastid separation in Arabidopsis
Yang Y, Sage TL, Liu Y, Ahmad TR, Marshall WF, Shiu SH, Froehlich JE, Imre KM, Osteryoung KW.
PNAS 2011 108:18530-18535.

Control of Mitotic Spindle Angle by the RAS-Regulated ERK1/2 Pathway Determines Lung Tube Shape
Tang N, Marshall WF, McMahon M, Metzger RJ, Martin GR.
Science 2011 333:342-345.

Ciliogenesis: building the cells antenna
Ishikawa H, Marshall WF.
Nat. Rev. Mol. Cell Biol. 2011 12:222-234.

Apparent diffusive motion of centrin foci in living cells: implications for diffusion-based motion in centriole duplication
Rafelski SM, Keller LC, Alberts JB, Marshall WF.
Phys. Biol. 2011 8:026010.

A cell-based screen for inhibitors of flagella-driven motility in Chlamydomonas reveals a novel modulator of ciliary length and retrograde actin flow
Engel BD, Ishikawa H, Feldman J, Wilson CW, Chuang PT, Snedecor J, Williams J, Sun Z, Marshall WF.
Cytoskeleton 2011 68:188-203.

Origins of cellular geometry
Marshall WF.
BMC Biol. 2011 9:57.

Centrosome size: scaling without measuring
Marshall WF.
Curr Biol. 2011 Sep 21:R594-596.

Regulation of flagellar motility by the conserved flagellar protein CG34110/Ccdc135/FAP50.
Yang Y, Cochran DA, Gargano MD, King I, Samhat NK, Burger BP, Sabourin KR, Hou Y, Awata J, Parry DA, Marshall WF, Witman GB, Lu X.
Mol. Biol. Cell . 2011 22:976-87.

Scaling properties of cell and organelle size
Chan YH, Marshall WF.
Organogenesis 2010 Apr;6(2):88-96.

Building the centriole
Azimzadeh J, Marshall WF.
Curr Biol. 2010 Sep 28;20(18):R816-25.

Influence of centriole number on mitotic spindle length and symmetry
Keller LC, Wemmer KA, Marshall WF.
Cytoskeleton . 2010 Aug;67(8):504-18.

Intraflagellar transport particle size scales inversely with flagellar length: revisiting the balance-point length control model
Engel BD, Ludington WB, Marshall WF.
J Cell Biol. 2009 Oct 5;187(1):81-9.

ASQ2 encodes a TBCC-like protein required for mother-daughter centriole linkage and mitotic spindle orientation
Feldman JL, Marshall WF.
Curr Biol. 2009 Jul 28;19(14):1238-43.

Quantitative high-throughput assays for flagella-based motility in chlamydomonas using plate-well image analysis and transmission correlation spectroscopy
Marshall WF.
J Biomol Screen. 2009 Feb;14(2):133-41. Epub 2009 Feb 4

Centriole evolution
Marshall WF.
Curr Opin Cell Biol. 2009 Feb;21(1):14-9. Epub 2009 Feb 3. Review

Total internal reflection fluorescence (TIRF) microscopy of Chlamydomonas flagella
Engel BD, Lechtreck KF, Sakai T, Ikebe M, Witman GB, Marshall WF.
Methods Cell Biol. 2009;93:157-77. Epub 2009 Dec 4.

Molecular architecture of the centriole proteome: the conserved WD40 domain protein POC1 is required for centriole duplication and length control
Keller LC, Geimer S, Romijn E, Yates J 3rd, Zamora I, Marshall WF.
Mol Biol Cell. 2009 Feb;20(4):1150-66. Epub 2008 Dec 24.

Basal bodies platforms for building cilia
Marshall WF.
Curr Top Dev Biol. 2008;85:1-22. Review.

Modeling recursive RNA interference
Marshall WF.
PLoS Comput Biol. 2008 Sep 19;4(9):e1000183.

Building the cell: design principles of cellular architecture
Rafelski SM, Marshall WF.
Nat Rev Mol Cell Biol. 2008 Aug;9(8):593-602. Review.

Use of transcriptomic data to support organelle proteomic analysis
Marshall WF.
Methods Mol Biol. 2008;432:403-14.

Isolation and proteomic analysis of Chlamydomonas centrioles
Keller LC, Marshall WF.
Methods Mol Biol. 2008;432:289-300.

The cell biological basis of ciliary disease
Marshall WF.
J Cell Biol. 2008 Jan 14;180(1):17-21. Epub 2008 Jan 7. Review

Stability and robustness of an organelle number control system: modeling and measuring homeostatic regulation of centriole abundance
Marshall WF.
Biophysical Journal 2007. 93,1818-1833.

The mother centriole plays an instructive role in defining cell geometry
Feldman JL, Geimer S, Marshall WF.
PLoS Biology 2007. 5,e149.

Flagellar length control in chlamydomonas--paradigm for organelle size regulation
Wemmer KA, Marshall WF.
Int Rev Cytol. 2007;260:175-212. Review.

Proteomic analysis of isolated Chlamydomonas centrioles reveals orthologs of ciliary disease genes
Keller LC, Romijn EP, Zamora I, Yates JR, Marshall WF.
Curr. Biol. 2005. 15,1090-8.

De novo formation of left-right asymmetry by posterior tilt of nodal cilia
Nonaka S, Yoshiba S, Watanabe D, Ikeuchi S, Goto T, Marshall WF, Hamada H.
PloS Biology 2005. 3,e268.

 

A mutation in the centriole-associated protein centrin causes genomic instability via increased chromosome loss in Chlamydomonas reinhardtii
Zamora I, Marshall WF.
BMC Biol. 2005. 3,15.

Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes
Stolc V, Samanta MP, Tonprasit W, Marshall WF.
PNAS 2005. 102,3703-7.

Flagellar length control system: testing a simple model based on intraflagellar transport and turnover
Marshall WF, Qin H, Rodrigo Brenni M, Rosenbaum JL.
Mol. Biol. Cell 2005. 16,270-8.

Flagellar motility: all pull together
Wemmer KA, Marshall WF.
Curr Biol. 2004 Dec 14;14(23):R992-3. Review.

Human cilia proteome contains homolog of zebrafish polycystic kidney disease gene qilin
Marshall WF.
Curr. Biol. 2004. 14,R913-4.

PCR-based assay for mating type and diploidy in Chlamydomonas
Zamora I, Feldman JL, Marshall WF.
Biotechniques 2004. 37,534-6.

Cellular length control systems
Marshall WF.
Ann. Rev. Cell Dev. Biol. 2004. 20,677-93.