Center Publications

Peer Reviewed Publications supported by Center for Cellular Construction 

bold indicates center faculty

1. Murrow LM, Weber RJ, Gartner ZJ. 2017. Dissecting the stem cell niche with organoid models: an engineering-based approach. Development 144, 998-1007.

2. Tang SKY, Marshall WF. 2017. Self-repairing cells: how single cells heal membrane ruptures and restore lost structures. Science. 2017 356, 1022-1025.

3. Blauch LR, Gai Y, Khor JW, Sood P, Marshall WF, Tang SKY. 2017. Microfluidic guillotine for single-cell wound repair studies. Proc Natl Acad Sci U S A. 114, 7283-88.

4. Eritano AS, Altamirano A, Beyeler S, Gaytan N, Velasquez M, Riggs B. 2017 The endoplasmic reticulum is partitioned asymmetrically during mitosis prior to cell fate selection in proneuronal cells in the early Drosophila embryo. Mol. Biol. Cell. 28, 1530-38.

5. Chang AY, Marshall WF. 2017. Organelles – understanding noise and heterogeneity in cell biology at an intermediate scale. J. Cell Sci. 130, 819-826.

6. Munoz NR, Black CJ, Young ET, Chu, DS. 2017. New alleles of C. elegans gene cls-2 (R107.6), called xc3, xc4, and xc5. Micropublication: biology. Dataset.

7. Fung, JC 2017. Kinetochores: Importance of Being Fashionably Late. Cell Systems 4:585-586

8. Hueschen CL, Kenny SJ, Xu K, Dumont S. 2017. NuMA recruits dynein activity to microtubule minus-ends at mitosis. eLife, 6:e29328

9. Zhang ZB, Wang QY, Ke YX, Liu SY, Ju JQ, Lim WA, Tang C, Wei P. 2017. Design of Tunable Oscillatory Dynamics in a Synthetic NF-κB Signaling Circuit. Cell Systems. pii: S2405-4712(17)30437-4.

10. Hughes AJ, Miyazaki H, Coyle MC, Zhang J, Laurie MT, Chu D, Vavrusova Z, Schneider RA, Klein OD, Gartner ZJ. 2018. Engineered tissue folding by mechanical compaction of the mesenchyme. Dev. Cell. 44, 165-178.

11. Kimmel JC, Chang AY, Brack AS, Marshall WF. 2018. Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance. PLoS Computational Biology 2018 14(1): e1005927.

12. Tang Z, Hu Y, Wang Z, Jiang K, Zhan C, Marshall WF, Tang N. 2018. Mechanical forces program the orientation of cell division during airway tube morphogenesis. Dev. Cell  44, 313-325.

13. Liang SI, van Lengerich B, Eichel K, Cha M, Patterson DM, Yoon TY, von Zastrow M, Jura N, Gartner ZJ. 2018 Phosphorylated EGFR Dimers Are Not Sufficient to Activate Ras. Cell Rep. 22, 2593-2600

14. Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ. 2018. Opportunities for organoids as new models of aging. J Cell Biol. 217, 39-50

15. King D, Ma J, Armendariz A, Yu K. 2018. Developing interactive exhibits with Scientists: Three example collaborations from the Life Sciences collection at the Exploratorium. Integr. Comp. Biol. 58, 94-102.  

16. Munoz, NR; Byrd, DT; Chu, D 2018. New allele of C. elegans gene spch-3 (T27A3.4), called xc2. Micropublication: biology. Dataset.

17. Galli LM, Santana F, Apollon C, Szabo LA, Ngo K, Burrus LW. 2018. Direct visualization of the Wntless-induced redistribution of WNT1 in developing chick embryos. Dev Biol. 439, 53-64

18. Chu DS 2018. Zinc: A small molecule with a big impact on sperm function. PLoS Biol 16, e2006204.

19. Vergara HM, Ramirez J, Rosing T, Nave C, Blandino R, Saw D, Saraf P, Piexoto G, Coombes C, Adams M, Domingo CR. 2018. miR-206 is required for changes in cell adhesion that drive muscle morphogenesis in Xenopus laevis. Dev. Biol. 438, 94-110.

20. Owens MT, Trujillo G, Seidel SB, Harrison CD, Farrar KM, Benton HP, Blair JR, Boyer KE, Breckler JL, Burrus LW, Byrd DT, Caporale N, Carpenter EJ, Chan YM, Chen JC, Chen L, Chen LH, Chu DS, Cochlan WP, Crook RJ, Crow KD, de la Torre JR, Denetclaw WF, Dowdy LM, Franklin D, Fuse M, Goldman MA, Govindan B, Green M, Harris HE, He ZH, Ingalls SB, Ingmire P, Johnson ARB, Knight JD, LeBuhn G, Light TL, Low C, Lund L, Márquez-Magaña LM, Miller-Sims VC, Moffatt CA, Murdock H, Nusse GL, Parker VT, Pasion SG, Patterson R, Pennings PS, Ramirez JC, Ramirez RM, Riggs B, Rohlfs RV, Romeo JM, Rothman BS, Roy SW, Russo-Tait T, Sehgal RNM, Simonin KA, Spicer GS, Stillman JH, Swei A, Tempe LC, Vredenburg VT, Weinstein SL, Zink AG, Kelley LA, Domingo CR, Tanner KD. 2018. Collectively Improving Our Teaching: Attempting Biology Department-wide Professional Development in Scientific Teaching. CBE Life Sci Educ. 17(1). pii: ar2.

21. Hughes AJ, Mornin JD, Biswas SK, Bauer DP, Bianco S, Gartner ZJ. 2018. A tool for rapid, flexible, crowd-based annotation of images.  Nature Methods 15, 587-590. 

22. Arter M, Hurtado-Nieves V, Oke A, Zhuge T, Wettstein R, Fung JC, Blanco MG and Matos J. 2018. Regulated crossing-over requires inactivation of Yen1/GEN1 resolvase during meiotic prophase I. Developmental Cell, 45, 785-800

23. Elting MW, Suresh P, Dumont S. 2018. The spindle: Integrating architecture and mechanics from molecular- to cellular-scales. Trends in Cell Biology 28, 896-910.   

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

25. Toda S, Blauch LR, Tang SKY, Morsut L, Lim WA. 2018. Synthetic morphologies: Programming self-organizing multicellular structures using engineered cell-cell signaling cascades. Science 361, 156-162. 

26. Chen E, Esquerra RM, Melendez PA, Chandrasekaran SS, Kliger DS. 2018. Microviscosity in E. coli cells from time-resolved linear dichroism measurements . J Phys Chem B. doi: 122, 11381-11389

27.  Gruber TD, Krishnamurthy C, Grimm JB,Tadross MR, Wysocki LM, Gartner ZJ, Lavis LD.  2018.  Cell-Specific Chemical Delivery Using a Selective Nitroreductase-Nitroaryl Pair.  ACS Chem Biol.  13, 2888-2896

28. Marshall WF. 2018. A dilution model for embryonic scaling. Dev. Cell. 46, 529-530.29.

29.  Yoon I, Kulkarni A, Okada K, Pennings P, Domingo C. 2018. Promoting Inclusivity in Computing (PINC) via Computing Application Minor. American Society for Engineering Education. ASEE 2018 CoNECD - The Collaborative Network for Engineering and Computing Diversity Conference, Crystal City, Virginia

30. Tang SKY, Marshall WF. 2018. Primer: Cell Learning. Curr. Biol. 28,:R1180-R1184.

31.  Gingold C, Douglas SM.  2018.  Gelbox - An Interactive Simulation Tool for Gel Electrophoresis.  bioRxiv

32. Allard CAH, Decker F, Weiner OD, Toettcher JE, Graziano BR. 2018. A size-invariant bud-length timer enables robustness in yeast cell size control. PLoS One 13, e0209301

33.  Rath KA, Peterfreund A, Bayliss F. 2018. Programmatic Mentoring: Providing Mentoring as a Community, Going Beyond Mentor/Protégé Pairs. Understanding Interventions 9, 2

34. Chowdhury A, Biswas S, Bianco S. 2018. Active deep learning reduces the annotation burden in automatic cell segmentation. bioRxiv,

35.  Riggs B.  2018.  Mutually Beneficial Research Partnerships for Equity and Innovation in Science.  ASCB Newsletter Dec 2018 issue. p 35-38.

36.  Liu F, Blauch LR, Tang SKY. 2018. Quantifying Phenotypes in Single Cells using Droplet Microfluidics. Meth. Cell Biol. 148,133-159. 

37.  Hueschen CL, Galstyan V, Amouzgar M, Phillips R, Dumont S.  2019.  Microtubule End-Clustering Maintains a Steady-State Spindle Shape.  Curr. Biol.  29, 700-708.

38.  Graziano BR, Town JP, Nagy TL, Fosnaric M, Penic C, Iglic A, Kralj-Iglic V, Gov N, DIaz-Munoz A, Weiner OD. 2019. Cell confinement reveals a branched-actin independent circuit for neutrophil polarity. PLoS Biology

39.  Biswas SK, Zimmerman T, Maini l, Adebiyi A, Bozano l, Brown C, Pastore VP, BIanco S.  2019.  High throughput analysis of plankton morphology and dynamicsProc. SPIE 1088109  

40.  Pastore VP, Zimmerman T, Biswas SK, Bianco S.   2019.  Establishing the baseline for using plankton as biosensor.  Proc. SPIE 108810H   

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

42.  Zimmerman T, Antipa N, Elnatan D, Murru A, Biswas S, Pastore V, Bonani M, Waller L, Fung J, Fennu G, Bianco S.  2019.  Stereo In-Line Holographic Digital Microscope.  Proc. SPIE 1088315 

43.  Eroy-Reveles AA, Hsu E, Rath KA, Peterfreund AR, Bayliss F.  2019.  History and Evolution of STEM Supplemental Instruction at San Francisco State University, a Large, Urban, Minority-Serving Institution.  In “Diversity in Higher Education” series, Emerald Publishing, Chapter 10.ISBN: 9781787569089.

44. Toda S, Brunger JM, Lim WA. 2019. Synthetic development: learning to program multicellular self-organization.  Curr. Opin. Systems Biol.  14, 41-49.  

45.  Tischer D, Weiner OD. 2019. Light-based tuning of ligand half-life supports kinetic proofreading model of T cell activation. Elife 8, e42498.

46.  Marshall WF, Fung JC. 2019. Modeling meiotic chromosome pairing: increased fidelity from a tug of war between telomere forces and a pairing-based Brownian ratchet. Phys. Biol. doi: 10.1088/1478-3975/ab15a7

47.  Mathijssen A, Culver J, Bhamla MS, Prakash M. 2019. Collective intercellular communication through ultra-fast hydrodynamic trigger waves. Nature 571, 560-564.

48.  Mclaurin J, Weiner OD. 2019. Multiple sources of signal amplification within the B cell Ras/MAPK pathway. Mol Biol Cell. 30, 1610-1620. 

49.  McGinnis CS, Murrow LM, Gartner ZJ. 2019. DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Systems 8,P329-337.  

50.  Castillo U, Gnazzo MM, Semaya E, Lam Y, Riggs B, Hall DH, Gelfand VI,and Skop AR. 2019. Conserved role for Ataxin-2 in mediating ER dynamics in embryos and neurons. Traffic. 20, 436-447

51.  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  

52.  Long AF, Kuhn J, Dumont S.  2019.  The mammalian kinetochore-microtubule interface:  robust mechanics and computation with many microtubules.   Curr. Opin. Cell Biol.  60, 60-67.

53.  Toda S, Frankel NW, Lim WA.  2019.   Engineering cell-cell communication networks:  programming multicellular behaviors.   Curr. Opin. Chem. Biol  52, 31-38..  

54.  McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. 2019. MULTI-seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nature Methods 16, 6190-626

55.  Kuhn JA, Dumont S. 2019. Mammalian kinetochores count attached microtubules in a sensitive and switch-like manner to control cell cycle progression. J. Cell Biol. DOI: 10.1083/jcb.201902105

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

57.  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

58.  Pastore VP, Zimmerman TG, Biswas SK, Bianco S. 2019. Annotation-free learning of plankton for classification and anomaly detection.  Submitted.  Preprint: bioRxiv

59. Coyle SM, Flaum E, Li H, Krishnamurthy D, Prakash M. 2019. Coupled active systems encode an emergent hunting behavior in the unicellular predator Lacrymaria olor. Currl Biol. 29, 3838-3850.

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

61.  Murrow LM, Gartner ZJ.  2019.  Balancing Act: Cell Polarity and Shape Compete to Ensure Robust Development.  Dev. Cell.  51, P545-547

62.  Prakash VM, Bull MS, Prakash M.  2019.  Motility induced fracture reveals a ductile to brittle crossover in the epithelial tissues of a simple animal.  preprint:  bioRxiv

63.  Li H, Soto-Montoya H, Voisin M, Fuentes Valenzuela L, Prakash M.  2019.  Octopi: Open configurable high-throughput imaging platform for infectious disease diagnosis in the field.   preprint:  bioRxiv

64.  Chan KMC,  Son S, Schmid EM, Fletcher DA.  2019.  A viral fusogen hijacks the actin cytoskeleton to drive cell-cell fusion.  preprint:  bioRxiv

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

66.  Pipathsouk A, Brunetti RM, Town JP, Breuer A, Pellett PA, Marchuk K,Tran NT, Krummel MF, Stamou D, Weiner OD.  2019.  WAVE complex self-organization templates lamellipodial formation.  preprint:  bioRxiv

67.  Wallach TE, Srivastava V, Reyes E, Klein OD, Gartner ZJ. 2019. Lactoferrin Reverses Methotrexate Driven Epithelial Barrier Defect by Inhibiting TGF-β Mediated Epithelial to Mesenchymal Transition. preprint: bioRxiv

68.  Long AF, Suresh P, Dumont S.  2019.  Individual kinetochore-fibers locally dissipate force to maintain robust mammalian spindle structure.  J. Cell Biol.  219 (8): e201911090

69.  Suresh P, Long AF, Dumont S.  2019.  Microneedle manipulation of the mammalian spindle reveals specialized, short-lived reinforcement near chromosomes.  eLife 2020;9:e53807

70.  Zhang JQ, Siltanen CA, Liu L, Chang KC, Gartner ZJ, Abate AR. 2019. Linked optical and gene expression profiling of single cells at high throughput. Genome Biology 21, 49

71.  McGinnis CS, Siegel DA, Xie G, Stone M, Gartner ZJ, Roan NR, Lee SA.  2020.  No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells.  preprint:  bioRxiv 

72.  Murow LM, Weber RJ, Caruso J, McGinnis CS, Gascard P, Borowsky AD, Desai TA, Thomson M, Tlsty T, Gartner ZJ.  2020.  Pregnancy and obesity modify the epithelial composition and hormone signaling state of the human breast.  Preprint:  bioRxiv

73. Kimmel JC, Hwang A, Scaramozza A, Marshall WF, Brack A. 2020. Aging induces aberrant state transition kinetics in murine muscle stem cells. Development. doi:10.1242/dev.183855

74.  Rohrberg J, Van de Mark D, Amouzgar M, Lee JV, Taileb M, Corella A, Kilinc S, Williams J, Jokisch ML, Camarda R, Balakrishnan S, Shankar R, Zhou A, Chang AN, Chen B, Rugo HS, Dumont S, Goga A.  2020.  MYC dysregulates mitosis, revealing cancer vulnerabilities.  Cell Rep. 30, 3368-3382.e7

75.  Gilpin W, Bull MS, Prakash M.  2020.  The multiscale physics of of cilia and flagella.  Nature Rev. Physics  2, 74–88. doi:10.1038/s42254-019-0129-0

76.  Fabig G, Kiewisz R, Lindow N, Powers JA, Cota V, Quintanilla LJ, Brugues J, Prohaska S, Chu D, Mueller-Reichert T. 2020. Male meiotic spindle features that efficiently segregate paired and lagging chromosomes. eLife 2020;9:e50988

77.  Bianco S, Chan YH, Marshall WF. 2020. Towards computer aided design of cellular structure. Phys. Biol.  17, 023001

78.  Jain N, Blauch LR, Szymanski MR, Das R, Tang SKY, Yin YW, Fire AZ.  2020.  Transcription polymerase–catalyzed emergence of novel RNA replicons.  Science  eaay0688
DOI: 10.1126/science.aay0688

79. Ramirez-San Juan GR, Mathijssen AJTM, He M, Jan L, Marshall WF, Prakash M. 2020. Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays. Nature Physics

80. Zhang JQ, Chang KC, Liu L, Gartner ZJ, Abate AR. 2020. High throughput yeast strain phenotyping with with droplet-based RNA sequencing. J. Vis. Exp. 159, e61014, doi:10.3791/61014

81.  Grewal PS, Samson JA, Baker JJ, Choi B, Dueber JE.  2020.  Repurposing the yeast peroxisome to compartmentalize a toxic enzyme enables improved (S)-reticuline production. Submitted.   Preprint:  bioRxiv

82.  Diaz U, Marshall WF, Riggs B.  2020.  Quantitative live cell microscopy of Drosophila embryonic development using automated high-content imaging.  Submitted.

83.  Gong X, Mathijssen A, Bryant Z, Prakash M.  2020.  Engineering configurable flow patterns via surface-driven light-controlled active matter.  Submitted.  Preprint:  arXiv 2004.01368

84.  Pollina T, Larson AG, Lombard F, Li H, Colin S, de Vargas C, Prakash M.  2020.  PlanktonScope: Affordable modular imaging platform for citizen oceanography.  Preprint:  bioRxiv

85.  Zimmerman T, Pastore VP, Bisawas S, Bianco S. 2020. Embedded System to Detect, Track and Classify Plankton Using a Lensless Video Microscope. Preprint: arXiv 2005.13064v1

86.  Molina A, Vyas P, Khlystov N, Kumar S, Kothari A, Deriso D, Liu Z, Banavar S, Flaum E, Prakash M.  2020.  Project 1000 x 1000: Centrifugal melt spinning for distributed manufacturing of N95 filtering facepiece respirators.  Preprint:  arXiv arXiv:2004.13494

87.  Serra-Marques A, Houtekamer R, Hintzen D, Canty JT, Yildiz A, Dumont S.  2020.  The mitotic protein NuMA plays a spindle-independent role in nuclear formation and mechanics.  Preprint:  bioRxiv

88.  Srivastava V, Huycke TR, Phong KT, Gartner ZJ.  2020.  Organoid models for mammary gland dynamics and breast cancer.  Curr. Opin. Cell Biol.  66, 51-58.

89.  Bonny AR, Foneca JP, Park JE, El-Samad H.  2020.  TuNR: Orthogonal Control of Mean and Variability of Endogenous Genes in a Human Cell Line.  Preprint: bioRxiv

90.  Kwak M, Southard KM, Kim NH, Gopalappa R, Kim WR, An M, Lee HJ, Farlow J, Georgakoplous A, Robakis NK, Seo D, Kim HB, Kim YH, Cheon J, Gartner ZJ, Jun Y.  2020.  Size-dependent protein segregation creates a spatial switch for Notch and APP signaling.  preprint:  bioRxiv doi:   

91.  Dods G, Gomez-Schiavon M, El-Samad H, Ng AH.  2020.  Accurate prediction of genetic circuit behavior requires multidimensional characterization of parts.  Preprint:  bioRxiv

92.  Marshall WF.  2020.  Scaling of subcellular structures. Ann. Rev. Cell Dev. Biol.

93.  Riggs B.  2020.  Misinformation in the age of COVID-19: What are our responsibilities as scientists?  ASCB Newsletter July 2020 Issue

94.  Ferguson P, Zimmerman T, Bianco S.  2020.  High throughput device for screening chemical sensitivity of plankton samples.  Science Matters  DOI pending

95.  Chadwick W, Biswas S, Bianco S, Chan YHM.  2020.   Non-random distribution of vacuoles in Schizosaccharomyces pombe.  Phys. Biol.  DOI

96.  Pastore VP, Zimmerman T, Biswas SK, Bianco S.  2020.  Monitoring Water Quality Using Plankton as Biosensor.  J. Interdisciplinary Res. Appl. Med.  4, 15-20.

97.  Zimmerman T, Barrera-Velasquez A, Cisneros R, Martin A, Ruiz D, Samperio E, Sanchez A, Antipa N, Elnatan D, Waller L, Phillips M, Esquerra RM, Chan YHM.  2020.  Direct in-line Holographic Video Microscope.  Am. J. Physics.  submitted

98.  Krishnamurthy D, Li H, du Rey FB, Cambournac P, Larson AG, Li E, Prakash M.  2020.  Scale-free vertical tracking microscopy.  Nature  Methods

99.  Shah DH, Biswas SK, Martin AM, Bianco S, Denetclaw WF.  2020.  Endoderm Nitric Oxide Signals to Regulate Nascent Development of Cardiac Progenitors in Chicken Embryos.  Preprint:  bioRxiv

100. Belardi B, Hamkins-Indik T, Harris AR, Fletcher DA. 2020. A weak link with actin organizes tight junctions to control epithelial permeability. Dev. Cell

101.  Molina A, Kumar S, Karpitschka S, Prakash M.  2020.  Evaporative self-assembly of motile droplets.   Preprint:  arXiv  arXiv:2009.05649v1

102.  Tischer D, Weiner OD.  2020.  Optogenetic tuning of protein-protein binding in bilayers using LOVTRAP.  bio-protocol  10(17): e3745

103.  Bauer D, Ishikawa H, Wemmer KA, Marshall WF.  2020.  Biological noise in an organelle size control system.  Preprint:  bioRxiv

104.  Grewal PS, Samson JA, Baker JJ, Choi B, Dueber JE.  2020.  Peroxisome compartmentalization of a toxic enzyme improves alkaloid production.  Nature Chem. Biol.