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.  Murrow LM, Weber RJ, Caruso J, McGinnis CS, Borowsky AD, Desai TA, Thomson M, Tlsty TD, Gartner ZJ.  2018.  Mapping the complex paracrine response to hormones in the human breast at single-cell resolution.  bioRxiv

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

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

38.  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.

39.  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

40.  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  

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

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

43.  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

44.  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.

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

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

47.  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

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

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

50.  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.

51.  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

52.  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

53.  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.

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

55.  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

56.  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

57. Douglas JV, Bianco S, Edlund S, Engelhardt T, Filter M, Guenther T, Hu K, Nixon EJ, Sevilla NL, Swaid A, Kaufman JH. 2019. STEM: An Open Source Tool for Disease Modeling. Health Security 17, 291-306.

58.   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,

59.  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

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

61. 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.

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

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

64.  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

65.  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

66.   Belardi B, Hamkins-Indik T, Harris AR, Fletcher DA.  2019.  A weak link with actin organizes tight junctions to control epithelial permeability.  preprint:  bioRxiv

67.  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

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

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

70.  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

71.  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

72.  Long AF, Suresh P, Dumont S.  2019.  Individual kinetochore-fibers locally dissipate force to maintain robust mammalian spindle structure.  Preprint: bioRxiv

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

74.  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

75.  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

76.  Murrow 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

77. 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

78.  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

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

80.  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

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

82.  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

83.  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.  Preprint:  bioRxiv

84.  Gong X, Mathijssen A, Bryant Z, Prakash M. 2021. Engineering reconfigurable flow patterns via surface-driven light-controlled active matter. Phys. Rev. Fluids 6, 123104 (Preprint 2020: arXiv 2004.01368) (Preprint 2020: arXiv 2004.01368)

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.

105.  Toda S, McKeithan WS, Hakkinen TJ, Lopez P, Klein OD, Lim WA.  2020.  Engineering synthetic morphogen systems that can program multicellular patterning.  Science  370, 327-331.

106.  Marshall WF.  2020.  Axopodia and the cellular “arms” race.  Cytoskeleton

107.  Armstrong M, Vahey MD, Hunt TP, Fletcher DA.  2020.  Forming and loading giant unilamellar vesicles with acoustic jetting.  Biomicrofluidics   14, 064105.

108.  Zhang KS, Blauch LR, Huang W, Marshall WF, Tang SKY.  2021.  Microfluidic guillotine reveals multiple timescales and mechanical modes of wound response in Stentor coeruleus. BMC Biol. 2021 Apr 2;19(1):63. doi: 10.1186/s12915-021-00970-0.
PMID: 33810789 (
preprint bioRxiv

109.  Belardi B, Son S, Felce JH, Dustin ML, Fletcher DA.  2020.  Cell-cell interfaces as specialized compartments directing cell function.  Nat. Rev. Mol. Cell Biol.  21, 750-764.

110.  Armon S, Bull MS, Moriel A, Aharoni H, Prakash M.  2021.  Modeling epithelial tissues as active-elastic sheets reproduce contraction pulses and predict rip resistance.  Comm. Physics  4, 216. (Preprint 2020: bioRxiv 2020.06.15.153163)

111.  Gómez-Schiavon M, Dods G, El-Samad H, Ng AH.  2020.  Multidimensional Characterization of Parts Enhances Modeling Accuracy in Genetic CircuitsACS Synth. Biol.2020, 9, 11, 2917–2926

112.  Gómez-Schiavon M and El-Samad H. 2020. CoRa – A general approach for quantifying biological feedback controlbioRxiv 2020.10.09.334078

113.  Harris AR, Jreij P. Belardi B, Joffe AM, Bausch AR, Fletcher DA.  2020.  Biased localization of actin binding proteins by actin filament conformation. Nat Commun11, 5973

114.  Li H, Krishnamurthy D, Li E, Vyas P, Akireddy Chai NC, Prakash M.  2020. Squid: Simplifying Quantitative Imaging Platform Development and Deployment.  bioRxiv  2020.12.28.42613

115. Li E, Larson A, Kothari A, Prakash M.  2020.  Handyfuge-LAMP: low-cost and electricity-free centrifugation for isothermal SARS-CoV-2 detection in saliva. medRxiv   2020.06.30.20143255

116. Zhang JQ, Chang KC, Liu L, Gartner ZJ, Abate AR.  2020.  High throughput yeast strain phenotyping with droplet based RNA sequencingJ. Vis. Exp.  Doi: 10.3791/61014

117. Diaz U, Marshall WFRiggs B. 2021. Drosophila Embryo Preparation and Microinjection for Live Cell Microscopy Performed using an Automated High Content AnalyzerJ. Vis. Exp. 167, e61589, doi:10.3791/61589

118. Beck LE, Lee J, Cote C, Dunagin MC, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Raj A.  2021.  Systematically quantifying morphological features reveals constraints on organoid phenotypes.  Preprint:  bioRxivdoi:

119. Zhang JQ, Siltanen CA, Dolatmoradi A, Sun C, Chang KC, Cole RH, Gartner ZJ, Abate AR.  2021.  High diversity droplet microfluidic libraries generated with a commercial liquid spotterSci. Rep.  11, 4351.

120. Zimmerman T, Park A, Bianco S.  2021.  Evaluating autofocusing metrics for plankton holographic microscope image reconstructionProc. SPIE 11710, 117100A

121. Capponi S, Wang SY, Navarro EJ, Bianco S.  .  2021.  AI-driven prediction of SARS-CoV-2 variant binding trend from atomistic simulations.  Eur. Phys. J. E 44 (10), 1-17. (Preprint 2021: bioRxiv

122.  Chan KMC, Arthur AL, Morstein J, Jin M, Bhat A, Schlesinger D, Son S, Stevens DA, Drubin DG, Fletcher DA.  2021.  Evolutionarily related small viral fusogens hijack distinct but modular actin nucleation pathways to drive cell-cell fusion.  PNAS 118, e2007526118

123.  Glaser M, Deb S, Seier F, Agrawal A, Liedl T, Douglas S, Gupta MK, Smith DM  2021. The Art of Designing DNA Nanostructures with CAD Software Molecules  26, 2287

124.  Hernandez-Lopez RA#, Yu W, Cabral KA, Creasey OA, Lopez Pazmino M, Tonai Y, De Guzman A, Makela A, Gartner ZJ, Lim WA.  2021.  T cell circuits that sense antigen density with an ultrasensitive threshold.  Science  371, 1166-1171

125.  Martyn I, Gartner ZJ.  2021.  Expanding the boundaries of synthetic development.  Dev. Biol. 474, 62-70.

126.  Neahring L, Cho NH, Dumont S.  2021. Opposing motors provide mechanical and functional robustness in the human spindle. Developmental Cell, 2021,

127.  Aranda ML, Diaz M, Mena LG, Ortiz JI, Rivera-Nolan C, Sanchez DC, Sanchez MJ, Upchurch AM, Williams CS, Boorstin SN, Cardoso LM, Dominguez M, Elias S, Lopez EE, Ramirez RE, Romero PJ, Tigress FN, Wilson JA, Winstead R, Cantley JT, Chen JC, Fuse M, Goldman MA, Govindan B, Ingmire P, Knight JD, Pasion SG, Pennings PS, Sehgal RNM, de Vera PT, Kelley L, Schinske JN, Riggs B, Burrus LW, Tanner KD. Student-Authored Scientist Spotlights: Investigating the Impacts of Engaging Undergraduates as Developers of Inclusive Curriculum through a Service-Learning Course.  CBE Life Sci Educ. 2021 Dec; 20(4):ar55. doi: 10.1187/cbe.21-03-0060. PMID: 34546103

128.  Galli LM, Anderson MO, Gabriel Fraley J, Sanchez L, Bueno R, Hernandez DN, Maddox EU, Lingappa VR, Burrus LW. Determination of the membrane topology of PORCN, an O-acyl transferase that modifies Wnt signalling proteins. Open Biol. 2021 Jun;11(6):200400. doi: 10.1098/rsob.200400. Epub 2021 Jun 30. PMID: 34186010

129.  Brunetti RM, Kockelkoren G, Raghavan P, Bell GRR, Britain D, Puri N, Collins SR, Leonetti MD, Stamou D, Weiner OD. 2021. WASP links substrate topology and cell polarity to guide neutrophil migration. J Cell Biol., 221:e202104046.

130.  Bull, Matthew S., and Manu Prakash. 2021.  Mobile defects born from an energy cascade shape the locomotive behavior of a headless animal.  arXiv preprint 2107.02940 

131.  Bull, Matthew S., Laurel A. Kroo, and Manu Prakash. 2021.  Excitable mechanics embodied in a walking cilium.  arXiv 2107.02930. 

132.  Bull, Matthew S., Vivek N. Prakash, and Manu Prakash. 2021.  Ciliary flocking and emergent instabilities enable collective agility in a non-neuromuscular animal.   arXiv  2107.02934.

133. Cabral KA, Patterson DM, Scheideler OJ, Cole R, Abate AR, Schaffer DV, Sohn LL, Gartner ZJ.  2021.  Simple, affordable, and mocular patterning of cells using DNA.  JoVE doi: 10.3791/61937

134.  Chang R, Prakash M.  2021.  Entangled architecture of rough endoplasmic reticulum (RER) and vacuoles enables topological damping in cytoplasm of an ultra-fast giant cell.  bioRxiv 10.1101/2021.12.13.472465v1

135.  Cordts SC, Castaño N, Koppaka S, Tang SKY.  2021.  Fabrication of a silicon μDicer for uniform microdissection of tissue samples.  Appl. Phys. Lett. 119, 011904

136.  Daniels KG, Wang S, Simic MS, Bhargava HK, Capponi S, Tonai Y, Yu W, Bianco S, Lim WA.  2022.  Exploring the rules of chimeric antigen receptor phenotypic output using combinatorial signaling motif libraries and machine learningbioRxiv  10.1101/2022.01.04.474985v2

137.  Doshi S, Banavar SP, Flaum E, Kulkarni S, Vaiydya U, Kumar S, Chen T, Bhattacharya A, Prakash M.  2021.  Applying heat and humidity using stove boiled water for decontamination of N95 respirators in low resource settingsPLoS One  doi: 10.1271/journal.pone.0255338

138. Ishikawa H, Tian JL, Yu JE, Marshall WF, Qin H. 2022. Biosynthesis of linear protein nanoarrays using the flagellar axoneme. ACS Synthetic Biology in press.

139. Kindberg AA, V Srivastava, JM Muncie, VM Weaver, ZJ Gartner, JO Bush. 2021. EPH/EPHRIN regulates cellular organization by actomyosin contractility effects on cell contacts.
Journal of Cell Biology 220, e202005216

140. Koppaka S, Zhang KS, Jalil MK, Blauch LR, Tang SKY, 2021. Fabrication of 3D Micro-Blades for the Cutting of Biological Structures in a Microfluidic Guillotine. Micromachines, 12(9), 1005, 2021.

141. Krishnamurthy D, Pepper R, Prakash M. 2021. Active Sinking Particles: Sessile Suspension Feeders significantly alter the Flow and Transport to Sinking Aggregates. bioRxiv 2021.08.05.455190

142. Kroo LA, Binagia JP, Eckman N, Prakash M, Shaqfe ESG. 2021. A Swimming Rheometer: Self-propulsion of a freely-suspended swimmer enabled by viscoelastic normal stresses. arXiv 2111.10515

143. Kumar S, Hol, FJH, Pujhari S, Ellington C, Narayanan HV, Li H, Rasgon JL, Prakash M. 2021. Vectorchip: Microfluidic platform for highly parallel bite by bite profiling of mosquito-borne pathogen transmission. Nature Commun. 12, 6018.

144. Kwak M, Kaden Southard, Woon Ryoung Kim, Annie Lin, Nam Hyeong Kim, Ramu Gopalappa, Minji An, Hyun Jung Lee, Seo Hyun Choi, Justin Farlow, Anastasios Georgakopoulos, Nikolaos Robakis, Min Kang, Matthew Kutys, Daeha Seo, Hyongbum Henry Kim, Yong Ho Kim, Jinwoo Cheon, Zev Gartner, Young-wook Jun. 2021. Membrane compartmentalization by adherens junctions creates a spatial switch for Notch signaling and function. Research Square (preprint)

145. Lewis GR, Marshall WF, Jones BA. 2021. Modeling the dynamics of within-host viral infection and evolution predicts quasispecies distributions and phase boundaries separating distinct classes of infections. bioRxiv 2021.12.16.473030; doi:

146. McGinn R. 2022. Startup Ethics: Ethically Responsible Conduct of Scientists and Engineers at Theranos Submitted

147. Molina, A., Kumar, S., Karpitschka, S., Prakash, M 2021. Droplet tilings for rapid exploration of spatially constrained many-body systems. PNAS 118, 34

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

149. Navarro EJ, Marshall WF, Fung JC. 2022. Modeling cell biological features of meiotic chromosome pairing. bioRxiv

150. Pastore VP, Oke A, Capponi S, Elnatan D, Fung JC, Bianco S. 2022. Phenotype to genotype mapping using supervised and unsupervised learning. bioRxiv 10.1101.2022.03.17.484826v1

151. Pipathsouk A, Brunetti RM, Town JP, Graziano BR, Breuer A, Pellett P, Marchuk K, Tran NHT, Krummel MF, Stamou D, Weiner OD (2021). The WAVE complex associates with sites of saddle membrane curvature. J. Cell Biol., 220: e202003086.

152. Rosas-Salvans M, Sutanto R, Suresh P, Dumont S. 2021. The Astrin-SKAP Complex Reduces Friction at the Kinetochore-Microtubule Interface. bioRxiv doi: 10.1101/

153. Singh S, Chu D, Roy S. 2022. Nematode histone H2A variant evolution reveals diverse histories of retention and loss, and evidence for conserved core-like variants. bioRxiv doi: 10.1101/2022.03.02.482035

154. Su-Feher L, Rubin A, Silberberg SN, Catta-Preta R, Lim KJ, Zdilar I, McGinnis CS, McKinsey GL, Rubino TE, Hawrylycz M, Thompson C, Gartner ZJ, Puelles L, Zeng H, Rubenstein JLR. 2021. Single Cell Enhancer Activity Maps Neuronal Lineages in Embryonic Mouse Basal Ganglia. bioRxiv

155. Suter, E. C., Schmid, E. M., Harris, A. R., Voets, E., Francica, B., & Fletcher, D. A. (2021). Antibody:CD47 ratio regulates macrophage phagocytosis through competitive receptor phosphorylation. Cell Reports, 36(8), 109587.

156. Wang S, Bianco S. 2021. AI-assisted biology: predict the conditional probability distributions from noisy measurements. bioRxiv

157. Zhang KS, Nadkarni AV, Paul R, Martin AM, Tang SKY, 2022. Microfluidic Surgery in Single Cells and Multicellular Systems. Chemical Reviews, doi: 10.1021/acs.chemrev.1c00616

158. Zimmerman T, Doung JKB, Dean Z, Bianco S, Esquerra RM. 2022. Evaluating Automated Reconstruction Methods for Digital Inline Holographic Images of Plankton. Proc. SPIE 12026, 1202603 doi: 10.1117/12.2607383

159. Shangying Wang, Sara Capponi, Simone Bianco, 2022. Inferring Conditional Probability Distributions of Noisy Gene Expression from Limited Observations by Deep Learning. GEN Biotechnology, 1 (6) (2022)

160. Kyle G. Daniels, Shangying Wang, Milos S. Simic, Hersh K. Bhargava, Sara Capponi, Yurie Tonai, Wei Yu, Simone Bianco, Wendell A. Lim, 2002. Decoding CAR T cell phenotype using combinatorial signaling motif libraries and machine learning, Science, 378, 1194-1200 (2022)