Publications supported by Center for Cellular Construction 

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 dynamics. Proc. 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  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)
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 Circuits.  ACS Synth. Biol.2020, 9, 11, 2917–2926
112 Gómez-Schiavon M and El-Samad H. 2020. CoRa – A general approach for quantifying biological feedback control.  bioRxiv 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 sequencing.  J. Vis. Exp.  Doi: 10.3791/61014
117 Diaz U, Marshall WF, Riggs B. 2021. Drosophila Embryo Preparation and Microinjection for Live Cell Microscopy Performed using an Automated High Content Analyzer. J. Vis. Exp. 167, e61589, doi:10.3791/61589
118 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 spotter.  Sci. Rep.  11, 4351.
119 Zimmerman T, Park A, Bianco S.  2021.  Evaluating autofocusing metrics for plankton holographic microscope image reconstruction.  Proc. SPIE 11710, 117100A
120 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
121 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
122 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
123 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
124 Martyn I, Gartner ZJ.  2021.  Expanding the boundaries of synthetic development.  Dev. Biol. 474, 62-70.
125 Neahring L, Cho NH, Dumont S.  2021. Opposing motors provide mechanical and functional robustness in the human spindle. Developmental Cell, 2021,
126 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
127 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
128 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.
129 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  
130 Bull, Matthew S., Laurel A. Kroo, and Manu Prakash. 2021.  Excitable mechanics embodied in a walking cilium.  arXiv 2107.02930.  
131 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. 
132 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
133 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
134 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
135 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 settings.  PLoS One  doi: 10.1271/journal.pone.0255338
136 Ishikawa H, Tian JL, Yu JE, Marshall WF, Qin H. 2022. Biosynthesis of linear protein nanoarrays using the flagellar axoneme. ACS  Synthetic Biol. 11, 1454-1465
137 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
138 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.
139 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
140 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
141 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.
142 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:
143 McGinn R. 2022. Startup Ethics: Ethically Responsible Conduct of Scientists and Engineers at Theranos. Sci Eng Ethics 28, 39
144 Molina, A., Kumar, S., Karpitschka, S., Prakash, M 2021. Droplet tilings for rapid exploration of spatially constrained many-body systems. PNAS 118, 34
145 Molina A, Kumar S, Karpitschka S, Prakash M. 2020. Evaporative self-assembly of motile droplets. Preprint: arXiv arXiv:2009.05649v1
146 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
147 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.
148 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
149 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
150 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.
151 Wang S, Bianco S. 2021. AI-assisted biology: predict the conditional probability distributions from noisy measurements. bioRxiv
152  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
153 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
154 Shangying Wang, Sara Capponi, Simone Bianco, 2022. Inferring Conditional Probability Distributions of Noisy Gene Expression from Limited Observations by Deep Learning. GEN Biotechnology 1, 504-513. 
155 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) (Preprint: 2022 bioRxiv )
156 Ascencio GA. de Cruz JA, Alvarado S, Arriaga Y, Conrad E, Castro A, Eichelberger K, Galvan L, Gundy G, Inojoza Garcia JA, Jimenez A#, Lu NT, Lugar C, Marania R, Mendsaikhan T, Ortega J, Nand N, Rodrigues NS, Shabazz K, Tam C, Valenciano E, Hayzelden C, Eritano, AS, Riggs B. 2023.   A deficiency screen of the 3rd chromosome for dominant modifiers of the Drosophila ER integral membrane protein, Jagunal. G3 Genes|Genomes|Genetics, jkad059,
157 Bayliss F, Gartner Z, Marshall W, Rath K, Peterfreund A.  2022. Training of a diverse science workforce in a university-industry-government research partnership: center for cellular construction.   ICERI2022 Proceedings, pp. 1099-1109. 
158 Beck LE, Lee J, Coté C, Dunagin MC, Lukonin I, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Liberali P, Raj A.  2022.  Systematically quantifying morphological features reveals constraints on organoid phenotypes.  Cell Systems 13, 547-560. (Preprint: 2021 bioRxiv)
159 Bianco S, Capponi S, Wang S.  2022. AI-Driven Design of Disease Sensors: Theoretical Foundations. Artificial Intelligence Applications In Human Pathology, 287.
160 Britain D, Town JP, Weiner OD. 2022. Progressive enhancement of kinetic proofreading in T cell antigen discrimination from receptor activation to DAG generation.  eLife, 11: e75263. DOI: 10.7554/eLife.75263
161 Cabral KA, Srivastava V, Graham AJ, Coyle MC, Stashko C, Weaver V, Gartner ZJ.  2023.   Programming the Self-Organization of Endothelial Cells into Perfusable Microvasculature.  Tissue Engineering Part A  29,
162 Chang KC, Rhodes CT, Zhang JQ, Moseley MC, Cardona SM, Huang SWA, Rawls A, Lemmon VP, Berger MS, Abate AR, Lin CHA.  2022.  The chromatin repressors EZH2 and Suv4-20h coregulate cell fate specification during hippocampal development. FEBS Letters 596, 294-308
163 De Belly H, Yan S, Borja da Rocha H, Ichbiah S, Town JP, Turlier H, Bustamante C, Weiner OD. 2023. Actin-driven protrusions generate rapid long-range membrane
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164 Denetclaw WF, Otto ZK, Christie S, Allen E, Cruz M#, Potter KA, Mehta KM.  2022.  Diné Navajo Resilience to the COVID-19 pandemic.  PLoS One. 17, e0272089. doi: 10.1371/journal.pone.0272089
165 Krishnamurthy D , Pepper R, Prakash M.  2023.  Active sinking particles: sessile suspension feeders significantly alter the flow and transport to sinking aggregates.   J. Royal Soc Interface
166 Krishnamurthy D,  Prakash M.  2022.  Emergent Programmable Behavior and Chaos in Dynamically Driven Active Filaments.   bioRxiv   doi:
167 Kwak M, Southard K, Kim WR, Lin A, Kim NH, Gopalappa R, An M, Lee HJ, Choi SH, Farlow J, Georgakopoulos A, Robakis N, Kang M, Kutys M, Seo D, Kim H, Kim YH, Cheon J, Gartner Z, Jun Y-W.  2022.  Membrane compartmentalization by adherens junctions creates a spatial switch for Notch signaling and function. Nature Cell Biol. 24, 1739–1753 (Preprint: 2021 Research Square)
168 Lee J, Brien HJ, Walton BL, Eidman ZM, Toda S, Lim WA, Burnger JM.  2023.  Instructional materials that control cellular activity through synthetic Notch receptors.  Biomaterials  297, 122099
169 Lourenço AL, Chuo SW, Bohn MF, Hann B, Khan S, Yevalekar N, Patel N, Yang T, Xu L, Lv D, Drakas R, Lively S, Craik CS.  2023.   High-throughput optofluidic screening of single B cells identifies novel cross-reactive antibodies as inhibitors of uPAR with antibody-dependent effector functions. MAbs. 15, 2184197
170 McGinn RE.  2023.  Ethically Responsible and Irresponsible Practices of Scientists and Engineers in Research and Innovation: A Synoptic Matrix.   Submitted to Science and Engineering Ethics
171 Meyer K, Lammers NC, Bugaj LJ, Garcia HH, Weiner OD. 2023. Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation. bioRxiv
172 Murrow LM, Weber RJ, Caruso JA, McGinnis CS, Phong K, Gascard P, Rabadam G, Borowsky AD, Desai TA, Thomson M, Tlsty T, Gartner ZJ. 2022. Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution. Cell Syst. 13, 644-664.e8.
173 Navarro EJ, Marshall WF, Fung JC.  2022.  Modeling cell biological features of meiotic chromosome pairing to study interlock resolution.  PLoS Computational Biol.  8, e1010252 (Preprint: 2022 bioRxiv)
174 Pastore VP, Megiddo N, Bianco S. 2022. An Anomaly Detection Approach for Plankton Species Discovery. In: Sclaroff, S., Distante, C., Leo, M., Farinella, G.M., Tombari, F. (eds) Image Analysis and Processing ICIAP 2022. Lecture Notes in Computer Science
175 Pastore VP, Alfano PD, Oke A, Capponi S, Woodruff-Madeira X, Nguyen A, Fung JC, Bianco S. 2023.  An unsupervised learning approach to resolve phenotype to genotype mapping in budding yeast vacuoles. ICIAP23 submitted.
176 Paul R, Zhang KS, Kurosu Jalil M, Castano N, Kim S, Tang SKY.  2022. Hydrodynamic dissection of Stentor coeruleus in a microfluidic cross junction.  Lab Chip  22, 3508-3520,
177 Rajan D, Makushok T, Kalish A, Acuna L, Bonville A, Correa Almanza K, Garibay B, Tang E, Voss M, Lin A, Barlow K, Harrigan P, Slabodnick MM, Marshall WF.  2022.  Single-cell analysis of habituation in Stentor coeruleus.  Curr. Biol.  S0960-9822, 01766-
178 Reyes RJ, Pham O, Fergusson R, Ceberio N,  Clark C, Cohen S, Fuse M, Pennings P.  2022.  SCIP: a self-paced summer coding program creates community and increases coding confidence.  bioRxiv doi:
179 Richter M, Neahring L, Tao J, Sutanto R, Cho NH, Dumont S. 2022.  Kinetochore-fiber lengths are maintained locally but coordinated globally by poles in the mammalian spindle.  bioRxiv
180 Rosas-Salvans M, Sutanto R, Suresh P, Dumont S. 2022. The Astrin-SKAP Complex Reduces Friction at the Kinetochore-Microtubule Interface. Current Biology 32, 1-11. (Preprint: 2021 bioRxiv)
181 Saha S, Town JP, Weiner OD.  2023. Mechanosensitive mTORC2 independently coordinates leading and trailing edge polarity programs during neutrophil migration, Mol Biol Cell  mbcE22050191. doi: 10.1091/mbc.E22-05-0191. 
182 Stevens AJ, Harris AR, Gerdts J, Kim KH, Trentesaux C, Ramirez JT, McKeithan WL, Fattahi F, Klein OD, Fletcher DA, Lim WA. 2023.  Programming multicellular assembly with synthetic cell adhesion molecules. Nature  614, 144-152. doi: 10.1038/s41586-022-05622-z
183 Suresh P, Galstayn V, Phillips R, Dumont S. 2022. Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle. eLife 11, e79558
184 Takatori SC, Son S, Lee D, Fletcher DA. 2022. Engineered molecular sensors of cell surface crowding. bioRxiv  doi: 
185 Town JP, Weiner OD. 2023. Rac negative feedback links local PIP3 rate-of-change to dynamic control of neutrophil guidance.  bioRxiv
186 Aksel T, Navarro EJ, Fong N, Douglas SM. 2024.  Design principles for accurate folding of DNA origami.  bioRxiv
187 J. Baker, J. Shi, S. Wang, S. Bianco, S. Capponi, J. Dueber.  2024.  Enhanced peroxisome capacity guided by machine learning enables compartmentalization of a multi-enzyme metabolic pathway. Nature Chemical Biology under review
188 S. Basu, J. Born, A. Bose, S. Capponi, et al.  2023.  Towards quantum-enabled cell-centric therapeutics.    arXiv
189 Capponi S., Daniels KG.  2023.  Harnessing the Power of Artificial Intelligence to Advance Cell Therapy.   Immunological Reviews   doi/full/10.1111/imr.13236
190 Capponi S, Wang S. 2024.  AI in Cellular Engineering and Reprogramming.   Biophys J.
191 R Chajwa, E Flaum, KD Bidle, B Van Mooy, M Prakash.  2023.  Hidden Comet-Tails of Marine Snow Impede Ocean-based Carbon Sequestration.   arXiv preprint arXiv:2310.01982.
192 Mark Chan, Michelle Phillips, Katherine Nielsen, Diana Chu. 2024.  Building interdisciplinary skills and mentorship opportunities in a two-week research experience.  The Biophysicist  in press.
193 Chang R, Davydov A, Jaroenlak P, Budaitis B, Ekiert DC, Bhabha G, Prakash M.  2023.  Energetics of the  G,  polar tube invasion machinery.  ELife 13:RP86638.
194 R Chang, M Prakash. Topological damping in an ultrafast giant cell.   Proceedings of the National Academy of Sciences U.S.A.  120 (41), e2303940120. 2023.  
195 Chung, D.H., Kong, S., Young, N. J….Craik, C.S. Rare antibody phage isolation and discrimination (RAPID) biopanning enables identification of high-affinity antibodies against challenging targets. Commun Biol 6, 1036 (2023).
196 Dai, T., Xiao, Z., Shan, D., Moreno, A., Li, H., Prakash, M., Banaei, N., Rao, J. 2023.   Culture- independent multiplexed detection of drug-resistant bacteria using surface-enhanced Raman scattering.  ACS Sensors   8, 3264–3271
197 De Belly H, Yan S, Borja da Rocha H, Ichbiah S, Town JP, Zager PJ, Estrada DC, Meyer K, Turlier H, Bustamante C, Weiner OD.  2023. Cell protrusions and contractions generate long-range membrane tension propagation.   Cell  14: 3049-3061.
198 E Flaum, M Prakash. 2023.  Curved crease origami and topological singularities at a cellular scale enable hyper-extensibility of Lacrymaria olor.   bioRxiv  10.1101/2023.08.04.551915
199 Andreana Gomez, Sergio Gonzalez, Ashwini Oke, Jiayu Luo, Johnny B. Duong, Raymond M. Esquerra, Thomas Zimmerman, Sara Capponi, Jennifer C. Fung, Todd G. Nystul. 2024.  A  high-throughput method for quantifying Drosophila fecundity. bioRxiv 2024.03.27.587093
200 Graham AJ, Khoo MWL, Srivastava V, Viragova S, Parekh K, Morley CD, Bird M, Lebel P, Kumar S, Klein O, Gomez-Sjoberg R, Gartner ZJ.  2024.  MAGIC matrices: freeform bioprinting materials to support complex and reproducible organoid morphogenesis.  bioRxiv
201 Larson BT, Marshall WF.  2024.  Cell motility: Bioelectrical control of behavior without neurons.  Curr Biol. 34, R137-R140.
202 Lee JC, Brien HJ, Walton BL, Eidman ZM, Toda S, Lim WA, Brunger JM. Instructional materials that control cellular activity through synthetic Notch receptors. Biomaterials. 2023 Jun;297:122099. doi: 10.1016/j.biomaterials.2023.122099. Epub 2023 Mar 29. PMID: 37023529; PMCID: PMC10320837.
203 Lewis G, Marshall WF.  2023.  Mitochondrial networks through the lens of mathematics.  Phys. Biol.  10.1088/1478-3975/acdcdb
204 E Li, V Saggiomo, W Ouyang, M Prakash, B Diederich.   2024.  ESPressoscope: a small and powerful platform for in situ microscopy.  bioRxiv, 2024.01. 20.576174
205 Marshall WF, Fung JC. 2024. Modeling homologous chromosome recognition via nonspecific interactions.  Proc. Natl. Acad. Sci. U.S.A.  in press.
206 McGinn, R.E. Startup Ethics: Ethically Responsible Conduct of Scientists and Engineers at Theranos. Sci Eng Ethics 28, 39 (2022).
207 Meyer K, Lammers NC, Bugaj LJ, Garcia HH, Weiner OD. 2023. Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation. Nature Communications  14,  6929.
208 A Molina, A Kothari, A Odundo, M Prakash. 2023.  Agave sisalana: towards distributed manufacturing of absorbent media for menstrual pads in semi-arid regions.  Communications Engineering 2 (1), 81.
209 TL Nagy, E Strickland, OD Weiner.  2023.   Neutrophils actively swell to potentiate rapid migration.   Elife
210 Ogunlade, B., Tadesse, L., Li, H., Vu N., Banaei, N., Barczak, A., Saleh, A., Prakash, M. and Dionne, J. (2023) Predicting tuberculosis drug resistance with machine learning-assisted Raman spectroscopy.    Proc. Natl. Acad. Sci. U.S.A.  in press.   (preprint arXiv
211 Pastore VP, Alfano PD, Oke A, Capponi S, Eltanan D, Woodruff-Madeira X, Nguyen A, Fung JC, Bianco S.  2023.  An Unsupervised Learning Approach to Resolve Phenotype to Genotype Mapping in Budding Yeasts Vacuoles. Image Analysis and Processing – ICIAP 2023: 22nd International Conference, ICIAP 2023, Udine, Italy, Proceedings, Part II, Berlin, Heidelberg: Springer-Verlag; 2023, p. 247–58.
212 Pastore VP, Ciranni M, Bianco S, Fung JC, Murino V, Odone F.  2023.  Efficient unsupervised learning of biological images with compressed deep features. Image and Vision Computing 2023;  137:104764.
213 Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Ye CJ, Kim S, Gartner Z, Sirota M, Neely J.  2023.  Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics.  bioRxiv 10.1101/2023.11.07.566033
214 K Shen, JJ Flood, Z Zhang, A Ha, BR Shy, JE Dueber, SM Douglas. 2024.  Engineering an Escherichia coli strain for production of long single-stranded DNA.   Nucleic Acids Res.  52, 4098–4107
215 Singh, S., Chu, D. and Roy, S., 2022. Nematode histone H2A variant evolution reveals diverse histories of retention and loss, and evidence for conserved core-like variants. bioRxiv, pp.2022-03. Accepted: PLoS ONE
216 Sho C. Takatori, Sungmin Son, Daniel Lee, Daniel A. Fletcher.  2023.   Engineered molecular sensors of cell surface crowding.   Proc. Natl. Acad. Sci. U.S.A.  120, e2219778120
217 Strickland E, Pan D, Godfrey C, Kim JS, Hopke A, Degrance M, Villavicencio B, Mansour MK, Zerbe CS, Irimia D, Amir A, Weiner OD.  2024.  Self-extinguishing relay waves enable homeostatic control of human neutrophil swarming.  bioRxiv 10.1101/2023.06.27.546744
218 Tang SKY, Marshall WF. 2024. Physical forces in regeneration of cells and tissues. Cold Spring Harbor Persp. Biol.  in press.
219 Town JP, Weiner OD. 2023.  Local negative feedback of Rac activity at the leading edge underlies a pilot pseudopod-like program for amoeboid guidance, PLoS Biology, 21: e3002307.
220 P Vyas, CM Brannon, L Formery, C Lowe, M Prakash.   2024.  Algorithmic construction of topologically complex biomineral lattices via cellular syncytia. bioRxiv, 2024.02. 20.580924
221 Zhang KS, Rodriguez R, Tang SKY. SMORES: A Simple Microfluidic Operating Room for the Examination and Surgery of Stentor coeruleus. Under review, available on bioRXiv. Preprint, posted 2/08/2024.
222 Q Zhu, DN Conrad, ZJ Gartner 2024.  deMULTIplex2: robust sample demultiplexing for scRNA-seq.  Genome Biology, 25, 37
223 Thomas Zimmerman, Raymond Esquerra, Mark Chan, Anagha Kulkarni, Nicole Adelstein, Ashley Albright, Jiayu Luo, Ziah Dean, Salma Ahmed, Michelle Phillips, Simone Bianco, and Sara Capponi.  2023.  Teaching Image Processing and Optical Engineering to University Biology Students”.   The Biophysicist 4 (1): 38–57.
224 T. Zimmerman, R. Esquerra, K. Yu, D. Carrison-Stone, J. Erwin, J. Ma, Z. He, S. Bianco, and S. Capponi.  2024.  Mentoring Strategies of the Center for Cellular Construction, an NSF Science and Technology Center.  The Biophysicist  under review.