PUBLICATIONS

Publications supported by Center for Cellular Construction

Updated: 05/23/25:     Peer-reveiwed: 199 / Preprints: 73

2025
1 Aksel, T., J. Navarro, E., Fong, N. and Douglas, S.M., 2024. Design principles for accurate folding of DNA origami. Proceedings of the National Academy of Sciences, 121(48), p.e2406769121. DOI: 10.1073/pnas.2406769121
2 Apedoe, X., Phillips, M. and Nielsen, K., 2024. Teacher and Student Perceptions of Co-Learning. Proceedings of the 18th International Conference of the Learning Sciences-ICLS 2024, 1374-1377.
3 Apedoe, X. and Nielsen, K. (2024). I’m a STEM Person, But do I Belong?   Proceedings of the 18th International Conference of the Learning Sciences – ICLS 2024 ,  1386-1389.
4 Asai R,  Prakash VN,  Sinha S,  Prakash, M, Mikawa T. 2024.  Coupling and uncoupling of midline morphogenesis and cell flow in amniote gastrulation.   eLife 12:RP89948.
5 Baker, J.J., Shi, J., Wang, S., Mujica, E.M., Bianco, S., Capponi, S. and Dueber, J.E., 2024. ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway. Nature chemical biology,  DOI: doi.org/10.1038/s41589-024-01759-2
6 Callahan TJ, Park NH, Capponi S.  2025.  Agentic Mixture-of-Workflows for Multi-Modal Chemical Search.  arXiv  2502.19629
7 Chajwa, R., Flaum, E., Bidle, K.D., Van Mooy, B. and Prakash, M., 2024. Hidden comet tails of marine snow impede ocean-based carbon sequestration. Science, 386(6718), p.eadl5767. DOI: 10.1126/science.adl5767
8 Chan M,  Phillips M, Nielsen K, Chu D. 2024.  Building interdisciplinary skills and mentorship opportunities in a two-week research experience.  The Biophysicist  DOI: 10.35459/tbp.2024.000266
9 Chen, J., Mirvis, M., Ekman, A., Vanslembrouck, B., Le Gros, M., Larabell, C. and Marshall, W.F. 2024. Automated segmentation of soft X-ray tomography: native cellular structure with sub-micron resolution at high throughput for whole-cell quantitative imaging in yeast. bioRxiv, 10.1101/2024.10.31.621371
10 Cheng, K.J., Shi, J., Pogorelov, T.V. and Capponi, S. 2024. Investigating the Bromoform Membrane Interactions Using Atomistic Simulations and Machine Learning: Implications for Climate Change Mitigation. The Journal of Physical Chemistry B, 128(50), 12493-12506. DOI: doi.org/10.1021/acs.jpcb.4c04930
11 Chong, M.K., Rosas-Salvans, M., Tran, V. and Dumont, S.  2024. Chromosome size-dependent polar ejection force impairs mammalian mitotic error correction. Journal of Cell Biology, 223(8), p.e202310010.
12 Chorlay, A., Agarwal, S., Blackmon, L. and Fletcher, D.A. 2024. SurFlex Microscopy: Measuring Flexibility of Surface-Tethered Biomolecules. bioRxiv  10.1101/2024.12.13.628410
13 Chung, D.H., Connelly, E.J., Unnikrishnan, A., Chuo, S.W., Wucherer, K., Nadel, C.M., Gestwicki, J.E., Southworth, D.R. and Craik, C.S. 2025. Recombinant antibodies inhibit enzymatic activity of the E3 ubiquitin ligase CHIP via multiple mechanisms. Journal of Biological Chemistry, 301(3):108220.  doi: 10.1016/j.jbc.2025.108220.
14 Conrad DN, Phong KT, Korotkevich E, McGinnis CS, Zhu Q, Chow ED, Gartner ZJ. 2025.  Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC.   bioRxiv   10.1101/2025.02.14.638353.
15 Cornell, C.E., Chorlay, A., Krishnamurthy, D., Martin, N.R., Baldauf, L. and Fletcher, D.A. 2024. Target cell tension regulates macrophage trogocytosis. bioRxiv  10.1101/2024.12.02.626490
16 Cyphert, E.L., Nand, S., Franco, G., Hajkowski, M., Soto, L., Lee, D.M., Ferner, M., Zabin, C., Blumenthal, J., Deck, A. Boyer, K., Burrus K, Hernandez CJ, Anand A.   2024. Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs. bioRxiv. 10.1101/2024.05.15.594453
17 Flaum E, Prakash M. 2024.  Curved crease origami and topological singularities enable hyperextensibility of L. olor.   Science   384(6700):eadk5511.  doi: 10.1126/science.adk5511
18 Hajkowski, M., Rafael-Mingoa, B., Crystal-Franco, G., Dick, K., Acholonu, M., Nand, S., Soto, L., Withers, B.N., Hernandez, M., Cheng, A. and Anand, A.  2024. A Resistance Persistence Index (RPI) for antimicrobial resistance in wastewater. medRxiv,  10.1101/2024.11.06.24316840
19 Huycke, T.R., Häkkinen, T.J., Miyazaki, H., Srivastava, V., Barruet, E., McGinnis, C.S., Kalantari, A., Cornwall-Scoones, J., Vaka, D., Zhu, Q. and Jo, H., …Gartner Z.J., 2024. Patterning and folding of intestinal villi by active mesenchymal dewetting. Cell, 187(12), 3072-3089. DOI: 10.1016/j.cell.2024.04.039
20 Gomez, A., Gonzalez, S., Oke, A., Luo, J., Duong, J.B., Esquerra, R.M., Zimmerman, T., Capponi, S., Fung, J.C. and Nystul, T.G.   2024. A high-throughput method for quantifying Drosophila fecundity. Toxics, 12(9), 658. DOI: 10.3390/toxics12090658
21 Kim, H., Hu, G., Graham, A.J., Gu, G.X. and Gartner, Z.J.  2024. Four-Dimensional Bioprinting: Harnessing Active Mechanics to Build with Living Inks. Cold Spring Harbor Perspectives in Biology, p.a041557. DOI: 10.1101/cshperspect.a041557
22 Larson, A.G., Chajwa, R., Li, H. and Prakash, M.  2024. Inflation-induced motility for long-distance vertical migration. Current Biology   34, 5149-5163. DOI: 10.1016/j.cub.2024.09.046.
23 Lee, D.S., Oster, L.F., Son, S. and Fletcher, D.A. 2024. Cell surface crowding is a tunable biophysical barrier to cell-cell fusion.  bioRxiv, DOI: 10.1101/2024.12.12.628283
24 Li H, Lin H, Shrestha P, Bhansali R, Yan Y, Pannu J, Marx K, Ouyang W, Valenzuela LF, Li E, Kothari A. … Prakash M.   2025.  Octopi 2.0: Point-of-care Multi-disease Detection and Diagnosis via Edge AI Imaging Platform.   medRxiv. 10.1101/2025.03.21.25324364
25 Mirvis, M., Weingard, B., Goodman, S. and Marshall, W.F.  2025. A scoping study of the whole-cell imaging literature: a foundational corpus, potential for data-mining and research synthesis, and a call for standardization of an emerging field.  bioRxiv  10.1101/2025.02.03.636363
26 Mostov, R., Lewis, G.R., Sturm, G. and Marshall, W.F.  2025. Representing Mitochondrial Dynamics with Abstract Algebra.   bioRxiv  10.1101/2025.03.17.643721
27 Park, N.H., Callahan, T.J., Hedrick, J.L., Erdmann, T. and Capponi, S.   2024. Leveraging chemistry foundation models to facilitate structure focused retrieval augmented generation in multi-agent workflows for catalyst and materials design.   arXiv:2408.11793. DOI: 10.48550/arXiv.2408.11793.
28 Rabadam, G., Wibrand, C., Flynn, E., Hartoularos, G.C., Sun, Y., Madubata, C., Fragiadakis, G.K., Ye, C.J., Kim, S., Gartner, Z.J. and Sirota, M., 2024. Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics.   JCI insight  9(12), p.e176963.
29 Rajan, D., Lee, B., Albright, A., Tang, E., Maravillas, A., Vargas, C., Marshall, W.F. and Cortes, D., 2024. Phylogeny, morphology, and behavior of the new ciliate species Stentor stipatus.   bioRxiv. 10.1101/2024.08.03.606273
30 Ramahi JS, Hokeness KL, Gonzales J, Allen J, Marquez RDP, Rojas RAA, Ingram S, Capponi S, Smith JE, von Herzen B, Dueber J, He Z-H.  2024.  Examining hydrogen peroxide-containing organelles in seaweeds.   MicroPubl Biol. 10.17912/micropub.biology.001217. doi: 10.17912/micropub.biology.001217
31 Reyes, R.J., Pham, O., Fergusson, R., Ceberio, N., Clark, C., Cohen, C.S., Fuse, M. and Pennings, P. 2024.  SCIP: a self-paced, community-based summer coding program creates community and increases coding confidence, lessons learned from the pandemic. bioRxiv  10.1101/2022.12.27.521952
32 Siu, K. Lee, V., Dueber J.E. Functional targeting of membrane transporters and enzymes to peroxisomes. Nature Chemical Biology. In review.
33 Strickland, E., Pan, D., Godfrey, C., Kim, J.S., Hopke, A., Ji, W., Degrange, M., Villavicencio, B., Mansour, M.K., Zerbe, C.S. Irimia, D., Amir A, and Weiner O.D.   2024. Self-extinguishing relay waves enable homeostatic control of human neutrophil swarming. Developmental Cell, 59(19), 2659-2671.
34 Winer, B.Y., Settle, A.H., Yakimov, A.M., Jeronimo, C., Lazarov, T., Tipping, M., Saoi, M., Sawh, A., Sepp, A.L.L., Galiano, M. and Perry, J.S., …Weiner, O.D., …  2024. Plasma membrane abundance dictates phagocytic capacity and functional cross-talk in myeloid cells. Science immunology, 9(96), p.eadl2388. DOI: 10.1126/sciimmunol.adl2388
35 Wu, M., Marchando, P., Meyer, K., Tang, Z., Woolfson, D.N. and Weiner, O.D.   2024. The WAVE complex forms linear arrays at negative membrane curvature to instruct lamellipodia formation. bioRxiv.  10.1101/2024.07.08.600855
36 Yamada, T., Trentesaux, C., Brunger, J.M., Xiao, Y., Stevens, A.J., Martyn, I., Kasparek, P., Shroff, N.P., Aguilar, A., Bruneau, B.G. and Boffelli, D., …Lim, W.A.  2025. Synthetic organizer cells guide development via spatial and biochemical instructions.   Cell  188(3), 778-795. DOI: 10.1016/j.cell.2024.11.017
37 Zhang, K.S., Rodriguez, R. and Tang, S.K.Y.  2024.   SMORES: a simple microfluidic operating room for the examination and surgery of Stentor coeruleus. Sci Rep 14, 8684 DOI: 10.1038/s41598-024-59286-y
38 Zhang, Q., Leng, H.T., Li, H., Arrigo, K.R. and Prakash, M.  2024. Ice gliding diatoms establish record-low temperature limit for motility in a eukaryotic cell.   bioRxiv 10.1101/2024.11.18.624199
39 Zhu Q, Jiang Z, Thomson M, Gartner Z.  2025.  Revealing a coherent cell state landscape across single cell datasets with CONCORD.   bioRxiv  10.1101/2025.03.13.643146.
40 Zimmerman, T., Yu, K., Carrison-Stone, D., Erwin, J., Ma, J., He, Z.H., Bianco, S., Esquerra, R. and Capponi, S.   2024. Dismantling silos: Academia, Industry, and a Science Museum working together. The Biophysicist 5(2), 147-150.
41 Mirvis, M., Weingard, B., Goodman, S.N. and Marshall, W.F., 2025. A scoping study of the whole-cell imaging literature: a foundational corpus, potential for mesoscale data synthesis, and implications for standardization of an emerging field. bioRxiv, pp.2025-02.

2024
1 Aksel T, Navarro EJ, Fong N, Douglas SM. 2024.  Design principles for accurate folding of DNA origami.  bioRxiv    doi.org/10.1101/2024.03.18.585609
2 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
3 Capponi S, Wang S. 2024.  AI in Cellular Engineering and Reprogramming.   Biophys J. doi.org/10.1016/j.bpj.2024.04.001
4 Chan, Y.H.M., Phillips, M., Nielsen, K. and Chu, D.S., 2024. Building Interdisciplinary Skills and Mentorship Opportunities in a 2-Week Research Experience. The Biophysicist.
5 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
6 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  doi.org/10.1101/2024.02.01.578324
7 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  https://doi.org/10.1101/2024.01.20.576174
8 Marshall, W.F. and Fung, J.C., 2024. Modeling homologous chromosome recognition via nonspecific interactions. Proceedings of the National Academy of Sciences, 121(20), p.e2317373121.
9 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. DOI: 10.1093/nar/gkae189
10 Singh S, Anderson N, Chu D, Roy SW (2024) Nematode histone H2A variant evolution reveals diverse histories of retention and loss and evidence for conserved core-like variant histone genes. PLoS ONE 19(5): e0300190. https://doi.org/10.1371/journal.pone.0300190
11 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
12 Tang SKY, Marshall WF. 2024. Physical forces in regeneration of cells and tissues. Cold Spring Harbor Persp. Biol., doi: 10.1101/cshperspect.a041527
13 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
14 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. https://doi.org/10.1101/2024.02.05.578956 Preprint, posted 2/08/2024.
15 Q Zhu, DN Conrad, ZJ Gartner 2024.  deMULTIplex2: robust sample demultiplexing for scRNA-seq.  Genome Biology, 25, 37
16 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.
17 Ramahi, JS; Hokeness, KL; Gonzales, J; Allen, J; Marquez , RDP; Rojas, RAA; et al.; He, ZH (2024). Examining hydrogen peroxide-containing organelles in seaweeds. microPublication Biology. 10.17912/micropub.biology.001217.
18 Zimmerman T, Yu K, Carrison-Stone D, et al. Dismantling Silos: Academia, Industry, and a Science Museum Working Together. The Biophysicist. Published online September 04, 2024. doi: 10.35459/tbp.2024.000269
19 Chajwa, R., Flaum, E., Bidle, K.D., Van Mooy, B. and Prakash, M., 2024. Hidden comet tails of marine snow impede ocean-based carbon sequestration. Science, 386(6718), p.eadl5767.
20 Rabadam, G., Wibrand, C., Flynn, E., Hartoularos, G.C., Sun, Y., Madubata, C., Fragiadakis, G.K., Ye, C.J., Kim, S., Gartner, Z.J. and Sirota, M., 2024. Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics. JCI insight, 9(12), p.e176963. (Preprint 2023)
21 Zhang, K.S., Rodriguez, R. & Tang, S.K.Y. SMORES: a simple microfluidic operating room for the examination and surgery of Stentor coeruleus. Sci Rep 14, 8684 (2024). https://doi.org/10.1038/s41598-024-59286-y (Preprint 2024)
22 Strickland, E., Pan, D., Godfrey, C., Kim, J.S., Hopke, A., Ji, W., Degrange, M., Villavicencio, B., Mansour, M.K., Zerbe, C.S. and Irimia, D., 2024. Self-extinguishing relay waves enable homeostatic control of human neutrophil swarming. Developmental Cell, 59(19), pp.2659-2671. (Preprint 2024) DOI: https://doi.org/10.1016/j.devcel.2024.06.003

2023
1 Krishnamurthy, D. and Prakash, M., 2023. Emergent programmable behavior and chaos in dynamically driven active filaments. Proceedings of the National Academy of Sciences, 120(28), p.e2304981120.
2 Richter, M., Neahring, L., Tao, J., Sutanto, R., Cho, N.H. and Dumont, S., 2023. Kinetochore-fiber lengths are maintained locally but coordinated globally by poles in the mammalian spindle. Elife, 12, p.e85208.
3 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, https://doi.org/10.1093/g3journal/jkad059
4 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,   https://doi.org/10.1089/ten.tea.2022.0072
5 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
tension propagation in cells.  bioRxiv, https://doi.org/10.1101/2022.09.07.507005
6 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    https://doi.org/10.1098/rsif.2022.0537
7 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
8 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
9 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
10 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 https://doi.org/10.1101/2022.10.17.512504
11 Pastore, V.P., Alfano, P.D., Oke, A., Capponi, S., Eltanan, D., Woodruff-Madeira, X., Nguyen, A., Fung, J.C. and Bianco, S., 2023, September. An Unsupervised Learning Approach to Resolve Phenotype to Genotype Mapping in Budding Yeasts Vacuoles. In International Conference on Image Analysis and Processing (pp. 247-258). Cham: Springer Nature Switzerland.
12 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. 
13 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
14 Town JP, Weiner OD. 2023. Rac negative feedback links local PIP3 rate-of-change to dynamic control of neutrophil guidance.  bioRxiv  https://doi.org/10.1101/2022.12.30.521706
15 S. Basu, J. Born, A. Bose, S. Capponi, et al.  2023.  Towards quantum-enabled cell-centric therapeutics.    arXiv  arxiv.org/abs/2307.05734
16 Capponi S., Daniels KG.  2023.  Harnessing the Power of Artificial Intelligence to Advance Cell Therapy.   Immunological Reviews   doi/full/10.1111/imr.13236
17 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.
18 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.  doi.org/10.7554/eLife.86638
19 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.  
20 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). https://doi.org/10.1038/s42003-023-05390-0
21 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
22 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.
23 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
24 Larson BT, Marshall WF.  2024.  Cell motility: Bioelectrical control of behavior without neurons.  Curr Biol. 34, R137-R140.
25 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.
26 Lewis G, Marshall WF.  2023.  Mitochondrial networks through the lens of mathematics.  Phys. Biol.  10.1088/1478-3975/acdcdb
27 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.
28 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.    https://www.nature.com/articles/s44172-023-00130-y
29 TL Nagy, E Strickland, OD Weiner.  2023.   Neutrophils actively swell to potentiate rapid migration.   Elife  doi.org/10.7554/eLife.90551.1
30 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  doi.org/10.48550/arXiv.2306.05653
31 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. https://doi.org/10.1007/978-3-031-43153-1_21.
32 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.   doi.org/10.1016/j.imavis.2023.104764.
33 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
34 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
35 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.
36 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.

2022
1 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
2 Su-Feher, L., Rubin, A.N., Silberberg, S.N., Catta-Preta, R., Lim, K.J., Ypsilanti, A.R., Zdilar, I., McGinnis, C.S., McKinsey, G.L., Rubino Jr, T.E. and Hawrylycz, M.J., 2022. Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia. Proceedings of the National Academy of Sciences, 119(15), p.e2108760119.
3 McGinn R. 2022. Startup Ethics: Ethically Responsible Conduct of Scientists and Engineers at Theranos. Sci Eng Ethics 28, 39   https://doi.org/10.1007/s11948-022-00393-2
4 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
5  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
6 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
7 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. https://doi.org/10.1089/genbio.2022.0030 
8 Kyle G. Daniels, Shangying Wang, Milos S. Simic, Hersh K. Bhargava, Sara Capponi, Yurie Tonai, Wei Yu, Simone Bianco, Wendell A. Lim, 2022. Decoding CAR T cell phenotype using combinatorial signaling motif libraries and machine learning, Science, 378, 1194-1200 (2022) (Preprint: 2022 bioRxiv )
9 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. https://doi.org/10.21125/iceri.2022.0300 
10 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)
11 Bianco S, Capponi S, Wang S.  2022. AI-Driven Design of Disease Sensors: Theoretical Foundations. Artificial Intelligence Applications In Human Pathology, 287.
12 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
13 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
14 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
15 Krishnamurthy D,  Prakash M.  2022.  Emergent Programmable Behavior and Chaos in Dynamically Driven Active Filaments.   bioRxiv   doi: https://doi.org/10.1101/2022.06.05.494577
16 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)
17 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.
18 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)
19 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
20 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, https://doi.org/10.1039/D2LC00527A
21 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-
22 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: https://doi.org/10.1101/2022.12.27.521952
23 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   https://www.biorxiv.org/content/10.1101/2022.11.26.517738v1
24 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)
25 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
26 Takatori SC, Son S, Lee D, Fletcher DA. 2022. Engineered molecular sensors of cell surface crowding. bioRxiv  doi: https://doi.org/10.1101/2022.11.18.517164 

2021
1 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 https://doi.org/10.1101/2020.11.12.379123)
2 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)
3 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)
4 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
5 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.
6 Zimmerman T, Park A, Bianco S.  2021.  Evaluating autofocusing metrics for plankton holographic microscope image reconstruction.  Proc. SPIE 11710, 117100A
7 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 doi.org/10.1101/2021.03.07.434295)
8 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
9 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
10 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
11 Martyn I, Gartner ZJ.  2021.  Expanding the boundaries of synthetic development.  Dev. Biol. 474, 62-70.
12 Neahring L, Cho NH, Dumont S.  2021. Opposing motors provide mechanical and functional robustness in the human spindle. Developmental Cell, 2021, https://doi.org/10.1016/j.devcel.2021.09.011.
13 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
14 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
15 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.
16 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  
17 Bull, Matthew S., Laurel A. Kroo, and Manu Prakash. 2021.  Excitable mechanics embodied in a walking cilium.  arXiv 2107.02930.  
18 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. 
19 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
20 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
21 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
22 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
23 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
24 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.
25 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
26 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
27 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.
28 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: https://doi.org/10.1101/2021.12.16.473030
29 Molina, A., Kumar, S., Karpitschka, S., Prakash, M 2021. Droplet tilings for rapid exploration of spatially constrained many-body systems. PNAS 118, 34
30 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.
31 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 doi.org/10.1101/2021.01.11.426285
32 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.
33 Wang S, Bianco S. 2021. AI-assisted biology: predict the conditional probability distributions from noisy measurements. bioRxiv doi.org/10.1101/2021.10.07.463577

2020
1 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 https://doi.org/10.1101/2020.02.12.946509
2 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 https://doi.org/10.1101/430611
3 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
4 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
5 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
6 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
7 Bianco S, Chan YH, Marshall WF. 2020. Towards computer aided design of cellular structure. Phys. Biol.  17, 023001
8 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
9 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  https://doi.org/10.1101/2020.03.23.000851
10 Gong X, Mathijssen A, Bryant Z, Prakash M. 2020. Engineering reconfigurable flow patterns via surface-driven light-controlled active matter. arXiv 2004.01368
11 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
12 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
13 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 https://doi.org/10.1101/2020.05.02.070680
14 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.
15 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  https://doi.org/10.1101/2020.05.23.112979
16 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: https://doi.org/10.1101/2020.06.28.176560
17 Dods G, Gomez-Schiavon M, El-Samad H, Ng AH.  2020.  Accurate prediction of genetic circuit behavior requires multidimensional characterization of parts.  Preprint:  bioRxiv   https://doi.org/10.1101/2020.05.30.122077
18 Marshall WF.  2020.  Scaling of subcellular structures. Ann. Rev. Cell Dev. Biol.  https://doi.org/10.1146/annurev-cellbio-020520-113246
19 Riggs B.  2020.  Misinformation in the age of COVID-19: What are our responsibilities as scientists?  ASCB Newsletter July 2020 Issue
20 Ferguson P, Zimmerman T, Bianco S.  2020.  High throughput device for screening chemical sensitivity of plankton samples.  Science Matters  DOI pending
21 Chadwick W, Biswas S, Bianco S, Chan YHM.  2020.   Non-random distribution of vacuoles in Schizosaccharomyces pombe.  Phys. Biol.  DOI https://doi.org/10.1088/1478-3975/aba510
22 Pastore VP, Zimmerman T, Biswas SK, Bianco S.  2020.  Monitoring Water Quality Using Plankton as Biosensor.  J. Interdisciplinary Res. Appl. Med.  4, 15-20.
23 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
24 Krishnamurthy D, Li H, du Rey FB, Cambournac P, Larson AG, Li E, Prakash M.  2020.  Scale-free vertical tracking microscopy. Nature  Methodshttps://doi.org/10.1038/s41592-020-0924-7
25 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  https://doi.org/10.1101/2020.08.29.272989
26 Belardi B, Hamkins-Indik T, Harris AR, Fletcher DA. 2020. A weak link with actin organizes tight junctions to control epithelial permeability. Dev. Cell  https://doi.org/10.1016/j.devcel.2020.07.022
27 Molina A, Kumar S, Karpitschka S, Prakash M.  2020.  Evaporative self-assembly of motile droplets.   Preprint:  arXiv  arXiv:2009.05649v1
28 Tischer D, Weiner OD.  2020.  Optogenetic tuning of protein-protein binding in bilayers using LOVTRAP.  bio-protocol  10(17): e3745
29 Bauer D, Ishikawa H, Wemmer KA, Marshall WF.  2020.  Biological noise in an organelle size control system.  Preprint:  bioRxiv  https://doi.org/10.1101/2020.08.31.276428
30 Grewal PS, Samson JA, Baker JJ, Choi B, Dueber JE.  2020.  Peroxisome compartmentalization of a toxic enzyme improves alkaloid production.  Nature Chem. Biol.  https://doi.org/10.1038/s41589-020-00668-4
31 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.
32 Marshall WF.  2020.  Axopodia and the cellular “arms” race.  Cytoskeleton  doi.org/10.1002/cm.21642
33 Armstrong M, Vahey MD, Hunt TP, Fletcher DA.  2020.  Forming and loading giant unilamellar vesicles with acoustic jetting.  Biomicrofluidics   14, 064105.
34 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.
35 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
36 Gómez-Schiavon M and El-Samad H. 2020. CoRa – A general approach for quantifying biological feedback control.  bioRxiv 2020.10.09.334078
37 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
38 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
39 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
40 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

2019
1 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.
2 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  https://doi.org/10.1371/journal.pbio.300
3 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  
4 Pastore VP, Zimmerman T, Biswas SK, Bianco S.   2019.  Establishing the baseline for using plankton as biosensor.  Proc. SPIE 108810H
5 Ishikawa H, Yu JE, Tian J, Tang SKY, Qin H, Marshall WF.  2019.  Cell-based biosynthesis of linear protein nanoarrays.  Proc. SPIE 108930F
6 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
7 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.
8 Toda S, Brunger JM, Lim WA. 2019. Synthetic development: learning to program multicellular self-organization.  Curr. Opin. Systems Biol.  14, 41-49.
9 Tischer D, Weiner OD. 2019. Light-based tuning of ligand half-life supports kinetic proofreading model of T cell activation. Elife 8, e42498.
10 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
11 Mathijssen A, Culver J, Bhamla MS, Prakash M. 2019. Collective intercellular communication through ultra-fast hydrodynamic trigger waves. Nature 571, 560-564.
12 Mclaurin J, Weiner OD. 2019. Multiple sources of signal amplification within the B cell Ras/MAPK pathway. Mol Biol Cell. 30, 1610-1620.
13 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.
14 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
15 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
16 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.
17 Toda S, Frankel NW, Lim WA.  2019.   Engineering cell-cell communication networks:  programming multicellular behaviors.   Curr. Opin. Chem. Biol  52, 31-38..
18 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
19 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
20 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.
21 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,
22 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
23 Pastore VP, Zimmerman TG, Biswas SK, Bianco S. 2019. Annotation-free learning of plankton for classification and anomaly detection.  Submitted.  Preprint: bioRxiv  https://doi.org/10.1101/856815
24 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. https://doi.org/10.1016/j.cub.2019.09.034
25 Chang AY, Marshall WF. 2019. Dynamics of living cells in a cytomorphological state space. Proc. Natl. Acad. Sci. U.S.A.  116, 21556-21562 
26 Murrow LM, Gartner ZJ.  2019.  Balancing Act: Cell Polarity and Shape Compete to Ensure Robust Development.  Dev. Cell.  51, P545-547
27 Ramirez-San Juan GR, Mathijssen AJTM, He M, Jan L, Marshall WF, Prakash M.  2019.  Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays.  Submitted   preprint:  bioRxiv  https://doi.org/10.1101/665125
28 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 https://doi.org/10.1101/676866
29 Belardi B, Hamkins-Indik T, Harris AR, Fletcher DA.  2019.  A weak link with actin organizes tight junctions to control epithelial permeability.  preprint:  bioRxiv  https://doi.org/10.1101/805689
30 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 https://doi.org/10.1101/684423
31 Chan KMC,  Son S, Schmid EM, Fletcher DA.  2019.  A viral fusogen hijacks the actin cytoskeleton to drive cell-cell fusion.  preprint:  bioRxiv https://doi.org/10.1101/761502
32 Marshall WF.  2019.  Cellular Cognition: sequential logic in a giant protist.  Curr. Biol.  29, R1303-R1305.
33 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  https://doi.org/10.1101/836585
34 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 https://doi.org/10.1101/2019.12.23.878207
35 Long AF, Suresh P, Dumont S.  2019.  Individual kinetochore-fibers locally dissipate force to maintain robust mammalian spindle structure.  Preprint: bioRxiv  https://doi.org/10.1101/846154
36 Suresh P, Long AF, Dumont S.  2019.  Microneedle manipulation of the mammalian spindle reveals specialized, short-lived reinforcement near chromosomes.  eLife 2020;9:e53807
37 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

2018
1 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.
2 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.
3 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.
4 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
5 Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ. 2018. Opportunities for organoids as new models of aging. J Cell Biol. 217, 39-50
6 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.
7 Munoz, NR; Byrd, DT; Chu, D 2018. New allele of C. elegans gene spch-3 (T27A3.4), called xc2. Micropublication: biology. Dataset. https://doi.org/10.17912/W2995W
8 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
9 Chu DS 2018. Zinc: A small molecule with a big impact on sperm function. PLoS Biol 16, e2006204.
10 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.
11 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.
12 Hughes AJ, Mornin JD, Biswas SK, Bauer DP, Bianco S, Gartner ZJ. 2018. Quanti.us: A tool for rapid, flexible, crowd-based annotation of images.  Nature Methods 15, 587-590.
13 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
14 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.  
15 Condon A, Kirchner H, Lariviere D, Marshall WF, Noireaux V, Tlusty T, Fourmentin E. 2018. Will biologists become computer scientists? EMBO Reports 19, E46628.  
16 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.
17 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
18 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
19 Marshall WF. 2018. A dilution model for embryonic scaling. Dev. Cell. 46, 529-530.29. 
20 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
21 Tang SKY, Marshall WF. 2018. Primer: Cell Learning. Curr. Biol. 28,:R1180-R1184.
22 Gingold C, Douglas SM.  2018.  Gelbox – An Interactive Simulation Tool for Gel Electrophoresis.  bioRxiv  https://doi.org/10.1101/406132
23 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
24 Rath KA, Peterfreund A, Bayliss F. 2018. Programmatic Mentoring: Providing Mentoring as a Community, Going Beyond Mentor/Protégé Pairs. Understanding Interventions 9, 2
25 Chowdhury A, Biswas S, Bianco S. 2018. Active deep learning reduces the annotation burden in automatic cell segmentation. bioRxiv, https://doi.org/10.1101/211060.
26 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  https://doi.org/10.1101/430611
27 Riggs B.  2018.  Mutually Beneficial Research Partnerships for Equity and Innovation in Science.  ASCB Newsletter Dec 2018 issue. p 35-38.
28 Liu F, Blauch LR, Tang SKY. 2018. Quantifying Phenotypes in Single Cells using Droplet Microfluidics. Meth. Cell Biol. 148,133-159.

2017
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. https://doi.org/10.17912/W2RQ2X
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.