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Peer-reveiwed: 175 | Preprints: 55 (Updated: 03/13/2025) |
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2024
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| 1 |
Aksel T, Navarro EJ, Fong N, Douglas SM. 2024. Design principles for accurate folding of DNA origami. bioRxiv https://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. http://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, DOI: https://www.doi.org/10.35459/tbp.2024.000266 |
| 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, https://doi.org/10.1101/2024.03.27.587093 |
| 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. https://doi.org/10.1073/pnas.2317373121 |
| 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. https://doi.org/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. https://doi.org/10.1016/j.devcel.2024.06.003 |
| 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. doi: https://doi.org/10.1101/2024.02.20.580924 |
| 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. doi: https://doi.org/10.1186/s13059-024-03177-y |
| 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. doi: https://doi.org/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: https://www.doi.org/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. doi: https://doi.org/10.1126/science.adl5767 |
| 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. doi: https://doi.org/10.1172/jci.insight.176963 (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. doi: https://doi.org/10.1016/j.devcel.2024.06.003 (Preprint 2024) |
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2023
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| 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. doi: https://doi.org/10.1073/pnas.2304981120. |
| 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. doi: https://doi.org/10.7554/eLife.85208 |
| 3 |
Ascencio, G., de Cruz, M.A., Abuel, J., Alvarado, S., Arriaga, Y., Conrad, E., Castro, A., Eichelberger, K., Galvan, L., Gundy, G. and Garcia, J.A.I., 2023. A deficiency screen of the 3rd chromosome for dominant modifiers of the Drosophila ER integral membrane protein, Jagunal. G3: Genes, Genomes, Genetics, 13(7), p.jkad059. doi: 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, doi: 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. doi: 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. doi: https://doi.org/10.1016/j.biomaterials.2023.122099. |
| 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. doi: https://doi.org/10.1080/19420862.2023.2184197. |
| 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. doi: https://doi.org/10.1007/978-3-031-43153-1_21 |
| 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: https://doi.org/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: https://doi.org/10.1038/s41586-022-05622-z |
| 14 |
Town, J. and Weiner, O., 2022. Rac negative feedback links local PIP3 rate-of-change to dynamic control of neutrophil guidance. bioRxiv, pp.2022-12. https://doi.org/10.1101/2022.12.30.521706 |
| 15 |
Basu, S., Born, J., Bose, A., Capponi, S., Chalkia, D., Chan, T.A., Doga, H., Flother, F.F., Getz, G., Goldsmith, M. and Gujarati, T., 2023. Towards quantum-enabled cell-centric therapeutics. arXiv preprint arXiv:2307.05734. doi: https://doi.org/10.48550/arXiv.2307.05734 |
| 16 |
Capponi, S. and Daniels, K.G., 2023. Harnessing the power of artificial intelligence to advance cell therapy. Immunological Reviews, 320(1), pp.147-165. doi: https://doi.org/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. doi: https://doi.org/10.48550/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: https://doi.org/10.7554/eLife.86638.3 |
| 19 |
Chang, R. and Prakash, M., 2023. Topological damping in an ultrafast giant cell. Proceedings of the National Academy of Sciences, 120(41), p.e2303940120. doi: https://doi.org/10.1073/pnas.2303940120 |
| 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. doi: https://doi.org/10.1021/acssensors.3c01345 |
| 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. doi: https://doi.org/10.1016/j.cell.2023.05.014 |
| 23 |
E Flaum, M Prakash. 2023. Curved crease origami and topological singularities at a cellular scale enable hyper-extensibility of Lacrymaria olor. bioRxiv doi: https://doi.org/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. doi: https://doi.org/10.1016/j.cub.2024.01.019 |
| 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. doi: https://doi.org/10.1016/j.biomaterials.2023.122099 |
| 26 |
Lewis G, Marshall WF. 2023. Mitochondrial networks through the lens of mathematics. Phys. Biol. https://doi.org/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. https://doi.org/10.1038/s41467-023-42643-2 |
| 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. https://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 https://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. https://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 https://doi.org/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. https://doi.org/10.1073/pnas.2219778120 |
| 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. https://doi.org/10.1371/journal.pbio.3002307 |
| 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. DOI: https://doi.org/10.35459/tbp.2022.000240 |
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2022
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| 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. https://doi.org/10.1021/acssynbio.1c00439 |
| 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. https://doi.org/10.1073/pnas.2108760119 |
| 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 https://doi.org/10.1101/2022.03.17.484826 |
| 5 |
Zhang KS, Nadkarni AV, Paul R, Martin AM, Tang SKY, 2022. Microfluidic Surgery in Single Cells and Multicellular Systems. Chemical Reviews, https://doi.org/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. https://doi.org/10.1117/12.2612438 |
| 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. https://doi.org/10.1126/science.abq0225 (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. https://doi.org/10.1016/j.cels.2022.05.008 (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. https://doi.org/10.1142/9781800611399_0011 |
| 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. https://doi.org/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. https://doi.org/10.1002/1873-3468.14254 |
| 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. https://doi.org/10.1371/journal.pone.0272089 |
| 15 |
Krishnamurthy D, Prakash M. 2022. Emergent Programmable Behavior and Chaos in Dynamically Driven Active Filaments. bioRxiv. 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. https://doi.org/10.1038/s41556-022-01031-6 (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. https://doi.org/10.1016/j.cels.2022.06.005 |
| 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. https://doi.org/10.1371/journal.pcbi.1010252 (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. https://doi.org/10.1007/978-3-031-06430-2_50 |
| 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- https://doi.org/10.1016/j.cub.2022.11.010 |
| 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. 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. https://doi.org/10.1016/j.cub.2022.04.061 (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. https://doi.org/10.7554/eLife.79558 |
| 26 |
Takatori SC, Son S, Lee D, Fletcher DA. 2022. Engineered molecular sensors of cell surface crowding. bioRxiv. https://doi.org/10.1101/2022.11.18.517164 |
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2021
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| 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. https://doi.org/10.1186/s12915-021-00970-0 (preprint bioRxiv) |
| 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. https://doi.org/10.1038/s42005-021-00712-2 (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. https://doi.org/10.1103/PhysRevFluids.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, https://dx-doi-org-s.vpn.cdutcm.edu.cn/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. https://doi.org/10.1038/s41598-021-83865-y |
| 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. https://doi.org/10.1140/epje/s10189-021-00119-5 (Preprint 2021: bioRxiv doi.org/10.1101/2021.03.07.434295) |
| 8 |
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Bull, Matthew S., and Manu Prakash. 2021. Mobile defects born from an energy cascade shape the locomotive behavior of a headless animal. arXiv https://doi.org/10.48550/arXiv.2107.02940 |
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Bull, Matthew S., Laurel A. Kroo, and Manu Prakash. 2021. Excitable mechanics embodied in a walking cilium. arXiv https://doi.org/10.48550/arXiv.2107.02930 |
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Bull, Matthew S., Vivek N. Prakash, and Manu Prakash. 2021. Ciliary flocking and emergent instabilities enable collective agility in a non-neuromuscular animal. arXiv https://doi.org/10.48550/arXiv.2107.02934 |
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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 https://doi.org/10.3791/61937 |
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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 https://doi.org/10.1101/2021.12.13.472465 |
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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. https://doi.org/10.1063/5.0053792 |
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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 https://doi.org/10.1371/journal.pone.0255338 |
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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. https://doi.org/10.1083/jcb.202005216 |
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Krishnamurthy D, Pepper R, Prakash M. 2021. Active Sinking Particles: Sessile Suspension Feeders significantly alter the Flow and Transport to Sinking Aggregates. bioRxiv https://doi.org/10.1101/2021.08.05.455190 |
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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 https://doi.org/10.48550/arXiv.2111.10515 |
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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. https://doi.org/10.1038/s41467-021-26300-0 |
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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 |
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Molina, A., Kumar, S., Karpitschka, S., Prakash, M 2021. Droplet tilings for rapid exploration of spatially constrained many-body systems. PNAS 118, 34. https://doi.org/10.1073/pnas.2020014118 |
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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. https://doi.org/10.1083/jcb.202003086 |
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Kimmel JC, Hwang A, Scaramozza A, Marshall WF, Brack A. 2020. Aging induces aberrant state transition kinetics in murine muscle stem cells. Development. https://doi.org/10.1242/dev.183855 |
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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 |
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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. https://doi.org/10.48550/arXiv.2004.13494 |
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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 |
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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. https://doi.org/10.1016/j.ceb.2020.05.003 |
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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 |
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Marshall WF. 2020. Scaling of subcellular structures. Ann. Rev. Cell Dev. Biol. https://doi.org/10.1146/annurev-cellbio-020520-113246 |
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Marshall WF. 2020. Axopodia and the cellular “arms” race. Cytoskeleton https://doi.org/10.1002/cm.21642 |
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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. https://doi.org/10.1016/j.devcel.2017.12.004 |
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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. https://doi.org/10.1371/journal.pcbi.1005927 |
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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. https://doi.org/10.1016/j.devcel.2017.12.013 |
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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. https://doi.org/10.1016/j.celrep.2018.02.031 |
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Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ. 2018. Opportunities for organoids as new models of aging. J Cell Biol. 217, 39-50. https://doi.org/10.1083/jcb.201709054 |
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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. https://doi.org/10.1093/icb/icy010 |
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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 |
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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. https://doi.org/10.1016/j.ydbio.2018.04.025 |
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Chu DS 2018. Zinc: A small molecule with a big impact on sperm function. PLoS Biol 16, e2006204. https://doi.org/10.1371/journal.pbio.2006204 |
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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. https://doi.org/10.1016/j.ydbio.2018.03.021 |
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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. https://doi.org/10.1187/cbe.17-06-0106 |
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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. https://doi.org/10.1038/s41592-018-0069-0 |
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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. https://doi.org/10.1016/j.devcel.2018.05.020 |
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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. https://doi.org/10.1016/j.tcb.2018.07.003 |
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Condon A, Kirchner H, Lariviere D, Marshall WF, Noireaux V, Tlusty T, Fourmentin E. 2018. Will biologists become computer scientists? EMBO Reports 19, E46628. https://doi.org/10.15252/embr.201846628 |
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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. https://doi.org/10.1126/science.aat0271 |
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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. https://doi.org/10.1021/acs.jpcb.8b07362 |
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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. https://doi.org/10.1021/acschembio.8b00524 |
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Marshall WF. 2018. A dilution model for embryonic scaling. Dev. Cell. 46, 529-530.29. https://doi.org/10.1016/j.devcel.2018.08.020 |
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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. https://doi.org/10.18260/1-2–29566 |
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Tang SKY, Marshall WF. 2018. Primer: Cell Learning. Curr. Biol. 28,:R1180-R1184. https://doi.org/10.1016/j.cub.2018.09.015 |
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Gingold C, Douglas SM. 2018. Gelbox – An Interactive Simulation Tool for Gel Electrophoresis. bioRxiv. https://doi.org/10.1101/406132 |
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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. https://doi.org/10.1371/journal.pone.0209301 |
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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. |
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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 |
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Riggs B. 2018. Mutually Beneficial Research Partnerships for Equity and Innovation in Science. ASCB Newsletter Dec 2018 issue. p 35-38. https://www.ascb.org/newsletter-pdf-archives/ |
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Liu F, Blauch LR, Tang SKY. 2018. Quantifying Phenotypes in Single Cells using Droplet Microfluidics. Meth. Cell Biol. 148,133-159. https://doi.org/10.1016/bs.mcb.2018.09.006 |
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2017
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Murrow LM, Weber RJ, Gartner ZJ. 2017. Dissecting the stem cell niche with organoid models: an engineering-based approach. Development 144, 998-1007. https://doi.org/10.1242/dev.140905 |
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Tang SKY, Marshall WF. 2017. Self-repairing cells: how single cells heal membrane ruptures and restore lost structures. Science. 2017 356, 1022-1025. https://doi.org/10.1126/science.aam6496 |
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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. https://doi.org/10.1073/pnas.1705059114 |
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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. https://doi.org/10.1091/mbc.e16-09-0690 |
| 5 |
Chang AY, Marshall WF. 2017. Organelles – understanding noise and heterogeneity in cell biology at an intermediate scale. J. Cell Sci. 130, 819-826. https://doi.org/10.1242/jcs.181024 |
| 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. |
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Fung, JC 2017. Kinetochores: Importance of Being Fashionably Late. Cell Systems 4:585-586. https://doi.org/10.1016/j.cels.2017.06.011 |
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Hueschen CL, Kenny SJ, Xu K, Dumont S. 2017. NuMA recruits dynein activity to microtubule minus-ends at mitosis. eLife, 6:e29328. https://doi.org/10.7554/eLife.29328 |
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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. https://doi.org/10.1016/j.cels.2017.09.016 |
