Arcadia Pubs (Contributors are in A-Z order)
1: Avasthi P, Celebi FM, McDaniel EA. (2023). Discovering shared protein structure signatures connected to polyphosphate accumulation in diverse bacteria. https://doi.org/10.57844/arcadia-ac10-23e7
2: Avasthi P, Bigge BM, Celebi FM, Gehring J, McGeever E, Radkov A, Sun DA. (2023). ProteinCartography: Comparing proteins with structure-based maps for interactive exploration. https://doi.org/10.57844/arcadia-a5a6-1068
3: Avasthi P, Mets DG, York R. (2023). Harnessing genotype-phenotype nonlinearity to accelerate biological prediction. https://doi.org/10.57844/arcadia-5953-995f
4: Avasthi P, Gehring J, Patton AH, Sun DA, York R. (2023). Comparing gene expression across species based on protein structure. https://doi.org/10.57844/arcadia-vw5e-2670
5: Avasthi P, Dutton RJ, Reiter T, Weiss ECP. (2023). Putative horizontal gene transfer events point to candidate genes involved in cross-species neuromodulation. https://doi.org/10.57844/arcadia-jqq0-y385
6: Avasthi P, Essock-Burns T, Garcia III G, Gehring J, Matus DQ, Mets DG, York R. (2023). Gotta catch ‘em all: Agar microchambers for high-throughput single-cell live imaging. https://doi.org/10.57844/arcadia-v1bg-6b60
7: Avasthi P, Patton AH, York R. (2023). Raman spectra reflect complex phylogenetic relationships. https://doi.org/10.57844/arcadia-x8wk-sf94
8: Avasthi P, MacQuarrie CD, Radkov A. (2023). Inducing protoplast formation in Phaeodactylum tricornutum by silica deprivation, enzymatic treatment, or cytoskeletal inhibition. https://doi.org/10.57844/arcadia-fh8f-xz51
9: Avasthi P, MacQuarrie CD. (2022). Chlorarachniophytes form light- and Arp2/3 complex-dependent extensions that are involved in motility and predation. https://doi.org/10.57844/arcadia-eqg7-kf54
10: Avasthi P, Bigge BM, Reiter T. (2022). Defining actin: Combining sequence, structure, and functional analysis to propose useful boundaries. https://doi.org/10.57844/arcadia-ynth-kh70
11: Avasthi P, York R. (2022). Distinct spatiotemporal movement properties reveal sub-modalities in crawling cell types. https://doi.org/10.57844/arcadia-h67a-0s36
12: Avasthi P, Garcia III G, York R. (2022). Microchamber slide design for cell confinement during imaging. https://doi.org/10.57844/arcadia-z6hb-fs28
13: Avasthi P, Gehring J. (2022). Designing genome-wide MERFISH probes for understudied species. https://doi.org/10.57844/arcadia-8926-7388
14: Avasthi P, Hochstrasser ML. (2022). The experiment begins: Arcadia publishing 1.0. https://doi.org/10.57844/arcadia-050a-q254
Academic Papers
1: Dougherty LL, Avasthi P. Determinants of cytoplasmic microtubule depolymerization during ciliogenesis in Chlamydomonas. Life Sci Alliance. 2023 Oct 9;7(1):e202302287. doi: 10.26508/lsa.202302287. PMID: 37813489; PMCID: PMC10561824.
2: Dougherty LL, Dutta S, Avasthi P. The ERK activator, BCI, inhibits ciliogenesis and causes defects in motor behavior, ciliary gating, and cytoskeletal rearrangement. Life Sci Alliance. 2023 Mar 13;6(6):e202301899. doi: 10.26508/lsa.202301899. PMID: 36914265; PMCID: PMC10011610.
3: Bigge BM, Rosenthal NE, Avasthi P. Initial ciliary assembly in Chlamydomonas requires Arp2/3 complex-dependent endocytosis. Mol Biol Cell. 2023 Apr 1;34(4):ar24. doi: 10.1091/mbc.E22-09-0443. Epub 2023 Feb 8. PMID: 36753382; PMCID: PMC10092647.
4: Bigge BM, Dougherty LL, Avasthi P. Lithium-induced ciliary lengthening sparks Arp2/3 complex-dependent endocytosis. Mol Biol Cell. 2023 Apr 1;34(4):ar26. doi: 10.1091/mbc.E22-06-0219. Epub 2023 Feb 8. PMID: 36753380; PMCID: PMC10092651.
5: Zhang N, Pazouki L, Nguyen H, Jacobshagen S, Bigge BM, Xia M, Mattoon EM, Klebanovych A, Sorkin M, Nusinow DA, Avasthi P, Czymmek KJ, Zhang R. Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background). Plants (Basel). 2022 Feb 22;11(5):585. doi: 10.3390/plants11050585. PMID: 35270055; PMCID: PMC8912731.
6: Avasthi P. From organism behaviour to molecular mechanisms. Nat Rev Mol Cell Biol. 2022 Jan;23(1):2. doi: 10.1038/s41580-021-00434-x. PMID: 34773101.
7: Goldstein B, Avasthi P. A guide to setting up and managing a lab at a research-intensive institution. BMC Proc. 2021 Jun 22;15(Suppl 2):8. doi: 10.1186/s12919-021-00214-7. PMID: 34158045; PMCID: PMC8218371.
8: Avasthi P. Finding your unique path in science. Mol Biol Cell. 2020 Dec 1;31(25):2749-2751. doi: 10.1091/mbc.E20-08-0565. PMID: 33253076; PMCID: PMC7851859.
9: Huang S, Dougherty LL, Avasthi P. Separable roles for RanGTP in nuclear and ciliary trafficking of a kinesin-2 subunit. J Biol Chem. 2021 Jan-
Jun;296:100117. doi: 10.1074/jbc.RA119.010936. Epub 2020 Dec 3. PMID: 33234597; PMCID: PMC7948393.
10: Avasthi P, Neill US, Pollack Porter KM, Weeraratna AT. Preserve junior faculty in biomedical sciences during and after the pandemic. Nat Med. 2020
Jul;26(7):1003-1004. doi: 10.1038/s41591-020-0943-z. PMID: 32514172.
11: Avasthi P, Feldman JL. Higher order cytoskeletal structures. Mol Biol Cell. 2020 Mar 15;31(6):398. doi: 10.1091/mbc.E19-12-0679. PMID: 32163347; PMCID: PMC7185890.
12: Christensen JR, Craig EW, Glista MJ, Mueller DM, Li Y, Sees JA, Huang S, Suarez C, Mets LJ, Kovar DR, Avasthi P. Chlamydomonas reinhardtii formin FOR1 and profilin PRF1 are optimized for acute rapid actin filament assembly. Mol Biol Cell. 2019 Dec 15;30(26):3123-3135. doi: 10.1091/mbc.E19-08-0463. Epub 2019 Oct 30. PMID: 31664873; PMCID: PMC6938247.
13: Craig EW, Mueller DM, Bigge BM, Schaffer M, Engel BD, Avasthi P. The elusive actin cytoskeleton of a green alga expressing both conventional and divergent actins. Mol Biol Cell. 2019 Oct 15;30(22):2827-2837. doi: 10.1091/mbc.E19-03-0141. Epub 2019 Sep 18. PMID: 31532705; PMCID: PMC6789165.
14: Craig EW, Avasthi P. Visualizing Filamentous Actin Using Phalloidin in Chlamydomonas reinhardtii. Bio Protoc. 2019 Jun 20;9(12):e3274. doi: 10.21769/BioProtoc.3274. PMID: 31363487; PMCID: PMC6667228.
15: Jack B, Mueller DM, Fee AC, Tetlow AL, Avasthi P. Partially Redundant ActinGenes in Chlamydomonas Control Transition Zone Organization and Flagellum-Directed Traffic. Cell Rep. 2019 May 21;27(8):2459-2467.e3. doi: 10.1016/j.celrep.2019.04.087. PMID: 31116988; PMCID: PMC6541019.
16: Avasthi P. Can microtubule motors use every available track? J Cell Biol. 2018 Dec 3;217(12):4055-4056. doi: 10.1083/jcb.201810083. Epub 2018 Nov 7. PMID: 30404947; PMCID: PMC6279381.
17: Jack B, Avasthi P. Erratum to: Chemical Screening for Flagella-Associated Phenotypes in Chlamydomonas reinhardtii. Methods Mol Biol. 2018;1795:E1. doi: 10.1007/978-1-4939-7874-8_19. Erratum for: Methods Mol Biol. 2018;1795:203-221.PMID: 30062533.
18: Avasthi P, Soragni A, Bembenek JN. Journal clubs in the time of preprints. Elife. 2018 Jun 11;7:e38532. doi: 10.7554/eLife.38532. PMID: 29889024; PMCID: PMC5995539.
19: Jack B, Avasthi P. Chemical Screening for Flagella-Associated Phenotypes in Chlamydomonas reinhardtii. Methods Mol Biol. 2018;1795:203-221. doi:
10.1007/978-1-4939-7874-8_17. Erratum in: Methods Mol Biol. 2018;1795:E1. PMID: 29846930.
20: Avasthi P, Maser RL, Tran PV. Primary Cilia in Cystic Kidney Disease. Results Probl Cell Differ. 2017;60:281-321. doi: 10.1007/978-3-319-51436-9_11.
PMID: 28409350; PMCID: PMC7065811.
21: Dutta S, Avasthi P. Flagellar Synchronization Is a Simple Alternative to Cell Cycle Synchronization for Ciliary and Flagellar Studies. mSphere. 2017 Mar
8;2(2):e00003-17. doi: 10.1128/mSphere.00003-17. PMID: 28289724; PMCID: PMC5343170.
22: Avasthi P, Onishi M, Karpiak J, Yamamoto R, Mackinder L, Jonikas MC, Sale WS, Shoichet B, Pringle JR, Marshall WF. Actin is required for IFT regulation in Chlamydomonas reinhardtii. Curr Biol. 2014 Sep 8;24(17):2025-32. doi: 10.1016/j.cub.2014.07.038. Epub 2014 Aug 21. PMID: 25155506; PMCID: PMC4160380.
23: Ying G, Avasthi P, Irwin M, Gerstner CD, Frederick JM, Lucero MT, Baehr W. Centrin 2 is required for mouse olfactory ciliary trafficking and development of ependymal cilia planar polarity. J Neurosci. 2014 Apr 30;34(18):6377-88. doi: 10.1523/JNEUROSCI.0067-14.2014. PMID: 24790208; PMCID: PMC4004820.
24: Avasthi P, Marshall WF. Ciliary regulation: disassembly takes the spotlight. Curr Biol. 2013 Nov 18;23(22):R1001-R1003. doi: 10.1016/j.cub.2013.09.052. PMID: 24262823.
25: Avasthi P. Signaling: Sifting at the ciliary base. Nat Chem Biol. 2013 Jul;9(7):414-5. doi: 10.1038/nchembio.1272. PMID: 23774872.
26: Avasthi P, Marshall W. Ciliary secretion: switching the cellular antenna to ‘transmit’. Curr Biol. 2013 Jun 3;23(11):R471-3. doi: 10.1016/j.cub.2013.04.056. PMID: 23743409.
27: Avasthi P, Scheel JF, Ying G, Frederick JM, Baehr W, Wolfrum U. Germline deletion of Cetn1 causes infertility in male mice. J Cell Sci. 2013 Jul
15;126(Pt 14):3204-13. doi: 10.1242/jcs.128587. Epub 2013 May 2. PMID: 23641067; PMCID: PMC3711207.
28: Avasthi P, Marshall WF. Chemical screening methods for flagellar phenotypes in Chlamydomonas. Methods Enzymol. 2013;525:351-69. doi:
10.1016/B978-0-12-397944-5.00017-1. PMID: 23522478.
29: Avasthi P, Marley A, Lin H, Gregori-Puigjane E, Shoichet BK, von Zastrow M, Marshall WF. A chemical screen identifies class a g-protein coupled receptors as regulators of cilia. ACS Chem Biol. 2012 May 18;7(5):911-9. doi: 10.1021/cb200349v. Epub 2012 Mar 8. PMID: 22375814; PMCID: PMC3356477.
30: Avasthi P, Marshall WF. Stages of ciliogenesis and regulation of ciliary length. Differentiation. 2012 Feb;83(2):S30-42. doi: 10.1016/j.diff.2011.11.015.
Epub 2011 Dec 16. PMID: 22178116; PMCID: PMC3269565.
31: Avasthi P, Watt CB, Williams DS, Le YZ, Li S, Chen CK, Marc RE, Frederick JM, Baehr W. Trafficking of membrane proteins to cone but not rod outer segments is dependent on heterotrimeric kinesin-II. J Neurosci. 2009 Nov 11;29(45):14287-98. doi: 10.1523/JNEUROSCI.3976-09.2009. PMID: 19906976; PMCID: PMC2788486.
32: Guo H, Hong S, Jin XL, Chen RS, Avasthi PP, Tu YT, Ivanco TL, Li Y. Specificity and efficiency of Cre-mediated recombination in Emx1-Cre knock-in
mice. Biochem Biophys Res Commun. 2000 Jul 5;273(2):661-5. doi: 10.1006/bbrc.2000.2870. PMID: 10873661.
33: Jin XL, Guo H, Mao C, Atkins N Jr, Wang H, Avasthi PP, Tu YT, Li Y. Emx1-specific expression of foreign genes using “knock-in” approach. Biochem
Biophys Res Commun. 2000 Apr 21;270(3):978-82. doi: 10.1006/bbrc.2000.2532. PMID: 10772936.
34: Guo H, Mao C, Jin XL, Wang H, Tu YT, Avasthi PP, Li Y. Cre-mediated cerebellum- and hippocampus-restricted gene mutation in mouse brain. Biochem
Biophys Res Commun. 2000 Mar 5;269(1):149-54. doi: 10.1006/bbrc.2000.2263. PMID: 10694492.