Publications

Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning.Unger EK, Keller JP, Altermatt M, Liang R, Matsui A, Dong C, Hon OJ, Yao Z, Sun J, Banala S, Flanigan ME, Jaffe DA, Hartanto S, Carlen J, Mizuno GO, Borden PM, Shivange AV, Cameron LP, Sinning S, Underhill SM, Olson DE, Amara SG, Temple Lang D, Rudnick G, Marvin JS, Lavis LD, Lester HA, Alvarez VA, Fisher AJ, Prescher JA, Kash TL, Yarov-Yarovoy V, Gradinaru V, Looger LL, Tian L.Cell. 2020 Dec 23;183(7):1986-2002.e26. doi: 10.1016/j.cell.2020.11.040. Epub 2020 Dec 16.PMID: 33333022 Free PMC article.

Voices in methods development.Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X.Nat Methods. 2019 Oct;16(10):945-951. doi: 10.1038/s41592-019-0585-6.PMID: 31562479 Free PMC article.

Author Correction: Kilohertz frame-rate two-photon tomography.Kazemipour A, Novak O, Flickinger D, Marvin JS, Abdelfattah AS, King J, Borden PM, Kim JJ, Al-Abdullatif SH, Deal PE, Miller EW, Schreiter ER, Druckmann S, Svoboda K, Looger LL, Podgorski K.Nat Methods. 2019 Sep;16(9):932. doi: 10.1038/s41592-019-0545-1.PMID: 31388143

Kilohertz frame-rate two-photon tomography.Kazemipour A, Novak O, Flickinger D, Marvin JS, Abdelfattah AS, King J, Borden PM, Kim JJ, Al-Abdullatif SH, Deal PE, Miller EW, Schreiter ER, Druckmann S, Svoboda K, Looger LL, Podgorski K.Nat Methods. 2019 Aug;16(8):778-786. doi: 10.1038/s41592-019-0493-9. Epub 2019 Jul 29.PMID: 31363222 Free PMC article.

Inaccurate secondary structure predictions often indicate protein fold switching.Mishra S, Looger LL, Porter LL.Protein Sci. 2019 Aug;28(8):1487-1493. doi: 10.1002/pro.3664. Epub 2019 Jun 17.PMID: 31148305 Free PMC article.

Recently, we developed a prediction method for fold-switching proteins using structure-based thermodynamic calculations and discrepancies between predicted and experimentally determined protein secondary structure (Porter and Looger, Proc Natl Acad Sci U S A 2018; 115:5968 …

Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians.Molineros JE, Looger LL, Kim K, Okada Y, Terao C, Sun C, Zhou XJ, Raj P, Kochi Y, Suzuki A, Akizuki S, Nakabo S, Bang SY, Lee HS, Kang YM, Suh CH, Chung WT, Park YB, Choe JY, Shim SC, Lee SS, Zuo X, Yamamoto K, Li QZ, Shen N, Porter LL, Harley JB, Chua KH, Zhang H, Wakeland EK, Tsao BP, Bae SC, Nath SK.PLoS Genet. 2019 Apr 25;15(4):e1008092. doi: 10.1371/journal.pgen.1008092. eCollection 2019 Apr.PMID: 31022184 Free PMC article.

Shared and distinct transcriptomic cell types across neocortical areas.Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo MN, Viswanathan S, Penn O, Bakken T, Menon V, Miller J, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirschstein D, Pendergraft J, Sullivan HA, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H.Nature. 2018 Nov;563(7729):72-78. doi: 10.1038/s41586-018-0654-5. Epub 2018 Oct 31.PMID: 30382198 Free PMC article.

Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR.Marvin JS, Scholl B, Wilson DE, Podgorski K, Kazemipour A, Müller JA, Schoch S, Quiroz FJU, Rebola N, Bao H, Little JP, Tkachuk AN, Cai E, Hantman AW, Wang SS, DePiero VJ, Borghuis BG, Chapman ER, Dietrich D, DiGregorio DA, Fitzpatrick D, Looger LL.Nat Methods. 2018 Nov;15(11):936-939. doi: 10.1038/s41592-018-0171-3. Epub 2018 Oct 30.PMID: 30377363 Free PMC article.

Falling apart.Marvin JS, Looger LL.Elife. 2016 Jun 27;5:e18203. doi: 10.7554/eLife.18203.PMID: 27345573 Free PMC article.

Sensitive red protein calcium indicators for imaging neural activity.Dana H, Mohar B, Sun Y, Narayan S, Gordus A, Hasseman JP, Tsegaye G, Holt GT, Hu A, Walpita D, Patel R, Macklin JJ, Bargmann CI, Ahrens MB, Schreiter ER, Jayaraman V, Looger LL, Svoboda K, Kim DS.Elife. 2016 Mar 24;5:e12727. doi: 10.7554/eLife.12727.PMID: 27011354 Free PMC article.

High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry.Sun C, Molineros JE, Looger LL, Zhou XJ, Kim K, Okada Y, Ma J, Qi YY, Kim-Howard X, Motghare P, Bhattarai K, Adler A, Bang SY, Lee HS, Kim TH, Kang YM, Suh CH, Chung WT, Park YB, Choe JY, Shim SC, Kochi Y, Suzuki A, Kubo M, Sumida T, Yamamoto K, Lee SS, Kim YJ, Han BG, Dozmorov M, Kaufman KM, Wren JD, Harley JB, Shen N, Chua KH, Zhang H, Bae SC, Nath SK.Nat Genet. 2016 Mar;48(3):323-30. doi: 10.1038/ng.3496. Epub 2016 Jan 25.PMID: 26808113 Free PMC article.

Green-to-Red Photoconversion of GCaMP.Ai M, Mills H, Kanai M, Lai J, Deng J, Schreiter E, Looger L, Neubert T, Suh G.PLoS One. 2015 Sep 18;10(9):e0138127. doi: 10.1371/journal.pone.0138127. eCollection 2015.PMID: 26382605 Free PMC article.

High-performance probes for light and electron microscopy.Viswanathan S, Williams ME, Bloss EB, Stasevich TJ, Speer CM, Nern A, Pfeiffer BD, Hooks BM, Li WP, English BP, Tian T, Henry GL, Macklin JJ, Patel R, Gerfen CR, Zhuang X, Wang Y, Rubin GM, Looger LL.Nat Methods. 2015 Jun;12(6):568-76. doi: 10.1038/nmeth.3365. Epub 2015 Apr 27.PMID: 25915120 Free PMC article.

Fixation-resistant photoactivatable fluorescent proteins for CLEM.Paez-Segala MG, Sun MG, Shtengel G, Viswanathan S, Baird MA, Macklin JJ, Patel R, Allen JR, Howe ES, Piszczek G, Hess HF, Davidson MW, Wang Y, Looger LL.Nat Methods. 2015 Mar;12(3):215-8, 4 p following 218. doi: 10.1038/nmeth.3225. Epub 2015 Jan 12.PMID: 25581799 Free PMC article.

Allelic heterogeneity in NCF2 associated with systemic lupus erythematosus (SLE) susceptibility across four ethnic populations.Kim-Howard X, Sun C, Molineros JE, Maiti AK, Chandru H, Adler A, Wiley GB, Kaufman KM, Kottyan L, Guthridge JM, Rasmussen A, Kelly J, Sánchez E, Raj P, Li QZ, Bang SY, Lee HS, Kim TH, Kang YM, Suh CH, Chung WT, Park YB, Choe JY, Shim SC, Lee SS, Han BG, Olsen NJ, Karp DR, Moser K, Pons-Estel BA, Wakeland EK, James JA, Harley JB, Bae SC, Gaffney PM, Alarcón-Riquelme M; GENLES, Looger LL, Nath SK.Hum Mol Genet. 2014 Mar 15;23(6):1656-68. doi: 10.1093/hmg/ddt532. Epub 2013 Oct 26.PMID: 24163247 Free PMC article.

Nanotools for neuroscience and brain activity mapping.Alivisatos AP, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X.ACS Nano. 2013 Mar 26;7(3):1850-66. doi: 10.1021/nn4012847. Epub 2013 Mar 20.PMID: 23514423 Free PMC article. Review.

Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.Akerboom J, Carreras Calderón N, Tian L, Wabnig S, Prigge M, Tolö J, Gordus A, Orger MB, Severi KE, Macklin JJ, Patel R, Pulver SR, Wardill TJ, Fischer E, Schüler C, Chen TW, Sarkisyan KS, Marvin JS, Bargmann CI, Kim DS, Kügler S, Lagnado L, Hegemann P, Gottschalk A, Schreiter ER, Looger LL.Front Mol Neurosci. 2013 Mar 4;6:2. doi: 10.3389/fnmol.2013.00002. eCollection 2013.PMID: 23459413 Free PMC article.

Admixture mapping in lupus identifies multiple functional variants within IFIH1 associated with apoptosis, inflammation, and autoantibody production.Molineros JE, Maiti AK, Sun C, Looger LL, Han S, Kim-Howard X, Glenn S, Adler A, Kelly JA, Niewold TB, Gilkeson GS, Brown EE, Alarcón GS, Edberg JC, Petri M, Ramsey-Goldman R, Reveille JD, Vilá LM, Freedman BI, Tsao BP, Criswell LA, Jacob CO, Moore JH, Vyse TJ, Langefeld CL, Guthridge JM, Gaffney PM, Moser KL, Scofield RH, Alarcón-Riquelme ME; BIOLUPUS Network, Williams SM, Merrill JT, James JA, Kaufman KM, Kimberly RP, Harley JB, Nath SK.PLoS Genet. 2013;9(2):e1003222. doi: 10.1371/journal.pgen.1003222. Epub 2013 Feb 18.PMID: 23441136 Free PMC article.

Imaging neural activity using Thy1-GCaMP transgenic mice.Chen Q, Cichon J, Wang W, Qiu L, Lee SJ, Campbell NR, Destefino N, Goard MJ, Fu Z, Yasuda R, Looger LL, Arenkiel BR, Gan WB, Feng G.Neuron. 2012 Oct 18;76(2):297-308. doi: 10.1016/j.neuron.2012.07.011. Epub 2012 Oct 17.PMID: 23083733 Free PMC article.

Optimization of a GCaMP calcium indicator for neural activity imaging.Akerboom J, Chen TW, Wardill TJ, Tian L, Marvin JS, Mutlu S, Calderón NC, Esposti F, Borghuis BG, Sun XR, Gordus A, Orger MB, Portugues R, Engert F, Macklin JJ, Filosa A, Aggarwal A, Kerr RA, Takagi R, Kracun S, Shigetomi E, Khakh BS, Baier H, Lagnado L, Wang SS, Bargmann CI, Kimmel BE, Jayaraman V, Svoboda K, Kim DS, Schreiter ER, Looger LL.J Neurosci. 2012 Oct 3;32(40):13819-40. doi: 10.1523/JNEUROSCI.2601-12.2012.PMID: 23035093 Free PMC article.

Retraction.Dwyer MA, Looger LL, Hellinga HW.Science. 2008 Feb 1;319(5863):569. doi: 10.1126/science.319.5863.569b.PMID: 18239106 No abstract available.

A novel analytical method for in vivo phosphate tracking.Gu H, Lalonde S, Okumoto S, Looger LL, Scharff-Poulsen AM, Grossman AR, Kossmann J, Jakobsen I, Frommer WB.FEBS Lett. 2006 Oct 30;580(25):5885-93. doi: 10.1016/j.febslet.2006.09.048. Epub 2006 Oct 2.PMID: 17034793 Free PMC article.

Genetically encoded sensors for metabolites.Deuschle K, Fehr M, Hilpert M, Lager I, Lalonde S, Looger LL, Okumoto S, Persson J, Schmidt A, Frommer WB.Cytometry A. 2005 Mar;64(1):3-9. doi: 10.1002/cyto.a.20119.PMID: 15688353 Free PMC article. Review.

Construction of a fluorescent biosensor family.de Lorimier RM, Smith JJ, Dwyer MA, Looger LL, Sali KM, Paavola CD, Rizk SS, Sadigov S, Conrad DW, Loew L, Hellinga HW.Protein Sci. 2002 Nov;11(11):2655-75. doi: 10.1110/ps.021860.PMID: 12381848 Free PMC article.