Selected Publications

2023

A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling.

den Berge KV, Chou HJ, Kunda D, Risso D, Street K, Purdom E, Dudoit S, Ngai J, Heavner W.

bioRxiv [Preprint]. 2023 Oct 31:2023.10.26.564041. doi: 10.1101/2023.10.26.564041.

PMID: 37961539 

Continuing trial responsibilities for implantable neural devices.

Hendriks S, Hsu N, Beckel-Mitchener AC, Ngai J, Grady C.

Neuron. 2023 Oct 18;111(20):3143-3149. doi: 10.1016/j.neuron.2023.07.008. Epub 2023 Aug 14.

PMID: 37582365

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2022

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects.

Van den Berge K, Chou HJ, Roux de Bézieux H, Street K, Risso D, Ngai J, Dudoit S.

Cell Rep Methods. 2022 Nov 1;2(11):100321. doi: 10.1016/j.crmeth.2022.100321. eCollection 2022 Nov 21.

PMID: 36452861 

 

BRAIN 2.0: Transforming neuroscience.

Ngai J.

Cell. 2022 Jan 6;185(1):4-8. doi: 10.1016/j.cell.2021.11.037.

PMID: 34995517

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2021

The International Brain Initiative: enabling collaborative science.

Quaglio G, Toia P, Moser EI, Karapiperis T, Amunts K, Okabe S, Poo MM, Rah JC, Koninck Y, Ngai J, Richards L, Bjaalie JG.

Lancet Neurol. 2021 Dec;20(12):985-986. doi: 10.1016/S1474-4422(21)00389-6.

PMID: 34800415

 

Advancing scientific excellence through inclusivity in the NIH BRAIN Initiative.

Richardson RR, Crawford DC, Ngai J, Beckel-Mitchener AC.

Neuron. 2021 Nov 3;109(21):3361-3364. doi: 10.1016/j.neuron.2021.10.021.

PMID: 34735787

 

A multimodal cell census and atlas of the mammalian primary motor cortex.

BRAIN Initiative Cell Census Network (BICCN).

Nature. 2021 Oct;598(7879):86-102. doi: 10.1038/s41586-021-03950-0. Epub 2021 Oct 6.

PMID: 34616075

 

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.

Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA.

Nature. 2021 Oct;598(7879):103-110. doi: 10.1038/s41586-021-03500-8. Epub 2021 Oct 6.

PMID: 34616066 

Generation of a DAT-P2A-Flpo mouse line for intersectional genetic targeting of dopamine neuron subpopulations.

Kramer DJ, Aisenberg EE, Kosillo P, Friedmann D, Stafford DA, Lee AY, Luo L, Hockemeyer D, Ngai J, Bateup HS.

Cell Rep. 2021 May 11;35(6):109123. doi: 10.1016/j.celrep.2021.109123.

PMID: 33979604

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Publications 2020 and Earlier

2020

The promise of the BRAIN initiative: NIH strategies for understanding neural circuit function.

Hsu NS, Fang HY, David KK, Gnadt JW, Peng GC, Talley EM, Ward JM, Ngai J, Koroshetz WJ.

Curr Opin Neurobiol. 2020 Dec;65:162-166. doi: 10.1016/j.conb.2020.10.008. Epub 2020 Dec 3.

PMID: 33279793 

 

The cellular basis of distinct thirst modalities.

Pool AH, Wang T, Stafford DA, Chance RK, Lee S, Ngai J, Oka Y.

Nature. 2020 Dec;588(7836):112-117. doi: 10.1038/s41586-020-2821-8. Epub 2020 Oct 14.

PMID: 33057193

 

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia.

Brann DH, Tsukahara T, Weinreb C, Lipovsek M, Van den Berge K, Gong B, Chance R, Macaulay IC, Chou HJ, Fletcher RB, Das D, Street K, de Bezieux HR, Choi YG, Risso D, Dudoit S, Purdom E, Mill J, Hachem RA, Matsunami H, Logan DW, Goldstein BJ, Grubb MS, Ngai J, Datta SR.

Sci Adv. 2020 Jul 31;6(31):eabc5801. doi: 10.1126/sciadv.abc5801. Epub 2020 Jul 24.

PMID: 32937591 

 

Transcriptome analysis of the zebrafish atoh7-/- Mutant, lakritz, highlights Atoh7-dependent genetic networks with potential implications for human eye diseases.

Covello G, Rossello FJ, Filosi M, Gajardo F, Duchemin AL, Tremonti BF, Eichenlaub M, Polo JM, Powell D, Ngai J, Allende ML, Domenici E, Ramialison M, Poggi L.

FASEB Bioadv. 2020 Jun 27;2(7):434-448. doi: 10.1096/fba.2020-00030. eCollection 2020 Jul.

PMID: 32676583 

 

Cellular mechanisms of epithelial stem cell self-renewal and differentiation during homeostasis and repair.

Das D, Fletcher RB, Ngai J.

Wiley Interdiscip Rev Dev Biol. 2020 Jan;9(1):e361. doi: 10.1002/wdev.361. Epub 2019 Aug 29.

PMID: 31468728

 

2019

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.

Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N.

Cell Syst. 2019 Apr 24;8(4):315-328.e8. doi: 10.1016/j.cels.2019.03.010.

PMID: 31022373

 

Complementary networks of cortical somatostatin interneurons enforce layer specific control.

Naka A, Veit J, Shababo B, Chance RK, Risso D, Stafford D, Snyder B, Egladyous A, Chu D, Sridharan S, Mossing DP, Paninski L, Ngai J, Adesnik H.

Elife. 2019 Mar 18;8:e43696. doi: 10.7554/eLife.43696.

PMID: 30883329

 

Perspectives on defining cell types in the brain.

Mukamel EA, Ngai J.

Curr Opin Neurobiol. 2019 Jun;56:61-68. doi: 10.1016/j.conb.2018.11.007. Epub 2018 Dec 6.

PMID: 30530112 

 

2018

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.

Risso D, Purvis L, Fletcher RB, Das D, Ngai J, Dudoit S, Purdom E.

PLoS Comput Biol. 2018 Sep 4;14(9):e1006378. doi: 10.1371/journal.pcbi.1006378. eCollection 2018 Sep.

PMID: 30180157 

 

Combinatorial Expression of Grp and Neurod6 Defines Dopamine Neuron Populations with Distinct Projection Patterns and Disease Vulnerability.

Kramer DJ, Risso D, Kosillo P, Ngai J, Bateup HS.

eNeuro. 2018 Jun 13;5(3):ENEURO.0152-18.2018. doi: 10.1523/ENEURO.0152-18.2018. eCollection 2018 May-Jun.

PMID: 30135866 

 

Creating Lineage Trajectory Maps Via Integration of Single-Cell RNA-Sequencing and Lineage Tracing: Integrating transgenic lineage tracing and single-cell RNA-sequencing is a robust approach for mapping developmental lineage trajectories and cell fate changes.

Fletcher RB, Das D, Ngai J.

Bioessays. 2018 Aug;40(8):e1800056. doi: 10.1002/bies.201800056. Epub 2018 Jun 26.

PMID: 29944188 

 

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S.

BMC Genomics. 2018 Jun 19;19(1):477. doi: 10.1186/s12864-018-4772-0.

PMID: 29914354

 

2017

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.

Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB.

Cell Stem Cell. 2017 Dec 7;21(6):775-790.e9. doi: 10.1016/j.stem.2017.10.014. Epub 2017 Nov 22.

PMID: 29174333 

 

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas.

Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H.

Neuron. 2017 Nov 1;96(3):542-557. doi: 10.1016/j.neuron.2017.10.007.

PMID: 29096072 

 

Anosmia-A Clinical Review.

Boesveldt S, Postma EM, Boak D, Welge-Luessen A, Schöpf V, Mainland JD, Martens J, Ngai J, Duffy VB.

Chem Senses. 2017 Sep 1;42(7):513-523. doi: 10.1093/chemse/bjx025.

PMID: 28531300 

 

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.

Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A, Cole MB, Flores Q, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J.

Cell Stem Cell. 2017 Jun 1;20(6):817-830.e8. doi: 10.1016/j.stem.2017.04.003. Epub 2017 May 11.

PMID: 28506465 

 

2014

Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

Ferreira T, Wilson SR, Choi YG, Risso D, Dudoit S, Speed TP, Ngai J.

Neuron. 2014 Feb 19;81(4):847-59. doi: 10.1016/j.neuron.2014.01.001.

PMID: 24559675

 

2013

Role of a ubiquitously expressed receptor in the vertebrate olfactory system.

DeMaria S, Berke AP, Van Name E, Heravian A, Ferreira T, Ngai J.

J Neurosci. 2013 Sep 18;33(38):15235-47. doi: 10.1523/JNEUROSCI.2339-13.2013.

PMID: 24048853

 

Intrinsic activity of odorant receptors guides sensory map formation.

Ngai J.

Cell. 2013 Sep 12;154(6):1186-7. doi: 10.1016/j.cell.2013.08.037.

PMID: 24034241 

 

2011

p63 regulates olfactory stem cell self-renewal and differentiation.

Fletcher RB, Prasol MS, Estrada J, Baudhuin A, Vranizan K, Choi YG, Ngai J.

Neuron. 2011 Dec 8;72(5):748-59. doi: 10.1016/j.neuron.2011.09.009.

PMID: 22153372

 

Transcription factors expressed in olfactory bulb local progenitor cells revealed by genome-wide transcriptome profiling.

Campbell GR, Baudhuin A, Vranizan K, Ngai J.

Mol Cell Neurosci. 2011 Feb;46(2):548-61. doi: 10.1016/j.mcn.2010.12.012. Epub 2010 Dec 29.

PMID: 21194568