Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N. Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq. Cell Syst. 2019 Apr 24;8(4):315-328.e8. doi: 10.1016/j.cels.2019.03.010.

Mukamel EA, Ngai J. Perspectives on defining cell types in the brain. Curr Opin Neurobiol. 2018 Dec 6;56:61-68. (published online 12/06/2018)

Risso D, Purvis L, Fletcher RB, Das D, Ngai J, Dudoit S, Purdom E. clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets. PLoS Comput Biol. 2018 Sep 4;14(9):e1006378.

Fletcher RB, Das D, Ngai J. Creating lineage trajectory maps via integration of single-cell RNA-sequencing and lineage tracing.  Bioessays. 2018 Aug;40(8):e1800056.

Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics. 2018 Jun 19;19(1):477.

Kramer DJ, Risso D, Kosillo P, Ngai J, Bateup HS. Combinatorial expression of Grp and Neurod6 defines dopamine neuron populations with distinct projection patterns and disease vulnerability. eNeuro. 2018 Jun 13;5(3). pii: ENEURO.0152-18.2018.

Gadye* L, Das* D, Sanchez* MA, Street KN, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB. Injury activates transient olfactory stem cell states with diverse lineage capacities. Cell Stem Cell. 2017 Dec 7;21(6):775-790.e9. (*equal contribution)

Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron. 2017 Nov 1;96(3), 542–557.

Boesveldt S, Postma EM, Boak D, Welge-Luessen A, Schöpf V, Mainland JD, Martens J, Ngai J, Duffy VB. Anosmia - A Clinical Review. Chem Senses. 2017 Sep 1;42(7):513-523.

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. Deconstructing olfactory stem cell trajectories at single-cell resolution. Cell Stem Cell. 2017 Jun 1;20(6):817-30. (*equal contribution)

Ferreira T, Wilson SR, Choi YG, Risso D, Dudoit S, Speed TP, Ngai J. Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron. Neuron. 2014 Feb 19;81(4):847-59.

Risso D, Ngai J, Speed TP, Dudoit S.  The Role of Spike-In Standards in the Normalization of RNA-Seq.  In: Statistical Analysis of Next Generation Sequence Data (S. Datta and D. Nettleton, editors), Frontiers in Probability and the Statistical Sciences.  Cham: Springer, 2014 pp. 169-190.

Risso D, Ngai J, Speed TP, Dudoit S.  Normalization of RNA-Seq data using factor analysis of control genes or samples.  Nature Biotechnology 2014 Sep 32(9): 896-902.

DeMaria S, Berke AP, Van Name E, Heravian A, Ferreira T, Ngai J. Role of a ubiquitously expressed receptor in the vertebrate olfactory system. J Neurosci. 2013 Sep 18;33(38):15235-47.

Ngai J. Intrinsic activity of odorant receptors guides sensory map formation. Cell. 2013 Sep 12;154(6):1186-7.

Viringipurampeer IA, Ferreira T, DeMaria S, Yoon JJ,  Shan X, Moosajee M, Gregory-Evans K, Ngai J, Gregory-Evans C.Y. Pax2 regulates a Fadd-dependent molecular switch that drives tissue fusion during eye development.  Hum. Molec. Genet. 2012  21, 2357-2369.

Logan DW, Brunet LJ, Webb WR, Cutforth T, Ngai J, Stowers L. Learned recognition of maternal signature odors mediates the first suckling episode in mice.  Curr. Biol. 2012  22, 1998-2007.

The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma.  Nature  2011 474, 609-615.

Fletcher RB, Prasol MS, Estrada J, Baudhuin A, Vranizan K, Choi YG, Ngai J. p63 regulates olfactory stem cell self-renewal and differentiation. Neuron. 2011 Dec 8;72(5):748-59. 

Campbell GR, Baudhuin A, Vranizan K, Ngai J. Transcription factors expressed in olfactory bulb local progenitor cells revealed by genome-wide transcriptome profiling. Mol Cell Neurosci. 2011 Feb;46(2):548-61.

DeMaria S, Ngai J. The cell biology of smell. J Cell Biol. 2010 Nov 1;191(3):443-52. 

Cameron P, Hiroi M, Ngai J, Scott K. The molecular basis for water taste in Drosophila. Nature. 2010 May 6;465(7294):91-5. Epub 2010 Apr 4.

Panchal HD, Vranizan K, Lee CY, Ho J, Ngai J, Timiras PS. Early anti-oxidative and anti-proliferative curcumin effects on neuroglioma cells suggest therapeutic targets.  Neurochem. Res. 2008  33, 1701-1710.

Triballeau N, Van Name E, Laslier G, Cai D, Paillard G, Sorensen PW, Hoffmann R, Bertrand HO, Ngai J, Acher FC. High-Potency Olfactory Receptor Agonists Discovered by Virtual High-Throughput Screening: Molecular Probes for Receptor Structure and Olfactory Function. Neuron. 2008 Dec 10;60(5):767-774

Cancer Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8

Duggan CD, Demaria S, Baudhuin A, Stafford D, Ngai J. Foxg1 is required for development of the vertebrate olfactory system. J Neurosci. 2008 May 14;28(20):5229-39

Scolnick JA, Cui K, Duggan CD, Xuan S, Yuan XB, Efstratiadis A, Ngai J. Role of IGF signaling in olfactory sensory map formation and axon guidance. Neuron. 2008 Mar 27;57(6):847-57

Ngai, J, Alioto TS.  Genomics of odor receptors in zebrafish.  In: The Senses: A Comprehensive Reference (A.I. Basbaum, A. Kaneko, G.M. Shepherd, and G. Westheimer, editors),  Vol 4, Olfaction & Taste (S. Firestein, and G.K. Beauchamp), San Diego: Academic Press, 2007 pp. 553-560.

French CR, Erickson T, Callander D, Berry KM, Koss R, Hagey DW, Stout J, Wuennenberg-Stapleton K, Ngai J, Moens CB, Waskiewicz AJ. Pbx homeodomain proteins pattern both the zebrafish retina and tectum.  BMC Develop. Biol. 2007 7, 85.

Szpara ML, Vranizan K, Tai YC, Goodman CS, Speed TP, Ngai J. Analysis of gene expression during neurite outgrowth and regeneration. BMC Neurosci. 2007 Nov 23;8:100

Duggan CD, Ngai J. Scent of a stem cell. Nat Neurosci. 2007 Jun;10(6):673-4.

Alioto TS, Ngai J. The repertoire of olfactory C family G protein-coupled receptors in zebrafish: candidate chemosensory receptors for amino acids. BMC Genomics. 2006 7:309.

Dugas JC, Tai YC, Speed TP, Ngai J, Barres BA. Functional genomic analysis of oligodendrocyte differentiation. J Neurosci. 2006 26(43):10967-83.

Ngai J. Neuroscience: an extra dimension to olfaction. Nature. 2006 442(7103):637-8.

Luu P, Acher F, Bertrand HO, Ngai J. Odorant receptor specificities and receptor combinatorials: implications for olfactory coding.  Chem. Senses Suppl. 2005 1, i97-i98.

Weidinger G, Thorpe CJ, Wuennenberg-Stapleton K, Ngai J, Moon RT. The Sp1-related transcription factors sp5 and sp5-like act downstream of Wnt/b-catenin signaling in mesoderm and neuroectoderm patterning.  Curr. Biol.  2005 15, 489-500.

Dybbs M, Ngai J, Kaplan JM. Using microarrays to facilitate positional cloning: identification of tomosyn as an inhibitor of neurosecretion.  PloS Genetics 2005 1, e2.

Alioto TS, Ngai J. The odorant receptor repertoire of teleost fish. BMC Genomics. 2005 6:173.

Luu P, Acher F, Bertrand HO, Ngai J. Odorant receptor specificities and receptor combinatorials: implications for olfactory coding. Chem Senses. 2005 30 Suppl 1:i97-i98.

Luu P, Acher F, Bertrand HO, Fan J, Ngai J. Molecular determinants of ligand selectivity in a vertebrate odorant receptor. J Neurosci. 2004 24(45):10128-37.

Lin DM, Yang YH, Scolnick JA, Brunet LJ, Marsh H, Peng V, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J. Spatial patterns of gene expression in the olfactory bulb. Proc Natl Acad Sci U S A. 2004 101(34):12718-23.

Ngai J. Science imitates art: the cloning of mice from olfactory sensory neurons. Cell. 2004 116(5):636-7.

Diaz E, Yang YH, Ferreira T, Loh KC, Okazaki Y, Hayashizaki Y, Tessier-Lavigne M, Speed TP, Ngai J. Analysis of gene expression in the developing mouse retina. Proc Natl Acad Sci U S A. 2003 100(9):5491-6.

Diaz E, Ge Y, Yang YH, Loh KC, Serafini TA, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J, Scheiffele P. Molecular analysis of gene expression in the developing pontocerebellar projection system. Neuron. 2002 36(3):417-34.

Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002 30(4):e15.

Kratz E, Dugas JC, Ngai J. Odorant receptor gene regulation: implications from genomic organization. Trends Genet. 2002 18(1):29-34.

Dugas JC, Ngai J. Analysis and characterization of an odorant receptor gene cluster in the zebrafish genome. Genomics 2001 71: 53-65.

Fan J, Ngai J. Onset of odorant receptor gene expression during olfactory sensory neuron regeneration. Develop. Biol. 2001 229: 119-127.

Lin DM., Wang F, Lowe G, Gold GH, Axel R, Ngai J, Brunet L. Formation of precise synaptic connections in the olfactory bulb occurs in the absence of odorant-evoked neuronal activity. Neuron 2000 26: 69-80.

Speca DJ, Lin DM, Sorensen PW, Isacoff EY, Ngai J, Dittman AH. Functional identification of a goldfish odorant receptor. Neuron 1999 23: 487Ð498.

Lin DM, Ngai J. Development of the vertebrate main olfactory system. Curr Opin Neurobiol. 1999 9(1):74-8. Review.

Dynes JL, Ngai J. Pathfinding of olfactory neuron axons to stereotyped glomerular targets revealed by dynamic imaging in living zebrafish embryos. Neuron 1997 20: 1081-1091.

Barth AL, Dugas JC, Ngai J. Noncoordinate expression of odorant receptor genes tightly linked in the zebrafish genome. Neuron 1997 19: 359-369.

Brunet LJ, Gold GH, Ngai J. General anosmia caused by a targeted disruption of the mouse olfactory cyclic nucleotide-gated cation channel. Neuron 1996 17: 681-693.

Barth AL, Justice NJ, Ngai J. Asynchronous onset of odorant receptor expression in the developing zebrafish olfactory system. Neuron 1996 16: 23-34