Recent Publications

For full list, see Pubmed 

BioRxiv Papers

• Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis

  Wan Y, El Kholtei J, Jenie I, Colomer-Rosell M, Liu J, Navajas Acedo J, Du LY, Codina-Tobias M, Wang M, Sawh A, Lin E, Chuang T, Mango SE,Yu G, Bintu B, Schier AF
  August 2024

• Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis

  Liu J, Castillo-Hair SM, Du LY, Wang Y, Carte AN, Colomer-Rosell M, Yin C, Seelig G, Schier AF
  August 2024

• Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes
  Nichols ALA+, Shafer MER+*, Indermaur A, Rüegg A, Gonzalez-Dominguez R, Malinsky M, Sommer-Trembo C, Fritschi L, Salzburger W, Schier AF
  June 2024 +co-contribution, *corresponding

• Optogenetic control of Nodal signaling patterns
  McNamara HM, Jia BZ, Guyer A, Parot VJ, Dobbs C, Schier AF, Cohen AE, Lord ND
  April 2024

• Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion
  Wang Y, Liu J, Du LY, Wyss JL, Farrell JA, Schier AF
  December 2023

• The regulatory landscape of 5′ UTRs in translational control during zebrafish embryogenesis
  Reimão-Pinto MM, Castillo-Hair SM, Seelig G, Schier AF
  November 2023

• Frequent transitions from night-to-day activity after mass extinctions.
  Shafer MER, Nichols ALA, Schier AF, Salzburger W
  November 2023

Peer reviewed Papers

• The dynamics and functional impact of tRNA repertoires during early embryogenesis in zebrafish
  Reimão-Pinto MM, Behrens A, Forcelloni S, Fröhlich K, Kaya S, Nedialkova DD. EMBO J. October 2024

• Complete persistence of the primary somatosensory system in zebrafish
  Navajas Acedo J. Dev. Biol. July 2024 (BioRxiv December 2023)

• The evolution of developmental biology through conceptual and technological revolutions.
  Liberali P, Schier AF. Cell. June 2024

• Axis formation in annual killifish: Nodal coordinates morphogenesis in absence of Huluwa prepatterning.
  Abitua PB, Stump L, Aksel DC, Schier AF. Science. June 2024. (BioRxiv April 2021)

• A vertebrate family without a functional Hypocretin/Orexin arousal system.
  Bitsikas V, Cubizolles F, Schier AF. Current Biology. March 2024

• A single-cell time-lapse of mouse prenatal development from gastrula to birth.
  Qiu C, Martin BK, Welsh IC, Daza RM, Le T, Huang X, Nichols EK, Taylor ML, Fulton O, O’Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J
  Feb 2024 (BioRxiv April 2023)

• Regulation of Vg1 biogenesis during mesendoderm induction.
  Dingal PCDP, Carte AN, Montague TG, Suan Jr MEL, Schier AF. PNAS October 2023

• Basic science under threat: Lessons from the Skirball Institute.
  Sfeir A, Fishell G, Schier AF, Dustin ML, Gan WB, Joyner A, Lehmann R, Ron D, Roth D, Talbot WS, Yelon D, Zychlinsky A.
  Cell. 2022 Mar

• Gene family evolution underlies cell-type diversification in the hypothalamus of teleosts.
  Shafer MER, Sawh AN, Schier AF.
  Nat Ecol Evol. 2022 Jan

• The pattern of nodal morphogen signaling is shaped by co-receptor expression.
  Lord ND, Carte AN, Abitua PB, Schier AF.
  Elife. 2021 May

• Emergence of Neuronal Diversity during Vertebrate Brain Development.
  Raj B, Farrell JA, Liu J, El Kholtei J, Carte AN, Navajas Acedo J, Du LY, McKenna A, Relić Đ, Leslie JM, Schier AF.
  Neuron. 2020 Dec

• Cerebellar Neurodynamics Predict Decision Timing and Outcome on the Single-Trial Level
  Lin Q, Manley J, Helmreich M, Schlumm F, Li JM, Robson DN, Engert F, Schier AF, Nöbauer T, Vaziri A
  Cell. 2020 Feb 6

• Single-cell Biology: Beyond the Sum of Its Parts
  Schier AF.
  Nature Methods. 2020 Jan 6

• Zebrafish dscaml1 Deficiency Impairs Retinal Patterning and Oculomotor Function
  Ma M, Ramirez AD, Wang T, Roberts RL, Harmon KE, Schoppik D, Sharma A, Kuang C, Goei SL, Gagnon JA, Zimmerman S, Tsai SQ, Reyon D, Joung JK, Aksay ERF, Schier AF, Pan YA
  J Neuroscience. 2020 Jan 2

• Convergent Temperature Representations in Artificial and Biological Neural Networks.
  Haesemeyer M, Schier AF, Engert F.
  Neuron. 2019 Sep 25

• Zebrafish oxytocin neurons drive nocifensive behavior via brainstem premotor targets.
  Wee CL, Nikitchenko M, Wang WC, Luks-Morgan SJ, Song E, Gagnon JA, Randlett O, Bianco IH, Lacoste AMB, Glushenkova E, Barrios JP, Schier AF, Kunes S, Engert F, Douglass AD.
  Nat Neurosci. 2019 Sep

• Distributed Plasticity Drives Visual Habituation Learning in Larval Zebrafish.
  Randlett O, Haesemeyer M, Forkin G, Shoenhard H, Schier AF, Engert F, Granato M.
  Curr Biol. 2019 Apr 22

• Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions.
  Thyme SB, Pieper LM, Li EH, Pandey S, Wang Y, Morris NS, Sha C, Choi JW, Herrera KJ, Soucy ER, Zimmerman S, Randlett O, Greenwood J, McCarroll SA, Schier AF.
  Cell. 2019 Apr 4

• Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility.
  Goudarzi M, Berg K, Pieper LM, Schier AF.
  Elife. 2019 Jan 8

• Conserved regulation of Nodal-mediated left-right patterning in zebrafish and mouse
  Montague TG, Gagnon JA, Schier AF.
  Development 2018 Dec 10
  

• Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT.
  Raj B, Gagnon JA, Schier AF.
  Nat Protoc. 2018 Oct 23
  

• A Brain-wide Circuit Model of Heat-Evoked Swimming Behavior in Larval Zebrafish.
  Haesemeyer M, Robson DN, Li JM, Schier AF, Engert F.
  Neuron. 2018 May 16
  

• Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis.
  Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF.
  Science. 2018 Apr 26
  

• Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain
  Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF.
  Nat Biotechnol. 2018 Mar 28
  

• Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq.
  Pandey S, Shekhar K, Regev A, Schier AF.
  Curr Biol. 2018 Mar 9
  

• A Massively Parallel Reporter Assay of 3' UTR Sequences Identifies In Vivo Rules for mRNA Degradation.
  Rabani M, Pieper L, Chew GL, Schier AF.
  Mol Cell. 2017 Dec 21
  

• Nodal patterning without Lefty inhibitory feedback is functional but fragile.
  Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S, Aksel DC, Reyon D, Tsai SQ, Joung JK, Schier AF.
  Elife. 2017 Dec 7
  

• Zebrafish nanog is primarily required in extraembryonic tissue.
  Gagnon JA, Obbad K, Schier AF.
  Development. 2017 Nov 27. pii: dev.147793. doi: 10.1242/dev.147793. [Epub ahead of print]
  

• Vg1-Nodal heterodimers are the endogenous inducers of mesendoderm.
  Montague TG, Schier AF.
  Elife. 2017 Nov 15
  

• Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling.
  Norris ML, Pauli A, Gagnon JA, Lord ND, Rogers KW, Mosimann C, Zon LI, Schier AF.
  Elife. 2017 Nov 9
  

• Gaze-stabilizing central vestibular neurons project asymmetrically to extraocular motoneuron pools.
  Schoppik D, Bianco IH, Prober DA, Douglass AD, Robson DN, Li JMB, Greenwood JSF, Soucy E, Engert F, Schier AF.
  J Neurosci. 2017 Sep 29
  

• Internal guide RNA interactions interfere with Cas9-mediated cleavage.
  Thyme SB, Akhmetova L, Montague TG, Valen E, Schier AF.
  Nat Commun. 2016 Jun 10
  

• Whole organism lineage tracing by combinatorial and cumulative genome editing.
  McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J.
  Science. 2016 May 26.
  

• Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish.
  Chew GL, Pauli A, Schier AF.
  Nat Commun. 2016 May 24
  

• CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering.
  Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E.
  Nucleic Acids Res. 2016 May 16
  

• Polq-Mediated End Joining Is Essential for Surviving DNA Double-Strand Breaks during EarlyZebrafish Development.
  Thyme SB, Schier AF.
  Cell Rep. 2016 Apr 13
  

• The structure and timescales of heat perception in larval zebrafish.
  Haesemeyer M, Robson DN, Li JM, Schier AF, Engert F.
  Cell Syst. 2015 Nov 25
  

• Whole-brain activity mapping onto a zebrafish brain atlas.
  Randlett O, Wee CL, Naumann EA, Nnaemeka O, Schoppik D, Fitzgerald JE, Portugues R, Lacoste AM, Riegler C, Engert F, Schier AF.
  Nat Methods. 2015 Nov
  

• Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish.
  Pauli A, Montague TG, Lennox KA, Behlke MA, Schier AF.
  PLoS One. 2015 Oct 5
  

• A convergent and essential interneuron pathway for Mauthner-cell-mediated escapes.
  Lacoste AM, Schoppik D, Robson DN, Haesemeyer M, Portugues R, Li JM, Randlett O, Wee CL, Engert F, Schier AF.
  Curr Biol. 2015 May 6
  

• Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus.
  Merkle FT, Neuhausser WM, Santos D, Valen E, Gagnon JA, Maas K, Sandoe J, Schier AF, Eggan K.
  Cell Rep. 2015 Apr 29
  

• Response to Nodal morphogen gradient is determined by the kinetics of target gene induction.
  Dubrulle J, Jordan BM, Akhmetova L, Farrell JA, Kim SH, Solnica-Krezel L, Schier AF.
  Elife. 2015 Apr 14
  

• Spatial reconstruction of single-cell gene expression data.
  Satija R, Farrell JA, Gennert D, Schier AF, Regev A.
  Nat Biotechnol. 2015 Apr 13
  

• Evolutionarily conserved regulation of hypocretin neuron specification by Lhx9.
  Liu J, Merkle FT, Gandhi AV, Gagnon JA, Woods IG, Chiu CN, Shimogori T, Schier AF, Prober DA.
  Development. 2015 Mar 15
  

• Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms.
  Mundell NA, Beier KT, Pan YA, Lapan SW, Göz Aytürk D, Berezovskii VK, Wark AR, Drokhlyansky E, Bielecki J, Born RT, Schier AF, Cepko CL.
  J Comp Neurol. 2015 Feb 17
  

• Generation of neuropeptidergic hypothalamic neurons from human pluripotent stem cells.
  Merkle FT, Maroof A, Wataya T, Sasai Y, Studer L, Eggan K, Schier AF.
  Development. 2015 Feb 15
  

• Measuring protein stability in living zebrafish embryos using fluorescence decay after photoconversion (FDAP).
  Rogers KW, Blässle A, Schier AF, Müller P.
  J Vis Exp. 2015 Jan 28
  

• The study of psychiatric disease genes and drugs in zebrafish.
  Haesemeyer M, Schier AF.
  Curr Opin Neurobiol. 2015 Feb
  

• High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.
  Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo DJ, Pauli A, Hacohen N, Schier AF, Blackshear PJ, Friedman N, Amit I, Regev A.
  Cell. 2014 Dec 18
  

• Identifying (non-)coding RNAs and small peptides: challenges and opportunities.
  Pauli A, Valen E, Schier AF
  Bioessays. 2015 Jan
  

• Obituary: Walter J. Gehring (1939-2014)
  Schier AF
  Development. 2014 Sep
  

• Neuropeptidergic control of sleep and wakefulness.
  Richter C, Woods IG, Schier AF
  Annu Rev Neurosci. 2014 Jul
  

• CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing.
  Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E
  Nucleic Acids Res. 2014 Jul
  

• Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs.
  Gagnon JA, Valen E, Thyme SB, Huang P, Ahkmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF
  PLoS One. 2014 May 29
  

• Neuropeptidergic signaling partitions arousal behaviors in zebrafish.
  Woods IG1, Schoppik D, Shi VJ, Zimmerman S, Coleman HA, Greenwood J, Soucy ER, Schier AF
  J Neurosci. 2014 Feb 26
  

• Toddler: an embryonic signal that promotes cell movement via Apelin receptors.
  Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF
  Science 2014 Feb 14
  

• Canonical nucleosome organization at promoters forms during genome activation.
  Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS
  Genome Res. 2014 Feb
  

• Should I stay or should I go: neuromodulators of behavioral states.
  Schier AF
  Cell. 2013 Aug
  

• Zebrabow: Multispectral cell labeling for cell tracing and lineage analysis in zebrafish.
  Pan YA, Freundlich T, Weissman TA, Schoppik D, Wang XC, Zimmerman S, Ciruna B, Sanes JR, Lichtman JW, Schier AF
  Development. 2013 July

For full publication list see PubMed.