Our research focuses on two areas: Vertebrate Development and Behavior. We mostly use zebrafish as a model system because genetic, genomic and imaging approaches can be combined to study complex behaviors and developmental processes in a vertebrate. But we are also beginning to use other fish (killifish, cavefish, loach, cichlids) and mouse as model systems. We are also committed to training the next generation of leaders in biomedical research.
Development
During development, cells acquire specialized fates and migrate to specific positions to form the embryo and generate functional organs. Our goal is to understand the molecular and cellular mechanisms underlying this process. How do signals move through fields of cells and elicit concentration dependent effects? How do cells differentiate into specialized cell types? How do cells arrive at the right place at the right time? And how can embryogenesis be both robust and flexible?
To address these questions, we use genetic, genomic, biophysical and in vivo imaging approaches in zebrafish. Most recently, we have developed single-cell technologies to reconstruct the lineage and specification trajectories of thousands of cells. We are applying these methods to construct lineage trees that capture the major decisions made by cells as they differentiate, with the long-term goal of understanding the rules and statistics of development.
Recent publications:
The pattern of nodal morphogen signaling is shaped by co-receptor expression.
Lord ND, Carte AN, Abitua PB, Schier AF.
Elife. 2021 MayEmergence 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 DecIndividual 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 8Conserved regulation of Nodal-mediated left-right patterning in zebrafish and mouse
Montague TG, Gagnon JA, Schier AF.
Development 2018 Dec 10Large-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
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis.
Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF.
Science. 2018 Apr 26Simultaneous 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
Sleep, wakefulness and other behaviors
We spend a third of our life asleep but the mechanisms that control sleep and waking states remain largely elusive. We seek to identify molecules and neurons that regulate sleep and the neuropeptides that promote sleep and wakefulness. What are the neurons that detect sleep deprivation and regulate recovery sleep? What is the role of genes that have been implicated in human sleep disorders? To address these questions and to study the basis of additional behaviors, we use genetic, genomic, and imaging approaches in fish and mouse.
Recent publications:
Gene family evolution underlies cell-type diversification in the hypothalamus of teleosts.
Shafer MER, Sawh AN, Schier AF.
Nat Ecol Evol. 2022 JanConvergent Temperature Representations in Artificial and Biological Neural Networks.
Haesemeyer M, Schier AF, Engert F.
Neuron. 2019 Sep 25Phenotypic 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 4A 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 16Comprehensive 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
Training the next generation of scientists
In addition to performing creative and rigorous research, we are committed to training the next generation of leaders in biomedicine. Graduate students are coached to become independent scientists, and postdoctoral fellows are mentored to develop the skills and projects that provide the foundations for their own labs. Following their training in the Schier lab 33 of 40 postdocs started their own labs at leading institutions such as Princeton, Caltech, UCLA, UCSD, NYU School of Medicine, University of Toronto, MPI Dresden, MPI Tuebingen, IMP Vienna, University of Utah, University College London, University of Cambridge and Yale. Please contact Alex if you are interested in joining us (alex.schier@unibas.ch).