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:
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 2024Dissecting 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 2024The regulatory landscape of 5′ UTRs in translational control during zebrafish embryogenesis
Reimão-Pinto MM, Castillo-Hair SM, Seelig G, Schier AF. Dev. Cell. January 2025 (BioRxiv November 2023)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. Dev. Cell. November 2024 (BioRxiv December 2023)The lives of cells, recorded
Askary A+, Chen W+, Choi J+, Du LY+, Elowitz MB, Gagnon JA, Schier AF, Seidel S+, Shendure J, Stadler T, Tran M+. Nat Rev Genet November 2024. +equal contributionThe 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 2024Complete 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 2024Axis 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)
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:
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 +equal contribution, *correspondingFrequent transitions from night-to-day activity after mass extinctions.
Shafer MER, Nichols ALA, Schier AF, Salzburger W
November 2023A vertebrate family without a functional Hypocretin/Orexin arousal system.
Bitsikas V, Cubizolles F, Schier AF. Current Biology. March 2024Gene 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 4
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).