
Tatjana Sauka-Spengler, Ph.D.
Investigator
Academia
• Dr. Ruth Williams—Assistant Professor, University of Manchester, UK
• Dr. Zhiyuan Hu—Assistant Professor, University of Wuhan, China
• Dr. Mara Artibani—Assistant Professor, University of Oxford UK
• Dr. Gunes Taylor—Assistant Professor, University of Edinburgh, UK
• Dr. Filipa Simoes Costa---Assistant Professor, University of Oxford, UK
• Dr. Dorit Hockman-- Assistant Professor, University of Cape Town, South Africa
• Dr. Aden Farrow—Assistant Professor, University of New Hampshire, USA
• Dr. Paola Betancur—Assistant Professor, University of San Francisco, USA
• Dr. Jane Khudyakov—Assistant Professor, University of the Pacific
• Dr. Pablo Strobl-Mazzulla—Assistant Professor, IIB-INTECH, Chascomus, Argentina.
Biotech
• Dr. Irving Ling,
• Dr. Bruno Steinkraus
• Dr. Muhammad Hanifi
• Dr. Amy Kenyon
• Dr. Daniel Fountain
Medical
• Dr. Upeka Senanayake,
• Dr. Muhammad Hanifi
• Dr. Daniel Fountain
Currently Postdocs in Academia
• Dr. Lucy Wheatley
• Dr. Oana Pelea
• Dr. Andrew Ramos
• Dr. Martyna Lukoseviciute
• Dr. Ivan Candido Ferreira
• Dr. Vanessa Chong
Support Staff
o Julianna Haug
o Erin Hiscock

Current Project: Neural crest (NC) cells are a vertebrate-specific multipotent cell population whose evolutionary origins remain incompletely understood. Although non-vertebrate chordates possess cell populations with partial neural crest–like properties, the cis-regulatory mechanisms underlying the emergence of neural crest identity remain unclear. In this project, we combine deep learning–based chromatin accessibility models within silico evolution to investigate how neural crest enhancers may evolve across chordates. Using convolutional neural network (CNN) models trained on chicken cranial NC ATAC-seq data, we evolved synthetic enhancers from random DNA sequences. In vivo assays in chick embryos demonstrated that active neural crest enhancers can emerge after 15 rounds of evolution. Large-scale evolution of random genomic sequences showed that in silico evolution is strongly influenced by the starting sequence. We are currently using this property to identify evolvable regions in the genomes of zebrafish and non-vertebrate chordates and investigate the motif features in the evolvable regions.



Ph.D. Student
Sauka-Spengler Lab
Joined: 2025
We study how P-E interactions contribute to cell-type-specific gene regulation during zebrafish gastrulation. Using high-temporal-resolution scMultiome and computational methods like SCENIC+ and RegVelo, we infer TF–enhancer–effector gene regulatory modules and their role in cell fate decisions. We use Micro-Capture-C to dissect how enhancers/repressors/other elements interact with the promoter in those modules. Ongoing efforts include functional perturbation of TFs/CREs and using additional modalities to explain the mechanism.

Ph.D. Student
B.S., Biology, Nara Women’s University, Japan
M.S., Biology, Kyoto University, Japan
Joined: 2023
Neural crest (NC) cells are multipotent progenitors that give rise to a remarkable diversity of cell types, including neurons, mesenchymal derivatives, and pigment cells. This developmental versatility makes them an ideal model for understanding how tissue-specific gene regulatory networks (GRNs) control cell fate decisions. While key regulators and GRNs governing mesenchymal NC development have been extensively characterized, those underlying neuronal NC specification remain poorly understood. My research aims to identify the key regulators of cranial neuronal NC specification and reconstruct the GRNs underlying this process in zebrafish embryos by integrating single-cell RNA sequencing, chromatin accessibility profiling, and spatial transcriptomics. This work will provide new insights into how cranial neuronal NC identity is established during vertebrate development.

Ph.D. Student
Sauka-Spengler Lab, Sanchez Alvarado Lab
B.S./M.S., Biological Sciences, Indian Institute of Science Education and Research, Thiruvananthapuram, India
Joined: 2023
Nothobranchius furzeri (African annual killifish), found in ephemeral ponds in eastern and south-eastern Africa live through harsh conditions during which the ponds that they live in dry up. These harsh conditions have led them to evolve a very peculiar embryonic cycle in which they are capable of undergoing diapause at 3 different stages of embryonic development [1]. One of these diapause (diapause 2) corresponds with neural crest (NC) development when the neural crest cells (NCCs) are migrating throughout the embryo to give rise to different tissues in the developing embryo. Furthermore, NC development is much slower in the annual killifish compared to other teleost model organism commonly used to study NC processes, like zebrafish. Understanding how these migrating NCCs retain the memory of migration even after months in diapause 2 and end up reaching their destination is very intriguing. Furthermore, no one has ever looked at NC development in the killifish and therefore understanding how these processes are regulated is crucial. My long-term goal is to dissect the gene regulatory network of neural crest cells during induction, migration and differentiation in killifish understanding how they maintain the NC development program intact during diapause 2.
Ultimately, we hope to clarify why specific melanocyte populations are particularly vulnerable in defined disease states and guide future strategies for targeted therapeutic intervention and regenerative medicine.

Research Technician
Sauka-Spengler Lab
I’m a lab technician with the Sauka-Spengler Lab. I’m currently working on the development of a CRISPR cas9 prime editing tool to work within zebrafish. In addition to this I am also working alongside our aquatics and invertebrate teams to establish a new working model organism Tunicate C.robusta

Ph.D. Student
Sauka-Spengler Lab
Joined: 2025

Investigator
Stowers Institute for Medical Research
Development and Regeneration, Genetics and Genomics, Evolutionary Biology, Molecular and Cell Biology, Systems Biology
Laboratory Rotation; Thesis Laboratory
Tatjana Sauka-Spengler, Ph.D., a physicist and developmental geneticist, is a Professor of developmental genomics and gene regulation at the University of Oxford. She joined the Stowers Institute as an Investigator in 2022.
