SHARIATI LAB

Understanding and Engineering Cell Fate

Join Us

Research

Synthetic Development

We use self-organizing properties of stem cells to build embryo-like structures

How cells make decsions?

We use biochemical and imaging approaches to determine fundamental principles of cell fate decsions

Engineering Cell Fate

We use genome and epigenome editing tools to control cell fate decsion in stem cells

Publications

Programmable stem cell-based models of human embryos

In this forum article, we discuss programmable stem cell-based models and their potential to understand early days human embryogenesis.

Link to Paper

CRISPRa-programmed embryo model

We programmed embryonic stem cells to self-organize into embryo-like structures—using only minimal epigenome editing (Lodewijk and Kozuki et al, 2025, Cell Stem Cell).

Featured in UCSC News and GEN news

Link to Paper

A precise and reversible method to disrupt transcription factor binding at specific genomic elements — featured in Shariati et al., Molecular Cell (2019).

Link to Paper

Exit from G0 state (quiescence)

Here we show that E2F1, a key cell cycle transcription factor, activates target genes without large-scale chromatin remodeling, redefining transcription factor–chromatin (Lodewijk, bioRxiv, Under Review, 2025).

Link to Paper

Our deep-learning model and software for segmentation and tracking single cells in time-lapse movies (Zargari et al, Cell Reports Methods, 2023).

Featured in UCSC News

Link to Paper

A customized CycleGAN model that boosts cell segmentation by generating realistic synthetic training images — Zargari et al., iScience (2023).

Featured in UCSC News

Link to Paper

A customized CycleGAN model that boosts cell tracking by generating realistic synthetic time-lapse videos of cells for training — Zargari et al., iScience (2025).

Link to Paper

Microtechnology-based methods for organoid models

Nature Microsystems & Nanoengineering

Link to Paper

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

Nature, 2016

Link to Paper

Zygotic Genome Activation in Vertebrates

Dev Cell, 2019

Link to Paper

Google Scholar Link

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Team

Ali Shariati, Principal Investigator

Ben Topacio, Visiting Scholar

Gerrald Lodewijk, Postdoc Fellow

Lida Langroudi, Postdoc Fellow

Estefania Sanchez-Vasquez, Postdoc Fellow

Seungho Lee, PhD Student (BME)

Carly Guiltinan, Postdoc Fellow

Abolfazl Zargari, PhD, Visiting Scholar

Eliana Moreno, Undergrad Researcher (BME)

Sofia Naderi, Undergrad Researcher (BME)

Ellison Lee, Undergrad Researcher (BME)

Amelia Sim, Undergrad Researcher (BME)

Avlyn Singer, Undergrad Researcher (BME)

Alia Azadi, Undergrad Researcher (BME)

Sayaka Kozuki

Subsequent Position: PhD Student at Caltech

Clara Han

Subsequent Position: Graduate Student at UC San Diego

Sage Brill

Subsequent Position: Postbac at Fred Hutchinson Cancer Center

Megna Chalamala

Subsequent Position: Research Specialist at UCSF

Silvart Arabian

Subsequent Position:

Znala Williams

Subsequent Position: UCLA PhD Student

Nathan Cook

Subsequent Position: UC Davis, PhD Student

Kimia Kashani

Subsequent Position: Dental School

Celine Neudorf

Subsequent Position: UCSC Grad Student

Rana Rahimi

Subsequent Position: Research Associate (Biotech)

Arshia Kapil

Subsequent Position: grad student at UCSC

Jonah Pierce

Subsequent Position: Research Associate at Arsenal Biotech

Lucy Suarez

Subsequent Position:

Taylor Ziccardi

Subsequent Position: Lab Manager at USC

Dami Ibrahim

Subsequent Position:

Shivani Rao

Subsequent Position: Grad student at UCB

Former Lab Members

Teaching

Stem Cell Engineering course covers the emerging concepts and technologies in the stem cell field. We will cover basic biology of stem cells as well as their engineering for improving human life. We will also discuss how different disciplines are coming together to generate synthetic tissues from stem cells. In addition, the potential of genome editing technologies for treating and modelling human diseases will be discussed.

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Computational Biology Tools

How do we sequence genomes? How do we represent genes and genomes? How do we compare genes across species? What can we learn from high-throughput sequencing data such as RNA-Sequencing or ATAC-Seq? What quantitative information is encoded in microscopy images? This course will focus on algorithms and tools that will prepare you to answer such questions.

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Cinema

A 3D projection of CRISPR-Programmed mouse pre-gasturlation embryo model

Dynamics of the MAPK signaling in single embryonic stem cells

A 3D representation of CRISPRa-induced embryonic patterns

Cell cycle progression in single embryonic stem cells

G0 Cells (Red) entering G1 by a single transcription factor (Green)

Contact/Join

Postdoctoral Position

We are currently looking for a postdoctoral fellow to join the lab. Postdoctoral fellows will receive interdisciplinary training by using computational and experimental approaches to understand stem cell biology broadly.

As your postdoc advisor, I will support you to reach the career goals that you set for yourself. Please email me (alish@ucsc.edu) a short cover letter stating your scientific background and interest, your CV and names/addresses of your advisors. Informal inquiries are welcomed!

Applicants from underrepresented groups in sciences are highly encouraged to apply.

Graduate Students

Students who are enrolled in Biomolecular Engineering and Bioinformatics (BMEB), Chemical Biology, Biochemistry and Biophysics (CB3) and Molecular, Cell and Developmental Biology (MCD) at UCSC can contact me to find out more about our research projects. Please email me (alish@ucsc.edu) to discuss rotation 2-3 weeks before you plan to start in the lab.

The success of my students is one of my top priorities. I don’t think there is a “one size fit all” mentorship strategy. I will, however, ensure fairness and will care about your success (however you define it!).

Applicants from underrepresented groups in sciences are highly encouraged to apply.

Undergraduate Students

UCSC undergrads are welcomed to email me (alish@ucsc.edu) their CV to explore research opportunities in my lab. In your email, please mention which projects you would like to contribute to and a rough estimate of how much time you can potentially commit to research. I look forward to hearing from you.

Students from underrepresented groups in sciences are highly encouraged to apply.