Research

Microfluidics

We build microfluidic and engineering tools for the high throughput analysis of single cells. We design new droplet microfluidic devices and assemble them into workflows for systems biology studies.

Molecular Tools

We develop methods to profile cell-cell interactions. Current projects are focused on genome-wide CRISPR screens and viral tracing of CNS networks.

HIV Latency

A major interest of the lab is understanding HIV latency in CD4 T cells. We use new droplet microfluidic sorting methods to study the transcriptional profiles of infected cells.

Postdoc positions

Single cell profiling of HIV-infected cells

Our lab aims to understand the molecular mechanisms that control HIV latency. Specifically what, if any, are the unique properties of CD4 cells that harbor replication competent HIV provirus during long term antiretroviral therapy (ART)? We have developed a unique method to detect and sort HIV+ cells using ultra-high throughput droplet microfluidics. We seek a talented postdoctoral researcher to use this method to study HIV latency ex vivo.

Single cell interaction networks

We are interested in developing tools to map cellular connections in the mouse brain at massive scale. Our approach is to combine virus tracing, molecular barcoding, and single cell sequencing to study both the connections and transcriptional profiles of cellular networks. We seek a talented postdoctoral researcher to further develop and apply this method to new experimental systems and animal models of disease.

News

June, 2021. Iain receives an NIH New Innovator award to study CNS immune cell interactions using RABID-seq.
May, 2021. Sakshi and Kevin join the lab!
April 22, 2021. Rabies barcode interaction detection followed by sequencing (RABID-seq) is published in Science.
April 15, 2021. Iain receives a NIH NIAID K22 transition award to continue work on PCR-activated cell sorting of latent HIV.
Feb, 2021. Our paper describing a hybrid droplet-valve microfluidic device for assembling rationally reduced DNA libraries is published in PNAS. In collaboration with Bruk Mensa and Bill DeGrado, we use this technique study domain coupling in the bacterial histidine kinase CpxA.
Jan, 2021. The lab opens. Many thanks to the tremendous mentors and collaborators who made this journey possible. Special thanks to Adam Abate, Francisco Quintana and Eli Boritz!
Nov, 2020. Our paper describing a method for targeted barcoding without sorting is published in Analytical Chemistry.
Feb, 2020. Mike Wheeler’s scRNA-seq paper deconstructing astrocyte heterogeneity during experimental autoimmunity is published in Nature.

Join

Training and advancing people of all races, gender identities, and ages, regardless of disability status, is a priority of this lab.

Postdoc positions – Please email Iain with a brief description of your interests, a CV, and the names of three references.
Bioinformatician – We are recruiting a full time bioinformatician to support projects in the lab.
PhD Students – Students are encouraged to apply to the Berkeley/UCSF Graduate Program in Bioengineering and join the lab for a rotation.
Undergraduates – Cal undergrads are encouraged to apply to projects posted on URAP. Due to the volume of inquiries, it may not always be possible to respond to email requests outside of this program.

Contact

Clark Lab

Department of Bioengineering
University of California, Berkeley
392 Stanley Hall
Berkeley, CA 94720

Iain Clark, PhD

Assistant Professor, Bioengineering
University of California, Berkeley
Office: 374 Stanley Hall MC #3220
Berkeley, CA 94720

iain.c.clark [at] berkeley.edu
607-592-8821