the Stephen Floor lab

Understanding how the information contained in RNA sequences
controls gene expression in development and cancer

Learn More

About the lab


What We Do

Our cells are like machines. Genes in our DNA are the instructions to produce each part (proteins, RNA, and other molecules). Each part must be accurately produced in the right amount for cells to work properly. Mistakes in these processes cause many diseases, including cancer.

Messenger RNA sequences instruct the cell what protein part to make and how much to make of it. Other RNA molecules also affect how cells work. Our lab studies how healthy cells make decisions and how decisions change in human diseases.

Left: phase separation like oil and water of RNA binding proteins and RNA into round foci under cellular stress.

A Scientific Description

We study the many ways RNA influences human gene expression. How do mRNA sequences specify protein production levels? How do changes to the biophysics of RNA in cells influence gene expression, and what role(s) do RNA chaperones play? How are these processes changed in human diseases, and can the changes be corrected?

The Floor lab uses genome editing, functional genomics, biochemistry, and cell biology to explore these and other questions. Learn more about our projects or recent work.

We are members of the Department of Cell and Tissue Biology & Helen Diller Family Comprehensive Cancer Center, and Biophysics, Biomedical Sciences, & Tetrad Graduate Programs.

Projects


RNA chaperones

Remodeling of RNA by DEAD-box RNA chaperones
DEAD-box proteins use the energy of ATP hydrolysis to remodel RNA structures and RNA-protein complexes. We study how DEAD-box proteins influence gene expression through mechanical work.

Transcript isoform translation

Translational output of the human transcriptome
Most human genes give rise to multiple mRNAs through alternative mRNA processing. Each mRNA may include different coding sequences, regulatory sequences, or both. We measure how well different mRNAs are translated and use this information to control transgene expression.

RNA in disease

RNA in developmental disorders and cancer
DEAD-box proteins and other aspects of RNA biology are altered in numerous human diseases. We are studying how alteration of the DEAD-box protein DDX3 drives formation of the brain tumor medulloblastoma, and other RNA-related processes in disease.

RNA granules

Cell biophysics & phase separation of RNA
RNA molecules exist in a crowded cytoplasm. RNA and RNA-binding proteins partition into phase-separated RNA granules under some conditions. We investigate the role of RNA chaperones like DEAD-box proteins in this balance.

The lab

Or most of us anyway

Lab members


...

Stephen N. Floor, PhD

Principal Investigator (CV)

stephen.floor@ucsf.edu

B.S. Physics, Computer Science: Univ. of Kansas
Ph.D.: UCSF Biophysics (John Gross lab)
Postdoc: Berkeley (Doudna lab)

...

Margaret Gadek

Graduate Student (BMS/MSTP)

B.S. Biological Sciences:
University of Chicago

...

Angela Gao

Technician

B.S. Mechanical Engineering:
University of California, Los Angeles

...

Ziad Jowhar

Graduate Student (BMS/MSTP)

B.S. Biology, Neuroscience: Emory University

...

Sam Kwok

Technician

B.A. Molecular and Cell Biology:
UC Berkeley

...

José Liboy Lugo

Graduate Student (Tetrad)

B.S. Industrial Biotechnology:
University of Puerto Rico, Mayaguez

UCSF Discovery Fellow

NIH/NIGMS F31 Fellow

...

Yizhu Lin, PhD

Postdoc

B.S. Biology, University of Science and Technology of China
Ph.D.: Carnegie Mellon University Biological Sciences (Joel McManus lab)

...

Jesslyn Park

Graduate Student (Tetrad)

B.S. Chemistry, Winthrop University

...

Srivats Venkataramanan, PhD

Postdoc

B. Tech & M. Tech: Indian Inst. of Tech. Madras, Biotechnology
PhD: UCLA Molecular, Cell, and Dev. Biology
(Tracy Johnson lab)

NIGMS F32 Fellow

...

Kevin Wilkins

Graduate Student (BMS)

B.S. Biologial Science, Medieval Studies:
Notre Dame

TRDRP Predoctoral Scholar

...

Albert Xu

Graduate Student (BMS/MSTP)

BS: UC Berkeley, Molecular and Cell Biology



Lab alumni



Name

Srivats Venkataramanan
Lorenzo Calviello
Ann Deng
Lesly Montano Zolano
Peter Bowman-Davis
Luisa Arake de Tacca
Emily Ehsan
Bao Thai
Malvika Tejura
Katie Blackwell

Time in lab

2018-2021
2018-2021
2019-2020
2020
2019-2020
2018-2019
2019
2017-2019
2017-2019
2018

Role

Postdoc
Postdoc
Technician
Biotech Partners Intern
High School Student
Joint Graduate Student with Jamie Cate
Visiting Undergrad
Technician
Technician
SRTP Summer Student

Next position

Scientist at Sardona Therapeutics
Group leader at the Human Technopole
Graduate School at Johns Hopkins
Returned to Berkeley High School
Returned to Justin-Siena High School
Scientist at Acrigen Biosciences
Returned to Cornell
MD/PhD program at Arizona
RA at Ultima Genomics. Now: Grad student at UW
Returned to UT Dallas. Now: Grad student at MIT

Select publications


DDX3 depletion represses translation of mRNAs with complex 5′ UTRs

Calviello L, Venkataramanan S, et al., Landthaler M, and Floor SN. (2021)

DDX3X and DDX3Y are redundant in protein synthesis

Venkataramanan S, Calviello L, Wilkins K, and Floor SN. (2020)

Pathogenic DDX3X mutations impair RNA metabolism and neurogenesis during fetal cortical development.

Lennox AL, Hoye ML, et al., Floor SN, Silver DL, and Sherr EH. (2020)

For a complete list of publications please click here or grab an RSS feed

Contact us


We're always excited to talk with people interested in the lab! Applicants, journalists, educators - get in touch!

Postdoc applicants email Stephen with your CV and why you'd like to work in the lab.
For info about what it's like to be a postdoc at UCSF and associated policies, click here.

Rotation students: multiple projects available! Email Stephen to discuss.

Prospective graduate students please apply through one of the UCSF graduate programs.

The Floor lab welcomes people of any race, religion, national origin, gender, political affiliation, sexual orientation, and eligible age or disability.

513 Parnassus Ave
HSW 740
San Francisco, CA 94143

News


July 2021: Welcome to Jesslyn joining as a graduate student and Angela joining as a technician!

June 2021: Stephen is a Pew Scholar in the Biomedical Sciences!

June 2021: José is awarded a NIGMS F31 fellowship!

May 2021: Welcome to Margaret Gadek, joining as a MSTP graduate student!

April 2021: Our paper with the Landthaler lab is published!

March 2021: Welcome to Sam Kwok, joining as a technician!

November 2020: Ziad joined as a BMS/MSTP graduate student!

September 2020: Two new preprints posted in the same week!

September 2020: Congratulations to José for being selected as a UCSF Discovery Fellow!

May 2020: Welcome to Peter Bowman-Davis and Lesly Montano Zolano who will join us for the summer!

May 2020: Albert Xu joined as a BMS/MSTP graduate student!

May 2020: Congratulations to José for passing his qualifying exam!

March 2020: Our paper with the Silver and Sherr labs is published!

August 2019: Welcome to Ann Deng, a new technician, and José Liboy who has joined the lab!

June 2019: Kevin is awarded a predoctoral fellowship from the TRDRP!

June 2019: Welcome to Emily Ehsan and Albert Xu who are joining us for the summer!

May 2019: Our preprint identifying the set of mRNAs that require DDX3 for translation is out!

May 2019: Congrats to Kevin, PhD candidate, for passing his qualifying exam!

December 2018: Welcome to Yizhu Lin, our new postdoc joining from Joel McManus's lab!

October 2018: The lab is funded by the NIH New Innovator program!

July 2018: Welcome to Lorenzo Calviello, our new postdoc joining us from Uwe Ohler's lab!

July 2018: Welcome to Luisa Tacca, a visiting graduate student from Jamie Cate's lab at UC Berkeley!

June 2018: Welcome to Kevin Wilkins, our first graduate student, and Katie Blackwell for the summer from SRTP!

March 2018: Welcome to Srivats Venkataramanan, our first postdoc from Tracy Johnson's lab!

February 2018: The lab is funded by the TRDRP for medulloblastoma research!

December 2017: The lab is funded by the UCSF PBBR!

July 2017: Bao and Malvika join in starting the lab!