Dr. Lei Qi

Associate Professor

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Biography

Dr. Lei (Stanley) Qi is an Associate Professor of Bioengineering at Stanford University, where he has been a faculty member since 2014. He is a member of the Chan Zuckerberg Biohub and serves as an Institute Scholar. Dr. Qi completed his Bachelor's degree in Mathematics and Physics at Tsinghua University, and earned both a Master's and a PhD in Bioengineering from the University of California, Berkeley. His research primarily focuses on CRISPR technology and its applications in genome engineering. His lab is known for pioneering the use of nuclease-deactivated Cas9 for targeted gene regulation through methods established as CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa). The lab's research integrates bioengineering, computer science, and machine learning to develop systems for multiplexed control of gene expression, real-time visualization of chromatin transcriptional dynamics, and synthetic cell–cell communication, particularly focusing on the interactions between immune cells and neurons. Throughout his career, Dr. Qi has received several accolades including the NIH Director's Independence Award, Pew Biomedical Scholar, and the NSF CAREER Award. His ongoing projects include the development of first-in-human clinical testing technology for treating facioscapulohumeral muscular dystrophy (FSHD), highlighting the translational potential of his research efforts. Dr. Qi continuously aims to identify generalizable rules linking molecular programs to systems-level physiology and disease trajectories, paving the way for next-generation therapeutics.

Research Interests

CRISPR Technology Genome Engineering Synthetic Biology Gene Regulation Computational Biology Cell Communication

Experience

Associate Professor

2022-01-01 — Present

Stanford University • Stanford, California

Member of the Institute and investigator in the Chan Zuckerberg Biohub.

Assistant Professor

2014-01-01 — 2022-01-01

Stanford University • Stanford, California

Started as a faculty member, focusing on CRISPR technology and genome editing.

Systems Biology Fellow

2012-01-01 — 2014-01-01

University of California San Francisco • San Francisco, California

Fellow focusing on systems biology.

Awards

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NIH Director's Independence Award

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Pew Biomedical Scholar

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Alfred P. Sloan Fellow

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Frontiers Science Award

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35 Innovators 35

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UC Berkeley Bioengineering Rising Star

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SN 10: Scientists Watch

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ACS Synthetic Biology Young Innovator Award

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NSF CAREER Award

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Thomas Salma Haider Biomedical Breakthrough Lectureship

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Blavatnik National Awards Young Scientists Finalist

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Kenneth Fong Young Investigator Award

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Elected Fellow AIMBE

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NIH Director’s Pioneer Award

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NIH TARGETED Prize

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Stein Innovation Award

Patents

Room Temperature-Stable CRISPRKit

U.S. Provisional Patent Application 63/791,209; 63/792,074 2025-06-01

CRISPR-Cas Guide Nucleic Acids Methods Use Thereof

U.S. Provisional Patent Application 63/762,301 2025-01-01

Method Composition Targeted Receptor-Mediated Programmable Macromolecule Delivery

U.S. Provisional Patent Application 63/606,711 2024-12-05

Composition Method Autonomous RNA Switches Translational Control

U.S. Provisional Patent Application 63/623,679 2024-11-12

Manipulating Spatial RNA Localization

U.S. Provisional Patent Application 63/594,147 2024-10-23

Engineered Nucleases, Compositions, Methods Use Thereof

12/054,756 2024-08-06

Multiplexed RNA Regulation Platform Primary Immune Cell Engineering

U.S. Provisional Patent Application 63/400,578 2023-08-24

Synthetic Miniature CRISPR-Cas System Eukaryotic Genome Engineering

18/174,552 2023-02-24

Gene Editing Delivery Myeloid Cells Promote Wound Healing

18/729,844 2023-01-24

Composition Method Valency Controlled Receptor Systems Cell Engineering Therapy

18/704,007 2022-11-15

Nuclease Systems Genetic Engineering

11/447,774 2022-09-20

Composition Method Universal Pseudotyped Retroviruses

U.S. Provisional Patent Application 63/405,720 2022-08-21

Compositions Methods Using Focused Ultrasound Multiplexed Gene Expression Control

U.S. Provisional Patent Application 62/347,259 2022-08-21

CRISPR/Cas Transcriptional Modulation

11/254,933 2022-02-22

Synthetic Cas12a Enhanced Multiplex Gene Control Editing

18/546,177 2022-02-11

Composition Method High-Multiplexed Genome Engineering Using Synthetic CRISPR Arrays

18/261,953 2022-01-18

Knock-in Large DNA Long-term High Genomic Expression

18/251,941 2021-11-10

Compositions Methods Identifying Using Stem Cell Differentiation Markers

17/496,275 2021-10-07

Mesophilic Argonaute Systems Uses Thereof

17/464,635 2021-09-01

Synthetic Oligomerization Systems Cell Engineering Therapy

18/007,283 2021-07-28

Systems Methods Viral Genome Targeting

17/911,079 2021-03-21

Optimized Small Guide RNAs Methods Use

10/822,606 2020-11-11

Chimeric Proteins Methods Regulating Gene Expression

10/457,961 2019-10-29

Systems Methods Polynucleotide Spatial Organization

provisional patent application 62/722,684 2018-09-01

Recombinant Chimeric Receptors Antigen Sensing Genome Manipulation

9,856,497 2018-01-02

Methods Compositions Controlling Gene Expression RNA Processing

9/745,610 2017-08-29

Methods Compositions RNA-Directed Target DNA Modification RNA-Directed Modulation Transcription

Patent App. 13/842,859 2013-03-15

Synthetic Transcriptional Control Elements Methods Generating Using Elements

9/593,338 2012-09-27

Courses

BIOE 141A BIOE 141B BIOE 191 BIOE 392 NEPR 299 STEMREM 299 BIOE 391 NEPR 399 STEMREM 399 CSB 370 STEMREM 370 BIOE 191X MATSCI 300 BIOE 299B STEMREM 199

Requirements for Stanford University

Doctorate Program
Requirements
GPA Requirement
Required:3.5
TOEFL
Listening
Required:26
Reading
Required:26
Writing
Required:26
Speaking
Required:26
Total
Required:100
GRE General
Verbal
Required:160
Quantitative
Required:165
Analytical Writing
Required:4.5
Overall
Required:4.5
Prerequisites
Bachelor degree from an accredited institution Strong background in mathematics and programming
Application Checklist
  • Statement of Purpose
  • Three letters of recommendation
  • Official transcripts
  • Resume/CV
Specialization Notes

The Computer Science department emphasizes research potential. GRE General is currently optional but recommended for some tracks.