Education
Duke University, Durham, North Carolina, USA
Ph.D., Computational Biology and Bioinformatics, 2012
Co-mentors: Professor Joshua Socolar and Professor David McClay
Thesis: Mechanistic modeling and experiments on cell fate specification in the sea urchin embryo
Tianjin University, Tianjin, China
B.E., Bioengineering, 2005
Mentor: Professor Pingsheng Ma
Thesis: Introduction of single point mutations to the carboxyl terminal of Sfi1p and its effect on yeast sporulation
Ph.D., Computational Biology and Bioinformatics, 2012
Co-mentors: Professor Joshua Socolar and Professor David McClay
Thesis: Mechanistic modeling and experiments on cell fate specification in the sea urchin embryo
Tianjin University, Tianjin, China
B.E., Bioengineering, 2005
Mentor: Professor Pingsheng Ma
Thesis: Introduction of single point mutations to the carboxyl terminal of Sfi1p and its effect on yeast sporulation
Positions
University of Southern California
01/2021 -- Present Assistant Professor, Department of Biological Sciences
Stanford University
05/2019 -- 12/2020 Basic Life Research Scientist, Department of Chemical and Systems Biology
05/2013 -- 04/2019 Postdoctoral Scholar, Department of Chemical and Systems Biology
Duke University
09/2012 -- 04/2013 Postdoctoral Associate, Department of Physics
07/2008 -- 08/2012 Research Assistant, Department of Biology
09/2006 -- 06/2008 Graduate Fellow, Computational Biology and Bioinformatics
01/2021 -- Present Assistant Professor, Department of Biological Sciences
Stanford University
05/2019 -- 12/2020 Basic Life Research Scientist, Department of Chemical and Systems Biology
05/2013 -- 04/2019 Postdoctoral Scholar, Department of Chemical and Systems Biology
Duke University
09/2012 -- 04/2013 Postdoctoral Associate, Department of Physics
07/2008 -- 08/2012 Research Assistant, Department of Biology
09/2006 -- 06/2008 Graduate Fellow, Computational Biology and Bioinformatics
Mentoring
University of Southern California
Graduate students
Ling Jin (Molecular and Computational Biology Ph.D. Program)
Jie Bai (Molecular and Computational Biology Ph.D. Program)
Undergraduate students
Betty Liu
Christopher Ahn
Carolyn Guo
Natalie Toma
Helen Ku
Stanford University
Ivan (Vanya) Zheludev (Biochemistry Ph.D. Program, rotation student, 2019)
Graduate students
Ling Jin (Molecular and Computational Biology Ph.D. Program)
Jie Bai (Molecular and Computational Biology Ph.D. Program)
Undergraduate students
Betty Liu
Christopher Ahn
Carolyn Guo
Natalie Toma
Helen Ku
Stanford University
Ivan (Vanya) Zheludev (Biochemistry Ph.D. Program, rotation student, 2019)
Teaching
USC
Instructor
Graduate Courses:
BISC 502B: Molecular Genetics and Biochemistry (Spring 2021, 2022)
BISC 502A: Molecular Genetics and Biochemistry (Fall 2022)
Undergraduate Courses:
BISC 372: Cell Biology (Spring 2023)
Stanford
Teaching Assistant
CSB 201: Chemical & Systems Biology Bootcamp
September 10 - September 14, 2015
Course instructor: Professor James Ferrell
Description: Supervised 6 first-year PhD students through a three-day research course project. Led the experiments, microscopy image data analysis and Q&A sessions.
Teaching Assistant
CSB 201: Chemical & Systems Biology Bootcamp
September 14 - September 18, 2016
Course instructor: Professor James Ferrell
Description: Supervised 7 first-year PhD students through a three-day research course project. Led the experiments, microscopy image data analysis and Q&A sessions.
Instructor
Graduate Courses:
BISC 502B: Molecular Genetics and Biochemistry (Spring 2021, 2022)
BISC 502A: Molecular Genetics and Biochemistry (Fall 2022)
Undergraduate Courses:
BISC 372: Cell Biology (Spring 2023)
Stanford
Teaching Assistant
CSB 201: Chemical & Systems Biology Bootcamp
September 10 - September 14, 2015
Course instructor: Professor James Ferrell
Description: Supervised 6 first-year PhD students through a three-day research course project. Led the experiments, microscopy image data analysis and Q&A sessions.
Teaching Assistant
CSB 201: Chemical & Systems Biology Bootcamp
September 14 - September 18, 2016
Course instructor: Professor James Ferrell
Description: Supervised 7 first-year PhD students through a three-day research course project. Led the experiments, microscopy image data analysis and Q&A sessions.
Service
Reviewer for:
SIAM Journal on Mathematics of Data Science
PLoS ONE
SIAM Journal on Mathematics of Data Science
PLoS ONE
Conference Presentations
(2017) Xianrui Cheng and James Ferrell.
Talk: Spatial propagation of apoptosis in Xenopus egg extracts via trigger waves.
Xenopus Resources and Emerging Technologies Meeting.
August 26 - 29, 2017, Marine Biological Laboratory, Woods Hole, MA.
(2015) Xianrui Cheng and James Ferrell.
Contributed talk: Apoptosis is spatially propagated by mitochondrion-dependent trigger waves.
The 3rd Annual Winter q-bio Meeting in Maui.
February 17 - 20, 2015, Maui, Hawai'i.
(2014) Xianrui Cheng and James Ferrell.
Poster prize
The 1st Annual Systems Biology Meeting.
May 27, 2014, Stanford, CA
(2012) Xianrui Cheng, Mengyang Sun and Joshua E. S. Socolar.
Poster: Autonomous Boolean modeling of developmental gene regulatory networks.
The 7th Annual Duke Systems Biology Symposium.
October 4, 2012, Durham, NC
(2011) Xianrui Cheng, Mengyang Sun and Joshua E. S. Socolar.
Spotlight talk: Autonomous Boolean models reveal timing constraints on embryonic developmental pattern formation.
The Fifth Annual International q-bio Conference on Cellular Information Processing.
August 10 - August 14, 2011, Santa Fe, NM
(2010) Xianrui Cheng and David R. McClay.
Poster: Skeletogenesis: under regulative control in the sea urchin embryo.
The Developmental Biology of the Sea Urchin XX.
April 27- May 1, 2011, Marine Biological Laboratory, Woods Hole, MA
(2010) Xianrui Cheng, David R. McClay and Joshua E. S. Socolar.
Poster: Boolean modeling of logic and timing in developmental regulatory networks.
The 5th Annual DREAM reverse engineering challenges, the 6th Annual RECOMB Satellite on Systems Biology, and the 7th Annual RECOMB Satellite on Regulatory Genomics.
November 16 - November 19, 2010, Columbia University, New York.
(2009) Xianrui Cheng, Joshua E. S. Socolar and David R. McClay.
Poster: An Autonomous Boolean Network Model for Sea Urchin Endomesoderm Specification.
The Developmental Biology of the Sea Urchin XIX.
September 30 - October 3, 2009, Marine Biological Laboratory, Woods Hole, MA.
Talk: Spatial propagation of apoptosis in Xenopus egg extracts via trigger waves.
Xenopus Resources and Emerging Technologies Meeting.
August 26 - 29, 2017, Marine Biological Laboratory, Woods Hole, MA.
(2015) Xianrui Cheng and James Ferrell.
Contributed talk: Apoptosis is spatially propagated by mitochondrion-dependent trigger waves.
The 3rd Annual Winter q-bio Meeting in Maui.
February 17 - 20, 2015, Maui, Hawai'i.
(2014) Xianrui Cheng and James Ferrell.
Poster prize
The 1st Annual Systems Biology Meeting.
May 27, 2014, Stanford, CA
(2012) Xianrui Cheng, Mengyang Sun and Joshua E. S. Socolar.
Poster: Autonomous Boolean modeling of developmental gene regulatory networks.
The 7th Annual Duke Systems Biology Symposium.
October 4, 2012, Durham, NC
(2011) Xianrui Cheng, Mengyang Sun and Joshua E. S. Socolar.
Spotlight talk: Autonomous Boolean models reveal timing constraints on embryonic developmental pattern formation.
The Fifth Annual International q-bio Conference on Cellular Information Processing.
August 10 - August 14, 2011, Santa Fe, NM
(2010) Xianrui Cheng and David R. McClay.
Poster: Skeletogenesis: under regulative control in the sea urchin embryo.
The Developmental Biology of the Sea Urchin XX.
April 27- May 1, 2011, Marine Biological Laboratory, Woods Hole, MA
(2010) Xianrui Cheng, David R. McClay and Joshua E. S. Socolar.
Poster: Boolean modeling of logic and timing in developmental regulatory networks.
The 5th Annual DREAM reverse engineering challenges, the 6th Annual RECOMB Satellite on Systems Biology, and the 7th Annual RECOMB Satellite on Regulatory Genomics.
November 16 - November 19, 2010, Columbia University, New York.
(2009) Xianrui Cheng, Joshua E. S. Socolar and David R. McClay.
Poster: An Autonomous Boolean Network Model for Sea Urchin Endomesoderm Specification.
The Developmental Biology of the Sea Urchin XIX.
September 30 - October 3, 2009, Marine Biological Laboratory, Woods Hole, MA.
Selected Graduate Courses
Genome tools and technologies
Design/analysis of algorithms
Introduction to statistical methods
Statistical methods in computational biology
Algorithms in computational biology
Nonlinear dynamics
Design/analysis of algorithms
Introduction to statistical methods
Statistical methods in computational biology
Algorithms in computational biology
Nonlinear dynamics
Skills
Programming:
Experimental skills:
Software skills:
- MATLAB: scientific computing, numerical analysis, cluster/parallel computing, GUI design/development, computer graphics/animation, image processing
- R: scientific computing, statistical analysis
- Perl: text mining, DNA/RNA/Protein sequence analysis, genomics
- Mathematica: scientific computing, symbolic algebra, graphics
- HTML/CSS
Experimental skills:
- standard molecular biology techniques: cloning, PCR, mutagenesis, etc.
- protein expression and purification
- quantitative real-time PCR (qPCR)
- recombinant protein production and purification
- Western blotting and quantitative analysis
- in situ hybridization: single/double color chromagenic/fluorescence in situ analysis
- microscopy: Fluorescent microscopy, confocal microscopy, image processing, tiling, stitching, image segmentation, intensity imaging and quantitative analysis
- micro-manipulation techniques: micro-injection, yeast tetrad dissection
Software skills:
- Operating systems: Windows, Linux, MacOS
- Software packages: LaTeX, Microsoft Word/Excel/PowerPoint, Adobe Illustrator/Photoshop, Graphviz, VectorNTI
Languages
Chinese (native), English (fluent)
Other Interests
Triathlon, rock climbing, swimming, weight lifting, jogging, hiking, piano, sculpture, drawing, comics, abstract mathematics