Genentech: Shiqi Xie | Principal Scientist, Discovery Oncology, Research Biology

Scientists / Our Scientists

"Proficiency in both the dry- and wet-lab skills is the key to success in modern biology research."

Years at Genentech

Publications at Genentech

Awards & Honors

I was trained as a wet-lab scientist during graduate school, investigating the innate immune response during virus infection. And then I was fascinated by the latest genomic technologies and joined Gary Hon’s lab in UT Southwestern, Dallas for my postdoc trainings. During which I learned the construction of NGS libraries as well as building computational tools for large-scale data analysis. I developed a highly multiplexed functional screen assay for enhancers in which the CRISPR-based enhancer perturbation is combined with the single-cell RNA-seq readout. I joined Genentech in 2020 and lead a team in to perform the large-scale single-cell functional genomics assays. I strongly believe that the combination of both the wet and dry lab is the key to success in the modern biology researches and my lab is actively working on both aspects.

Featured Publication

Multiplexed engineering and analysis of combinatorial enhancer activity in single cells

Molecular cell, 2017

S Xie, J Duan, B Li, P Zhou, GC Hon

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My lab is focused on understanding the impact of genes, regulator elements and genomic variations on genome function and phenotypes. We leverage the latest single-cell genomics assays to acquire rich phenotypic readout coupled with systematic perturbations. The lab has three general research goals: 1) understanding of drug response in complex model systems; 2) evaluation of diseases-associated mutations to identify new therapeutic targets and 3) identification of key genes for cell fate engineering.

Chemically-inducible CRISPR/Cas9 circuits for ultra-high dynamic range gene perturbation

Nature Communications,

Rajini Srinivasan; Tao Sun; Azalia Sandles; Diana Wu; Liang Wang; Hetal Patel; Ryan Pabalate; Maram Bader; Amy J. Heidersbach; Clark Ho; Shiqi Xie; Andrew H. Ng; Benjamin Haley

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Dynamic transitioning between MAPK-driven and WNT-driven cell states drives intestinal cancer and shapes therapy response

Nature Genetics, ISSN: 10614036

Amanda R. Moore; Brian Biehs; Noelyn M. Kljavin; Thi Thu Thao Nguyen; Akansha M. Shah; Jeremy B. Burton; Honglin Jiang; Jenille Tan; Deepankar Chakroborty; Lisa Wang; Nayan Chaudhary; Dongze He; William Lin; Kathryn Mesh; Xin Ye; Kamakoti P. Bhat; Lisa Tai; Shiqi Xie; Weilan Ye; Lisa M. McGinnis; Shiva Malek; Sandra P. Melo; Frédéric J. de Sauvage

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KRAS Codon-Specific Mutations Differentially Toggle PI3K Pathway Signaling and Alter Sensitivity to Inavolisib (GDC-0077)

Molecular Cancer Therapeutics,

Kyung W. Song; Christy C. Ong; Eva Lin; Jeffrey T. Lau; Nicole M. Sodir; Dexter X. Jin; Katherine E. Hutchinson; Shiqi Xie; Jenille Tan; Yuxin Liang; Zora D. Modrusan; Scott E. Martin; Danilo Maddalo; Marc Hafner; Anwesha Dey

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Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition

Nature Communications, ISSN: 20411723

Sayantanee Paul; Thijs Hagenbeek; Julien Tremblay; Vasumathi Kameswaran; Christy C. Ong; Chad Liu; Alissa D. Guarnaccia; James A. Mondo; Peter L. Hsu; Noelyn Kljavin; Bartosz Czech; Janina Smola; Dieu An H. Nguyen; Jennifer A. Lacap; Trang Pham; Yuxin Liang; Robert A. Blake; Luca Gerosa; Matthew R. Grimmer; Shiqi Xie; Bence Daniel; Xiaosai Yao; Anwesha Dey

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Epiregulon: Single-cell transcription factor activity inference to predict drug response and drivers of cell states

Nature Communications,

Tomasz Włodarczyk; Aaron T.L. Lun; Diana Wu; Minyi Shi; Xiaofen Ye; Shreya Menon; Shushan Toneyan; Kerstin Seidel; Liang Wang; Jenille Tan; Shangyang Chen; Timothy J. Keyes; Aleksander Chlebowski; Adrian Waddell; Wei Zhou; Yangmeng Wang; Qiuyue Yuan; Yu Guo; Liangfu Chen; Bence Dániel; Antonina Hafner; Meng He; Alejandro Martinez Chibly; Yuxin Liang; Zhana Duren; Ciara Metcalfe; Marc Hafner; Christian W. Siebel; M. Ryan Corces; Robert L. Yauch; Shiqi Xie; Xiaosai Yao

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Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes

Genome Biology, ISSN: 1474760X 14747596

Yihan Wang; Daniel A. Armendariz; Lei Wang; Huan Zhao; Shiqi Xie; Gary C. Hon

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Systematic perturbation screens identify regulators of inflammatory macrophage states and a role for TNF mRNA m6A modification

Nature Genetics, ISSN: 10614036

Simone M. Haag; Shiqi Xie; Celine Eidenschenk; Jean-Philippe Fortin; Marinella G. Callow; Michael Costa; Aaron T. L. Lun; Christian Cox; Sunny Z. Wu; Rachana Pradhan; Jaclyn Y. Lock; Julia A. Kuhn; Loryn Holokai; Minh Thai; Emily C. Freund; Ariane Nissenbaum; Mary E. Keir; Christopher J. Bohlen; Scott E. Martin; Kathryn R. Geiger-Schuller; Hussein A. Hejase; Brian L. Yaspan; Sandra Melo Carlos; Shannon J. Turley; Aditya Murthy

View on Scopus

Transcriptional Regulation of the Hippo Pathway: Current Understanding and Insights from Single-Cell Technologies

Cells, ISSN: 20734409

Sayantanee Paul; Shiqi Xie; Xiaosai Yao; Anwesha Dey

View on Scopus

UT Southwestern Medical Center, Dallas, TX, Postdoc – 2020
Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China, Ph.D. in Microbiology – 2014
Sichuan University, Chengdu, China, B.S. in Biotechnology – 2008

AHA Postdoc Fellowship, American Heart Association – 2016

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Shiqi Xie

Principal Scientist, Discovery Oncology, Research Biology

Featured Publication

Multiplexed engineering and analysis of combinatorial enhancer activity in single cells