Steve Quake

Stephen R. Quake, D.Phil., Lee Otterson Professor, Departments of Bioengineering, Applied Physics and (by courtesy) Physics, Stanford University School of Medicine, Engineering, and Humanities & Sciences; Co-President, Chan Zuckerberg Biohub 

Research Description: Dr. Quake’s research program has made important contributions to multiple biomedical fields. His innovative technologies have been capitalized in research and clinical applications. His work on single cell RNA sequencing has resulted in the understanding and identification of cell physiologies in various tissues. One such project, in collaboration with Seung Kim and colleagues, is aimed at understanding the lineage, gene expression and epigenetic characteristics of normal somatic stem cells and premalignant or malignant cells from the human pancreas to define markers to identify and remove these cells from contaminated cell cultures intended for regenerative medicine. This work will build an openly accessible database for pancreas with lists of gene expression and epigenetic signatures that identify subpopulations. Quake’s group has also collaborated with Seung Kim to assess conversion of primary islet alpha-cells to beta- cells in a project supported by the NIH Beta-cell biology consortium (BCBC), Human Islet Resource Network (HIRN), and JDRF. Finally, Dr. Quake’s single cell RNA-profiling methods have been widely adopted by collaborating investigators in SDRC and others at Stanford, and in collaborations worldwide.

Selected relevant publications (Stanford DRC Members in BOLD):

  1. Camunas-Soler J, Dai XQ, Hang Y, Bautista A, Lyon J, Suzuki K, Kim SK, Quake SR, MacDonald PE. Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes. Cell Metab. 2020 May 5;31(5):1017-1031.e4. doi: 10.1016/j.cmet.2020.04.005. PMID: 32302527; PMCID: PMC7398125. [cites P30DK116074] 

  2. Enge Kim S, Whitener RL, Peiris H, Gu X, Chang CA, Lam JY, Camunas-Soler J, Park I, Bevacqua RJ, Tellez K, Quake SR, Lakey JRT, Bottino R, Ross PJ, Kim SK. Molecular and genetic regulation of pig pancreatic islet cell development. Development. 2020 Mar 30;147(6):dev186213. doi: 10.1242/dev.186213. PMID: 32108026; PMCID: PMC7132804. [cites P30DK116074] 

  3. Guler GD, Ning Y, Ku CJ, Phillips T, McCarthy E, Ellison CK, Bergamaschi A, Collin F, Lloyd P, Scott A, Antoine M, Wang W, Chau K, Ashworth A, Quake SR, Levy S. Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA. Nat Commun. 2020 Oct 19;11(1):5270. doi: 10.1038/s41467-020-18965-w. PMID: 33077732; PMCID: PMC7572413. 

  4. Wang W, Penland L, Gokce O, Croote D, Quake SR. High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis. BMC Genomics. 2018 Feb 13;19(1):140. doi: 10.1186/s12864-018-4512-5. PMID: 29439658; PMCID: PMC5811979.