Stanford
Gu Lab

Publications

Selected Publications

Members of Gu Lab in Bold, * Co-authors

Minimally Invasive Testing (Cancer, Infectious Disease, Other):

  • W. Gu, A. M. Rauschecker, E. Hsu, K. C. Zorn, Y. Sucu, S. Federman, A. Gopez, S. Arevalo, H. A. Sample, E. Talevich, E. D. Nguyen, M. Gottschall, B. Nourbakhsh, C. A. Gold, B. A. C. Cree, V. C. Douglas, M. B. Richie, M. P. Shah, S. A. Josephson, J. M. Gelfand, S. Miller, L. Wang, T. Tihan, J. L. DeRisi, C. Y. Chiu, M. R. Wilson, Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid. JAMA Neurol (2021), doi:10.1001/jamaneurol.2021.3088.
  • Gu, W., Talevich, E., Hsu, E., Qi, Z., Urisman, A., Federman, S., Gopez, A., Arevalo, S., Gottschall, M., Liao, L., et al. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. Genome Med 13, 98 (2021).
  • (Gu, W., Deng, X., Lee, M.)*, Sucu, Y., Arevalo, S., Stryke, D., Federman, S., Gopez, A., Reyes, K., Zorn, K., Sample, H., Yu, G., Ishpuniani, G., Briggs, B., Chow, E. D., Berger, A., Wilson, M., Wang, C., Hsu, E., Miller, S., DeRisi, J., Chiu, C.  “Rapid Pathogen Detection by Metagenomic Next-Generation Sequencing of Infected Body Fluids”, Nature Med, 27, 115–124 (2021). https://doi.org/10.1038/s41591-020-1105-z
  • Pan, W., Gu, W., Nagpal, S., Gephart, M., Quake, S.R. “Brain tumor mutations detected in cerebral spinal fluid” Clin. Chem. 2015, 61(3), 514-22.

Noninvasive Prenatal Testing:

  • (Fan, H.C., Gu, W.)*, Wang J.B., Blumenfeld, Y.J., El-Sayed, Y.Y., Quake, S.R. “Noninvasive Prenatal Measurement of the Fetal Genome” Nature 2012, 489(7415), 326.
  • Gu, W., Koh, W., Blumenfeld, Y.J., El-Sayed, Y.Y., Hudgins, L., Hintz, S., Quake, S.R. “Noninvasive Prenatal Diagnosis of Methylmalonic Acidemia” Genet. Med. 2014, 16(7), 564-7.

Technology Development:

  • (Gu, W., Crawford, E.)*, O’Donovan, B., Wilson, M., Chow, E., Retallack, H., DeRisi, J. “Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications” Genome Biology 2016, 17(41).
  • Gu, W., Zhu, X., Futai, N., Cho, B. S., Takayama, S. “Computerized Microfluidic Cell Culture Using Elastomeric Channels and Braille Displays” Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15861-15866.

COVID-19:

  • (W. Gu, X. Deng)*, K. Reyes, E. Hsu, C. Wang, A. Sotomayor-Gonzalez, S. Federman, B. Bushnell, S. Miller, C. Chiu, Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel. Clin Infect Dis, 2020, doi:10.1093/cid/ciaa599.
  • (X. Deng, W. Gu, S. Federman, L. du Plessis)*, O. G. Pybus, N. R. Faria, C. Wang, G. Yu, B. Bushnell, C.-Y. Pan, H. Guevara, A. Sotomayor-Gonzalez, K. Zorn, A. Gopez, V. Servellita, E. Hsu, S. Miller, T. Bedford, A. L. Greninger, P. Roychoudhury, L. M. Starita, M. Famulare, H. Y. Chu, J. Shendure, K. R. Jerome, C. Anderson, K. Gangavarapu, M. Zeller, E. Spencer, K. G. Andersen, D. MacCannell, C. R. Paden, Y. Li, J. Zhang, S. Tong, G. Armstrong, S. Morrow, M. Willis, B. T. Matyas, S. Mase, O. Kasirye, M. Park, G. Masinde, C. Chan, A. T. Yu, S. J. Chai, E. Villarino, B. Bonin, D. A. Wadford, C. Y. Chiu, Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science. 369, 582–587 (2020).
  • (A. P. Cheng , M. Cheng , W. Gu*), J. Lenz , E. Hsu , E. Schurr , G. Bourque , M. Bourgey , J. Ritz , F. Marty , C. Y. Chiu , D. Vinh, I. D. Vlaminck, “Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity”, Cell Med. 2021.

 

All Publications

24) C. Loy, L. Ahmann, (I. De Vlaminck, W. Gu)* Liquid Biopsy based on Cell-Free DNA and RNA. Annu. Rev. Biomed. Eng. (2024), doi: 10.1146/annurev-bioeng-110222-111259.

23) W. Gu, A. M. Rauschecker, E. Hsu, K. C. Zorn, Y. Sucu, S. Federman, A. Gopez, S. Arevalo, H. A. Sample, E. Talevich, E. D. Nguyen, M. Gottschall, B. Nourbakhsh, C. A. Gold, B. A. C. Cree, V. C. Douglas, M. B. Richie, M. P. Shah, S. A. Josephson, J. M. Gelfand, S. Miller, L. Wang, T. Tihan, J. L. DeRisi, C. Y. Chiu, M. R. Wilson, Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid. JAMA Neurol (2021), doi:10.1001/jamaneurol.2021.3088.

22) Gu, W., Talevich, E., Hsu, E., Qi, Z., Urisman, A., Federman, S., Gopez, A., Arevalo, S., Gottschall, M., Liao, L., et al. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. Genome Med, 13, 98 (2021). doi: 10.1186/s13073-021-00912-z

21) (A. P. Cheng , M. Cheng , W. Gu)*, J. Lenz , E. Hsu , E. Schurr , G. Bourque , M. Bourgey , J. Ritz , F. Marty , C. Y. Chiu , D. Vinh, I. D. Vlaminck, “Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity”, Cell Med. 2021. https://doi.org/10.1016/j.medj.2021.01.001

20) (Gu, W., Deng, X., Lee, M.)*, Sucu, Y., Arevalo, S., Stryke, D., Federman, S., Gopez, A., Reyes, K., Zorn, K., Sample, H., Yu, G., Ishpuniani, G., Briggs, B., Chow, E. D., Berger, A., Wilson, M., Wang, C., Hsu, E., Miller, S., DeRisi, J., Chiu, C.  “Rapid Pathogen Detection by Metagenomic Next-Generation Sequencing of Infected Body Fluids”, Nature Med, 27, 115–124 (2021). https://doi.org/10.1038/s41591-020-1105-z

19) (W. Gu, X. Deng)*, K. Reyes, E. Hsu, C. Wang, A. Sotomayor-Gonzalez, S. Federman, B. Bushnell, S. Miller, C. Chiu, Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel. Clin Infect Dis, doi:10.1093/cid/ciaa599.

18) (X. Deng, W. Gu, S. Federman, L. du Plessis)*, O. G. Pybus, N. R. Faria, C. Wang, G. Yu, B. Bushnell, C.-Y. Pan, H. Guevara, A. Sotomayor-Gonzalez, K. Zorn, A. Gopez, V. Servellita, E. Hsu, S. Miller, T. Bedford, A. L. Greninger, P. Roychoudhury, L. M. Starita, M. Famulare, H. Y. Chu, J. Shendure, K. R. Jerome, C. Anderson, K. Gangavarapu, M. Zeller, E. Spencer, K. G. Andersen, D. MacCannell, C. R. Paden, Y. Li, J. Zhang, S. Tong, G. Armstrong, S. Morrow, M. Willis, B. T. Matyas, S. Mase, O. Kasirye, M. Park, G. Masinde, C. Chan, A. T. Yu, S. J. Chai, E. Villarino, B. Bonin, D. A. Wadford, C. Y. Chiu, Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science. 369, 582–587 (2020). 10.1126/science.abb9263

17) T. Bedford, A. L. Greninger, P. Roychoudhury, L. M. Starita, M. Famulare, M.-L. Huang, A. Nalla, G. Pepper, A. Reinhardt, H. Xie, L. Shrestha, T. N. Nguyen, A. Adler, E. Brandstetter, S. Cho, D. Giroux, P. D. Han, K. Fay, C. D. Frazar, M. Ilcisin, K. Lacombe, J. Lee, A. Kiavand, M. Richardson, T. R. Sibley, M. Truong, C. R. Wolf, D. A. Nickerson, M. J. Rieder, J. A. Englund, T. S. F. S. Investigators‡, J. Hadfield, E. B. Hodcroft, J. Huddleston, L. H. Moncla, N. F. Müller, R. A. Neher, X. Deng, W. Gu, S. Federman, C. Chiu, J. S. Duchin, R. Gautom, G. Melly, B. Hiatt, P. Dykema, S. Lindquist, K. Queen, Y. Tao, A. Uehara, S. Tong, D. MacCannell, G. L. Armstrong, G. S. Baird, H. Y. Chu, J. Shendure, K. R. Jerome, Cryptic transmission of SARS-CoV-2 in Washington state. Science (2020), doi:10.1126/science.abc0523.

16) J. D. Whitman, J. Hiatt, C. T. Mowery, B. R. Shy, R. Yu, T. N. Yamamoto, U. Rathore, G. M. Goldgof, C. Whitty, J. M. Woo, A. E. Gallman, T. E. Miller, A. G. Levine, D. N. Nguyen, S. P. Bapat, J. Balcerek, S. Bylsma, A. M. Lyons, S. Li, A. W. Wong, E. M. Gillis-Buck, Z. B. Steinhart, Y. Lee, R. Apathy, M. J. Lipke, J. A. Smith, T. Zheng, I. C. Boothby, E. Isaza, J. Chan, D. D. Acenas, J. Lee, T. A. Macrae, T. S. Kyaw, D. Wu, D. L. Ng, W. Gu, V. A. York, H. A. Eskandarian, P. C. Callaway, L. Warrier, M. E. Moreno, J. Levan, L. Torres, L. Farrington, R. Loudermilk, K. Koshal, K. C. Zorn, W. F. Garcia-Beltran, D. Yang, M. G. Astudillo, B. E. Bernstein, J. A. Gelfand, E. T. Ryan, R. C. Charles, A. J. Iafrate, J. K. Lennerz, S. Miller, C. Y. Chiu, S. L. Stramer, M. R. Wilson, A. Manglik, C. J. Ye, N. J. Krogan, M. S. Anderson, J. G. Cyster, J. D. Ernst, A. H. B. Wu, K. L. Lynch, C. Bern, P. D. Hsu, A. Marson, “Test performance evaluation of SARS-CoV-2 serological assays” Nature Biotechnology, (2020), doi:10.1038/s41587-020-0659-0.

15) C. R. Zamecnik, J. V. Rajan, K. A. Yamauchi, S. A. Mann, R. P. Loudermilk, G. M. Sowa, K. C. Zorn, B. D. Alvarenga, C. Gaebler, M. Caskey, M. Stone, P. J. Norris, W. Gu, C. Y. Chiu, D. Ng, J. R. Byrnes, X. X. Zhou, J. A. Wells, D. F. Robbiani, M. C. Nussenzweig, J. L. DeRisi, M. R. Wilson, ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens. Cell Reports. Medicine, 100123 (2020). doi:10.1016/j.xcrm.2020.100123.

14) D. Ng, G. Goldgof, B. Shy, A. Levine, J. Balcerek, S. P. Bapat, J. Prostko, M. Rodgers, K. Coller, S. Pearce, S. Franz, L. Du, M. Stone, S. Pillai, A. Sotomayor-Gonzalez, V. Servellita, C. Sanchez-San Martin, A. Granados, D. R. Glasner, L. M. Han, K. Truong, N. Akagi, D. N. Nguyen, N. Neumann, D. Qazi, E. Hsu, W. Gu, Y. A. Santos, B. Custer, V. Green, P. Williamson, N. K. Hills, C. M. Lu, J. D. Whitman, S. Stramer, C. Wang, K. Reyes, J. Hakim, K. Sujishi, F. Alazzeh, L. Pharm, C.-Y. Oon, S. Miller, T. Kurtz, J. Hackett, G. Simmons, M. P. Busch, C. Y. Chiu, Nat. Commun., 11, 4698 (2020). 10.1038/s41467-020-18468-8

13) J. P. Broughton, X. Deng, G. Yu, C. L. Fasching, V. Servellita, J. Singh, X. Miao, J. A. Streithorst, A. Granados, A. Sotomayor-Gonzalez, K. Zorn, A. Gopez, E. Hsu, W. Gu, S. Miller, C.-Y. Pan, H. Guevara, D. A. Wadford, J. S. Chen, C. Y. Chiu, CRISPR–Cas12-based detection of SARS-CoV-2. Nature Biotechnology, 1–5 (2020). 10.1038/s41587-020-0513-4

12) (Gu, W., Crawford, E.)*, O’Donovan, B., Wilson, M., Chow, E., Retallack, H., DeRisi, J. “Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications” Genome Biology 2016, 17(41). doi: 10.1186/s13059-016-0904-5

11) Pan, W., Gu, W., Nagpal, S., Gephart, M., Quake, S.R. “Brain tumor mutations detected in cerebral spinal fluid” Clin. Chem. 2015, 61(3), 514-22. doi: 10.1373/clinchem.2014.235457

10) Gu, W., Koh, W., Blumenfeld, Y.J., El-Sayed, Y.Y., Hudgins, L., Hintz, S., Quake, S.R. “Noninvasive Prenatal Diagnosis of Methylmalonic Acidemia” Genet. Med. 2014, 16(7), 564-7. http://dx.doi.org/10.1038/gim.2013.194

9)  (Fan, H.C., Gu, W.)*, Wang J.B., Blumenfeld, Y.J., El-Sayed, Y.Y., Quake, S.R. “Noninvasive Prenatal Measurement of the Fetal Genome” Nature 2012, 489(7415), 326. 10.1038/nature11251

8)  Chen, H., Gu, W., Cellar, N., Kennedy, R., Takayama, S., and Meiners, J.  “Electromechanical properties of pressure-actuated PDMS microfluidic push-down valves”  Anal. Chem.  2008, 80, 6110-6113.

7)  Gu, W., Chen, H., Tung, Y.C., Meiners, J.C., Takayama, S.  “Multiplexed Hydraulic Valve Actuation Using Ionic Liquid Filled Soft Channels and Braille Displays” Appl. Phys. Lett. 2007, 90(3), 033505.

6)   Futai, N., Gu, W., Song, J.W., Takayama, S.  “Handheld recirculation system and customized media for microfluidic cell culture” Lab Chip 2006, 6, 149-154.

5) Chung, Y., Zhu, X., Gu, W., Smith, G., Takayama S. “Microscale Integrated Sperm Sorter” Methods Mol. Biol.  2006, 321, 227-44.

4) Song, J. W., Gu, W., Futai, N., Warner, K. A., Nor, J. E., Takayama, S. “Computer-Controlled Microcirculatory System for Endothelial Cell Culture and Shearing” Anal. Chem. 2005, 77, 3993-3999.

3) Huh, D., Gu, W., Kamotani, Y., Grotberg, J. B., Takayama, S. “Microfluidics for Flow Cytometric Analysis of Cells and Particles” Physiol. Meas. 2005, 26, R73-98.

2)  Gu, W., Zhu, X., Futai, N., Cho, B. S., Takayama, S. “Computerized Microfluidic Cell Culture Using Elastomeric Channels and Braille Displays” Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15861-15866. (Cover Image)

1) Futai, N., Gu, W., Takayama, S. “Rapid Prototyping of Microstructures with Bell-Shaped Cross-Sections and Its Application to Deformation-Based Microfluidic Valves” Adv. Mater. 2004, 16, 1320-1323.