Hanlee P. Ji

Medical oncologist, GI specialist

Assistant Professor of Medicine (Oncology)

Gastrointestinal (GI) Cancer Program

  • 875 Blake Wilbur Drive
  • Palo Alto, CA 94304
  • Phone: 650-498-6000
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Professional Education

Residency: University Of Iowa Hospitals and Clinics (1996) IA

Fellowship: Stanford University Hospital -Internal Medicine Residency Training Program (2005) CA

Board Certification: Medical Oncology, American Board of Internal Medicine (2004)

Residency: University of Washington (2001) WA

Medical Education: John Hopkins University School of Medicine (1994) MD

B.A., Reed College, Biology

M.D., Johns Hopkins University, Medicine

Honors & Awards

Research Scholar Award, American Cancer Society (2013)

Clinical Scientist Development Award, Doris Duke Charitable Foundation (2009)

Physician Scientist Early Career Award, Howard Hughes Medical Institute (2008)

Merit Award for Research Achievement, American Society Clinical Oncology Foundation (2006)

American Association Cancer Research, Scholar-in-Training Award for Research Achievement (2005)

Physician-Scientist Fellowship Award, Howard Hughes Medical Institute (1998)

Administrative Appointments

Senior Associate Director, Stanford Genome Technology Center, 2008

Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture
Li, X., Nadauld, L., Ootani, A., Corney, D. C., Pai, R. K., & Kuo, C. J. (2014). Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture. NATURE MEDICINE, 20(7), 769-777.

A programmable method for massively parallel targeted sequencing.
Hopmans, E. S., Natsoulis, G., Bell, J. M., Grimes, S. M., Sieh, W., & Ji, H. P. (2014). A programmable method for massively parallel targeted sequencing. Nucleic acids research, 42(10).

High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR.
Miotke, L., Lau, B. T., Rumma, R. T., & Ji, H. P. (2014). High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR. Analytical chemistry, 86(5), 2618-2624.

RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing.
Cushing, A., Flaherty, P., Hopmans, E., Bell, J. M., & Ji, H. P. (2013). RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing. BMC research notes, 6, 206-?.

Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis.
Lee, H., Flaherty, P., & Ji, H. P. (2013). Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis. BMC medical genomics, 6, 54-?.

Identification of Insertion Deletion Mutations from Deep Targeted Resequencing.
Natsoulis, G., Zhang, N., Welch, K., Bell, J., & Ji, H. P. (2013). Identification of Insertion Deletion Mutations from Deep Targeted Resequencing. Journal of data mining in genomics & proteomics, 4(3).

DETECTING MUTATIONS IN MIXED SAMPLE SEQUENCING DATA USING EMPIRICAL BAYES
Muralidharan, O., Natsoulis, G., Bell, J., Ji, H., & Zhang, N. R. (2012). DETECTING MUTATIONS IN MIXED SAMPLE SEQUENCING DATA USING EMPIRICAL BAYES. ANNALS OF APPLIED STATISTICS, 6(3), 1047-1067.

Improving bioinformatic pipelines for exome variant calling
Ji, H. P. (2012). Improving bioinformatic pipelines for exome variant calling. GENOME MEDICINE, 4.

Performance comparison of whole-genome sequencing platforms
Lam, H. Yk., Clark, M. J., Chen, R., Chen, R., Natsoulis, G., & Snyder, M. (2012). Performance comparison of whole-genome sequencing platforms. NATURE BIOTECHNOLOGY, 30(1), 78-U118.

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome
Newburger, D. E., Natsoulis, G., Grimes, S., Bell, J. M., Davis, R. W., & Ji, H. P. (2012). The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. NUCLEIC ACIDS RESEARCH, 40(D1), D1137-D1143.

A cross-sample statistical model for SNP detection in short-read sequencing data
Muralidharan, O., Natsoulis, G., Bell, J., Newburger, D., Xu, H., & Zhang, N. (2012). A cross-sample statistical model for SNP detection in short-read sequencing data. NUCLEIC ACIDS RESEARCH, 40(1).

Quantitative and Sensitive Detection of Cancer Genome Amplifications from Formalin Fixed Paraffin Embedded Tumors with Droplet Digital PCR.
Nadauld, L., Regan, J. F., Miotke, L., Pai, R. K., Longacre, T. A., & Ji, H. P. (2012). Quantitative and Sensitive Detection of Cancer Genome Amplifications from Formalin Fixed Paraffin Embedded Tumors with Droplet Digital PCR. Translational medicine (Sunnyvale, Calif.), 2(2).

Identification of a novel deletion mutant strain in Saccharomyces cerevisiae that results in a microsatellite instability phenotype.
Ji, H. P., Morales, S., Welch, K., Yuen, C., Farnam, K., & Ford, J. M. (2012). Identification of a novel deletion mutant strain in Saccharomyces cerevisiae that results in a microsatellite instability phenotype. BioDiscovery, (1).

Ultrasensitive detection of rare mutations using next-generation targeted resequencing
Flaherty, P., Natsoulis, G., Muralidharan, O., Winters, M., Buenrostro, J., & Ji, H. P. (2012). Ultrasensitive detection of rare mutations using next-generation targeted resequencing. NUCLEIC ACIDS RESEARCH, 40(1).

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.
Newburger, D. E., Natsoulis, G., Grimes, S., Bell, J. M., Davis, R. W., & Ji, H. P. (2012). The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. Nucleic acids research, 40(Database issue), D1137-43.

Targeted sequencing library preparation by genomic DNA circularization
Myllykangas, S., Natsoulis, G., Bell, J. M., & Ji, H. P. (2011). Targeted sequencing library preparation by genomic DNA circularization. BMC BIOTECHNOLOGY.

Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing
Myllykangas, S., Buenrostro, J. D., Natsoulis, G., Bell, J. M., & Ji, H. P. (2011). Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing. NATURE BIOTECHNOLOGY, 29(11), 1024-U95.

A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing
Natsoulis, G., Bell, J. M., Xu, H., Buenrostro, J. D., Ordonez, H., & Ji, H. P. (2011). A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. PLOS ONE, 6(6).

Genetic-based biomarkers and next-generation sequencing: the future of personalized care in colorectal cancer
Kim, R. Y., Xu, H., Myllykangas, S., & Ji, H. (2011). Genetic-based biomarkers and next-generation sequencing: the future of personalized care in colorectal cancer. PERSONALIZED MEDICINE, 8(3), 331-345.

Oncogenic BRAF Mutation with CDKN2A Inactivation Is Characteristic of a Subset of Pediatric Malignant Astrocytomas
Schiffman, J. D., Hodgson, J. G., VandenBerg, S. R., Flaherty, P., Polley, M.-Y. C., & James, C. D. (2010). Oncogenic BRAF Mutation with CDKN2A Inactivation Is Characteristic of a Subset of Pediatric Malignant Astrocytomas. CANCER RESEARCH, 70(2), 512-519.

Detecting simultaneous changepoints in multiple sequences.
Zhang, N. R., Siegmund, D. O., Ji, H., & Li, J. Z. (2010). Detecting simultaneous changepoints in multiple sequences. Biometrika, 97(3), 631-645.

Targeted deep resequencing of the human cancer genome using next-generation technologies
Myllykangas, S., & Ji, H. P. (2010). Targeted deep resequencing of the human cancer genome using next-generation technologies. BIOTECHNOLOGY AND GENETIC ENGINEERING REVIEWS, VOL 27, 27, 135-158.

Identification of a biomarker panel using a multiplex proximity ligation assay improves accuracy of pancreatic cancer diagnosis
Chang, S. T., Zahn, J. M., Horecka, J., Kunz, P. L., Ford, J. M., & Koong, A. C. (2009). Identification of a biomarker panel using a multiplex proximity ligation assay improves accuracy of pancreatic cancer diagnosis. JOURNAL OF TRANSLATIONAL MEDICINE, 7.

Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia
Schiffman, J. D., Wang, Y., McPherson, L. A., Welch, K., Zhang, N., & Ji, H. P. (2009). Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia. CANCER GENETICS AND CYTOGENETICS, 193(1), 9-18.

Disperse-a software system for design of selector probes for exon resequencing applications
Stenberg, J., Zhang, M., & Ji, H. (2009). Disperse-a software system for design of selector probes for exon resequencing applications. BIOINFORMATICS, 25(5), 666-667.

Molecular inversion probe assay for allelic quantitation.
Ji, H., & Welch, K. (2009). Molecular inversion probe assay for allelic quantitation. Methods in molecular biology (Clifton, N.J.), 556, 67-87.

Next-generation DNA sequencing
Shendure, J., & Ji, H. (2008). Next-generation DNA sequencing. NATURE BIOTECHNOLOGY, 26(10), 1135-1145.

Multigene amplification and massively parallel sequencing for cancer mutation discovery
Dahl, F., Stenberg, J., Fredriksson, S., Welch, K., Zhang, M., & Ji, H. (2007). Multigene amplification and massively parallel sequencing for cancer mutation discovery. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104(22), 9387-9392.

Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector
Fredriksson, S., Baner, J., Dahl, F., Chu, A., Ji, H., & Davis, R. W. (2007). Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. NUCLEIC ACIDS RESEARCH, 35(7).

Multiplexed protein detection by proximity ligation for cancer biomarker validation
Fredriksson, S., Dixon, W., Ji, H., Koong, A. C., Mindrinos, M., & Davis, R. W. (2007). Multiplexed protein detection by proximity ligation for cancer biomarker validation. NATURE METHODS, 4(4), 327-329.

Under-expression of Kalirin-7 increases iNOS activity in cultured cells and correlates to elevated iNOS activity in Alzheimer's disease hippocampus
Youn, Hs., Ji, I., Ji, H. P., Markesbery, W. R., & Ji, T. H. (2007). Under-expression of Kalirin-7 increases iNOS activity in cultured cells and correlates to elevated iNOS activity in Alzheimer's disease hippocampus. JOURNAL OF ALZHEIMERS DISEASE, 12(3), 271-281.

Reproducibility Probability Score - incorporating measurement variability across laboratories for gene selection
Lin, G., He, X., Ji, H., Shi, L., Davis, R. W., & Zhong, S. (2006). Reproducibility Probability Score - incorporating measurement variability across laboratories for gene selection. NATURE BIOTECHNOLOGY, 24(12), 1476-1477.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., & Slikker, W. (2006). The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. NATURE BIOTECHNOLOGY, 24(9), 1151-1161.

Data quality in genomics and microarrays
Ji, H., & Davis, R. W. (2006). Data quality in genomics and microarrays. NATURE BIOTECHNOLOGY, 24(9), 1112-1113.

Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma
Ji, H., Kumm, J., Zhang, M., Farnam, K., Salari, K., & Davis, R. W. (2006). Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma. CANCER RESEARCH, 66(16), 7910-7919.

A functional assay for mutations in tumor suppressor genes caused by mismatch repair deficiency
Ji, H. P., & King, M. C. (2001). A functional assay for mutations in tumor suppressor genes caused by mismatch repair deficiency. HUMAN MOLECULAR GENETICS, 10(24), 2737-2743.

Spondyloepimetaphyseal dysplasia with joint laxity (SEMDJL): Presentation in two unrelated patients in the United States
Smith, W., Ji, H. Lp., Mouradian, W., & Pagon, R. A. (1999). Spondyloepimetaphyseal dysplasia with joint laxity (SEMDJL): Presentation in two unrelated patients in the United States. AMERICAN JOURNAL OF MEDICAL GENETICS, 86(3), 245-252.

Molecular classification of the inherited hamartoma polyposis syndromes: Clearing the muddied waters
Eng, C., & Ji, H. L. (1998). Molecular classification of the inherited hamartoma polyposis syndromes: Clearing the muddied waters. AMERICAN JOURNAL OF HUMAN GENETICS, 62(5), 1020-1022.

Inherited mutations in PTEN that are associated with breast cancer, Cowden disease, and juvenile polyposis
Lynch, E. D., OSTERMEYER, E. A., Lee, M. K., Arena, J. F., Ji, H. L., & KING, M. C. (1997). Inherited mutations in PTEN that are associated with breast cancer, Cowden disease, and juvenile polyposis. AMERICAN JOURNAL OF HUMAN GENETICS, 61(6), 1254-1260.

HOTSPOTS FOR UNSELECTED TY1 TRANSPOSITION EVENTS ON YEAST CHROMOSOME-III ARE NEAR TRANSFER-RNA GENES AND LTR SEQUENCES
Ji, H., Moore, D. P., BLOMBERG, M. A., Braiterman, L. T., Voytas, D. F., & Boeke, J. D. (1993). HOTSPOTS FOR UNSELECTED TY1 TRANSPOSITION EVENTS ON YEAST CHROMOSOME-III ARE NEAR TRANSFER-RNA GENES AND LTR SEQUENCES. CELL, 73(5), 1007-1018.