Professional Summary
Education & Certifications
- Board Certification: American Board of Internal Medicine, Medical Oncology (2004)
- Residency: University of Iowa Hospitals and Clinics (1996) IA
- Residency: University of Washington Medical Center Dept of Medicine (2001) WA
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- Medical Education: Johns Hopkins University School of Medicine (1994) MD
- Fellowship: Stanford University Hospital -Clinical Excellence Research Center (2005) CA
- B.A., Reed College, Biology
- M.D., Johns Hopkins University, Medicine
Honors & Awards
- American Association Cancer Research, Scholar-in-Training Award for Research Achievement (2005)
- Clinical Scientist Development Award, Doris Duke Charitable Foundation (2009)
- Merit Award for Research Achievement, American Society Clinical Oncology Foundation (2006)
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- Physician Scientist Early Career Award, Howard Hughes Medical Institute (2008)
- Physician-Scientist Fellowship Award, Howard Hughes Medical Institute (1998)
- Research Scholar Award, American Cancer Society (2013)
Administrative Appointments
- Department of Medicine Team Science Division Representative, Department of Medicine, Stanford University (2022 - Present)
- Senior Associate Director, Stanford Genome Technology Center (2008 - 2020)
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Publications
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Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma
Ji, H., Kumm, J., Zhang, M., Farnam, K., Salari, K., Faham, M., … Davis, R. W. (2006). Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma. CANCER RESEARCH, 66(16), 7910–19. -
Data quality in genomics and microarrays
Ji, H., & Davis, R. W. (2006). Data quality in genomics and microarrays. NATURE BIOTECHNOLOGY, 24(9), 1112–13. -
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., Baker, S. C., … Slikker, W. (2006). The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. NATURE BIOTECHNOLOGY, 24(9), 1151–61. -
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Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector
Fredriksson, S., Baner, J., Dahl, F., Chu, A., Ji, H., Welch, K., & 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), 327–29. -
Multigene amplification and massively parallel sequencing for cancer mutation discovery
Dahl, F., Stenberg, J., Fredriksson, S., Welch, K., Zhang, M., Nilsson, 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), 9387–92. -
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), 666–67. -
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. -
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., Davis, R., … 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. -
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., Fisher, G. A., … 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. -
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., Yu, M., … James, C. D. (2010). Oncogenic BRAF Mutation with CDKN2A Inactivation Is Characteristic of a Subset of Pediatric Malignant Astrocytomas. CANCER RESEARCH, 70(2), 512–19. -
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, 135–58. -
A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing
Natsoulis, G., Bell, J. M., Xu, H., Buenrostro, J. D., Ordonez, H., Grimes, S., … Ji, H. P. (2011). A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. PLOS ONE, 6(6). -
Ultrasensitive detection of rare mutations using next-generation targeted resequencing
Flaherty, P., Natsoulis, G., Muralidharan, O., Winters, M., Buenrostro, J., Bell, J., … Ji, H. P. (2012). Ultrasensitive detection of rare mutations using next-generation targeted resequencing. NUCLEIC ACIDS RESEARCH, 40(1). -
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 cross-sample statistical model for SNP detection in short-read sequencing data
Muralidharan, O., Natsoulis, G., Bell, J., Newburger, D., Xu, H., Kela, I., … Zhang, N. (2012). A cross-sample statistical model for SNP detection in short-read sequencing data. 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., Batzoglou, S., & 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, 11. -
Improving bioinformatic pipelines for exome variant calling
Ji, H. P. (2012). Improving bioinformatic pipelines for exome variant calling. GENOME MEDICINE, 4. -
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), 631–45. -
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). -
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., Kwok, S. S., … 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). -
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., Batzoglou, S., & 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. -
Gene-specific delineation of copy number aberrations in follicular lymphoma with molecular inversion probes
Ji, H. P., Welch, K. M., Wang, Y., Faham, M., Akasaka, T., Czerwinski, D., … Levy, R. (2007). Gene-specific delineation of copy number aberrations in follicular lymphoma with molecular inversion probes. BLOOD, 110(11), 766A–767A. -
Performance comparison of whole-genome sequencing platforms
Lam, H. Y. K., Clark, M. J., Chen, R., Chen, R., Natsoulis, G., O'Huallachain, M., … Snyder, M. (2012). Performance comparison of whole-genome sequencing platforms. NATURE BIOTECHNOLOGY, 30(1), 78–U118. -
Identification of Novel LNK Mutations In Patients with Chronic Myeloproliferative Neoplasms and Related Disorders
Oh, S. T., Zahn, J. M., Jones, C. D., Zhang, B., Loh, M. L., Kantarjian, H., … Gotlib, J. (2010). Identification of Novel LNK Mutations In Patients with Chronic Myeloproliferative Neoplasms and Related Disorders. BLOOD. ORLANDO,FL,FL,FL,FL,FL,FL,FL,FL: AMER SOC HEMATOLOGY. -
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), 1047–67. -
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), 1476–77. -
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), 331–45. -
Under-expression of Kalirin-7 increases iNOS activity in cultured cells and correlates to elevated iNOS activity in Alzheimer's disease hippocampus
Youn, H. S., 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. -
Next-generation DNA sequencing
Shendure, J., & Ji, H. (2008). Next-generation DNA sequencing. NATURE BIOTECHNOLOGY, 26(10), 1135–1145. -
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). -
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), 2618–24. -
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. L. P., 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. -
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., Dann, J., … 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), 1254–60. -
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. -
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., Natsoulis, G., & 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. -
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). -
Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture
Li, X., Nadauld, L., Ootani, A., Corney, D. C., Pai, R. K., Gevaert, O., … Kuo, C. J. (2014). Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture. NATURE MEDICINE, 20(7), 769–77. -
Allele-specific copy number profiling by next-generation DNA sequencing.
Chen, H., Bell, J. M., Zavala, N. A., Ji, H. P., & Zhang, N. R. (2015). Allele-specific copy number profiling by next-generation DNA sequencing. Nucleic Acids Research, 43(4). -
Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer
Nadauld, L. D., Garcia, S., Natsoulis, G., Bell, J. M., Miotke, L., Hopmans, E. S., … Ji, H. P. (2014). Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer. GENOME BIOLOGY, 15(8). -
Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy
Miotke, L., Maity, A., Ji, H., Brewer, J., & Astakhova, K. (2015). Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy. PLOS ONE, 10(8). -
MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.
Grimes, S. M., & Ji, H. P. (2014). MendeLIMS: a web-based laboratory information management system for clinical genome sequencing. BMC Bioinformatics, 15(1), 290-? -
Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy.
Miotke, L., Maity, A., Ji, H., Brewer, J., & Astakhova, K. (2015). Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy. PloS One, 10(8). -
Emergence of Hemagglutinin Mutations During the Course of Influenza Infection.
Cushing, A., Kamali, A., Winters, M., Hopmans, E. S., Bell, J. M., Grimes, S. M., … Ji, H. P. (2015). Emergence of Hemagglutinin Mutations During the Course of Influenza Infection. Scientific Reports, 5, 16178-? -
Pan-cancer analysis of the extent and consequences of intratumor heterogeneity.
Andor, N., Graham, T. A., Jansen, M., Xia, L. C., Aktipis, C. A., Petritsch, C., … Maley, C. C. (2016). Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nature Medicine, 22(1), 105–13. -
The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations.
Lee, H., Palm, J., Grimes, S. M., & Ji, H. P. (2015). The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations. Genome Medicine, 7(1), 112-? -
The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations
Lee, H., Palm, J., Grimes, S. M., & Ji, H. P. (2015). The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations. GENOME MEDICINE, 7. -
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.
Zheng, G. X. Y., Lau, B. T., Schnall-Levin, M., Jarosz, M., Bell, J. M., Hindson, C. M., … Ji, H. P. (2016). Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nature Biotechnology, 34(3), 303–11. -
A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
Xia, L. C., Sakshuwong, S., Hopmans, E. S., Bell, J. M., Grimes, S. M., Siegmund, D. O., … Zhang, N. R. (2016). A genome-wide approach for detecting novel insertion-deletion variants of mid-range size. Nucleic Acids Research, 44(15). -
Genomic Instability in Cancer: Teetering on the Limit of Tolerance
Andor, N., Maley, C. C., & Ji, H. P. (2017). Genomic Instability in Cancer: Teetering on the Limit of Tolerance. CANCER RESEARCH, 77(9), 2179–85. -
Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence
Taskova, M., Uhd, J., Miotke, L., Kubit, M., Bell, J., Ji, H. P., & Astakhova, K. (2017). Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence. ANALYTICAL CHEMISTRY, 89(8), 4363–66. -
CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis
Shin, G. W., Grimes, S. M., Lee, H., Lau, B. T., Xia, L. C., & Ji, H. P. (2017). CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis. NATURE COMMUNICATIONS, 8. -
Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity
Yan, K., Gevaert, O., Zheng, G., Anchang, B., & Probert, C. (2017). Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity. Cell Stem Cell, 21(1), 78–90.e6. -
Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases.
Greer, S. U., Nadauld, L. D., Lau, B. T., Chen, J., Wood-Bouwens, C., Ford, J. M., … Ji, H. P. (2017). Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases. Genome Medicine, 9(1), 57. -
Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity.
Yan, K. S., Gevaert, O., Zheng, G. X., Anchang, B., Probert, C. S., Larkin, K. A., … Kuo, C. J. (2017). Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity. Cell Stem Cell, 21(1), 78–90.e6. -
High Performance Detection of Cancer Mutations from Circulating DNA Using Single Color Digital PCR
Lau, B. T., Handy, C. M., Lee, H., Wood-Bouwens, C. M., & Ji, H. P. (2017). High Performance Detection of Cancer Mutations from Circulating DNA Using Single Color Digital PCR. JOURNAL OF MOLECULAR DIAGNOSTICS, 19(6), 1064. -
Single-Color, Multiplexed, Droplet Digital PCR Analysis of the Clinical Significance of Hemizygous Loss of WRN Gene in Colorectal Cancer
Lee, H., Lau, B., Zavala, N. A., & Ji, H. P. (2014). Single-Color, Multiplexed, Droplet Digital PCR Analysis of the Clinical Significance of Hemizygous Loss of WRN Gene in Colorectal Cancer. JOURNAL OF MOLECULAR DIAGNOSTICS, 16(6), 768. -
Identification of large rearrangements in cancer genomes with barcode linked reads.
Xia, L. C., Bell, J. M., Wood-Bouwens, C., Chen, J. J., Zhang, N. R., & Ji, H. P. (2018). Identification of large rearrangements in cancer genomes with barcode linked reads. Nucleic Acids Research, 46(4), e19. -
Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy
Bell, J. M., Lau, B. T., Greer, S. U., Wood-Bouwens, C., Xia, L. C., Connolly, I. D., … Ji, H. P. (2017). Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy. NUCLEIC ACIDS RESEARCH, 45(19), e162. -
A new multiple feature approach for rapid and highly accurate somatic structural variation discovery from whole cancer genome sequencing
Xia, L. C., Bell, J., Chen, J., Zhang, N. R., & Ji, H. P. (2015). A new multiple feature approach for rapid and highly accurate somatic structural variation discovery from whole cancer genome sequencing. CANCER RESEARCH, 75. -
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
Xia, L. C., Ai, D., Lee, H., Andor, N., Li, C., Zhang, N. R., & Ji, H. P. (2018). SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution. GigaScience. -
A phase II study of capecitabine, carboplatin, and bevacizumab for metastatic or unresectable gastroesophageal junction and gastric adenocarcinoma.
Kunz, P. L., Nandoskar, P., Koontz, M. Z., Ji, H., Ford, J. M., Balise, R. R., … Fisher, G. A. (2014). A phase II study of capecitabine, carboplatin, and bevacizumab for metastatic or unresectable gastroesophageal junction and gastric adenocarcinoma. JOURNAL OF CLINICAL ONCOLOGY, 32(3). -
Robust Multiplexed Clustering and Denoising of Digital PCR Assays by Data Gridding
Lau, B. T., Wood-Bouwens, C., & Ji, H. P. (2017). Robust Multiplexed Clustering and Denoising of Digital PCR Assays by Data Gridding. ANALYTICAL CHEMISTRY, 89(22), 11913–17. -
Synthetic lethality screen identifies novel druggable targets in the MYC pathway
Li, Y., Deutzmann, A., Bell, J., Ji, H., & Felsher, D. (2017). Synthetic lethality screen identifies novel druggable targets in the MYC pathway. MOLECULAR CANCER THERAPEUTICS. AMER ASSOC CANCER RESEARCH. -
Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes
Lau, B. T., & Ji, H. P. (2017). Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes. BMC GENOMICS, 18, 745. -
Massively Parallel Single Cell RNA-Seq of Primary Lymphomas Reveals Distinct Cellular Lineages and Diverse, Intratumoral Transcriptional States
Andor, N., Simonds, E., Chen, J., Grimes, S., Wood, C., Czerwinski, D. K., … Ji, H. P. (2016). Massively Parallel Single Cell RNA-Seq of Primary Lymphomas Reveals Distinct Cellular Lineages and Diverse, Intratumoral Transcriptional States. BLOOD, 128(22). -
Paired phospho-proteomic and genomic analyses reveal functionally distinct subclones in refractory pediatric acute myeloid leukemia
Simonds, E., Schiffman, J., Gramatges, M. M., Dahl, G., Ford, J., Lacayo, N., … Nolan, G. (2009). Paired phospho-proteomic and genomic analyses reveal functionally distinct subclones in refractory pediatric acute myeloid leukemia. CANCER RESEARCH, 69. -
Clonal structure analysis of cancer genomes at single molecule resolution
Lau, B., & Ji, H. (2015). Clonal structure analysis of cancer genomes at single molecule resolution. CANCER RESEARCH, 75. -
Megabase-scale phased haplotypes of genetic aberrations from whole cancer genome sequencing of primary colorectal tumors
Lau, B., Bell, J. M., Schnall-Levin, M., Jarosz, M., Hopmans, E., Wood, C. M., … Ji, H. P. (2015). Megabase-scale phased haplotypes of genetic aberrations from whole cancer genome sequencing of primary colorectal tumors. CANCER RESEARCH, 75. -
Identification of novel tumor suppressor candidates and characterizing their potential driver role in familial cholangiocarcinoma
Greer, S., Nadauld, L. D., Lau, B., Miotke, L., Hopmans, E., Wood, C. M., … Ji, H. P. (2015). Identification of novel tumor suppressor candidates and characterizing their potential driver role in familial cholangiocarcinoma. CANCER RESEARCH, 75. -
Pan-cancer analysis of the causes and consequences of Intra-tumor heterogeneity
Andor, N., Graham, T. A., Aktipis, A. C., Petritsch, C., Ji, H. P., & Maley, C. C. (2015). Pan-cancer analysis of the causes and consequences of Intra-tumor heterogeneity. CANCER RESEARCH, 75. -
Pan-cancer analysis of the etiology and consequences of intra-tumor heterogeneity
Andor, N., Graham, T. A., Petritsch, C., Ji, H. P., & Maley, C. C. (2015). Pan-cancer analysis of the etiology and consequences of intra-tumor heterogeneity. CANCER RESEARCH, 75(22). -
Pan-cancer analysis of the etiology and consequences of intratumor heterogeneity
Andor, N., Graham, T. A., Petritsch, C., Ji, H. P., & Maley, C. C. (2015). Pan-cancer analysis of the etiology and consequences of intratumor heterogeneity. CANCER RESEARCH, 75(22). -
A robust and rapid targeted sequencing technology for iterative multiple genomic features in cancer
Lau, B., Cushing, A., & Ji, H. (2014). A robust and rapid targeted sequencing technology for iterative multiple genomic features in cancer. CANCER RESEARCH, 74(19). -
Highly sensitive and specific digital quantification of cancer genetic aberrations
Miotke, L. K., Lau, B., Rumma, R., & Ji, H. (2014). Highly sensitive and specific digital quantification of cancer genetic aberrations. CANCER RESEARCH, 74(19). -
Analysis of Genomic Instability in Colorectal Carcinoma
Flaherty, P., Davis, R. W., & Ji, H. (2008). Analysis of Genomic Instability in Colorectal Carcinoma. FASEB JOURNAL, 22. -
ASSOCIATION OF 7Q34 COPY NUMBER GAINS AND KIAA1549-BRAF GENE FUSIONS WITH JUVENILE PILOCYTIC ASTROCYTOMA
Hodgson, J. G., VandenBerg, S. R., James, C. D., Perry, A., Gutmann, D., Fisher, P., … Schiffman, J. (2009). ASSOCIATION OF 7Q34 COPY NUMBER GAINS AND KIAA1549-BRAF GENE FUSIONS WITH JUVENILE PILOCYTIC ASTROCYTOMA. NEURO-ONCOLOGY, 11(6), 960. -
FOXM1 OVEREXPRESSION AND DNA AMPLIFICATION IN PEDIATRIC ASTROCYTOMAS
Hodgson, G., Vandenberg, S., Fisher, P., Yu, M., James, C. D., Rowitch, D., … Schiffman, J. (2008). FOXM1 OVEREXPRESSION AND DNA AMPLIFICATION IN PEDIATRIC ASTROCYTOMAS. NEURO-ONCOLOGY, 10(5), 805–6. -
Multi-patient Longitudinal Monitoring of Cancer Mutations from Circulating DNA of using Personalized Single Color Digital PCR Assays
Wood-Bouwens, C. M., Haslem, D., Lau, B. T., Almeda, A., Moulton, B., Romero, R., … Ji, H. P. (2018). Multi-patient Longitudinal Monitoring of Cancer Mutations from Circulating DNA of using Personalized Single Color Digital PCR Assays. JOURNAL OF MOLECULAR DIAGNOSTICS, 20(6), 1039. -
Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints.
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Covalent 'click chemistry'-based attachment of DNA onto solid phase enables iterative molecular analysis.
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Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562.
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Single Cell RNA Sequencing of Serial Tumor and Blood Biopsies from Lymphoma Patients on an in Situ Vaccination Clinical Trial
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Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2.
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Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model.
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Molecular Inversion Probes (MIPs) identify novel areas of allelic imbalance in childhood leukemia
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Analysis of genomic DNA copy number alterations in chromosome arm 18q demonstrates distinct molecular categories of colorectal carcinoma.
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Adapting molecular inversion probe (MIP) technology for allele quantification in childhood leukemia
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Structural variant analysis for linked-read sequencing data with gemtools.
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Precision Oncology Strategy in Trastuzumab-Resistant Human Epidermal Growth Factor Receptor 2-Positive Colon Cancer: Case Report of Durable Response to Ado-Trastuzumab Emtansine
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Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture.
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Single-Color Digital PCR Provides High-Performance Detection of Cancer Mutations from Circulating DNA.
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Genetic-based biomarkers and next-generation sequencing: the future of personalized care in colorectal cancer.
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Detecting simultaneous changepoints in multiple sequences.
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A functional CRISPR/Cas9 screen identifies kinases that modulate FGFR inhibitor response in gastric cancer
Chen, J., Bell, J., Lau, B. T., Whittaker, T., Stapleton, D., & Ji, H. P. (2019). A functional CRISPR/Cas9 screen identifies kinases that modulate FGFR inhibitor response in gastric cancer. ONCOGENESIS, 8. -
Mapping the comprehensive landscape of missense-mutation neoantigens across the human genome
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High-quality CNV segments from low-coverage whole genome sequencing from FFPE cancer biopsies based on an evaluation of multiple CNV tools
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Improved detection and identification of microsatellite instability features in colorectal cancer: Implications for immunotherapy
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Highly sensitive digital detection of circulating DNA cancer mutations using synthetic genome standards
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Chromosome-scale haplotyping enables comprehensive discovery of cancer rearrangements and germline-related susceptibility mutations
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Characterization of colorectal liver metastasis at single-cell resolution reveals dynamic interplay in the tumor microenvironment
Sathe, A., Chen, J., Wood-Bouwens, C., Almeda, A., Lau, B., Grimes, S. M., … Ji, H. (2018). Characterization of colorectal liver metastasis at single-cell resolution reveals dynamic interplay in the tumor microenvironment. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Integrated single-cell DNA and RNA analysis of intratumoral heterogeneity and immune lineages in colorectal and gastric tumor biopsies
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Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer
Xia, L. C., Bell, J. M., Wood-Bouwens, C., King, D. A., Shin, G. W., Greer, S., … Ji, H. P. (2018). Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer. CANCER RESEARCH, 78(13). -
Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes.
Shin, G. W., Greer, S. U., Xia, L. C., Lee, H. J., Zhou, J., Boles, T. C., & Ji, H. P. (2019). Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes. Nucleic Acids Research. -
Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model
Chen, J., Lau, B. T., Andor, N., Grimes, S. M., Handy, C., Wood-Bouwens, C., & Ji, H. P. (2019). Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model. SCIENTIFIC REPORTS, 9. -
Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints
Andor, N., Simonds, E. F., Czerwinski, D. K., Chen, J., Grimes, S. M., Wood-Bouwens, C., … Ji, H. P. (2019). Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints. BLOOD, 133(10), 1119–29. -
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
Zhou, B., Ho, S. S., Greer, S. U., Zhu, X., Bell, J. M., Arthur, J. G., … Urban, A. E. (2019). Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. GENOME RESEARCH, 29(3), 472–84. -
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
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Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant Genotyping
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Comprehensive characterization of gastric cancer at single-cell resolution
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Single cell RNA sequencing of serial tumor and blood biopsies from lymphoma patients undergoing in situ vaccination
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Single cell RNA sequencing reveals multiple adaptive resistance mechanisms to regorafenib in colon cancer
Sathe, A., Lau, B. T., Grimes, S., Greer, S., & Ji, H. (2019). Single cell RNA sequencing reveals multiple adaptive resistance mechanisms to regorafenib in colon cancer. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
iGRAMMy: Cloud-based characterization of microbial landscape in colorectal cancers
Xia, L. C., Ai, D., Guo, M., & Ji, H. (2019). iGRAMMy: Cloud-based characterization of microbial landscape in colorectal cancers. CANCER RESEARCH, 79(13). -
scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data.
Alquicira-Hernandez, J., Sathe, A., Ji, H. P., Nguyen, Q., & Powell, J. E. (2019). scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data. Genome Biology, 20(1), 264. -
Structural variant analysis for linked-read sequencing data with gemtools
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Therapeutic Monitoring of Circulating DNA Mutations in Metastatic Cancer with Personalized Digital PCR.
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Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment.
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CRISPRpic: fast and precise analysis for CRISPR-induced mutations via prefixed index counting.
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One Size Does Not Fit All: Marked Heterogeneity in Incidence of and Survival from Gastric Cancer among Asian American Subgroups.
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Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer.
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Identify biomarkers associated with immunotoxicities using single-cell RNAseq.
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Joint single cell DNA-seq and RNA-seq of gastric cancer cell lines reveals rules of in vitro evolution.
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Comparative Genomic Analysis of High Grade Neuroendocrine Neoplasms across Diverse Organs
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Entire landscape of epitopes from all possible missense mutations in human coding sequences.
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Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale.
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Comprehensive genomic sequencing of high-grade neuroendocrine neoplasms
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Gastric Cancer Registry: A comprehensive patient-reported resource for multidisciplinary and translational genomic approaches to gastric cancer
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Improved read/write cost tradeoff in DNA-based data storage using LDPC codes
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Loss of TP53 as a prognostic biomarker of poor survival in stage III colorectal cancer patients.
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Ultra-fast detection and quantification of nucleic acids by amplification-free fluorescence assay.
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A Summary of the 2020 Gastric Cancer Summit at Stanford University.
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The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing.
MacKay, M. J., Hooker, A. C., Afshinnekoo, E., Salit, M., Kelly, J., Feldstein, J. V., … Mason, C. E. (2020). The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing. Nature Biotechnology. -
Precision Oncology Strategy in Trastuzumab-Resistant Human Epidermal Growth Factor Receptor 2-Positive Colon Cancer: Case Report of Durable Response to Ado-Trastuzumab Emtansine.
Haslem, D. S., Ji, H. P., Ford, J. M., & Nadauld, L. D. (2017). Precision Oncology Strategy in Trastuzumab-Resistant Human Epidermal Growth Factor Receptor 2-Positive Colon Cancer: Case Report of Durable Response to Ado-Trastuzumab Emtansine. JCO Precision Oncology, 1. -
Site to Site Comparison of Follicular Lymphoma Biopsies By Single Cell RNA Sequencing
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A Targeted Resequencing Approach to Identify Actionable Somatic Copy Number Alterations with High Sensitivity Alongside SNVs and Indels from Clinical Tumor Specimens
De La Vega, F. M., Mendoza, D., Bouhlai, Y., Vilborg, A., Koehler, R., Pouliot, Y., … Ji, H. P. (2017). A Targeted Resequencing Approach to Identify Actionable Somatic Copy Number Alterations with High Sensitivity Alongside SNVs and Indels from Clinical Tumor Specimens. JOURNAL OF MOLECULAR DIAGNOSTICS, 19(2), S48. -
Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations.
Lee, H. J., Shuaibi, A., Bell, J. M., Pavlichin, D. S., & Ji, H. P. (2020). Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations. NAR Cancer, 2(4), zcaa034. -
Dynamic Immune Modulation Seen By Single Cell RNA-Sequencing of Serial Lymphoma Biopsies in Patients Undergoing in Situ Vaccination
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Pepsinogens and Gastrin Demonstrate Low Discrimination for Gastric Precancerous Lesions in a Multi-Ethnic United States Cohort.
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SPATIAL SINGLE-CELL ANALYSIS OF COLORECTAL CANCER TUMOUR USING MULTIPLEXED IMAGING MASS CYTOMETRY
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IDENTIFY IMMUNE CELL TYPES AND BIOMARKERS ASSOCIATED WITH IMMUNE-RELATED ADVERSE EVENTS USING SINGLE CELL RNA SEQUENCING
Chen, J., Pflieger, L., Grimes, S., Baker, T., Brems, M., Fulde, G., … Rhodes, T. (2020). IDENTIFY IMMUNE CELL TYPES AND BIOMARKERS ASSOCIATED WITH IMMUNE-RELATED ADVERSE EVENTS USING SINGLE CELL RNA SEQUENCING. JOURNAL FOR IMMUNOTHERAPY OF CANCER. BMJ PUBLISHING GROUP. -
OVERCOMING HIGH NANOPORE BASECALLER ERROR RATES FOR DNA STORAGE VIA BASECALLER-DECODER INTEGRATION AND CONVOLUTIONAL CODES
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An expanded universe of cancer targets.
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Modeling the Evolution of Ploidy in a Resource Restricted Environment
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Single Cell Analysis Can Define Distinct Evolution of Tumor Sites in Follicular Lymphoma.
Haebe, S. E., Shree, T., Sathe, A., Day, G., Czerwinski, D. K., Grimes, S., … Levy, R. (2021). Single Cell Analysis Can Define Distinct Evolution of Tumor Sites in Follicular Lymphoma. Blood. -
Goblet Cell Origins of Human Appendiceal Mucinous Neoplasms and Pseudomyxoma Peritonei Tumors
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Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies.
Lau, B. T., Pavlichin, D., Hooker, A. C., Almeda, A., Shin, G., Chen, J., … Ji, H. P. (2021). Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies. Genome Medicine, 13(1), 62. -
Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer.
Wu, C.-Y., Lau, B. T., Kim, H. S., Sathe, A., Grimes, S. M., Ji, H. P., & Zhang, N. R. (2021). Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer. Nature Biotechnology. -
New Approaches to Moderate CRISPR-Cas9 Activity: Addressing Issues of Cellular Uptake and Endosomal Escape.
van Hees, M., Slott, S., Hansen, A. H., Kim, H. S., Ji, H. P., & Astakhova, K. (2021). New Approaches to Moderate CRISPR-Cas9 Activity: Addressing Issues of Cellular Uptake and Endosomal Escape. Molecular Therapy : the Journal of the American Society of Gene Therapy. -
Patient-derived ex vivo TME-models and single-cell sequencing reveal transcriptional responses to immunotherapy.
Sathe, A., Chen, J., Grimes, S. M., Ayala, C. I., Poultsides, G., & Ji, H. P. (2021). Patient-derived ex vivo TME-models and single-cell sequencing reveal transcriptional responses to immunotherapy. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8.
Shin, G. W., Greer, S. U., Hopmans, E., Grimes, S. M., Lee, H. J., Zhao, L., … Ji, H. P. (2021). Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8. Genome Medicine, 13(1), 145. -
A Predictive Model to Guide Brain MRI Surveillance in Patients With Metastatic Lung Cancer: Impact on Real World Outcomes
Wu, J., Ding, V., Luo, S., Choi, E., Hellyer, J., Myall, N., … Han, S. (2021). A Predictive Model to Guide Brain MRI Surveillance in Patients With Metastatic Lung Cancer: Impact on Real World Outcomes. JOURNAL OF THORACIC ONCOLOGY. ELSEVIER SCIENCE INC. -
Single-Cell Transcriptomic Analysis of a Patient with Metastatic Appendiceal Adenocarcinoma: A Stem or Crypt Cell-Like Neoplasm?
Ayala, C., Grimes, S. M., Lee, B., & Ji, H. (2021). Single-Cell Transcriptomic Analysis of a Patient with Metastatic Appendiceal Adenocarcinoma: A Stem or Crypt Cell-Like Neoplasm? JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS. ELSEVIER SCIENCE INC. -
Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing.
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Characterization of the consensus mucosal microbiome of colorectal cancer.
Zhao, L., Grimes, S. M., Greer, S. U., Kubit, M., Lee, H. J., Nadauld, L. D., & Ji, H. P. (1800). Characterization of the consensus mucosal microbiome of colorectal cancer. NAR Cancer, 3(4), zcab049. -
A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images.
Su, A., Lee, H. J., Tan, X., Suarez, C. J., Andor, N., Nguyen, Q., & Ji, H. P. (2022). A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images. NPJ Precision Oncology, 6(1), 14. -
Analysis of 16S rRNA sequencing in advanced colorectal cancer tissue samples
An, H., Partha, M. A., Lee, H., Lau, B., Shin, G., Almeda, A. F., & Ji, H. P. (2022). Analysis of 16S rRNA sequencing in advanced colorectal cancer tissue samples. JOURNAL OF CLINICAL ONCOLOGY. LIPPINCOTT WILLIAMS & WILKINS. -
The Human Pangenome Project: a global resource to map genomic diversity.
Wang, T., Antonacci-Fulton, L., Howe, K., Lawson, H. A., Lucas, J. K., Phillippy, A. M., … Haussler, D. (2022). The Human Pangenome Project: a global resource to map genomic diversity. Nature, 604(7906), 437–446. -
KmerKeys: a web resource for searching indexed genome assemblies and variants.
Pavlichin, D. S., Lee, H. J., Greer, S. U., Grimes, S. M., Weissman, T., & Ji, H. P. (2022). KmerKeys: a web resource for searching indexed genome assemblies and variants. Nucleic Acids Research. -
Mucinous Epithelial Cell Secretion Drives Mucinous Ascites Formation in Pseudomyxoma Peritonei Patients
Ayala, C., Sathe, A., Grimes, S., Zhao, L., Bai, X., Poultsides, G., … Ji, H. (2022). Mucinous Epithelial Cell Secretion Drives Mucinous Ascites Formation in Pseudomyxoma Peritonei Patients. ANNALS OF SURGICAL ONCOLOGY. SPRINGER. -
ALTEN: A High-Fidelity Primary Tissue-Engineering Platform to Assess Cellular Responses Ex Vivo.
Law, A. M., Chen, J., Colino-Sanguino, Y., Fuente, L. R., Fang, G., Grimes, S. M., … Gallego-Ortega, D. (2022). ALTEN: A High-Fidelity Primary Tissue-Engineering Platform to Assess Cellular Responses Ex Vivo. Advanced Science (Weinheim, Baden-Wurttemberg, Germany), e2103332. -
Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62.
Greer, S. U., Chen, J., Ogmundsdottir, M. H., Ayala, C., Lau, B. T., Delacruz, R. G., … Nadauld, L. D. (2022). Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62. Scientific Reports, 12(1), 10333. -
The Gastric Cancer Registry: A Genomic Translational Resource for Multidisciplinary Research in Gastric Cancer.
Almeda, A. F., Grimes, S. M., Lee, H. J., Greer, S., Shin, G. W., McNamara, M., … Ji, H. P. (2022). The Gastric Cancer Registry: A Genomic Translational Resource for Multidisciplinary Research in Gastric Cancer. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology. -
In Situ Vaccination Induces Changes in Follicular Lymphoma Tumor Cells That Correlate with Abscopal Clinical Regressions
Haebe, S., Shree, T., Day, G., Sathe, A., Czerwinski, D. K., Grimes, S. M., … Levy, R. (2021). In Situ Vaccination Induces Changes in Follicular Lymphoma Tumor Cells That Correlate with Abscopal Clinical Regressions. BLOOD. AMER SOC HEMATOLOGY. -
Therapeutic and Immunologic Responses Elicited By in Situ Vaccination with CpG, Ibrutinib, and Low-Dose Radiation
Shree, T., Haebe, S., Czerwinski, D. K., Day, G., Sathe, A., Khodadoust, M. S., … Levy, R. (2021). Therapeutic and Immunologic Responses Elicited By in Situ Vaccination with CpG, Ibrutinib, and Low-Dose Radiation. BLOOD. AMER SOC HEMATOLOGY. -
Exploratory genomic analysis of high grade neuroendocrine neoplasms across diverse primary sites.
Sun, T. Y., Zhao, L., Van Hummelen, P., Martin, B., Hornbacker, K., Lee, H. J., … Kunz, P. (2022). Exploratory genomic analysis of high grade neuroendocrine neoplasms across diverse primary sites. Endocrine-Related Cancer. -
Predictive Model to Guide Brain Magnetic Resonance Imaging Surveillance in Patients With Metastatic Lung Cancer: Impact on Real-World Outcomes.
Wu, J., Ding, V., Luo, S., Choi, E., Hellyer, J., Myall, N., … Han, S. S. (2022). Predictive Model to Guide Brain Magnetic Resonance Imaging Surveillance in Patients With Metastatic Lung Cancer: Impact on Real-World Outcomes. JCO Precision Oncology, 6, e2200220. -
Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblasts.
Sathe, A., Mason, K., Grimes, S. M., Zhou, Z., Lau, B. T., Bai, X., … Ji, H. P. (2022). Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblasts. Clinical Cancer Research : an Official Journal of the American Association for Cancer Research. -
RESOLVING THE EXACT BREAKPOINTS AND SEQUENCE REARRANGEMENTS OF LARGE NEUROPSYCHIATRIC COPY NUMBER VARIATIONS (CNVS) AT SINGLE BASE-PAIR RESOLUTION USING CRISPR-TARGETED ULTRALONG READ SEQUENCING (CTLR-SEQ)
Zhou, B., Shin, G. W., Vervoort, L., Greer, S., Huang, Y., Roychowdhury, T., … Urban, A. (2022). RESOLVING THE EXACT BREAKPOINTS AND SEQUENCE REARRANGEMENTS OF LARGE NEUROPSYCHIATRIC COPY NUMBER VARIATIONS (CNVS) AT SINGLE BASE-PAIR RESOLUTION USING CRISPR-TARGETED ULTRALONG READ SEQUENCING (CTLR-SEQ). EUROPEAN NEUROPSYCHOPHARMACOLOGY. ELSEVIER. -
Large Cancer Pedigree Involving Multiple Cancer Genes including Likely Digenic MSH2 and MSH6 Lynch Syndrome (LS) and an Instance of Recombinational Rescue from LS.
Vogelaar, I. P., Greer, S., Wang, F., Shin, G. W., Lau, B., Hu, Y., … Hitchins, M. P. (2022). Large Cancer Pedigree Involving Multiple Cancer Genes including Likely Digenic MSH2 and MSH6 Lynch Syndrome (LS) and an Instance of Recombinational Rescue from LS. Cancers, 15(1). -
Activating Immune Effectors and Dampening Immune Suppressors Generates Successful Therapeutic Cancer Vaccination in Patients with Lymphoma
Shree, T., Haebe, S., Czerwinski, D. K., Eckhert, E., Day, G., Sathe, A., … Levy, R. (2022). Activating Immune Effectors and Dampening Immune Suppressors Generates Successful Therapeutic Cancer Vaccination in Patients with Lymphoma. BLOOD. AMER SOC HEMATOLOGY. -
Prevalence of Acquired N-Glycosylation Sites at the Single Cell Level in Follicular Lymphoma
Haebe, S., Shree, T., Day, G., Czerwinski, D. K., Sathe, A., Grimes, S. M., … Levy, R. (2022). Prevalence of Acquired N-Glycosylation Sites at the Single Cell Level in Follicular Lymphoma. BLOOD. AMER SOC HEMATOLOGY. -
Reconstructing the spatial evolution of cancer through subclone detection on copy number profiles in tumor sequencing data
Wu, C.-Y., Hess, P. R., Sathe, A., Rong, J., Lau, B. T., Grimes, S. M., … Zhang, N. R. (2022). Reconstructing the spatial evolution of cancer through subclone detection on copy number profiles in tumor sequencing data. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
A single-cell solution for solid tumors to detect mutations and quantify copy number variations.
Wu, C.-Y., Hess, P. R., Sathe, A., Rong, J., Lau, B. T., Grimes, S. M., … Zhang, N. R. (2022). A single-cell solution for solid tumors to detect mutations and quantify copy number variations. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Reconstructing the spatial evolution of cancer through subclone detection on copy number profiles in tumor sequencing data.
Wu, C.-Y., Hess, P. R., Sathe, A., Rong, J., Lau, B. T., Grimes, S. M., … Zhang, N. R. (2022). Reconstructing the spatial evolution of cancer through subclone detection on copy number profiles in tumor sequencing data. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing.
Lau, B. T., Almeda, A., Schauer, M., McNamara, M., Bai, X., Meng, Q., … Ji, H. P. (2023). Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing. Genome Medicine, 15(1), 33. -
A draft human pangenome reference.
Liao, W.-W. W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., … Paten, B. (2023). A draft human pangenome reference. Nature, 617(7960), 312–324. -
Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay.
Hernandez Bustos, A., Martiny, E., Bom Pedersen, N., Parvathaneni, R. P., Hansen, J., Ji, H. P., & Astakhova, K. (2023). Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay. Analytical Chemistry. -
Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing.
Lau, B., Chandak, S., Roy, S., Tatwawadi, K., Wootters, M., Weissman, T., & Ji, H. P. (2023). Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing. Scientific Reports, 13(1), 8514. -
Transitioning single-cell genomics into the clinic.
Lim, J., Chin, V., Fairfax, K., Moutinho, C., Suan, D., Ji, H., & Powell, J. E. (2023). Transitioning single-cell genomics into the clinic. Nature Reviews. Genetics. -
Pangenome graph construction from genome alignments with Minigraph-Cactus
Hickey, G., Monlong, J., Ebler, J., Novak, A. M., Eizenga, J. M., Gao, Y., … Zook, J. M. (2023). Pangenome graph construction from genome alignments with Minigraph-Cactus. NATURE BIOTECHNOLOGY. -
Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer.
Grimes, S. M., Kim, H. S., Roy, S., Sathe, A., Ayala, C. I., Bai, X., … Ji, H. P. (2023). Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer. NAR Cancer, 5(3), zcad034. -
Single Cell Transcriptomic Analysis of Human Extra- and Intra-Hepatic Cholangiocarcinoma
Ayala, C. I., Sathe, A., Grimes, S., Bae, X., Dua, M., Poultsides, G., … Ji, H. (2023). Single Cell Transcriptomic Analysis of Human Extra- and Intra-Hepatic Cholangiocarcinoma. ANNALS OF SURGICAL ONCOLOGY. SPRINGER. -
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.
Lee, H. J., Greer, S. U., Pavlichin, D. S., Zhou, B., Urban, A. E., Weissman, T., & Ji, H. P. (2023). Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome. Cell Reports Methods, 3(8), 100543. -
Follicular lymphoma evolves with a surmountable dependency on acquired glycosylation motifs in the B cell receptor.
Haebe, S. E., Day, G., Czerwinski, D. K., Sathe, A., Grimes, S. M., Chen, T., … Levy, R. (2023). Follicular lymphoma evolves with a surmountable dependency on acquired glycosylation motifs in the B cell receptor. Blood. -
Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells.
Kim, H. S., Grimes, S. M., Chen, T., Sathe, A., Lau, B. T., Hwang, G.-H. H., … Ji, H. P. (2023). Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells. Nature Biotechnology. -
GITR and TIGIT immunotherapy provokes divergent multi-cellular responses in the tumor microenvironment of gastrointestinal cancers.
Sathe, A., Ayala, C., Bai, X., Grimes, S. M., Lee, B., Kin, C., … Ji, H. P. (2023). GITR and TIGIT immunotherapy provokes divergent multi-cellular responses in the tumor microenvironment of gastrointestinal cancers. BioRxiv : the Preprint Server for Biology. -
A spatially mapped gene expression signature for intestinal stem-like cells identifies high-risk precursors of gastric cancer.
Huang, R. J., Wichmann, I. A., Su, A., Sathe, A., Shum, M. V., Grimes, S. M., … Ji, H. P. (2023). A spatially mapped gene expression signature for intestinal stem-like cells identifies high-risk precursors of gastric cancer. BioRxiv : the Preprint Server for Biology. -
Single cell and spatial alternative splicing analysis with long read sequencing.
Fu, Y., Kim, H., Adams, J. I., Grimes, S. M., Huang, S., Lau, B. T., … Zhang, N. R. (2023). Single cell and spatial alternative splicing analysis with long read sequencing. Research Square. -
A clinical trial of therapeutic vaccination in lymphoma with serial tumor sampling and single cell analysis.
Shree, T., Haebe, S. E., Czerwinski, D. K., Eckhert, E., Day, G., Sathe, A., … Levy, R. (2023). A clinical trial of therapeutic vaccination in lymphoma with serial tumor sampling and single cell analysis. Blood Advances. -
GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers.
Sathe, A., Ayala, C., Bai, X., Grimes, S. M., Lee, B., Kin, C., … Ji, H. P. (2023). GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers. Genome Medicine, 15(1), 100. -
The Gastric Cancer Registry Genome Explorer: A tool for genomic discovery.
Almeda, A. F., Grimes, S. M., Shin, G., Lee, H., Wichmann, I. A., Greer, S., & Ji, H. P. (2023). The Gastric Cancer Registry Genome Explorer: A tool for genomic discovery. JOURNAL OF CLINICAL ONCOLOGY. LIPPINCOTT WILLIAMS & WILKINS. -
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions.
Mason, K., Sathe, A., Hess, P. R., Rong, J., Wu, C.-Y. Y., Furth, E., … Zhang, N. (2024). Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions. Genome Biology, 25(1), 14. -
Tumor-associated microbiome features of metastatic colorectal cancer and clinical implications.
An, H. J., Partha, M. A., Lee, H. J., Lau, B. T., Pavlichin, D. S., Almeda, A., … Ji, H. P. (2023). Tumor-associated microbiome features of metastatic colorectal cancer and clinical implications. Frontiers in Oncology, 13, 1310054. -
Co-Occurrence of Clonally Related Follicular Lymphoma and Histiocytic Sarcoma
Haebe, S., Czerwinski, D. K., Sathe, A., Grimes, S., Chen, T., Martin, B., … Shree, T. (2023). Co-Occurrence of Clonally Related Follicular Lymphoma and Histiocytic Sarcoma. BLOOD. AMER SOC HEMATOLOGY. -
Single cell transcriptomic analysis reveals differences between primary appendiceal tumors
Ayala, C. I., Sathe, A., Bai, X., Grimes, S., Lee, B., & Ji, H. P. (2024). Single cell transcriptomic analysis reveals differences between primary appendiceal tumors. ANNALS OF SURGICAL ONCOLOGY. SPRINGER. -
Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints.
Zhou, B., Purmann, C., Guo, H., Shin, G. W., Huang, Y., Pattni, R., … Urban, A. E. (2024). Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints. Proceedings of the National Academy of Sciences of the United States of America, 121(31), e2322834121. -
Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders
Zhou, B., Arthur, J. G., & Guo, H. (2024). Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. Cell, Published online September 30, 2024.
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Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector
Clinical Trials
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