James Hicks

Department of Biological Sciences, University of Southern California

Affiliated withUniversity of Southern California

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 36	2021

Other Publications

Article	Year
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome research\| PubMed ID: 19581485	2009
Updates to the RMAP short-read mapping software. Bioinformatics (Oxford, England)\| PubMed ID: 19736251	2009
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome research\| PubMed ID: 23739895	2013
Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells. PloS one\| PubMed ID: 25084170	2014
Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Physical biology\| PubMed ID: 25574741	2015
Paired High-Content Analysis of Prostate Cancer Cells in Bone Marrow and Blood Characterizes Increased Androgen Receptor Expression in Tumor Cell Clusters. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 27702818	2017
Vasculogenic mimicry in small cell lung cancer. Nature communications\| PubMed ID: 27827359	2016
TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells. eLife\| PubMed ID: 28092266	2017
Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Nature medicine\| PubMed ID: 28165479	2017
Unravelling biology and shifting paradigms in cancer with single-cell sequencing. Nature reviews. Cancer\| PubMed ID: 28835719	2017
Potential of Aqueous Humor as a Surrogate Tumor Biopsy for Retinoblastoma. JAMA ophthalmology\| PubMed ID: 29049475
Effect of Blood Collection Tube Type and Time to Processing on the Enumeration and High-Content Characterization of Circulating Tumor Cells Using the High-Definition Single-Cell Assay. Archives of pathology & laboratory medicine\| PubMed ID: 29144792	2018
Potential of Aqueous Humor as a Surrogate Tumor Biopsy for Retinoblastoma-Reply. JAMA ophthalmology\| PubMed ID: 29566117	2018
When it comes to genomic analysis of tumours, don't buy in bulk. British journal of cancer\| PubMed ID: 29743553	2018
Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 29997387	2019
Improved molecular karyotyping in glioblastoma. Mutation research\| PubMed ID: 30055482	2018
Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome research\| PubMed ID: 30061114	2018
Genomic cfDNA Analysis of Aqueous Humor in Retinoblastoma Predicts Eye Salvage: The Surrogate Tumor Biopsy for Retinoblastoma. Molecular cancer research : MCR\| PubMed ID: 30061186
Correction: Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 30158693	2019
Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harbor perspectives in medicine\| PubMed ID: 30617056	2019
Single-Cell Analysis of Circulating Tumor Cells. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 30649733	2019
Multiplex protein detection on circulating tumor cells from liquid biopsies using imaging mass cytometry. Convergent science physical oncology\| PubMed ID: 30906572	2018
SMURF-seq: efficient copy number profiling on long-read sequencers. Genome biology\| PubMed ID: 31287019	2019
Circulating tumor cells as a response monitor in stage IV non-small cell lung cancer. Journal of translational medicine\| PubMed ID: 31462312	2019
Circulating Tumor Cells Exhibit Metastatic Tropism and Reveal Brain Metastasis Drivers. Cancer discovery\| PubMed ID: 31601552	2020
Aqueous Humor Is Superior to Blood as a Liquid Biopsy for Retinoblastoma. Ophthalmology\| PubMed ID: 31767439
A truncating mutation in the autophagy gene UVRAG drives inflammation and tumorigenesis in mice. Nature communications\| PubMed ID: 31831743	2019
Single cell correlation analysis of liquid and solid biopsies in metastatic colorectal cancer. Oncotarget\| PubMed ID: 31903162	2019
Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. The Journal of molecular diagnostics : JMD\| PubMed ID: 31978562	2020
Minimum Technical Data Elements for Liquid Biopsy Data Submitted to Public Databases. Clinical pharmacology and therapeutics\| PubMed ID: 32017048	2020
Whole-Exome Sequencing Analysis of the Progression from Non-Low-Grade Ductal Carcinoma to Invasive Ductal Carcinoma. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 32220886	2020
Single-Cell Circulating Tumor Cell Analysis Reveals Genomic Instability as a Distinctive Feature of Aggressive Prostate Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 32341031	2020
Variability in retinoblastoma genome stability is driven by age and not heritability. Genes, chromosomes & cancer\| PubMed ID: 32390242
Chromosome 6p Amplification in Aqueous Humor Cell-Free DNA Is a Prognostic Biomarker for Retinoblastoma Ocular Survival. Molecular cancer research : MCR\| PubMed ID: 32434859
Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges. Cancers\| PubMed ID: 32471160	2020
Clonal diversity revealed by morphoproteomic and copy number profiles of single prostate cancer cells at diagnosis. Convergent science physical oncology\| PubMed ID: 32670616	2018
Correction: Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 32719393	2020
Simultaneous identification of clinically relevant mutations and copy number alterations in aqueous humor of retinoblastoma eyes. Ophthalmic genetics\| PubMed ID: 32799607
Author Correction: SMURF-seq: efficient copy number profiling on long-read sequencers. Genome biology\| PubMed ID: 32843071	2020
Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC's Analytical Variables Working Group. Clinical chemistry\| PubMed ID: 32870995	2020
Modeling the Onset of Symptoms of COVID-19. Frontiers in public health\| PubMed ID: 32903584	2020
Cell-Free DNA Tumor Fraction in the Aqueous Humor Is Associated With Therapeutic Response in Retinoblastoma Patients. Translational vision science & technology\| PubMed ID: 33062393	2020
Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient. Cold Spring Harbor molecular case studies\| PubMed ID: 33203646	2020
Correction: Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 33288881	2020
N-Acetyl-L-cysteine Promotes Growth and Expansion of Single Circulating Tumor Cells by Mitigating Cellular Stress Responses. Molecular cancer research : MCR\| PubMed ID: 33303691	2021
Large Extracellular Vesicle Characterization and Association with Circulating Tumor Cells in Metastatic Castrate Resistant Prostate Cancer. Cancers\| PubMed ID: 33801459	2021
Establishing the Clinical Utility of ctDNA Analysis for Diagnosis, Prognosis, and Treatment Monitoring of Retinoblastoma: The Aqueous Humor Liquid Biopsy. Cancers\| PubMed ID: 33805776	2021
Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma. Cancers\| PubMed ID: 34283049	2021
Inter-eye genomic heterogeneity in bilateral retinoblastoma via aqueous humor liquid biopsy. NPJ precision oncology\| PubMed ID: 34316014	2021
Platelet-coated circulating tumor cells are a predictive biomarker in patients with metastatic castrate resistant prostate cancer. Molecular cancer research : MCR\| PubMed ID: 34462330	2021

Article	Year
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome research\| PubMed ID: 19581485	2009
Updates to the RMAP short-read mapping software. Bioinformatics (Oxford, England)\| PubMed ID: 19736251	2009
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome research\| PubMed ID: 23739895	2013
Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells. PloS one\| PubMed ID: 25084170	2014
Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Physical biology\| PubMed ID: 25574741	2015
Paired High-Content Analysis of Prostate Cancer Cells in Bone Marrow and Blood Characterizes Increased Androgen Receptor Expression in Tumor Cell Clusters. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 27702818	2017
Vasculogenic mimicry in small cell lung cancer. Nature communications\| PubMed ID: 27827359	2016
TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells. eLife\| PubMed ID: 28092266	2017
Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Nature medicine\| PubMed ID: 28165479	2017
Unravelling biology and shifting paradigms in cancer with single-cell sequencing. Nature reviews. Cancer\| PubMed ID: 28835719	2017
Potential of Aqueous Humor as a Surrogate Tumor Biopsy for Retinoblastoma. JAMA ophthalmology\| PubMed ID: 29049475
Effect of Blood Collection Tube Type and Time to Processing on the Enumeration and High-Content Characterization of Circulating Tumor Cells Using the High-Definition Single-Cell Assay. Archives of pathology & laboratory medicine\| PubMed ID: 29144792	2018
Potential of Aqueous Humor as a Surrogate Tumor Biopsy for Retinoblastoma-Reply. JAMA ophthalmology\| PubMed ID: 29566117	2018
When it comes to genomic analysis of tumours, don't buy in bulk. British journal of cancer\| PubMed ID: 29743553	2018
Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 29997387	2019
Improved molecular karyotyping in glioblastoma. Mutation research\| PubMed ID: 30055482	2018
Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome research\| PubMed ID: 30061114	2018
Genomic cfDNA Analysis of Aqueous Humor in Retinoblastoma Predicts Eye Salvage: The Surrogate Tumor Biopsy for Retinoblastoma. Molecular cancer research : MCR\| PubMed ID: 30061186
Correction: Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 30158693	2019
Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harbor perspectives in medicine\| PubMed ID: 30617056	2019
Single-Cell Analysis of Circulating Tumor Cells. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 30649733	2019
Multiplex protein detection on circulating tumor cells from liquid biopsies using imaging mass cytometry. Convergent science physical oncology\| PubMed ID: 30906572	2018
SMURF-seq: efficient copy number profiling on long-read sequencers. Genome biology\| PubMed ID: 31287019	2019
Circulating tumor cells as a response monitor in stage IV non-small cell lung cancer. Journal of translational medicine\| PubMed ID: 31462312	2019
Circulating Tumor Cells Exhibit Metastatic Tropism and Reveal Brain Metastasis Drivers. Cancer discovery\| PubMed ID: 31601552	2020
Aqueous Humor Is Superior to Blood as a Liquid Biopsy for Retinoblastoma. Ophthalmology\| PubMed ID: 31767439
A truncating mutation in the autophagy gene UVRAG drives inflammation and tumorigenesis in mice. Nature communications\| PubMed ID: 31831743	2019
Single cell correlation analysis of liquid and solid biopsies in metastatic colorectal cancer. Oncotarget\| PubMed ID: 31903162	2019
Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. The Journal of molecular diagnostics : JMD\| PubMed ID: 31978562	2020
Minimum Technical Data Elements for Liquid Biopsy Data Submitted to Public Databases. Clinical pharmacology and therapeutics\| PubMed ID: 32017048	2020
Whole-Exome Sequencing Analysis of the Progression from Non-Low-Grade Ductal Carcinoma to Invasive Ductal Carcinoma. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 32220886	2020
Single-Cell Circulating Tumor Cell Analysis Reveals Genomic Instability as a Distinctive Feature of Aggressive Prostate Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 32341031	2020
Variability in retinoblastoma genome stability is driven by age and not heritability. Genes, chromosomes & cancer\| PubMed ID: 32390242
Chromosome 6p Amplification in Aqueous Humor Cell-Free DNA Is a Prognostic Biomarker for Retinoblastoma Ocular Survival. Molecular cancer research : MCR\| PubMed ID: 32434859
Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges. Cancers\| PubMed ID: 32471160	2020
Clonal diversity revealed by morphoproteomic and copy number profiles of single prostate cancer cells at diagnosis. Convergent science physical oncology\| PubMed ID: 32670616	2018
Correction: Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 32719393	2020
Simultaneous identification of clinically relevant mutations and copy number alterations in aqueous humor of retinoblastoma eyes. Ophthalmic genetics\| PubMed ID: 32799607
Author Correction: SMURF-seq: efficient copy number profiling on long-read sequencers. Genome biology\| PubMed ID: 32843071	2020
Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC's Analytical Variables Working Group. Clinical chemistry\| PubMed ID: 32870995	2020
Modeling the Onset of Symptoms of COVID-19. Frontiers in public health\| PubMed ID: 32903584	2020
Cell-Free DNA Tumor Fraction in the Aqueous Humor Is Associated With Therapeutic Response in Retinoblastoma Patients. Translational vision science & technology\| PubMed ID: 33062393	2020
Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient. Cold Spring Harbor molecular case studies\| PubMed ID: 33203646	2020
Correction: Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 33288881	2020
N-Acetyl-L-cysteine Promotes Growth and Expansion of Single Circulating Tumor Cells by Mitigating Cellular Stress Responses. Molecular cancer research : MCR\| PubMed ID: 33303691	2021
Large Extracellular Vesicle Characterization and Association with Circulating Tumor Cells in Metastatic Castrate Resistant Prostate Cancer. Cancers\| PubMed ID: 33801459	2021
Establishing the Clinical Utility of ctDNA Analysis for Diagnosis, Prognosis, and Treatment Monitoring of Retinoblastoma: The Aqueous Humor Liquid Biopsy. Cancers\| PubMed ID: 33805776	2021
Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma. Cancers\| PubMed ID: 34283049	2021
Inter-eye genomic heterogeneity in bilateral retinoblastoma via aqueous humor liquid biopsy. NPJ precision oncology\| PubMed ID: 34316014	2021
Platelet-coated circulating tumor cells are a predictive biomarker in patients with metastatic castrate resistant prostate cancer. Molecular cancer research : MCR\| PubMed ID: 34462330	2021