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Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome

Nature communications, 2018-09, Vol.9 (1), p.3962-13, Article 3962

2018

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CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

Genome Biology, 2020-05, Vol.21 (1), p.126-126, Article 126

2020

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MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

Genome Biology, 2021-01, Vol.22 (1), p.24-24, Article 24

2021

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Genetic Risk for Subsequent Neoplasms Among Long-Term Survivors of Childhood Cancer

Journal of clinical oncology, 2018-07, Vol.36 (20), p.2078-2087

2018

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NetBID2 provides comprehensive hidden driver analysis

Nature communications, 2023-05, Vol.14 (1), p.2581-2581, Article 2581

2023

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Inflammation, Active Fibroplasia, and End-stage Fibrosis in 172 Biliary Atresia Remnants Correlate Poorly With Age at Kasai Portoenterostomy, Visceral Heterotaxy, and Outcome

The American journal of surgical pathology, 2018-12, Vol.42 (12), p.1625-1635

2018

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Abstract 6252: Driver indel discovery and allelic imbalance in >9,000 tumor RNA-Seq samples from the Cancer Genome Atlas (TCGA)

Cancer research (Chicago, Ill.), 2024-03, Vol.84 (6_Supplement), p.6252-6252

2024

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Abstract PO-046: MethylationToActivity: A deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

Clinical cancer research, 2021-03, Vol.27 (5_Supplement), p.PO-046-PO-046

2021

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St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem

Cancer discovery, 2021-05, Vol.11 (5), p.1082-1099

2021

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Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing

Cancer discovery, 2021-12, Vol.11 (12), p.3008-3027

2021

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VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

Nucleic acids research, 2012-01, Vol.40 (Database issue), p.D729-D734

2012

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Abstract 2289: Empowering point-and-click genomic analysis with large pediatric genomic reference data on St. Jude Cloud

Cancer research (Chicago, Ill.), 2021-07, Vol.81 (13_Supplement), p.2289-2289

2021

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The 5% Canary

SSRN Electronic Journal, 2023

Thrasher, Andrew

2023

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Abstract 5478: CICERO: An accurate method for detecting complex and diverse driver fusions using cancer transcriptome sequencing (RNA-seq) data

Cancer research (Chicago, Ill.), 2020-08, Vol.80 (16_Supplement), p.5478-5478

2020

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Forecasting a Volatility Tsunami

SSRN Electronic Journal

Thrasher, CMT, Andrew

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Abstract 642: Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in pediatric cancer

Cancer research (Chicago, Ill.), 2021-07, Vol.81 (13_Supplement), p.642-642

2021

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Abstract 1901: VisComm: A cloud-based platform for accessing and creating scientific visualization for the pediatric cancer research community

Cancer research (Chicago, Ill.), 2022-06, Vol.82 (12_Supplement), p.1901-1901

2022

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A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids

IEEE transactions on parallel and distributed systems, 2012-12, Vol.23 (12), p.2189-2197

2012

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Abstract 4092: Fuzzion2: Fast, sensitive detection of known gene fusions by fuzzy pattern matching for clinical testing and large-scale data mining

Cancer research (Chicago, Ill.), 2022-06, Vol.82 (12_Supplement), p.4092-4092

2022

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Scaling up genome annotation using MAKER and work queue

International journal of bioinformatics research and applications, 2014, Vol.10 (4-5), p.447

2014

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Abstract 2628: Molecular diagnosis for pediatric cancer through integrative analysis of whole-genome, whole-exome and transcriptome sequencing

Cancer research (Chicago, Ill.), 2016-07, Vol.76 (14_Supplement), p.2628-2628

2016

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Abstract 3001: Germline mutations in cancer predisposition genes and risk for subsequent neoplasms among long-term survivors of childhood cancer in the St. Jude Lifetime Cohort

Cancer research (Chicago, Ill.), 2017-07, Vol.77 (13_Supplement), p.3001-3001

2017

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Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

Genetic Risk for Subsequent Neoplasms Among Long-Term Survivors of Childhood Cancer

NetBID2 provides comprehensive hidden driver analysis

Inflammation, Active Fibroplasia, and End-stage Fibrosis in 172 Biliary Atresia Remnants Correlate Poorly With Age at Kasai Portoenterostomy, Visceral Heterotaxy, and Outcome

Abstract 6252: Driver indel discovery and allelic imbalance in >9,000 tumor RNA-Seq samples from the Cancer Genome Atlas (TCGA)

Abstract PO-046: MethylationToActivity: A deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem

Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

Abstract 2289: Empowering point-and-click genomic analysis with large pediatric genomic reference data on St. Jude Cloud

Cancer Germline Predisposing Variants and Late-Mortality from Subsequent Malignant Neoplasms among Long-Term Survivors of Childhood Cancer: A Report from the St. Jude Lifetime Cohort and the Childhood Cancer Survivor Study

The 5% Canary

Cancer germline predisposing variants and late mortality from subsequent malignant neoplasms among long-term childhood cancer survivors: a report from the St Jude Lifetime Cohort and the Childhood Cancer Survivor Study

Abstract 5478: CICERO: An accurate method for detecting complex and diverse driver fusions using cancer transcriptome sequencing (RNA-seq) data

Forecasting a Volatility Tsunami

Abstract 642: Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in pediatric cancer

Abstract 1901: VisComm: A cloud-based platform for accessing and creating scientific visualization for the pediatric cancer research community

Precision Medicine for Sickle Cell Disease through Whole Genome Sequencing

A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids

Abstract 4092: Fuzzion2: Fast, sensitive detection of known gene fusions by fuzzy pattern matching for clinical testing and large-scale data mining

Scaling up genome annotation using MAKER and work queue

Abstract 2628: Molecular diagnosis for pediatric cancer through integrative analysis of whole-genome, whole-exome and transcriptome sequencing

Abstract 3001: Germline mutations in cancer predisposition genes and risk for subsequent neoplasms among long-term survivors of childhood cancer in the St. Jude Lifetime Cohort

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