Author

Helio A. Costa

Stanford Medicine

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 3 Bioinformatics· 1 Genetic & Genomic Medicine· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Research Focus:variant calling· 4 Approach:experimental assay· 3 Assay:bulk RNA-seq· 2 Research Focus:database / resource· 2 Approach:statistical model· 2 Assay:whole-exome sequencing· 2 Assay:whole-genome sequencing· 2

Frequent Co-Authors

Carlos D. BustamanteiD· 3 shared Christian A. KunderiD· 3 shared James L. ZehnderiD· 3 shared Afshin BeheshtiiD· 1 shared Aleksander Milosavljevic· 1 shared Alice B. PopejoyiD· 1 shared Alicia VillacampaiD· 1 shared Amanda Saravia-ButleriD· 1 shared

Activity by Year

2018-2022 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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3 shared papersGenomics

Carlos D. BustamanteORCID

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Author profile →

5 papers

Recent·Most cited

ClinGen Variant Curation Interface: A Variant Classification Platform for the Application of Evidence Criteria from ACMG/AMP Guidelines

Christine G. Preston, Matt W. Wright, Rao Madhavrao, Steven M. Harrison, Jennifer Goldstein, Xi Luo, Hannah Wand, Bryan Wulf, Gloria Cheung, Mark E. Mandell, Howard Tong, Shaung Cheng, Michael A. Iacocca, Arturo López Pineda, Alice B. Popejoy, , Helio A. Costa

The paper introduces the ClinGen Variant Curation Interface, a platform for applying ACMG/AMP guidelines to classify genetic variants, enabling collaboration and standardization in clinical variant interpretation.

Genome Medicine · Jan 17, 2022Peer-reviewedGenetic & Genomic Medicine

NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data

Eliah G. Overbey, Amanda Saravia-Butler, Zhe Zhang, Komal S. Rathi, Homer W. Fogle, Willian A. da Silveira, Richard John Barker, Joseph J. Bass, Afshin Beheshti, Daniel C. Berrios, Elizabeth A. Blaber, Egle Cekanaviciute, Helio A. Costa, Laurence B Davin, Kathleen M Fisch, , Jonathan M. Galazka

The paper describes a standardized RNA-Seq pipeline for spaceflight data, enabling reproducible analysis of gene expression changes in astronauts and organisms exposed to spaceflight.

iScience · Mar 26, 2021Peer-reviewedBioinformatics

STAMPede: A Precision Oncology Catalogue of Solid Tumors

Jessica W. Chen, Haik Kalantarian, Christian A. Kunder, James L. Zehnder, Henning Stehr, Helio A. Costa

STAMPede is a web-based portal for visualizing somatic tumor sequencing data from a solid tumor oncology panel, enabling query and display of gene-, variant-, and cancer-level summary statistics.

bioRxiv · Sep 18, 2020 · PreprintGenomics

Development and clinical validation of a targeted RNAseq panel (Fusion-STAMP) for diagnostic and predictive gene fusion detection in solid tumors

Erik Nohr, Christian A. Kunder, Carol D. Jones, Shirley C. Sutton, Eula Fung, Hongbo Zhu, Sharon J. Feng, Linda Gojenola, Carlos D. Bustamante, James L. Zehnder, Helio A. Costa

The paper develops and validates a targeted RNAseq panel (Fusion-STAMP) for detecting gene fusions in solid tumors, showing high sensitivity and specificity.

bioRxiv · Dec 10, 2019 · PreprintGenomics

Structural variation detection by proximity ligation from FFPE tumor tissue

Chris J. Troll, Nicholas H. Putnam, Paul D. Hartley, Brandon Rice, Marco Blanchette, Sameed M. Siddiqui, Javkhlan-Ochir Ganbat, Martin P. Powers, Christian A. Kunder, Carlos D. Bustamante, James L. Zehnder, Richard Edward Green, Helio A. Costa

This paper develops a method called Fix-C to detect structural variations in FFPE tumor samples, achieving high concordance with FISH assays and identifying novel variations.

bioRxiv · Feb 27, 2018 · PreprintGenomics