Author

Philip Fremont‐Smith

MIT Lincoln LaboratoryORCID 0000-0002-2061-5809Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:DNA methylation· 4 Approach:statistical model· 4 Research Focus:deconvolution· 3 Research Focus:variant calling· 3 Assay:whole-genome sequencing· 3 Assay:ATAC-seq· 1 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Darrell O. RickeiD· 6 shared Eric D. Schwoebel· 3 shared James Watkins· 3 shared Tara BoettcheriD· 3 shared Adam M. MichaleasiD· 2 shared Aliza B. Rubenstein· 1 shared Anna ShcherbinaiD· 1 shared Arianna Comendul· 1 shared

Activity by Year

2017-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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6 shared papersBioinformatics

Darrell O. RickeORCID

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6 papers

Recent·Most cited

Comprehensive Guide of Epigenetics and Transcriptomics Data Quality Control

Arianna Comendul, Frederique Murielle Ruf-Zamojski, Colby T. Ford, Pankaj Agarwal, Elena Zaslavsky, German Nudelman, Manoj Hariharan, Aliza B. Rubenstein, Hanna Pinças, Venugopalan D. Nair, Adam M. Michaleas, Philip Fremont‐Smith, Darrell O. Ricke, Stuart C. Sealfon, Christopher W. Woods, , Rafael Jaimes

This paper provides a comprehensive guide for quality control metrics and mitigation strategies for 11 epigenetics and transcriptomics assays to improve exposure signature discovery.

STAR Protocols · Jan 26, 2025Peer-reviewedBioinformatics

The Genetic Chain Rule for Probabilistic Kinship Estimation

Brian S. Helfer, Philip Fremont‐Smith, Darrell O. Ricke

This paper introduces a method for kinship estimation using large SNP panels, resolving parent-sibling relationships and distinguishing degrees of kinship.

bioRxiv · Apr 25, 2019 · PreprintBioinformatics

Estimating Individual Contributions to Complex DNA SNP Mixtures

Darrell O. Ricke, Philip Fremont‐Smith, James Watkins, Sara H. Stankiewicz, Tara Boettcher, Eric D. Schwoebel

The paper introduces three methods to estimate individual DNA contributions in forensic SNP mixtures using HTS/MPS data.

Journal of Forensic Sciences · Feb 22, 2019Peer-reviewedBioinformatics

TranslucentID: Detecting Individuals with High Confidence in Saturated DNA SNP Mixtures

Darrell O. Ricke, James Watkins, Philip Fremont‐Smith, Tara Boettcher, Eric D. Schwoebel

TranslucentID identifies contributors in saturated DNA SNP mixtures by desaturating them using minor allele ratios, improving detection confidence in forensic analysis.

bioRxiv · Aug 13, 2018 · PreprintBioinformatics

GrigoraSNPs: Optimized HTS DNA Forensic SNP Analysis

Darrell O. Ricke, Anna Shcherbina, Adam M. Michaleas, Philip Fremont‐Smith

GrigoraSNPs optimizes SNP calling in DNA forensics by improving runtime efficiency for high-throughput sequencing data.

Journal of Forensic Sciences · Apr 16, 2018Peer-reviewedBioinformatics

The Plateau Method for Forensic DNA SNP Mixture Deconvolution

Darrell O. Ricke, Joe Isaacson, James Watkins, Philip Fremont‐Smith, Tara Boettcher, Martha S. Petrovick, Edward C. Wack, Eric D. Schwoebel

The paper introduces the Plateau method to deconvolve DNA mixtures into individual sub-profiles using SNP data without reference profiles, detecting contributors as low as 1/200 in concentration.

bioRxiv · Nov 27, 2017 · PreprintBioinformatics