Kristin H. Jarman

MARLOWE: taxonomic characterization of unknown samples for forensics using de novo peptide identification

Sarah C. Jenson, Fanny Chu, Gelio Alves, Aleksey Y. Ogurtsov et autres

We present a computational tool, MARLOWE, for source organism characterization of unknown, forensic biological samples. The intent of MARLOWE is to address a gap in applying proteomics data analysis to forensic applications. MARLOWE produces a list of potential source organisms given confident …

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Microbial cell-free DNA sequencing for diagnosing lung infections in immunocompromised patients

Kevin Brick, Kristin H. Jarman, Frederick S. Nolte, Igor D. Vilfan et autres

Abstract Rationale Rapid and comprehensive detection of respiratory pathogens is essential for immunocompromised patients with suspected pneumonia. Conventional diagnostic methods are limited in scope, often slow, and lack sensitivity, leading to reduced diagnostic yield. Objectives To analytically and clinically validate a microbial …

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In-matrix library preparation for metagenomic sequencing of microbial cell-free DNA

Paul L. Babb, Jamilla Akhund‐Zade, Damek V. Spacek, Kevin Brick et autres

Metagenomic sequencing of microbial cell-free DNA (mcfDNA) enables comprehensive identification and quantification of diverse pathogens from blood and other biofluids. This approach enables minimally invasive diagnosis of deep-seated infectious disease, provides culture-free identification of antimicrobial resistance, and powers the discovery of novel …

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MARLOWE: An Untargeted Proteomics, Statistical Approach to Taxonomic Classification for Forensics

Fanny Chu, Sarah C. Jenson, Anthony S. Barente, Natalie C. Heller et autres

General proteomics research for fundamental science typically addresses laboratory- or patient-derived samples of known origin and composition. However, in a few research areas, such as environmental proteomics, clinical identification of infectious organisms, archeology, art/cultural history, and forensics, attributing the origin of a …

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Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing

Fred C. Christians, Jamilla Akhund‐Zade, Kristin H. Jarman, Shivkumar Venkatasubrahmanyam et autres

ABSTRACT Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the …

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Analytical and Clinical Validation of Direct Detection of Antimicrobial Resistance Markers by Plasma Microbial Cell-free DNA Sequencing

Fred C. Christians, Jamilla Akhund‐Zade, Kristin H. Jarman, Shivkumar Venkatasubrahmanyam et autres

ABSTRACT Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the …

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Method of identifying features in indexed data

Kristin H. Jarman

The present invention is a method of identifying features in indexed data, especially useful for distinguishing signal from noise in data provided as a plurality of ordered pairs. Each of the plurality of ordered pairs has an index and a response. The …

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Identification of features in indexed data and equipment therefore

Kristin H. Jarman

Embodiments of the present invention provide methods of identifying a feature in an indexed dataset. Such embodiments encompass selecting an initial subset of indices, the initial subset of indices being encompassed by an initial window-of-interest and comprising at least one beginning index …

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Model for spectral and chromatographic data

Kristin H. Jarman

A method and apparatus using a spectral analysis technique are disclosed. In one form of the invention, probabilities are selected to characterize the presence (and in another form, also a quantification of a characteristic) of peaks in an indexed data set for …

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Peptide identification

Kristin H. Jarman

Peptides are identified from a list of candidates using collision-induced dissociation tandem mass spectrometry data. A probabilistic model for the occurrence of spectral peaks corresponding to frequently observed partial peptide fragment ions is applied. As part of the identification procedure, a probability …

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Compound specific stable isotope analysis of aromatics in diesel fuel to identify potential cocktailing

Megan K. Nims, Angela M. Melville, James J. Moran, Kristin H. Jarman et autres

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Metaproteomic Characterization of Forensic Samples

Kristin H. Jarman, Sarah C. Jenson, Natalie C. Heller, Dustin L. Crockett et autres

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