Garrett Jenkinson
YOU?
Author Swipe
View article: UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP Open
Clonal hematopoiesis (CH) of indeterminate potential (CHIP), driven by somatic mutations in leukemia-associated genes, confers increased risk of hematologic malignancies, cardiovascular disease, and all-cause mortality. In blood of healthy…
View article: A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions Open
Our findings demonstrate that PPAR, a method developed from the clinical knowledge graph, effectively ranks causal genes based on patient-derived HPO terms in rare and Mendelian disease contexts. PPAR has shown superior performance compare…
View article: Corrigendum to “Identification of gene regulatory networks associated with breast cancer patient survival using an interpretable deep neural network model” [Expert Syst. Appl. 262 (2025) 125632]
Corrigendum to “Identification of gene regulatory networks associated with breast cancer patient survival using an interpretable deep neural network model” [Expert Syst. Appl. 262 (2025) 125632] Open
View article: Unified somatic calling and machine learning-based classification enhance the discovery of clonal hematopoiesis of indeterminate potential
Unified somatic calling and machine learning-based classification enhance the discovery of clonal hematopoiesis of indeterminate potential Open
Clonal hematopoiesis (CH) of indeterminate potential (CHIP), driven by somatic mutations in leukemia-associated genes, confers increased risk of hematologic malignancies, cardiovascular disease and all-cause mortality. In blood of healthy …
View article: Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease
Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease Open
Background X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential inactivation of either…
View article: A supervised learning method for classifying methylation disorders
A supervised learning method for classifying methylation disorders Open
Background DNA methylation is one of the most stable and well-characterized epigenetic alterations in humans. Accordingly, it has already found clinical utility as a molecular biomarker in a variety of disease contexts. Existing methods fo…
View article: MICon Contamination Detection Workflow for Next-Generation Sequencing Laboratories Using Microhaplotype Loci and Supervised Learning
MICon Contamination Detection Workflow for Next-Generation Sequencing Laboratories Using Microhaplotype Loci and Supervised Learning Open
Innovation in sequencing instrumentation is increasing the per-batch data volumes and decreasing the per-base costs. Multiplexed chemistry protocols after the addition of index tags have further contributed to efficient and cost-effective …
View article: Real-world performance of SARS-Cov-2 serology tests in the United States, 2020
Real-world performance of SARS-Cov-2 serology tests in the United States, 2020 Open
Background Real-world performance of COVID-19 diagnostic tests under Emergency Use Authorization (EUA) must be assessed. We describe overall trends in the performance of serology tests in the context of real-world implementation. Methods S…
View article: Multiomics single timepoint measurements to predict severe COVID-19 – Authors' reply
Multiomics single timepoint measurements to predict severe COVID-19 – Authors' reply Open
View article: P570: Getting it right on the first test: Machine learning plus genome-wide methylation profiling resolves equivocal cases of Beckwith-Wiedemann syndrome
P570: Getting it right on the first test: Machine learning plus genome-wide methylation profiling resolves equivocal cases of Beckwith-Wiedemann syndrome Open
View article: P651: Early results from a multiomics cohort: Unique RIPK1 fusions identified in two individuals with irritable bowel disease
P651: Early results from a multiomics cohort: Unique RIPK1 fusions identified in two individuals with irritable bowel disease Open
View article: Authorized SARS-CoV-2 molecular methods show wide variability in the limit of detection.
Authorized SARS-CoV-2 molecular methods show wide variability in the limit of detection. Open
View article: Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study
Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study Open
Eric and Wendy Schmidt.
View article: Role of immune mediators in predicting hospitalization of SARS-CoV-2 positive patients
Role of immune mediators in predicting hospitalization of SARS-CoV-2 positive patients Open
View article: Improved Characterization of Complex β-Globin Gene Cluster Structural Variants Using Long-Read Sequencing
Improved Characterization of Complex β-Globin Gene Cluster Structural Variants Using Long-Read Sequencing Open
View article: SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA
SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA Open
Detecting gene fusions involving driver oncogenes is pivotal in clinical diagnosis and treatment of cancer patients. Recent developments in next-generation sequencing (NGS) technologies have enabled improved assays for bioinformatics-based…
View article: Universally Rank Consistent Ordinal Regression in Neural Networks
Universally Rank Consistent Ordinal Regression in Neural Networks Open
Despite the pervasiveness of ordinal labels in supervised learning, it remains common practice in deep learning to treat such problems as categorical classification using the categorical cross entropy loss. Recent methods attempting to add…
View article: COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation
COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation Open
Background COVID-19 is caused by the SARS-CoV-2 virus and has strikingly heterogeneous clinical manifestations, with most individuals contracting mild disease but a substantial minority experiencing fulminant cardiopulmonary symptoms or de…
View article: COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation (Preprint)
COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation (Preprint) Open
BACKGROUND COVID-19 is caused by the SARS-CoV-2 virus and has strikingly heterogeneous clinical manifestations, with most individuals contracting mild disease but a substantial minority experiencing fulminant cardiopulmonary symptoms or d…
View article: Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis
Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis Open
View article: Comparison of In Situ Hybridization, Immunohistochemistry, and Reverse Transcription–Droplet Digital Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Testing in Tissue
Comparison of In Situ Hybridization, Immunohistochemistry, and Reverse Transcription–Droplet Digital Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Testing in Tissue Open
Context.— Small case series have evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in formalin-fixed, paraffin-embedded tissue using reverse transcription–polymerase chain reaction, immunohistochemistry (IHC)…
LeafCutterMD: an algorithm for outlier splicing detection in rare diseases Open
View article: A Dysregulated DNA Methylation Landscape Linked to Gene Expression in MLL-Rearranged AML
A Dysregulated DNA Methylation Landscape Linked to Gene Expression in MLL-Rearranged AML Open
Translocations of the KMT2A (MLL) gene define a biologically distinct and clinically aggressive subtype of acute myeloid leukaemia (AML), marked by a characteristic gene expression profile and few cooperating mutations. Although dys…
View article: Computational Detection of Known Pathogenic Gene Fusions in a Normal Tissue Database and Implications for Genetic Disease Research
Computational Detection of Known Pathogenic Gene Fusions in a Normal Tissue Database and Implications for Genetic Disease Research Open
Several recent studies have demonstrated the utility of RNA-Seq in the diagnosis of rare inherited disease. Diagnostic rates 35% higher than those previously achievable with DNA-Seq alone have been attained. These studies have primarily pr…
View article: A Dysregulated DNA Methylation Landscape Linked to Gene Expression in MLL-Rearranged AML
A Dysregulated DNA Methylation Landscape Linked to Gene Expression in MLL-Rearranged AML Open
Translocations of the KMT2A (MLL) gene define a biologically distinct and clinically aggressive subtype of acute myeloid leukaemia (AML), marked by a characteristic gene expression profile and few cooperating mutations. Although dys…
View article: An intragenic duplication of <i>TRPS1</i> leading to abnormal transcripts and causing trichorhinophalangeal syndrome type I
An intragenic duplication of <i>TRPS1</i> leading to abnormal transcripts and causing trichorhinophalangeal syndrome type I Open
Trichorhinophalangeal syndrome type I (TRPSI) is a rare disorder that causes distinctive ectodermal, facial, and skeletal features affecting the hair (tricho-), nose (rhino-), and fingers and toes (phalangeal) and is inherited in an autoso…
View article: The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight
The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight Open
What to expect after a year in space Space is the final frontier for understanding how extreme environments affect human physiology. Following twin astronauts, one of which spent a year-long mission on the International Space Station, Garr…
View article: Ranking genomic features using an information-theoretic measure of epigenetic discordance
Ranking genomic features using an information-theoretic measure of epigenetic discordance Open
View article: Additional file 2 of Ranking genomic features using an information-theoretic measure of epigenetic discordance
Additional file 2 of Ranking genomic features using an information-theoretic measure of epigenetic discordance Open
Supplementary tables. This file contains supplementary tables summarizing our results. (XLSX 17,856 kb)
View article: DIPG-74. DNA METHYLATION STOCHASTICITY IN DIPG
DIPG-74. DNA METHYLATION STOCHASTICITY IN DIPG Open
Diffuse intrinsic pontine glioma (DIPG) is a childhood brainstem tumor with a dismal prognosis and no effective treatment. Recent studies point to a critical role for epigenetic dysregulation in this disease. Nearly 80% of DIPGs harbor mut…