A5039416459- Molecular Biology Techniques and Applications
- DNA and Nucleic Acid Chemistry
- Gene expression and cancer classification
- Cancer Genomics and Diagnostics
- Management of metastatic bone disease
- Lung Cancer Treatments and Mutations
- Geochemistry and Geologic Mapping
- Radiomics and Machine Learning in Medical Imaging
- Cancer Diagnosis and Treatment
- Genetic factors in colorectal cancer
- Bayesian Methods and Mixture Models
- RNA modifications and cancer
- Machine Learning in Healthcare
- Advanced Radiotherapy Techniques
- Software Engineering Research
- Scientific Computing and Data Management
- Global Maternal and Child Health
- Data-Driven Disease Surveillance
- Statistical Methods and Bayesian Inference
- Genomics and Chromatin Dynamics
- Bayesian Modeling and Causal Inference
- COVID-19 and healthcare impacts
- Advanced Data Storage Technologies
- Pancreatic and Hepatic Oncology Research
- Domain Adaptation and Few-Shot Learning
Vertex Pharmaceuticals (United States)
2024
University of Pennsylvania
2023
Johns Hopkins University
2017-2023
Sidney Kimmel Comprehensive Cancer Center
2017-2023
Johns Hopkins Medicine
2022
University of Baltimore
2018
Noninvasive liquid biopsy analysis of circulating tumor DNA permits direct detection early-stage cancers.
Abstract Liquid biopsies are providing new opportunities for detection of residual disease in cell-free DNA (cfDNA) after surgery but may be confounded through identification alterations arising from clonal hematopoiesis. Here, we identify circulating tumor-derived (ctDNA) ultrasensitive targeted sequencing analyses matched cfDNA and white blood cells the same patient. We apply this approach to analyze samples patients CRITICS trial, a phase III randomized controlled study perioperative...
Risk factors for progression of coronavirus disease 2019 (COVID-19) to severe or death are underexplored in U.S. cohorts.
With the advent of precision oncology, there is an urgent need to develop improved methods for rapidly detecting responses targeted therapies. Here, we have developed ultrasensitive measure cell-free tumor load using and whole-genome sequencing approaches assess tyrosine kinase inhibitors in patients with advanced lung cancer. Analyses 28 treated anti-EGFR or HER2 therapies revealed a bimodal distribution circulating DNA (ctDNA) after therapy initiation, molecular responders having nearly...
Git and GitHub are common tools for keeping track of multiple versions data analytic content, which allow more than one person to simultaneously work on a project. Classroom aims provide way students submit their assignments via GitHub, giving teachers an opportunity facilitate the integration these version control into undergraduate statistics courses. In Fall 2017 semester, we implemented in two educational settings—an introductory computational lab advanced course. We found many benefits...
BackgroundNonalcoholic fatty liver disease (NAFLD) is a major cause of liver-related morbidity in people with and without diabetes, but it underdiagnosed, posing challenges for research clinical management. Here, we determine if natural language processing (NLP) data the electronic health record (EHR) could identify undiagnosed patients hepatic steatosis based on pathology radiology reports.MethodsA rule-based NLP algorithm was built using Linguamatics literature text mining tool to search...
The RAS family of small GTPases represents the most commonly activated oncogenes in human cancers. To better understand prevalence somatic mutations and compendium genes that are coaltered RAS-mutant tumors, we analyzed targeted next-generation sequencing data 607,863 from 66,372 tumors 51 cancer types AACR Project GENIE Registry. Bayesian hierarchical models were implemented to estimate cancer-specific non-RAS mutations, evaluate co-occurrence mutual exclusivity, model effects tumor...
Abstract Background Risk factors for poor outcomes from COVID-19 are emerging among US cohorts, but patient trajectories during hospitalization ranging mild-moderate, severe, and death the associated with these have been underexplored. Methods We performed a cohort analysis of consecutive hospital admissions at 5 Johns Hopkins hospitals in Baltimore/DC area between March 4 April 24, 2020. Disease severity were classified using WHO disease ordinal scale. Cox proportional-hazards regressions...
Abstract Swedish Interactive Threshold Algorithm (SITA) Faster is the most recent and fastest testing algorithm for evaluation of Humphrey visual fields (VF). However, existing evidence suggests that there are some differences in global measures VF loss eyes transitioning from SITA Standard to newer Faster. These may be relevant, especially glaucoma, where changes over time influence clinical decisions around treatment. Furthermore, characterization localizable patterns between algorithms,...
The Countrywide Mortality Surveillance for Action platform is collecting verbal autopsy (VA) records from a nationally representative sample in Mozambique. These are used to estimate the national and subnational cause-specific mortality fractions (CSMFs) children (1-59 months) neonates (1-28 days). Cross-tabulation of VA-based cause-of-death (COD) determination against that minimally invasive tissue sampling (MITS) Child Health Prevention project revealed important misclassification errors...
Computer-coded verbal autopsy (CCVA) algorithms predict cause of death from high-dimensional family questionnaire data (verbal autopsy) a deceased individual, which are then aggregated to generate national and regional estimates cause-specific mortality fractions. These may be inaccurate if CCVA is trained on non-local training different the local population interest. This problem special case transfer learning, i.e., improving classification within target domain (e.g., particular...
Compositional data are common in many fields, both as outcomes and predictor variables. The inventory of models for the case when outcome variables compositional is limited, existing often difficult to interpret space, due their use complex log-ratio transformations. We develop a transformation-free linear regression model where expected value expressed single Markov transition from predictor. Our approach based on estimating equations thereby not requiring complete specification likelihood...
The Bone Metastases Ensemble Trees for Survival (BMETS) model uses a machine learning algorithm to estimate survival time following consultation palliative radiation therapy symptomatic bone metastases (SBM). BMETS was developed at tertiary-care, academic medical center, but its validity and stability when applied external data sets are unknown.Patients treated with SBM from May 2013 2016 two hospital-based community oncology clinics were included, records retrospectively reviewed collect...
Quantification learning is the task of prevalence estimation for a test population using predictions from classifier trained on different population. methods assume that sensitivities and specificities are either perfect or transportable training to These assumptions inappropriate in presence dataset shift, when misclassification rates not representative those under shift has been addressed only single-class (categorical) assuming knowledge true labels small subset We propose generalized...
Randomization-based inference using the Fisher randomization test allows for computation of Fisher-exact P-values, making it an attractive option analysis small, randomized experiments with non-normal outcomes. Two common statistics used to perform tests are difference-in-means between treatment and control groups covariate-adjusted version covariance. Modern computing fast P-value, but confidence intervals have typically been obtained by inverting over a range possible effect sizes. The...
The Bone Metastases Ensemble Trees for Survival Decision Support Platform (BMETS-DSP) provides patient-specific survival predictions and evidence-based recommendations to guide multidisciplinary management symptomatic bone metastases. We assessed the clinical utility of BMETS-DSP through a pilot prepost design in simulated environment.