The Role of Environmental Exposures on Survival After Non-Small Cell Lung Cancer Resection.

Background: Socioeconomic status and pollution exposure have been described as risk factors for poor survival in patients with non-small cell lung cancer (NSCLC). However, the relationship between these factors is complex and inadequately studied. This study aimed to evaluate the relationship between environmental and social factors and their impact on survival after NSCLC resection.

Disparities Associated with Decision to Undergo Oncologic Surgery: A Prospective Mixed-Methods Analysis.

Background: Underrepresented minority patients with surgical malignancies experience disparities in outcomes. The impact of provider-based factors, including communication, trust, and cultural competency, on outcomes is not well understood. This study examines modifiable provider-based barriers to care experienced by patients with surgical malignancies.

VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.

Next-generation sequencing (NGS) is a powerful tool for detecting and investigating viral pathogens; however, analysis and management of the enormous amounts of data generated from these technologies remains a challenge. Here, we present VPipe (the Viral NGS Analysis Pipeline and Data Management System), an automated bioinformatics pipeline optimized for whole-genome assembly of viral sequences and identification of diverse species. VPipe automates the data quality control, assembly, and contig identification steps typically performed when analyzing NGS data.

Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP.

Natural language processing (NLP) technologies have been successfully applied to cancer research by enabling automated phenotypic information extraction from narratives in electronic health records (EHRs) such as pathology reports; however, developing customized NLP solutions requires substantial effort. To facilitate the adoption of NLP in cancer research, we have developed a set of customizable modules for extracting comprehensive types of cancer-related information in pathology reports (e.g.

Computerized Approach to Creating a Systematic Ontology of Hematology/Oncology Regimens.

Purpose: The systemic treatment of cancer is primarily through the administration of complex chemotherapy protocols. To date, this knowledge has not been systematized, because of the lack of a consistent nomenclature and the variation in which regimens are documented. For example, recording of treatment events in electronic health record notes is often through shorthand and acronyms, limiting secondary use.