A Potential Answer to the Alert Override Riddle: Using Patient Attributes to Predict False Positive Alerts.

Electronic health records (EHRs) use alerts to help prevent medical errors, yet clinicians override many of these alerts due to desensitization from constant exposure (alert fatigue). We hypothesize that a clinician might override an alert warning about the dangers of a treatment if the patient's health is so poor that the treatment is worth the risk or if a patient's health suggests the treatment is not needed. We used logistic regression with general estimating equations to determine if the Early Warning Score (EWS), a measurement used to predict critical care need, could be used to predict alert overrides.

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data.

Background: The Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics. Access of the HPA data is mainly via web-based interface allowing views of individual proteins, which may not be optimal for data analysis of a gene set, or automatic retrieval of original images.

Results: HPAanalyze is an R package for retrieving and performing exploratory analysis of data from HPA.

MRLR: unraveling high-resolution meiotic recombination by linked reads.

Motivation: Meiotic recombination facilitates the transmission of exchanged genetic material between homologous chromosomes and plays a crucial role in increasing the genetic variations in eukaryotic organisms. In humans, thousands of crossover events have been identified by genotyping related family members. However, most of these crossover regions span tens to hundreds of kb, which is not sufficient resolution to accurately identify the crossover breakpoints in a typical trio family.

Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data.

Kinomics is an emerging field of science that involves the study of global kinase activity. As kinases are essential players in virtually all cellular activities, kinomic testing can directly examine protein function, distinguishing kinomics from more remote, upstream components of the central dogma, such as genomics and transcriptomics. While there exist several different approaches for kinomic research, peptide microarrays are the most widely used and involve kinase activity assessment through measurement of phosphorylation of peptide substrates on the array.

Clinical Informatics Researcher's Desiderata for the Data Content of the Next Generation Electronic Health Record.

Objective: Clinical informatics researchers depend on the availability of high-quality data from the electronic health record (EHR) to design and implement new methods and systems for clinical practice and research. However, these data are frequently unavailable or present in a format that requires substantial revision. This article reports the results of a review of informatics literature published from 2010 to 2016 that addresses these issues by identifying categories of data content that might be included or revised in the EHR.