[HTML][HTML] Comprehensive analysis of normal adjacent to tumor transcriptomes

…, R Camarda, J Odegaard, H Paik, B Oskotsky… - Nature …, 2017 - nature.com
Histologically normal tissue adjacent to the tumor (NAT) is commonly used as a control in
cancer studies. However, little is known about the transcriptomic profile of NAT, how it is …

Mortality risk among patients with COVID-19 prescribed selective serotonin reuptake inhibitor antidepressants

T Oskotsky, I Marić, A Tang, B Oskotsky… - JAMA network …, 2021 - jamanetwork.com
Importance Antidepressant use may be associated with reduced levels of several proinflammatory
cytokines suggested to be involved with the development of severe COVID-19. An …

Assessment of a deep learning model based on electronic health record data to forecast clinical outcomes in patients with rheumatoid arthritis

…, D Lituiev, M Gianfrancesco, B Oskotsky… - JAMA network …, 2019 - jamanetwork.com
Importance Knowing the future condition of a patient would enable a physician to customize
current therapeutic options to prevent disease worsening, but predicting that future condition …

[PDF][PDF] Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

JL Golob, TT Oskotsky, AS Tang, A Roldan… - Cell Reports …, 2024 - cell.com
Every year, 11% of infants are born preterm with significant health consequences, with the
vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) …

[HTML][HTML] Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes

…, G Schenk, E Rutenberg, B Oskotsky… - NPJ digital …, 2020 - nature.com
There is a great and growing need to ascertain what exactly is the state of a patient, in terms
of disease progression, actual care practices, pathology, adverse events, and much more, …

[HTML][HTML] Deep phenotyping of Alzheimer's disease leveraging electronic medical records identifies sex-specific clinical associations

AS Tang, T Oskotsky, S Havaldar, WG Mantyh… - Nature …, 2022 - nature.com
Alzheimer’s Disease (AD) is a neurodegenerative disorder that is still not fully understood.
Sex modifies AD vulnerability, but the reasons for this are largely unknown. We utilize two …

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model

BS Glicksberg, B Oskotsky, PM Thangaraj… - …, 2019 - academic.oup.com
Motivation Electronic health records (EHRs) are quickly becoming omnipresent in healthcare,
but interoperability issues and technical demands limit their use for biomedical and clinical …

[PDF][PDF] A certified de-identification system for all clinical text documents for information extraction at scale

…, G Schenk, K Muenzen, B Oskotsky… - JAMIA …, 2023 - academic.oup.com
Objectives Clinical notes are a veritable treasure trove of information on a patient’s disease
progression, medical history, and treatment plans, yet are locked in secured databases …

A biomedical open knowledge network harnesses the power of AI to understand deep human biology

…, R Pearce, T Reza, B Smith, B Herr II, B Oskotsky… - AI magazine, 2022 - ojs.aaai.org
Abstract Knowledge representation and reasoning (KR&R) has been successfully implemented
in many fields to enable computers to solve complex problems with AI methods. However…

Comparing ethnicity-specific reference intervals for clinical laboratory tests from EHR data

N Rappoport, H Paik, B Oskotsky, R Tor… - The journal of …, 2018 - academic.oup.com
Background The results of clinical laboratory tests are an essential component of medical
decision-making. To guide interpretation, test results are returned with reference intervals …