457 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Harvard UniversityUS15 papers
- Johns Hopkins UniversityUS10 papers
- University of Colorado DenverUS10 papers
- University of Wisconsin–MadisonUS9 papers
- Colorado School of Public HealthUS8 papers
- Lawrence Berkeley National LaboratoryUS8 papers
- Stanford UniversityUS8 papers
- University of California, San FranciscoUS8 papers
- Columbia UniversityUS6 papers
- Cornell UniversityUS6 papers
- Imperial College LondonGB6 papers
- University of North Carolina at Chapel HillUS6 papers
47 papers
Evaluating Retrieval-Augmented Generation vs. Long-Context Input for Clinical Reasoning over EHRs
Skatje Myers, Dmitriy Dligach, Timothy A. Miller +6
Objective: To evaluate whether retrieval-augmented generation (RAG) can serve as an efficient alternative to long-context prompting for clinical reasoning over electronic health re…
BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool
Vicente Ramos, Sundous Hussein, Mohamed Abdel-Hafiz +6
Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical chall…
Combining multiplexed functional data to improve variant classification
Atlas of Variant Effects Alliance, :, Jeffrey D. Calhoun +10
With the surge in the number of variants of uncertain significance (VUS) reported in ClinVar in recent years, there is an imperative to resolve VUS at scale. Multiplexed assays of…
Genetic studies through the lens of gene networks
Marc Subirana-Granés, Jill Hoffman, Haoyu Zhang +4
Understanding the genetic basis of complex traits is a longstanding challenge in the field of genomics. Genome-wide association studies (GWAS) have identified thousands of variant-…
Learning and teaching biological data science in the Bioconductor community
Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva +15
Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of…
Environment Scan of Generative AI Infrastructure for Clinical and Translational Science
Betina Idnay, Zihan Xu, William G. Adams +54
This study reports a comprehensive environmental scan of the generative AI (GenAI) infrastructure in the national network for clinical and translational science across 36 instituti…
Lessons Learned on Information Retrieval in Electronic Health Records: A Comparison of Embedding Models and Pooling Strategies
Skatje Myers, Timothy A. Miller, Yanjun Gao +4
Objective: Applying large language models (LLMs) to the clinical domain is challenging due to the context-heavy nature of processing medical records. Retrieval-augmented generation…
Computational strategies for cross-species knowledge transfer
Hao Yuan, Christopher A. Mancuso, Kayla Johnson +2
Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However,…
The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization
Kathleen R. Mullen, Imke Tammen, Nicolas A. Matentzoglu +13
Background: Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the app…
Box Filtration
Enrique Alvarado, Prashant Gupta, Bala Krishnamoorthy
We define a new framework that unifies the filtration and mapper approaches from TDA, and present efficient algorithms to compute it. Termed the box filtration of a PCD, we grow bo…
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
Sabrina Toro, Anna V Anagnostopoulos, Sue Bello +27
Background: Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in…
Walking fingerprinting
Lily Koffman, Ciprian Crainiceanu, Andrew Leroux
We consider the problem of predicting an individual's identity from accelerometry data collected during walking. In a previous paper we introduced an approach that transforms the a…
Current and future directions in network biology
Marinka Zitnik, Michelle M. Li, Aydin Wells +34
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseas…
The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)
Russell A. Poldrack, Christopher J. Markiewicz, Stefan Appelhoff +111
The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is mean…
Leveraging Medical Knowledge Graphs Into Large Language Models for Diagnosis Prediction: Design and Application Study
Yanjun Gao, Ruizhe Li, Emma Croxford +6
Electronic Health Records (EHRs) and routine documentation practices play a vital role in patients' daily care, providing a holistic record of health, diagnoses, and treatment. How…
Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning
J. Harry Caufield, Harshad Hegde, Vincent Emonet +9
Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases,…
Successful and sustainable undergraduate research in data science
Audrey E Hendricks
Undergraduate research experiences hold many potential benefits. Students can learn about new areas opening up previously unknown paths in academia and industry. The hands-on exper…
Fast, effective, and coherent time series modeling using the sparsity-ranked lasso
Ryan Peterson, Joseph Cavanaugh
The sparsity-ranked lasso (SRL) has been developed for model selection and estimation in the presence of interactions and polynomials. The main tenet of the SRL is that an algorith…
The Coming of Age of Nucleic Acid Vaccines during COVID-19
Halie M. Rando, Ronan Lordan, Likhitha Kolla +8
In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing SAR…
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies
Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan +24
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dep…
Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome
Tiffany J. Callahan, Adrianne L. Stefanski, Jin-Dong Kim +3
Preeclampsia is a leading cause of maternal and fetal morbidity and mortality. Currently, the only definitive treatment of preeclampsia is delivery of the placenta, which is centra…
Federated Learning Enables Big Data for Rare Cancer Boundary Detection
Sarthak Pati, Ujjwal Baid, Brandon Edwards +276
Although machine learning (ML) has shown promise in numerous domains, there are concerns about generalizability to out-of-sample data. This is currently addressed by centrally shar…
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada +21
Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the int…
Breath analysis by ultra-sensitive broadband laser spectroscopy detects SARS-CoV-2 infection
Qizhong Liang, Ya-Chu Chan, Jutta Toscano +6
Rapid testing is essential to fighting pandemics such as COVID-19, the disease caused by the SARS-CoV-2 virus. Exhaled human breath contains multiple volatile molecules providing p…