18 Result(s)

Article

Author Correction: Detecting visually significant cataract using retinal photograph-based deep learning

Yih-Chung Tham, Jocelyn Hui Lin Goh, Ayesha Anees, **aofeng Lei… in Nature Aging (2022)

Article

Detecting visually significant cataract using retinal photograph-based deep learning

Age-related cataracts are the leading cause of visual impairment among older adults. Many significant cases remain undiagnosed or neglected in communities, due to limited availability or accessibility to catar...

Yih-Chung Tham, Jocelyn Hui Lin Goh, Ayesha Anees, **aofeng Lei… in Nature Aging (2022)

Article

DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks

An orphan disease is any disease that affects a small percentage of the population. Orphan diseases are a great burden to patients and society, and most of them are genetic in origin. Unfortunately, our curren...

**aoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons, Zhiyong Lu in BMC Systems Biology (2017)

Article

Identifying named entities from PubMed® for enriching semantic categories

Controlled vocabularies such as the Unified Medical Language System (UMLS®) and Medical Subject Headings (MeSH®) are widely used for biomedical natural language processing (NLP) tasks. However, the standard te...

Sun Kim, Zhiyong Lu, W John Wilbur in BMC Bioinformatics (2015)

Article

Pathway-based drug repositioning using causal inference

Recent in vivo studies showed new hopes of drug repositioning through causality inference from drugs to disease. Inspired by their success, here we present an in silico method for building a causal network (Cause...

Jiao Li, Zhiyong Lu in BMC Bioinformatics (2013)

Article

The gene normalization task in BioCreative III

We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 full...

Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, **gchen Liu… in BMC Bioinformatics (2011)

Article

BioCreative III interactive task: an overview

The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of bi...

Cecilia N Arighi, Phoebe M Roberts, Shashank Agarwal… in BMC Bioinformatics (2011)

Article

Overview of the BioCreative III Workshop

The overall goal of the BioCreative Workshops is to promote the development of text mining and text processing tools which are useful to the communities of researchers and database curators in the biological s...

Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen… in BMC Bioinformatics (2011)

Article

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional ...

Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado… in BMC Bioinformatics (2011)

Article

A context-blocks model for identifying clinical relationships in patient records

Patient records contain valuable information regarding explanation of diagnosis, progression of disease, prescription and/or effectiveness of treatment, and more. Automatic recognition of clinically important ...

Rezarta Islamaj Doğan, Aurélie Névéol, Zhiyong Lu in BMC Bioinformatics (2011)

Article

Nuclear entry of active caspase-3 is facilitated by its p3-recognition-based specific cleavage activity

As a critical apoptosis executioner, caspase-3 becomes activated and then enters into the nucleus to exert its function. However, the molecular mechanism of this nuclear entry of active caspase-3 is still unkn...

Min Luo, Zhiyong Lu, He Sun, Kehu Yuan, Quancang Zhang, Sha Meng… in Cell Research (2010)

Article

Overview of BioCreative II gene normalization

The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a cha...

Alexander A Morgan, Zhiyong Lu, **nglong Wang, Aaron M Cohen… in Genome Biology (2008)

Article

Concept recognition for extracting protein interaction relations from biomedical text

Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasin...

William A Baumgartner Jr, Zhiyong Lu, Helen L Johnson, J Gregory Caporaso… in Genome Biology (2008)

Article

Semantic role labeling for protein transport predicates

Automatic semantic role labeling (SRL) is a natural language processing (NLP) technique that maps sentences to semantic representations. This technique has been widely studied in the recent years, but mostly w...

Steven Bethard, Zhiyong Lu, James H Martin, Lawrence Hunter in BMC Bioinformatics (2008)

Article

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a ...

Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner Jr… in BMC Bioinformatics (2008)