Recent advances in biomedical literature mining

Remdesivir as a possible therapeutic option for the COVID-19

(2020) Jaffar A. Al-Tawfiq et al.   Travel Medicine and Infectious Disease

Bi-directional differentiation of single bronchioalveolar stem cells during lung repair

(2020) Kuo Liu et al.   Cell Discovery

Keep up with the latest coronavirus research

(2020) Qingyu Chen et al.   NATURE

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

(2019) Jinhyuk Lee et al.   BIOINFORMATICS

Deep learning for drug–drug interaction extraction from the literature: a review

(2019) Tianlin Zhang et al.   BRIEFINGS IN BIOINFORMATICS

A Systematic Review on Literature-based Discovery

(2019) Menasha Thilakaratne et al.   ACM COMPUTING SURVEYS

Should Health Care Demand Interpretable Artificial Intelligence or Accept “Black Box” Medicine?

(2019) Fei Wang et al.   ANNALS OF INTERNAL MEDICINE

A gene–phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach

(2018) Wenhui Xing et al.   BIOINFORMATICS

SemaTyP: a knowledge graph based literature mining method for drug discovery

(2018) Shengtian Sang et al.   BMC BIOINFORMATICS

Recent Trends in Deep Learning Based Natural Language Processing [Review Article]

(2018) Tom Young et al.   IEEE Computational Intelligence Magazine

Automatic extraction of protein-protein interactions using grammatical relationship graph

(2018) Kaixian Yu et al.   BMC Medical Informatics and Decision Making

Biomedical literature classification with a CNNs-based hybrid learning network

(2018) Yan Yan et al.   PLoS One

OUP accepted manuscript

(2018)   Database-The Journal of Biological Databases and Curation

Deep Learning in Medicine—Promise, Progress, and Challenges

(2018) Fei Wang et al.   JAMA Internal Medicine

Extracting chemical–protein interactions from literature using sentence structure analysis and feature engineering

(2018) Pei-Yau Lung et al.   Database-The Journal of Biological Databases and Curation

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)

(2017) Xiangying Jiang et al.   Database-The Journal of Biological Databases and Curation

MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank

(2017) Yuqing Mao et al.   Journal of Biomedical Semantics

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

(2016) Robert Leaman et al.   BIOINFORMATICS

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing

(2016) Shengwen Peng et al.   BIOINFORMATICS

Drug-Drug Interaction Extraction via Convolutional Neural Networks

(2016) Shengyu Liu et al.   Computational and Mathematical Methods in Medicine

Spark, an application based on Serendipitous Knowledge Discovery

(2016) T. Elizabeth Workman et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Using Literature-Based Discovery to Explain Adverse Drug Effects

(2016) Dimitar Hristovski et al.   JOURNAL OF MEDICAL SYSTEMS

Link Prediction on a Network of Co-occurring MeSH Terms: Towards Literature-based Discovery

(2016) Thomas Rindflesch et al.   METHODS OF INFORMATION IN MEDICINE

Event causality extraction based on connectives analysis

(2016) Sendong Zhao et al.   NEUROCOMPUTING

AuDis: an automatic CRF-enhanced disease normalization in biomedical text

(2016) Hsin-Chun Lee et al.   Database-The Journal of Biological Databases and Curation

Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine

(2016) Ayush Singhal et al.   PLoS Computational Biology

MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence

(2015) Ke Liu et al.   BIOINFORMATICS

Community challenges in biomedical text mining over 10 years: success, failure and the future

(2015) Chung-Chi Huang et al.   BRIEFINGS IN BIOINFORMATICS

Normalizing clinical terms using learned edit distance patterns

(2015) Rohit J Kate   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Deep learning

(2015) Yann LeCun et al.   NATURE

Phenolyzer: phenotype-based prioritization of candidate genes for human diseases

(2015) Hui Yang et al.   NATURE METHODS

PhenoMiner: from text to a database of phenotypes associated with OMIM diseases

(2015) Nigel Collier et al.   Database-The Journal of Biological Databases and Curation

tmChem: a high performance approach for chemical named entity recognition and normalization

(2015) Robert Leaman et al.   Journal of Cheminformatics

A novel feature-based approach to extract drug-drug interactions from biomedical text

(2014) Q.-C. Bui et al.   BIOINFORMATICS

Identifying plausible adverse drug reactions using knowledge extracted from the literature

(2014) Ning Shang et al.   JOURNAL OF BIOMEDICAL INFORMATICS

NCBI disease corpus: A resource for disease name recognition and concept normalization

(2014) Rezarta Islamaj Doğan et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature

(2013) R. Xu et al.   BIOINFORMATICS

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

(2013) Makoto Miwa et al.   BIOINFORMATICS

DNorm: disease name normalization with pairwise learning to rank

(2013) R. Leaman et al.   BIOINFORMATICS

A Review on Multi-Label Learning Algorithms

(2013) Min-Ling Zhang et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

The DDI corpus: An annotated corpus with pharmacological substances and drug–drug interactions

(2013) María Herrero-Zazo et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Extracting Drug-Drug Interaction from the Biomedical Literature Using a Stacked Generalization-Based Approach

(2013) Linna He et al.   PLoS One

ChemSpot: a hybrid system for chemical named entity recognition

(2012) Tim Rocktäschel et al.   BIOINFORMATICS

Biomedical text mining and its applications in cancer research

(2012) Fei Zhu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Using rule-based natural language processing to improve disease normalization in biomedical text

(2012) Ning Kang et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Identifying Novel Drug Indications through Automated Reasoning

(2012) Luis Tari et al.   PLoS One

Discovering and visualizing indirect associations between biomedical concepts

(2011) Y. Tsuruoka et al.   BIOINFORMATICS

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation

(2011) Antonio J Jimeno-Yepes et al.   BMC BIOINFORMATICS

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

(2011) Martin Krallinger et al.   BMC BIOINFORMATICS

Literature mining, ontologies and information visualization for drug repurposing

(2011) C. Andronis et al.   BRIEFINGS IN BIOINFORMATICS

Recommending MeSH terms for annotating biomedical articles

(2011) Minlie Huang et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Drug repurposing and adverse event prediction using high-throughput literature analysis

(2011) Spyros N. Deftereos et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

PathText: a text mining integrator for biological pathway visualizations

(2010) B. Kemper et al.   BIOINFORMATICS

Creating Reference Datasets for Systems Biology Applications Using Text Mining

(2009) Martin Krallinger et al.   Annals of the New York Academy of Sciences

MeSH Up: effective MeSH text classification for improved document retrieval

(2009) Dolf Trieschnigg et al.   BIOINFORMATICS

A dictionary to identify small molecules and drugs in free text

(2009) Kristina M. Hettne et al.   BIOINFORMATICS

Bayesian inference of protein–protein interactions from biological literature

(2009) Rajesh Chowdhary et al.   BIOINFORMATICS

Detection of IUPAC and IUPAC-like chemical names

(2008) R. Klinger et al.   BIOINFORMATICS

Literature mining method RaJoLink for uncovering relations between biomedical concepts

(2008) Ingrid Petriĕ et al.   JOURNAL OF BIOMEDICAL INFORMATICS

CoPub: a literature-based keyword enrichment tool for microarray data analysis

(2008) R. Frijters et al.   NUCLEIC ACIDS RESEARCH