A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries

Mining clinical attributes of genomic variants through assisted literature curation in Egas

(2016) Sérgio Matos et al.   Database-The Journal of Biological Databases and Curation

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies

(2016) Qiongshi Lu et al.   PLoS Genetics

Large-scale extraction of gene interactions from full-text literature using DeepDive

(2015) Emily K. Mallory et al.   BIOINFORMATICS

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature

(2015) Komandur Elayavilli Ravikumar et al.   BMC BIOINFORMATICS

A scoping review of cloud computing in healthcare

(2015) Lena Griebel et al.   BMC Medical Informatics and Decision Making

Bioinformatics tools for the analysis of NMR metabolomics studies focused on the identification of clinically relevant biomarkers

(2015) Leonor Puchades-Carrasco et al.   BRIEFINGS IN BIOINFORMATICS

Biochemical mechanism of DSB end resection and its regulation

(2015) James M. Daley et al.   DNA REPAIR

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information

(2015) Manabu Torii et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Novel Systems Modeling Methodology in Comparative Microbial Metabolomics: Identifying Key Enzymes and Metabolites Implicated in Autism Spectrum Disorders

(2015) Colin Heberling et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways

(2015) Suresh Subramani et al.   JOURNAL OF BIOMEDICAL INFORMATICS

DISEASES: Text mining and data integration of disease–gene associations

(2015) Sune Pletscher-Frankild et al.   METHODS

Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles

(2015) Denis Bertrand et al.   NUCLEIC ACIDS RESEARCH

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

(2015) Yifeng Liu et al.   NUCLEIC ACIDS RESEARCH

Use of Genome-Wide Association Studies for Cancer Research and Drug Repositioning

(2015) Jizhun Zhang et al.   PLoS One

Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci

(2015) Lam C. Tsoi et al.   Nature Communications

miRTex: A Text Mining System for miRNA-Gene Relation Extraction

(2015) Gang Li et al.   PLoS Computational Biology

Design of Automatic Extraction Algorithm of Knowledge Points for MOOCs

(2015) Haijian Chen et al.   Computational Intelligence and Neuroscience

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions

(2015) Junguk Hur et al.   Journal of Biomedical Semantics

Biomarkers of An Autoimmune Skin Disease—Psoriasis

(2015) Shan Jiang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A hybrid named entity tagger for tagging human proteins/genes

(2015) Kalpana Raja et al.   International Journal of Data Mining and Bioinformatics

Assembly of a Comprehensive Regulatory Network for the Mammalian Circadian Clock: A Bioinformatics Approach

(2015) Robert Lehmann et al.   PLoS One

Translational research platforms integrating clinical and omics data: a review of publicly available solutions

(2014) V. Canuel et al.   BRIEFINGS IN BIOINFORMATICS

Event-based text mining for biology and functional genomics

(2014) S. Ananiadou et al.   Briefings in Functional Genomics

Text summarization in the biomedical domain: A systematic review of recent research

(2014) Rashmi Mishra et al.   JOURNAL OF BIOMEDICAL INFORMATICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Prioritisation and Network Analysis of Crohn's Disease Susceptibility Genes

(2014) Daniele Muraro et al.   PLoS One

BC4GO: a full-text corpus for the BioCreative IV GO task

(2014) K. Van Auken et al.   Database-The Journal of Biological Databases and Curation

Prediction of gene-based drug indications using compendia of public gene expression data and PubMed abstracts

(2014) Ala Qabaja et al.   Journal of Bioinformatics and Computational Biology

Big data: the next frontier for innovation in therapeutics and healthcare

(2014) Naiem T Issa et al.   Expert Review of Clinical Pharmacology

Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing

(2013) Rosemarie Weikard et al.   BMC GENOMICS

3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data

(2013) Tien-Chueh Kuo et al.   BMC Systems Biology

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants

(2013) Thomas A. Peterson et al.   JOURNAL OF MOLECULAR BIOLOGY

Genetic data and electronic health records: a discussion of ethical, logistical and technological considerations

(2013) Kimberly Shoenbill et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

PPInterFinder—a mining tool for extracting causal relations on human proteins from literature

(2013) Kalpana Raja et al.   Database-The Journal of Biological Databases and Curation

Cloud computing for comparative genomics

(2012) Dennis P Wall et al.   BMC BIOINFORMATICS

A text-mining system for extracting metabolic reactions from full-text articles

(2012) Jan Czarnecki et al.   BMC BIOINFORMATICS

Biomedical text mining and its applications in cancer research

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

Text mining for the biocuration workflow

(2012) L. Hirschman et al.   Database-The Journal of Biological Databases and Curation

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

(2012) Aurélie Névéol et al.   Database-The Journal of Biological Databases and Curation

Preimplantation development regulatory pathway construction through a text-mining approach

(2011) Elisa Donnard et al.   BMC GENOMICS

Combining literature text mining with microarray data: advances for system biology modeling

(2011) A. Faro et al.   BRIEFINGS IN BIOINFORMATICS

Search terms and a validated brief search filter to retrieve publications on health-related values in Medline: a word frequency analysis study

(2011) M. Petrova et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Bring on the biomarkers

(2011) George Poste   NATURE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

(2011) George A. Khoury et al.   Scientific Reports

A hybrid approach to extract protein-protein interactions

(2010) Q.-C. Bui et al.   BIOINFORMATICS

A view of cloud computing

(2010) Michael Armbrust et al.   COMMUNICATIONS OF THE ACM

The FEBS Letters SDA corpus: A collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community

(2010) Florian Leitner et al.   FEBS LETTERS

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)

(2009) Thomas C Wiegers et al.   BMC BIOINFORMATICS

Construction of an annotated corpus to support biomedical information extraction

(2009) Paul Thompson et al.   BMC BIOINFORMATICS

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS