A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model

Improving genomic prediction accuracy for meat tenderness in Nellore cattle using artificial neural networks

(2020) Fernando Brito Lopes et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Sparse Convolutional Neural Networks for Genome-Wide Prediction

(2020) Patrik Waldmann et al.   Frontiers in Genetics

Genome-wide association study identifies markers associated with meat ultimate pH in Duroc pigs

(2019) R. Davoli et al.   ANIMAL GENETICS

A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive

(2019) Nedenia Bonvino Stafuzza et al.   BMC GENOMICS

A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data

(2019) Quan Wang et al.   NATURE NEUROSCIENCE

Bayes Factor-Based Regulatory Gene Network Analysis of Genome-Wide Association Study of Economic Traits in a Purebred Swine Population

(2019) Lee et al.   Genes

Genome-Wide Association Study Reveals Candidate Genes for Growth Relevant Traits in Pigs

(2019) Zhenshuang Tang et al.   Frontiers in Genetics

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

(2019) Himel Mallick et al.   Nature Communications

QTG-Finder: A Machine-Learning Based Algorithm To Prioritize Causal Genes of Quantitative Trait Loci in Arabidopsis and Rice

(2019) Fan Lin et al.   G3-Genes Genomes Genetics

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

(2019) Anurag Priyam et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2018) Wenhui Xing et al.   BIOINFORMATICS

Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design

(2018) Jacob W. Metch et al.   Nature Nanotechnology

DNA methylation-based biomarkers and the epigenetic clock theory of ageing

(2018) Steve Horvath et al.   NATURE REVIEWS GENETICS

RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments

(2018) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Integrated analysis of methylome, transcriptome and miRNAome of three pig breeds

(2018) Yuhua Fu et al.   Epigenomics

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

Deep learning in omics: a survey and guideline

(2018) Zhiqiang Zhang et al.   Briefings in Functional Genomics

Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding

(2018) Hong-Kyu Choi   Genes & Genomics

A powerful method to integrate genotype and gene expression data for dissecting the genetic architecture of a disease

(2018) Sarmistha Das et al.   GENOMICS

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Integrating co-expression networks with GWAS to prioritize causal genes in maize

(2018) Robert Schaefer et al.   PLANT CELL

Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma

(2018) Li Zhang et al.   Frontiers in Genetics

Multi-omics at single-cell resolution: comparison of experimental and data fusion approaches

(2018) Karolis Leonavicius et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genetic correlation of fatty acid composition with growth, carcass, fat deposition and meat quality traits based on GWAS data in six pig populations

(2018) Yifeng Zhang et al.   MEAT SCIENCE

A genome-wide association study identifies genomic loci associated with backfat thickness, carcass weight, and body weight in two commercial pig populations

(2017) Yuanmei Guo et al.   JOURNAL OF APPLIED GENETICS

Genome Variation Map: a data repository of genome variations in BIG Data Center

(2017) Shuhui Song et al.   NUCLEIC ACIDS RESEARCH

PigVar: a database of pig variations and positive selection signatures

(2017) Zhong-Yin Zhou et al.   Database-The Journal of Biological Databases and Curation

More Is Better: Recent Progress in Multi-Omics Data Integration Methods

(2017) Sijia Huang et al.   Frontiers in Genetics

Methods for the integration of multi-omics data: mathematical aspects

(2016) Matteo Bersanelli et al.   BMC BIOINFORMATICS

PCA-based polling strategy in machine learning framework for coronary artery disease risk assessment in intravascular ultrasound: A link between carotid and coronary grayscale plaque morphology

(2016) Tadashi Araki et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Predicting the Future — Big Data, Machine Learning, and Clinical Medicine

(2016) Ziad Obermeyer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs

(2016) Nadezda Kryuchkova-Mostacci et al.   PLoS Computational Biology

Expression Profiles of miRNA Subsets Distinguish Human Colorectal Carcinoma and Normal Colonic Mucosa

(2016) Daniel F Pellatt et al.   Clinical and Translational Gastroenterology

QTLMiner: QTL database curation by mining tables in literature

(2015) J. Peng et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Strong signatures of selection in the domestic pig genome

(2012) C.-J. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Proteomics as a tool for the modelling of biological processes and biomarker development in nutrition research

(2008) Baukje de Roos et al.   BRITISH JOURNAL OF NUTRITION