DiSignAtlas: an atlas of human and mouse disease signatures based on bulk and single-cell transcriptomics

Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data

(2022) Aleksandr Ianevski et al.   Nature Communications

OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids

(2022) Qinfeng Ma et al.   NUCLEIC ACIDS RESEARCH

PertOrg 1.0: a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation

(2022) Zhaoyu Zhai et al.   NUCLEIC ACIDS RESEARCH

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA

(2021) Chenwei Li et al.   NUCLEIC ACIDS RESEARCH

Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures

(2021) Arutha Kulasinghe et al.   EUROPEAN RESPIRATORY JOURNAL

The Human Disease Ontology 2022 update

(2021) Lynn M Schriml et al.   NUCLEIC ACIDS RESEARCH

IFP35 as a promising biomarker and therapeutic target for the syndromes induced by SARS-CoV-2 or influenza virus

(2021) Yang Yu et al.   Cell Reports

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

From ArrayExpress to BioStudies

(2020) Ugis Sarkans et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

The Human Phenotype Ontology in 2021

(2020) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Identifying novel biomarkers of the pediatric influenza infection by weighted co-expression network analysis

(2019) Mohadeseh Zarei Ghobadi et al.   Virology Journal

OUP accepted manuscript

(2018)   BIOINFORMATICS

Integrative omics for health and disease

(2018) Konrad J. Karczewski et al.   NATURE REVIEWS GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

OMIM.org: leveraging knowledge across phenotype–gene relationships

(2018) Joanna S Amberger et al.   NUCLEIC ACIDS RESEARCH

A novel immune biomarkerIFI27discriminates between influenza and bacteria in patients with suspected respiratory infection

(2017) Benjamin M. Tang et al.   EUROPEAN RESPIRATORY JOURNAL

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery

(2017) Hayley M Dingerdissen et al.   NUCLEIC ACIDS RESEARCH

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

(2017) Beryl B. Cummings et al.   Science Translational Medicine

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS

Importing ArrayExpress datasets into R/Bioconductor

(2009) Audrey Kauffmann et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS