Standout Papers
Citation Impact
Citing Papers
A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules
2003 StandoutScience
The Sequence Alignment/Map format and SAMtools
2009 Standout
Induced Systemic Resistance by Beneficial Microbes
2014 Standout
Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways
2013 StandoutScience
One thousand plant transcriptomes and the phylogenomics of green plants
2019 StandoutNature
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
2008
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
2023 StandoutNobel
WGCNA: an R package for weighted correlation network analysis
2008 Standout
IDconverter and IDClight: Conversion and annotation of gene and protein IDs
2007
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
2007
High-throughput functional annotation and data mining with the Blast2GO suite
2008 Standout
A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals
2012 StandoutNobel
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
2008
Primer3—new capabilities and interfaces
2012 Standout
STRING v10: protein–protein interaction networks, integrated over the tree of life
2014 Standout
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
2008 Standout
ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery
2009
PHASTER: a better, faster version of the PHAST phage search tool
2016 Standout
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
2011 Standout
The Human Transcription Factors
2018 Standout
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
2007 Standout
CD-HIT: accelerated for clustering the next-generation sequencing data
2012 Standout
The molecular ecologist's guide to expressed sequence tags
2006
PlantTribes: a gene and gene family resource for comparative genomics in plants
2007
Using the Acropora digitifera genome to understand coral responses to environmental change
2011 StandoutNature
Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification
2012
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
2008 Standout
WebGestalt: an integrated system for exploring gene sets in various biological contexts
2005
Biosynthesis of the flavour precursors of onion and garlic
2004
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
2016 Standout
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
2012 Standout
Detecting the number of clusters of individuals using the software structure : a simulation study
2005 Standout
Applications of next-generation sequencing technologies in functional genomics
2008
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
2003 Standout
HaMStR: Profile hidden markov model based search for orthologs in ESTs
2009
Ancestral polyploidy in seed plants and angiosperms
2011 StandoutNature
Origin, Biogenesis, and Activity of Plant MicroRNAs
2009 Standout
QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR
2008
The DExD/H-box helicase Dicer-2 mediates the induction of antiviral activity in drosophila
2008 StandoutNobel
A framework for variation discovery and genotyping using next-generation DNA sequencing data
2011 Standout
The TIGR Rice Genome Annotation Resource: improvements and new features
2006
The development and impact of 454 sequencing
2008
The Sequence Analysis and Management System – SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies
2009
eggNOG: automated construction and annotation of orthologous groups of genes
2007
Insights into social insects from the genome of the honeybee Apis mellifera
2006 StandoutNature
Creating a honey bee consensus gene set
2007
Phytome: a platform for plant comparative genomics
2005
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
2010 Standout
RNA-Seq: a revolutionary tool for transcriptomics
2008 Standout
Next-generation sequencing transforms today's biology
2007
The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss
2007
Broad phylogenomic sampling improves resolution of the animal tree of life
2008 StandoutNature
Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA
2013 StandoutNobel
Diamonds in the rough: mRNA-like non-coding RNAs
2008
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
2007
The Pfam protein families database
2011 Standout
Compagen, a comparative genomics platform for early branching metazoan animals, reveals early origins of genes regulating stem‐cell differentiation
2008
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database
2006
EnsMart: A Generic System for Fast and Flexible Access to Biological Data
2004
A hitchhiker's guide to expressed sequence tag (EST) analysis
2006
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
2009
Applied bioinformatics for the identification of regulatory elements
2004
Applications of Ultra-high-Throughput Sequencing
2009
Multi-Platform, Multi-Site, Microarray-Based Human Tumor Classification
2004
Phytozome: a comparative platform for green plant genomics
2011 Standout
Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
2009
Engineering the third wave of biocatalysis
2012 StandoutNature
Recent Developments in the Chemistry of Deoxyribonucleic Acid (DNA) Intercalators: Principles, Design, Synthesis, Applications and Trends
2009
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
2009
Improving Protein Expression, Stability, and Function with ProteinMPNN
2024 StandoutNobel
Drug Discovery and Natural Products: End of an Era or an Endless Frontier?
2009 StandoutScience
Creation of a Productive, Highly Enantioselective Nitrilase through Gene Site Saturation Mutagenesis (GSSM)
2003
Babel's tower revisited: a universal resource for cross-referencing across annotation databases
2006
A Perspective on Cancer Cell Metastasis
2011 StandoutScience
Genome sequencing and analysis of the model grass Brachypodium distachyon
2010 StandoutNature
Modeling hepatitis C virus infection using human induced pluripotent stem cells
2012 StandoutNobel
Complex networks: Structure and dynamics
2006 Standout
Ancient class of translocated oomycete effectors targets the host nucleus
2010
Pungent products from garlic activate the sensory ion channel TRPA1
2005 StandoutNobel
Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
2016 StandoutScienceNobel
Highly Oxidized Peroxisomes Are Selectively Degraded via Autophagy in Arabidopsis
2013 StandoutNobel
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
2018 Standout
Proteomic Identification and Characterization of a Novel Peroxisomal Adenine Nucleotide Transporter Supplying ATP for Fatty Acid β-Oxidation in Soybean and Arabidopsis
2008
UniRef: comprehensive and non-redundant UniProt reference clusters
2007
Activatable Photosensitizers for Imaging and Therapy
2010 Standout
PartiGene—constructing partial genomes
2004
Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales
2009
Next-Generation DNA Sequencing Methods
2008
Structural Basis of Type II Topoisomerase Inhibition by the Anticancer Drug Etoposide
2011 StandoutScience
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
2013 Standout
Trimmomatic: a flexible trimmer for Illumina sequence data
2014 Standout
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)
2022 Standout
Works of Foo Cheung being referenced
Comparative Genomics of Brassica oleracea and Arabidopsis thaliana Reveal Gene Loss, Fragmentation, and Dispersal after Polyploidy
2006
A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and Poales[W]
2004
Sequencing and analysis of the gene-rich space of cowpea
2008
TIGR Gene Indices clustering tools (TGICL): a softwaresystem for fast clustering of large EST datasets
2003 Standout
Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems
2011
The TIGR Plant Transcript Assemblies database
2006
Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches
2008
Arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots
2007
RESOURCERER: a database for annotating and linking microarray resources within and across species
2001
Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice
2006
Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)
2002
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
2006
The Institute for Genomic Research Osa1 Rice Genome Annotation Database
2005