Standout Papers
Citation Impact
Citing Papers
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
2014 Standout
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
2016
NCBI BLAST+ integrated into Galaxy
2015
RepeatModeler2 for automated genomic discovery of transposable element families
2020 Standout
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
2015 Standout
A Genomewide Search for Ribozymes Reveals an HDV-Like Sequence in the Human CPEB3 Gene
2006 StandoutScienceNobel
One thousand plant transcriptomes and the phylogenomics of green plants
2019 StandoutNature
Gene finding in novel genomes
2004 Standout
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
2023 StandoutNobel
A survey of best practices for RNA-seq data analysis
2016 Standout
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
2017
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
2008 Standout
Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED
2015 StandoutNobel
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences
2012
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
2011 Standout
Beyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage
2014
Discovery and engineering of enhanced SUMO protease enzymes
2018 StandoutNobel
Exploring the rice dispensable genome using a metagenome-like assembly strategy
2015
The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy
2015 StandoutNobel
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
2011 Standout
lincRNAs: Genomics, Evolution, and Mechanisms
2013 Standout
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
2014 Standout
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
2019
Phased diploid genome assembly with single-molecule real-time sequencing
2016
Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees
2016
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
2012 StandoutNature
Circular RNAs are a large class of animal RNAs with regulatory potency
2013 StandoutNature
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
2012 Standout
Genome annotation past, present, and future: How to define an ORF at each locus
2005
Rewiring of the Fruit Metabolome in Tomato Breeding
2018 Standout
Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus
2009
Modular regulatory principles of large non-coding RNAs
2012 StandoutNature
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
2015 Standout
High‐Throughput Screening for Terpene‐Synthase‐Cyclization Activity and Directed Evolution of a Terpene Synthase
2013 StandoutNobel
APPRIS: annotation of principal and alternative splice isoforms
2012
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
2011 Standout
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
2009 StandoutNature
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
2010
A new coronavirus associated with human respiratory disease in China
2020 StandoutNature
The Human Intestinal Microbiome in Health and Disease
2016 Standout
GeSeq – versatile and accurate annotation of organelle genomes
2017 Standout
Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
2014 Standout
Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile
2011
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
2011
vasa mRNA accumulates at the posterior pole during blastoderm formation in the flour beetle Tribolium castaneum
2006
Integrating single-cell transcriptomic data across different conditions, technologies, and species
2018 Standout
Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
2015
Using the Acropora digitifera genome to understand coral responses to environmental change
2011 StandoutNature
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
2007 Standout
Revisiting the protein-coding gene catalog ofDrosophila melanogasterusing 12 fly genomes
2007
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection
2010 Standout
The pangenome of an agronomically important crop plant Brassica oleracea
2016 Standout
Biogeography and individuality shape function in the human skin metagenome
2014 Nature
2016 update of the PRIDE database and its related tools
2015 Standout
Meeting the Global Food Demand of the Future by Engineering Crop Photosynthesis and Yield Potential
2015 Standout
Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
2017
Unexpected Repertoire of Metazoan Transcription Factors in the Unicellular Holozoan Capsaspora owczarzaki
2010
Insights into social insects from the genome of the honeybee Apis mellifera
2006 StandoutNature
NCBI prokaryotic genome annotation pipeline
2016 Standout
Realistic artificial DNA sequences as negative controls for computational genomics
2014
WormBase ParaSite − a comprehensive resource for helminth genomics
2016
The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure
2014 Standout
A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives
2011
The UCSC Genome Browser Database: update 2006
2005
A beginner's guide to eukaryotic genome annotation
2012
Long noncoding RNAs are rarely translated in two human cell lines
2012
Long Noncoding RNAs: Cellular Address Codes in Development and Disease
2013 Standout
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
2012
Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
2013
Methods to Study Splicing from High-Throughput RNA Sequencing Data
2014
Assessment of transcript reconstruction methods for RNA-seq
2013
Cell‐type specific analysis of translating RNAs in developing flowers reveals new levels of control
2010
Minimap2: pairwise alignment for nucleotide sequences
2018 Standout
Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography
2015
Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences
2016
The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals
2011 StandoutScience
Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment
2022
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
2017 StandoutScience
Protein Analysis by Shotgun/Bottom-up Proteomics
2013
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
2017 Standout
Evidence of ancient genome reduction in red algae (Rhodophyta)
2015
Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
2014
AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development
2009
The Genome 10K Project: A Way Forward
2015
Quality Assessment of Domesticated Animal Genome Assemblies
2015
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)
2019 Standout
Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach
2009
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
2018 Standout
Interactive Tree Of Life (iTOL) v4: recent updates and new developments
2019 Standout
Identification of novel transcripts in annotated genomes using RNA-Seq
2011
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
2011 Standout
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution
2012 StandoutNobel
RDP3: a flexible and fast computer program for analyzing recombination
2010
Chemical Glycoproteomics
2016 StandoutNobel
Works of Mario Stanke being referenced
Discovery and revision of Arabidopsis genes by proteogenomics
2008
Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote
2013 Science
Draft genome sequence of the oilseed species Ricinus communis
2010
Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
2008
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
2006
AUGUSTUS: ab initio prediction of alternative transcripts
2006 Standout
The Chlamydomonas genome project: a decade on
2014
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
2006
Gene prediction with a hidden Markov model and a new intron submodel
2003
AUGUSTUS: a web server for gene finding in eukaryotes
2004
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
2005
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
2006
A novel hybrid gene prediction method employing protein multiple sequence alignments
2011
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
2008
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
2015