Citation Impact
Citing Papers
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
2014 Standout
Prokka: rapid prokaryotic genome annotation
2014 Standout
Unusual DNA Structures Associated With Germline Genetic Activity in Caenorhabditis elegans
2006 StandoutNobel
Protein structure determination using metagenome sequence data
2017 StandoutScienceNobel
WGCNA: an R package for weighted correlation network analysis
2008 Standout
Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway
2015 StandoutNobel
GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses
2017 Standout
Altered splicing of ATP6AP2 causes X-linked parkinsonism with spasticity (XPDS)
2013
Protein families and TRIBES in genome sequence space
2003
Functions of DNA methylation: islands, start sites, gene bodies and beyond
2012 Standout
A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern
2012
Genetic effects on gene expression across human tissues
2017 StandoutNature
High-throughput functional annotation and data mining with the Blast2GO suite
2008 Standout
Co-expression networks reveal the tissue-specific regulation of transcription and splicing
2017
Estimating the annotation error rate of curated GO database sequence annotations
2007
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
2009
BayGO: Bayesian analysis of ontology term enrichment in microarray data
2006
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
2015 Standout
The Spliceosome: Design Principles of a Dynamic RNP Machine
2009 Standout
Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis
2002
Applying genomic and transcriptomic advances to mitochondrial medicine
2021
Hallmarks of aging: An expanding universe
2023 Standout
Chromatin-Driven Behavior of Topologically Associating Domains
2014
The automatic annotation of bacterial genomes
2012
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
2008 Standout
The mini-driver model of polygenic cancer evolution
2015 StandoutNobel
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
2011 Standout
Modeling Heart Rate Variability in Healthy Humans: A Turbulence Analogy
2001
A general framework for estimating the relative pathogenicity of human genetic variants
2014 Standout
Biological Functions of Autophagy Genes: A Disease Perspective
2019 Standout
Transcription as a source of genome instability
2012
The carbohydrate-active enzymes database (CAZy) in 2013
2013 Standout
Reactive oxygen species (ROS) as pleiotropic physiological signalling agents
2020 Standout
High-performance medicine: the convergence of human and artificial intelligence
2018 Standout
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
2008 Standout
A categorization approach to automated ontological function annotation
2006
Ortholog identification in the presence of domain architecture rearrangement
2011
RNA and Disease
2009
rSeqDiff: Detecting Differential Isoform Expression from RNA-Seq Data Using Hierarchical Likelihood Ratio Test
2013
Expansion of the eukaryotic proteome by alternative splicing
2010 StandoutNature
Speeding disease gene discovery by sequence based candidate prioritization
2005
Linear motifs confer functional diversity onto splice variants
2012
Assessing the Mechanical Properties of a Molecular Spring
2007
Replication timing and epigenetic reprogramming of gene expression: a two-way relationship?
2009
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
2005
Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins
2012 Standout
A guide to deep learning in healthcare
2018 Standout
The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012
2012
Genome-wide analysis of noncoding regulatory mutations in cancer
2014
Applying negative rule mining to improve genome annotation
2007
Chromatin remodeller SMARCA4 recruits topoisomerase 1 and suppresses transcription-associated genomic instability
2016 StandoutNobel
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
2010 Standout
The Pfam protein families database
2011 Standout
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
2006
Whole genome sequencing for quantifying germline mutation frequency in humans and model species: Cautious optimism
2011
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
2011
iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data
2012
Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription
2009
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
2014 Standout
CLOCK:BMAL1 is a pioneer-like transcription factor
2014 StandoutNobel
ModelFinder: fast model selection for accurate phylogenetic estimates
2017 Standout
Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes
2006
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
2009 Standout
RNA processing enables predictable programming of gene expression
2012 StandoutNobel
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
2018 Standout
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
2017 StandoutScience
Decrease in topoisomerase I is responsible for activation-induced cytidine deaminase (AID)-dependent somatic hypermutation
2011 StandoutNobel
Genome sequencing and analysis of the model grass Brachypodium distachyon
2010 StandoutNature
A Bioinformatician's Guide to Metagenomics
2008
Oxidative Stress and Diabetic Complications
2010 Standout
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
2018 Standout
Classification of Intrinsically Disordered Regions and Proteins
2014 Standout
PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences
2010
Splicing in disease: disruption of the splicing code and the decoding machinery
2007
Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions
2016 Standout
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
2018 Standout
Fractal dynamics in physiology: Alterations with disease and aging
2002 Standout
Helical Polymers: Synthesis, Structures, and Functions
2009 Standout
Long-Chain N -Acyl Amino Acid Synthases Are Linked to the Putative PEP-CTERM/Exosortase Protein-Sorting System in Gram-Negative Bacteria
2011
Cancer Genome Landscapes
2013 StandoutScience
Protein Annotation at Genomic Scale: The Current Status
2007
Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks
2006
Interpreting non-coding variation in complex disease genetics
2012
2018
Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets
2015
Information Content and Complexity in the High-Order Organization of DNA
2004
The Microbial Engines That Drive Earth's Biogeochemical Cycles
2008 StandoutScience
Oxidative Stress Signaling to Chromatin in Health and Disease
2016
Evolutionary Comparison of the Mechanism of DNA Cleavage with Respect to Immune Diversity and Genomic Instability
2012 StandoutNobel
The Organization of the Bacterial Genome
2008
InterProScan 5: genome-scale protein function classification
2014 Standout
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
2019 Standout
Works of Benjamin Audit being referenced
From DNA Sequence Analysis to Modeling Replication in the Human Genome
2005
Long-range Correlations between DNA Bending Sites: Relation to the Structure and Dynamics of Nucleosomes
2002
Influence of the sequence on elastic properties of long DNA chains
2003
Percolation of annotation errors through hierarchically structured protein sequence databases
2005
Long-Range Correlations in Genomic DNA: A Signature of the Nucleosomal Structure
2001
Human Genome Replication Proceeds through Four Chromatin States
2013
Modeling the percolation of annotation errors in adatabase of protein sequences
2002
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
2010
Are splicing mutations the most frequent cause of hereditary disease?
2005
Probabilistic annotation of protein sequences based on functional classifications
2005
An Exponential Core in the Heart of the Yeast Protein Interaction Network
2004
From Genes to Genomes: Universal Scale-invariant Properties of Microbial Chromosome Organisation
2003
A novel strategy of transcription regulation by intragenic nucleosome ordering
2009
CoGenT++: an extensive and extensible data environment for computational genomics
2005
Human gene organization driven by the coordination of replication and transcription
2007
Thermodynamics of fractal signals based on wavelet analysis: application to fully developed turbulence data and DNA sequences
1998
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics
2003
Long-Range Correlations in Genomic DNA
2001
Replication-associated strand asymmetries in mammalian genomes: Toward detection of replication origins
2005