Citation Impact
Citing Papers
Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes
2020 StandoutNobel
Prediction of Individual Brain Maturity Using fMRI
2010 StandoutScience
Removing T-cell epitopes with computational protein design
2014 StandoutNobel
Development of siRNA Payloads to Target KRAS -Mutant Cancer
2014
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era
2013 StandoutNobel
Predicting protein–protein interactions in the context of protein evolution
2009
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
2014 Standout
WGCNA: an R package for weighted correlation network analysis
2008 Standout
Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution
2024 StandoutNobel
Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs
2019 StandoutNobel
Network‐based classification of breast cancer metastasis
2007
Massively multiplex single-cell Hi-C
2017
Support Vector Machines and Kernels for Computational Biology
2008
Improved residue contact prediction using support vector machines and a large feature set
2007
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites
2003
A Survey on Filter Techniques for Feature Selection in Gene Expression Microarray Analysis
2012
The Pfam Protein Families Database
2002 Standout
Advantages and limitations of current network inference methods
2010
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
2019 Standout
STRING v10: protein–protein interaction networks, integrated over the tree of life
2014 Standout
Pfam: the protein families database
2013 Standout
CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification
2019 StandoutNobel
An Optimized microRNA Backbone for Effective Single-Copy RNAi
2013
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
2016 Standout
Template-based structure modeling of protein–protein interactions
2013
Machine Learning methods for Quantitative Radiomic Biomarkers
2015 Standout
The single-cell transcriptional landscape of mammalian organogenesis
2019 StandoutNature
GC-Content Normalization for RNA-Seq Data
2011
Why we need more ecology for genetic models such as C. elegans
2015
Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch
2016 StandoutNobel
Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay
2011
VisANT: an integrative framework for networks in systems biology
2008
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
2019 Standout
A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function
2006 StandoutNature
Deep generative modeling for single-cell transcriptomics
2018
A Combined Transmembrane Topology and Signal Peptide Prediction Method
2004 Standout
SwissTargetPrediction: a web server for target prediction of bioactive small molecules
2014
MHC Class II epitope predictive algorithms
2010
Wisdom of crowds for robust gene network inference
2012
Insights into RNA structure and function from genome-wide studies
2014 StandoutNobel
NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure
2010
Improved Prediction of Signal Peptides: SignalP 3.0
2004 Standout
EMT: 2016
2016 Standout
Exploring protein-protein interactions at the proteome level
2022
Clonal Expansion and Diversification of Cancer-Associated Mutations in Endometriosis and Normal Endometrium
2018
Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells
2021 StandoutNobel
Exosomes facilitate therapeutic targeting of oncogenic KRAS in pancreatic cancer
2017 StandoutNature
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
2009
Transcription factor Ikzf1 associates with Foxp3 to repress gene expression in Treg cells and limit autoimmunity and anti-tumor immunity
2024 StandoutNobel
SHAPE-directed Discovery of Potent shRNA Inhibitors of HIV-1
2012
SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules
2017 Standout
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
2013 StandoutNobel
Whole-organism clone tracing using single-cell sequencing
2018 Nature
Rapid non-uniform adaptation to conformation-specific KRAS(G12C) inhibition
2020 Nature
Network and Data Integration for Biomarker Signature Discovery via Network Smoothed T-Statistics
2013
Comprehensive Integration of Single-Cell Data
2019 Standout
Mapping the multiscale structure of biological systems
2021
Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications
2017 StandoutNobel
PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles
2015 StandoutNobel
Deep learning in neural networks: An overview
2014 Standout
Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods
2010
A GPT‐4 Reticular Chemist for Guiding MOF Discovery**
2023 StandoutNobel
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
2010 Standout
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system
2016 StandoutNobel
Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules
2013
A review of network-based approaches to drug repositioning
2017
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
2017 StandoutScience
Systematic discovery of natural CRISPR-Cas12a inhibitors
2018 StandoutScienceNobel
SWISS-MODEL: homology modelling of protein structures and complexes
2018 Standout
Prediction of Synthesis of 2D Metal Carbides and Nitrides (MXenes) and Their Precursors with Positive and Unlabeled Machine Learning
2019
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
2022 Standout
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
2018 Standout
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
2018 Standout
Endometriosis
2020 Standout
Mining Insights on Metal–Organic Framework Synthesis from Scientific Literature Texts
2022
The world of two-dimensional carbides and nitrides (MXenes)
2021 StandoutScience
Computational Approaches for Integrative Analysis of the Metabolome and Microbiome
2017
Definitions, methods, and applications in interpretable machine learning
2019 Standout
Estimation Stability With Cross-Validation (ESCV)
2015
A survey on feature selection methods
2013 Standout
ChatGPT Chemistry Assistant for Text Mining and the Prediction of MOF Synthesis
2023 StandoutNobel
Chemistry and Biology Of Multicomponent Reactions
2012 Standout
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
2020 Standout
Integrated Computational Pipeline for Single-Cell Genomic Profiling
2020
Establishing neural crest identity: a gene regulatory recipe
2015
Caenorhabditis elegans responses to bacteria from its natural habitats
2016 StandoutNobel
Protein contact prediction using metagenome sequence data and residual neural networks
2019 StandoutNobel
Works of Jean‐Philippe Vert being referenced
Large-scale prediction of protein-protein interactions from structures
2010
An accurate and interpretable model for siRNA efficacy prediction
2006
Classification of microarray data using gene networks
2007
A general and flexible method for signal extraction from single-cell RNA-seq data
2018
Accurate identification of centromere locations in yeast genomes using Hi-C
2015
Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers
2013
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
2015
Protein network inference from multiple genomic data: a supervised approach
2004
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
2018
Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons
2012
A novel representation of protein sequences for prediction of subcellular location using support vector machines
2005
Machine Learning for In Silico Virtual Screening and Chemical Genomics: New Strategies
2008
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection
2012
Supervised reconstruction of biological networks with local models
2007
The Influence of Feature Selection Methods on Accuracy, Stability and Interpretability of Molecular Signatures
2011
Graph kernels based on tree patterns for molecules
2008
A tree kernel to analyse phylogenetic profiles
2002
Global alignment of protein–protein interaction networks by graph matching methods
2009
A statistical approach for inferring the 3D structure of the genome
2014
Protein-ligand interaction prediction: an improved chemogenomics approach
2008
Efficient peptide–MHC-I binding prediction for alleles with few known binders
2007
A Primer on Kernel Methods
2004
A bagging SVM to learn from positive and unlabeled examples
2013
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
2010
SUPPORT VECTOR MACHINE PREDICTION OF SIGNAL PEPTIDE CLEAVAGE SITE USING A NEW CLASS OF KERNELS FOR STRINGS
2001
SIRENE: supervised inference of regulatory networks
2008