Citation Impact
Citing Papers
High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding
2017 StandoutNobel
Improved protein structure prediction using predicted interresidue orientations
2020 StandoutNobel
A sex-biased imbalance between Tfr, Tph, and atypical B cells determines antibody responses in COVID-19 patients
2023 StandoutNobel
Infrared molecular fingerprinting of blood-based liquid biopsies for the detection of cancer
2021 StandoutNobel
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
2015
ENNET: inferring large gene regulatory networks from expression data using gradient boosting
2013
A survey of best practices for RNA-seq data analysis
2016 Standout
cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture
2017
State-of-the-art in artificial neural network applications: A survey
2018 Standout
A genetic method specifically delineates Th1-type Treg cells and their roles in tumor immunity
2023 StandoutNobel
Transcriptional regulatory networks underlying gene expression changes in Huntington's disease
2018
Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil
2016
An Expanded View of Complex Traits: From Polygenic to Omnigenic
2017 Standout
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument
2011
Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease
2017
Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8+ T Cells in Chronic versus Acute Infection
2017
Genetic effects on gene expression across human tissues
2017 StandoutNature
Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance
2018 StandoutNobel
A paradigm shift in medicine: A comprehensive review of network-based approaches
2019
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
2010
Plant–microbiome interactions: from community assembly to plant health
2020 Standout
Advantages and limitations of current network inference methods
2010
Multi-omics approaches to disease
2017
The multidimensional mechanisms of long noncoding RNA function
2017 Standout
Microbiome Datasets Are Compositional: And This Is Not Optional
2017 Standout
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update
2017 Standout
SCENIC: single-cell regulatory network inference and clustering
2017 Standout
The Human Transcription Factors
2018 Standout
Somewhat in control — the role of transcription in regulating microbial metabolic fluxes
2013
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
2015 Standout
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
2016 Standout
Microbial Co-occurrence Relationships in the Human Microbiome
2012 Standout
High-performance medicine: the convergence of human and artificial intelligence
2018 Standout
Human diseases through the lens of network biology
2012
Multimodal biomedical AI
2022 Standout
Systematic evaluation of spliced alignment programs for RNA-seq data
2013
Transcription Factor NRF2 as a Therapeutic Target for Chronic Diseases: A Systems Medicine Approach
2018 Standout
A comparison of single-cell trajectory inference methods
2019
Microbial interactions: from networks to models
2012 Standout
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
2018
Integrative omics for health and disease
2018
HISAT: a fast spliced aligner with low memory requirements
2015 Standout
Functional mapping and annotation of genetic associations with FUMA
2017 Standout
Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19
2020 Standout
Defining roles of specific reactive oxygen species (ROS) in cell biology and physiology
2022 Standout
Dimensionality reduction for visualizing single-cell data using UMAP
2018 Standout
Applications of machine learning in drug discovery and development
2019 Standout
Keystone taxa as drivers of microbiome structure and functioning
2018 Standout
Transcription factor Ikzf1 associates with Foxp3 to repress gene expression in Treg cells and limit autoimmunity and anti-tumor immunity
2024 StandoutNobel
Therapeutic targeting of the NRF2 and KEAP1 partnership in chronic diseases
2019 Standout
Field-resolved infrared spectroscopy of biological systems
2020 StandoutNatureNobel
Regulatory T Cell-Specific Epigenomic Region Variants Are a Key Determinant of Susceptibility to Common Autoimmune Diseases
2020 StandoutNobel
Evaluation of methods for modeling transcription factor sequence specificity
2013
Soil microbiomes and climate change
2019 Standout
Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning
2018
Gene regulation by long non-coding RNAs and its biological functions
2020 Standout
Next-Generation Machine Learning for Biological Networks
2018
Towards revealing the functions of all genes in plants
2013
Redox Systems Biology: Harnessing the Sentinels of the Cysteine Redoxome
2019
CADD: predicting the deleteriousness of variants throughout the human genome
2018 Standout
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system
2016 StandoutNobel
Applications of Deep Learning and Reinforcement Learning to Biological Data
2018
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China
2016
Conversion of antigen-specific effector/memory T cells into Foxp3-expressing T reg cells by inhibition of CDK8/19
2019 StandoutNobel
Neuroevolution: from architectures to learning
2008
R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter
2016
Significant Impacts of Increasing Aridity on the Arid Soil Microbiome
2017
ProTox-II: a webserver for the prediction of toxicity of chemicals
2018 Standout
Functional association networks as priors for gene regulatory network inference
2014
The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads
2019 Standout
A Survey of Autonomous Driving: Common Practices and Emerging Technologies
2020 Standout
Acquisition of chess knowledge in AlphaZero
2022 StandoutNobel
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
2018 Standout
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks
2019
Comprehensive Review of Artificial Neural Network Applications to Pattern Recognition
2019 Standout
Tox21Challenge to Build Predictive Models of Nuclear Receptor and Stress Response Pathways as Mediated by Exposure to Environmental Chemicals and Drugs
2016
A Theory of Usable Information Under Computational Constraints
2020
From hairballs to hypotheses–biological insights from microbial networks
2018
The return of metabolism: biochemistry and physiology of the pentose phosphate pathway
2014 Standout
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
2020 Standout
Transcription factor and chromatin features predict genes associated with eQTLs
2012
A modular framework for gene set analysis integrating multilevel omics data
2013
SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
2015
Protein contact prediction using metagenome sequence data and residual neural networks
2019 StandoutNobel
Works of Daniel Marbach being referenced
GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods
2011
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics
2016
Wisdom of crowds for robust gene network inference
2012
Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases
2016
Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges
2010
Network deconvolution as a general method to distinguish direct dependencies in networks
2013
Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods
2009
Revealing strengths and weaknesses of methods for gene network inference
2010
The Age of Analog Networks
2008
Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges
2010