Citation Impact
Citing Papers
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
2014 StandoutNobel
Spatially resolved, highly multiplexed RNA profiling in single cells
2015 StandoutScience
Iterative random forests to discover predictive and stable high-order interactions
2018
Limits of long-term selection against Neandertal introgression
2019 StandoutNobel
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
2015 Science
Alteration of enzyme specificity by computational loop remodeling and design
2009 StandoutNobel
The Ensembl Regulatory Build
2015
Improved metagenomic analysis with Kraken 2
2019 Standout
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease
2015 Nature
The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation
2020 Standout
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
2012
An integrated encyclopedia of DNA elements in the human genome
2012 StandoutNature
An Expanded View of Complex Traits: From Polygenic to Omnigenic
2017 Standout
lincRNAs: Genomics, Evolution, and Mechanisms
2013 Standout
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions
2016
Phased diploid genome assembly with single-molecule real-time sequencing
2016
SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
2020 Standout
deepTools2: a next generation web server for deep-sequencing data analysis
2016 Standout
Genetic effects on gene expression across human tissues
2017 StandoutNature
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
2014
Increased Diels-Alderase activity through backbone remodeling guided by Foldit players
2012 StandoutNobel
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
2011 StandoutNobel
Ten quick tips for machine learning in computational biology
2017
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
2015 Standout
The GENCODE pseudogene resource
2012
The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia
2017 StandoutNobel
Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin
2016
Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs
2018
Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure
2013 StandoutNobel
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
2019 Standout
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology
2015 Standout
In vitro DNA-binding profile of transcription factors: methods and new insights
2011
The Human Transcription Factors
2018 Standout
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
2018
The multilayered complexity of ceRNA crosstalk and competition
2014 StandoutNature
Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
2014 StandoutNobel
A general framework for estimating the relative pathogenicity of human genetic variants
2014 Standout
Super-Enhancers in the Control of Cell Identity and Disease
2013 Standout
The single-cell transcriptional landscape of mammalian organogenesis
2019 StandoutNature
Massively parallel determination and modeling of endonuclease substrate specificity
2014 StandoutNobel
High resolution mapping of modified DNA nucleobases using excision repair enzymes
2014
Translation of new cancer treatments from pet dogs to humans
2008 Standout
Genome-wide map of regulatory interactions in the human genome
2014
NCBI GEO: archive for functional genomics data sets—update
2012 Standout
Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment
2016 StandoutNobel
De Novo Enzyme Design Using Rosetta3
2011 StandoutNobel
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
2013 Standout
The long-range interaction landscape of gene promoters
2012 Nature
Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs
2013
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases
2015
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
2010
Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment
2014 Standout
Comprehensive Integration of Single-Cell Data
2019 Standout
Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits
2014
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
2014 Standout
Single-cell transcriptomic analysis of Alzheimer’s disease
2019 StandoutNature
CLOCK:BMAL1 is a pioneer-like transcription factor
2014 StandoutNobel
Organoid single-cell genomic atlas uncovers human-specific features of brain development
2019 StandoutNatureNobel
Motif‐directed flexible backbone design of functional interactions
2009 StandoutNobel
Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery
2018
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
2013 Standout
Massively parallel kinetic profiling of natural and engineered CRISPR nucleases
2020 StandoutNobel
Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution
2015 StandoutNobel
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
2013 Standout
The role of chromatin dynamics in immune cell development
2014
Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches
2012
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system
2016 StandoutNobel
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
2017 StandoutScience
Protein Side-Chain Dynamics and Residual Conformational Entropy
2008
Reprogramming homing endonuclease specificity through computational design and directed evolution
2013 StandoutNobel
An Interactive Analysis and Exploration Tool for Epigenomic Data
2013
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19
2020
Definitions, methods, and applications in interpretable machine learning
2019 Standout
Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs
2011
Identifying Causal Variants at Loci with Multiple Signals of Association
2014
Accurate proteome-wide missense variant effect prediction with AlphaMissense
2023 StandoutScienceNobel
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design
2011 StandoutNobel
Works of Michael M. Hoffman being referenced
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome
2022
ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data
2016
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types
2019
Estimating the Neutral Rate of Nucleotide Substitution Using Introns
2006
Integrative annotation of chromatin elements from ENCODE data
2012
Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
2018
AANT: the Amino Acid-Nucleotide Interaction Database
2003
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
2012
Extending reference assembly models
2015
Top considerations for creating bioinformatics software documentation
2016
A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data
2010