Citation Impact
Citing Papers
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
2015 StandoutNobel
Limits of long-term selection against Neandertal introgression
2019 StandoutNobel
A sex-biased imbalance between Tfr, Tph, and atypical B cells determines antibody responses in COVID-19 patients
2023 StandoutNobel
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells
2016 Science
Predicting enhancer‐promoter interaction from genomic sequence with deep neural networks
2019
HiFive: a tool suite for easy and efficient HiC and 5C data analysis
2015
Single-cell immunology of SARS-CoV-2 infection
2021
Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases
2024 StandoutNobel
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
2016 Standout
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
2016
A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions
2020
Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions
2020 StandoutNobel
dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region
2022 StandoutNobel
Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome
2020
Function and evolution of local repeats in the Firre locus
2016
Long COVID: major findings, mechanisms and recommendations
2023 Standout
Massively multiplex single-cell Hi-C
2017
Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X
2019
Long Noncoding RNAs in Development and Regeneration of the Neural Lineage
2019
HiChIP: efficient and sensitive analysis of protein-directed genome architecture
2016
Transcriptional architecture of the mammalian circadian clock
2016 Standout
The Biogenesis, Functions, and Challenges of Circular RNAs
2018 Standout
Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
2020 StandoutNobel
The T-box factor MLS-1 acts as a molecular switch during specification of nonstriated muscle in C. elegans
2002 StandoutNobel
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
2018
The multidimensional mechanisms of long noncoding RNA function
2017 Standout
Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects
2020 Standout
Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression
2017
Effective gene expression prediction from sequence by integrating long-range interactions
2021 StandoutNobel
SCENIC: single-cell regulatory network inference and clustering
2017 Standout
Functional Classification and Experimental Dissection of Long Noncoding RNAs
2018 Standout
The ground state of embryonic stem cell self-renewal
2008 StandoutNature
22q11.21 Deletion Syndromes: A Review of Proximal, Central, and Distal Deletions and Their Associated Features
2015 Standout
Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation
2017
REPuter: the manifold applications of repeat analysis on a genomic scale
2001 Standout
Prediction of enhancer-promoter interactions via natural language processing
2018
The single-cell transcriptional landscape of mammalian organogenesis
2019 StandoutNature
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
2015
Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly
2017
Wisdom of crowds for robust gene network inference
2012
Dictionary learning for integrative, multimodal and scalable single-cell analysis
2023 Standout
DeepC: predicting 3D genome folding using megabase-scale transfer learning
2020
Functional mapping and annotation of genetic associations with FUMA
2017 Standout
Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression
2018
Towards a comprehensive catalogue of validated and target-linked human enhancers
2020
Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells
2021 StandoutNobel
SARS-CoV-2-specific T cells associate with inflammation and reduced lung function in pulmonary post-acute sequalae of SARS-CoV-2
2022
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
2019
Regulation of Neuroregeneration by Long Noncoding RNAs
2018
Mechanistic insights in X-chromosome inactivation
2017
Organization and function of the 3D genome
2016
Interpreting neural networks for biological sequences by learning stochastic masks
2022 StandoutNobel
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
2015
22q11.2 deletion syndrome
2015 Standout
Comprehensive Integration of Single-Cell Data
2019 Standout
Mapping the multiscale structure of biological systems
2021
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
2014 Standout
Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States
2019
Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection
2021 Standout
Gene regulation by long non-coding RNAs and its biological functions
2020 Standout
Organoid single-cell genomic atlas uncovers human-specific features of brain development
2019 StandoutNatureNobel
Modeling Development and Disease with Organoids
2016 Standout
Adaptive immunity to SARS-CoV-2 and COVID-19
2021
Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression
2016
Functional organization of the human 4D Nucleome
2015
CADD: predicting the deleteriousness of variants throughout the human genome
2018 Standout
The Fibroblast Growth Factor signaling pathway
2015 Standout
Reversed graph embedding resolves complex single-cell trajectories
2017 Standout
A review of wheat diseases—a field perspective
2017 Standout
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
Genomes in Focus: Development and Applications of CRISPR‐Cas9 Imaging Technologies
2017 StandoutNobel
The Impact of Evolving SARS-CoV-2 Mutations and Variants on COVID-19 Vaccines
2022
Structural organization of the inactive X chromosome in the mouse
2016 Nature
AnFgf8mouse mutant phenocopies human 22q11 deletion syndrome
2002 StandoutNobel
A multivalent nucleoside-modified mRNA vaccine against all known influenza virus subtypes
2022 StandoutScienceNobel
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
2022 Standout
Conditional Deletion of Focal Adhesion Kinase Leads to Defects in Ventricular Septation and Outflow Tract Alignment
2007 StandoutNobel
Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development
2016 StandoutNobel
Liquid phase condensation in cell physiology and disease
2017 StandoutScience
Works of Ferhat Ay being referenced
Identification of copy number variations and translocations in cancer cells from Hi-C data
2017
Bipartite structure of the inactive mouse X chromosome
2015
Measuring the reproducibility and quality of Hi-C data
2019
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
2014
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
2014
Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome
2013
Analysis methods for studying the 3D architecture of the genome
2015
Accurate identification of centromere locations in yeast genomes using Hi-C
2015
A predictive modeling approach for cell line-specific long-range regulatory interactions
2015
The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain
2018
Comprehensive identification and analysis of human accelerated regulatory DNA
2015
Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19
2020
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
2012
17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells
2016
Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
2015
Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2–reactive CD8 + T cells
2021
A statistical approach for inferring the 3D structure of the genome
2014