| 9.50 |
independent |
0/2 |
2026 |
Causal variant underestimation is a major overlooked driver of sequence-to-function model underperformance
score:
bench +1.5, crit +8
words: baseline, compare, fail, fails, fails to, overlooked, systematic, underestimat, underperform
|
| 6.00 |
independent |
0/6 |
2025 |
Early feature extraction drives model performance in high-resolution chromatin accessibility prediction: A systematic evaluation of deep learning architectures
score:
bench +6
words: benchmark, evaluate, evaluation, systematic
|
| 5.50 |
independent |
0/3 |
2025 |
Comparative evaluation of genomic footprinting algorithms for predicting transcription factor binding sites in single-cell data
score:
bench +5.5
words: benchmark, benchmarking, comparative, evaluate, evaluation
|
| 4.50 |
independent |
0/2 |
2026 |
DNA-aware evaluation and debiasing of sequence-to-function models
score:
bench +3, name_abstract +1.5
words: evaluate, evaluation
|
| 4.25 |
partial |
1/17 |
2026 |
Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens
score:
bench +3.5, crit +0.75
words: benchmark, evaluating, fail, systematic
shared authors:
Anshul Bharat Kundaje
|
| 4.00 |
independent |
0/3 |
2025 |
Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants
score:
bench +4
words: assess, assessment, benchmark, comparative, compare, comparison, evaluate, evaluation, we evaluate
|
| 4.00 |
independent |
0/13 |
2025 |
mRNABench: A curated benchmark for mature mRNA property and function prediction
score:
bench +4
words: assess, benchmark, benchmarking, evaluate
|
| 3.75 |
independent |
0/1 |
2025 |
Molecular phenotyping of Parkinson's disease
score:
bench +1.5, crit +2.25
words: assess, assessment, fail, fails, fails to, systematic
|
| 3.75 |
independent |
0/4 |
2026 |
Evaluation of Active Learning Selection Strategies and Characterization of Informative Sequences for Sequence-to-Expression Models
score:
bench +3, crit +0.75
words: benchmark, evaluation, poorly, we benchmark
|
| 3.50 |
independent |
0/34 |
2025 |
Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex
score:
bench +3.5
words: assess, benchmark, evaluate, evaluating
|
| 3.50 |
independent |
0/5 |
2025 |
Evaluating the contribution of genome 3D folding to variation in human height using machine learning
score:
bench +3.5
words: assess, assessing, evaluating
|
| 3.25 |
independent |
0/37 |
2026 |
Single-cell multiomics and chromatin structure reveal gene-regulatory dynamics in heart failure
score:
crit +3.25
words: fail
|
| 3.00 |
independent |
0/14 |
2026 |
Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling
score:
bench +3
words: benchmark, evaluating, systematic
|
| 2.75 |
independent |
0/2 |
2026 |
Genetic risk and inflammatory signaling converge on cell type-specific regulatory programs in type 1 diabetes
score:
bench +0.5, crit +0.75, name_abstract +1.5
words: evaluate, poorly
|
| 2.50 |
independent |
0/20 |
2025 |
Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium
score:
bench +2.5
words: compare, comparison
|
| 2.50 |
independent |
0/4 |
2025 |
Characterizing homology-induced data leakage and memorization in genome-trained sequence models
score:
bench +1, crit +1.5
words: evaluation, fail, overestimat, systematic
|
| 2.00 |
independent |
0/6 |
2025 |
Integration of Deep Learning Annotations with Functional Genomics Improves Identification of Causal Alzheimer's Disease Variants
score:
bench +0.5, name_abstract +1.5
words: compare
|
| 2.00 |
independent |
0/3 |
2025 |
Polygenic prediction of phenotypes with a neural empirical Bayes approach
score:
bench +2
words: benchmark, benchmarking, evaluate, we evaluate
|
| 2.00 |
independent |
0/5 |
2026 |
TFBSpedia: a comprehensive human and mouse transcription factor binding sites database
score:
bench +2
words: assess, benchmark, evaluation, systematic
|
| 2.00 |
independent |
0/6 |
2026 |
Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
score:
bench +2
words: benchmark, evaluate, evaluation, systematic
|
| 2.00 |
independent |
0/2 |
2026 |
AutoNovo: Agentic Program Search Discovers Transferable Nucleic Acid Design Algorithms
score:
bench +0.5, crit +1.5
words: artifact, evaluate, fail
|
| 1.75 |
independent |
0/3 |
2026 |
Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts
score:
bench +1, crit +0.75
words: cannot, evaluate, systematic
|
| 1.75 |
independent |
0/24 |
2025 |
A multispecies foundation model for genome function prediction, gene annotation and sequence design
score:
bench +1, crit +0.75
words: comparative, evaluate, spurious
|
| 1.75 |
independent |
0/13 |
2026 |
Deep learning as a bridge between sequencing-derived biological data and functional interpretation
score:
bench +1, crit +0.75
words: benchmark, benchmarking, limitation
|
| 1.50 |
independent |
0/15 |
2026 |
CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species
score:
bench +1.5
words: assess, compare, we assess
|
| 1.50 |
partial |
2/18 |
2025 |
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci
score:
name_abstract +1.5
shared authors:
Soumya Kundu, Anshul Bharat Kundaje
|
| 1.50 |
independent |
0/2 |
2026 |
GUANinE v1.1 reveals complementarity of supervised and genomic language models
score:
bench +1.5
words: benchmark, evaluate, evaluation
|
| 1.50 |
independent |
0/21 |
2025 |
Context-dependent regulatory variants in Alzheimer’s disease
score:
bench +1.5
words: assess, assessing, systematic
|
| 1.50 |
independent |
0/10 |
2026 |
BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era
score:
bench +1.5
words: baseline, benchmark, evaluation
|
| 1.50 |
independent |
0/27 |
2026 |
Massive-scale single-nucleus multi-omics identifies novel rare noncoding drivers of Parkinson’s disease
score:
crit +1.5
words: fail, often fail
|
| 1.50 |
independent |
0/12 |
2026 |
Using sequence-to-function models to interpret archaic hominin introgression
score:
crit +1.5
words: limitation, no better than
|
| 1.50 |
independent |
0/2 |
2026 |
fp-tools: A Reproducible Platform for ATAC-seq Footprinting and Regulatory Motif Analysis
score:
bench +1.5
words: benchmark, benchmarking, compare
|
| 1.50 |
independent |
0/3 |
2026 |
ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility
score:
bench +1.5
words: compare, comparison, systematic
|
| 1.25 |
independent |
0/3 |
2025 |
In silico prediction of variant effects: promises and limitations for precision plant breeding
score:
bench +1, crit +3.25, demote_type -3
words: comparative, compare, limitation
|
| 1.25 |
partial |
1/8 |
2026 |
Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models
score:
bench +0.5, crit +0.75
words: confound, systematic
shared authors:
Anshul Bharat Kundaje
|
| 1.25 |
independent |
0/21 |
2026 |
Modeling cis -regulatory variation in human brain enhancers across a large Parkinson’s Disease cohort
score:
bench +0.5, crit +0.75
words: assess, limitation
|
| 1.25 |
independent |
0/3 |
2026 |
When Less Is Enough: Low-Rank Structure in DNA Sequence-to-Function Models
score:
bench +0.5, crit +0.75
words: artifact, benchmark
|
| 1.25 |
independent |
0/6 |
2026 |
Regulatory network architecture constrains inflammatory responses in tissue-resident alveolar macrophages
score:
bench +0.5, crit +0.75
words: compare, poorly
|
| 1.00 |
partial |
2/10 |
2026 |
Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration
score:
bench +1
words: assess, systematic
shared authors:
Surag Nair, Anshul Bharat Kundaje
|
| 1.00 |
independent |
0/5 |
2026 |
Refining sequence-to-activity models by increasing model resolution
score:
bench +1
words: compare, systematic
|
| 1.00 |
independent |
0/7 |
2025 |
IceQream: Quantitative chromosome accessibility analysis using physical TF models
score:
bench +1
words: baseline, compare
|
| 1.00 |
independent |
0/16 |
2026 |
Single-cell multiomics across nine mammals reveals cell-type-specific regulatory conservation in the brain
score:
bench +1
words: assess, comparative
|
| 1.00 |
partial |
2/24 |
2025 |
Enhancer-targeting CRISPR screens at coronary artery disease loci suggest shared mechanisms of disease risk
score:
bench +1
words: evaluation, systematic
shared authors:
Soumya Kundu, Anshul Bharat Kundaje
|
| 1.00 |
independent |
0/11 |
2025 |
Enigma: An Efficient Model for Deciphering Regulatory Genomics
score:
bench +1
words: benchmark, compare
|
| 1.00 |
independent |
0/4 |
2025 |
A machine-learning framework to characterize functional disease architectures and prioritize disease variants
score:
bench +1
words: benchmark, we benchmark
|
| 1.00 |
independent |
0/3 |
2025 |
A machine-learning framework to characterize functional disease architectures and prioritize disease variants
score:
bench +1
words: benchmark, we benchmark
|
| 1.00 |
independent |
0/9 |
2026 |
Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
score:
bench +1
words: evaluate, systematic
|
| 1.00 |
independent |
0/3 |
2026 |
FABIAN-variant 2026: improved prediction of the effects of DNA variants on transcription factor binding
score:
bench +1
words: assess, assessment
|
| 1.00 |
independent |
0/4 |
2026 |
Gene regulatory innovations from transposable elements in primate cerebellum development
score:
bench +1
words: assess, systematic
|
| 1.00 |
independent |
0/5 |
2026 |
DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference
score:
bench +1
words: baseline, benchmark
|
| 0.75 |
independent |
0/7 |
2025 |
scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution
score:
crit +0.75
words: fail
|
| 0.75 |
independent |
0/15 |
2026 |
Distinctive DNA sequence features define epigenetic longevity of inflammatory memory
score:
crit +0.75
words: poorly
|
| 0.75 |
independent |
0/16 |
2025 |
YAP-Induced Glycolysis Drives Fibroinflammation and Disrupts Fibroblast Fidelity
score:
crit +0.75
words: poorly
|
| 0.75 |
independent |
0/9 |
2025 |
Synergistic and antagonistic activities of IRF8 and FOS enhancer pairs during an immune-cell fate switch
score:
crit +0.75
words: poorly
|
| 0.75 |
independent |
0/23 |
2025 |
Multi-scale gene regulatory networks for resolving transcription factor and autoimmune variant impacts on human B cell fate dynamics
score:
crit +0.75
words: poorly
|
| 0.75 |
partial |
2/8 |
2025 |
Cancer cell phagocytosis induces an anti-inflammatory gene regulatory program in macrophages
score:
crit +0.75
words: poorly
shared authors:
Anshul Bharat Kundaje, William James Greenleaf
|
| 0.75 |
independent |
0/24 |
2025 |
The craniofacial shape of modern humans embodies genomic signatures of evolution, diversity, and clinical conditions
score:
crit +0.75
words: poorly
|
| 0.75 |
independent |
0/10 |
2026 |
Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers
score:
crit +0.75
words: poorly
|
| 0.75 |
independent |
0/9 |
2026 |
Current challenges in GWAS integration and fine-mapping for variant interpretation
score:
crit +0.75
words: limitation
|
| 0.75 |
independent |
0/4 |
2025 |
InfluenceNet: Encoding Motif Influence for Interpretable Modeling of Cis-Regulatory Syntax
score:
crit +0.75
words: poorly
|
| 0.75 |
independent |
0/7 |
2026 |
Reconstitution of the Spinal Cord Injury Microenvironment in Adult Neural Stem Cell-Derived Organoids
score:
crit +0.75
words: fail
|
| 0.75 |
independent |
0/9 |
2026 |
Temporal regulation of a spatial patterning factor in Drosophila neurogenesis
score:
crit +0.75
words: poorly
|
| 0.75 |
independent |
0/4 |
2026 |
Predicting single-molecule chromatin distribution from DNA sequence
score:
crit +0.75
words: cannot
|
| 0.50 |
independent |
0/26 |
2026 |
Advancing regulatory variant effect prediction with AlphaGenome
score:
bench +0.5
words: evaluation
|
| 0.50 |
partial |
1/5 |
2025 |
gReLU: a comprehensive framework for DNA sequence modeling and design
score:
bench +0.5
words: evaluation
shared authors:
Surag Nair
|
| 0.50 |
independent |
0/5 |
2026 |
EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles
score:
bench +0.5
words: compare
|
| 0.50 |
independent |
0/31 |
2026 |
Genetic variants shape single-cell chromatin accessibility and disease risk
score:
bench +0.5
words: compare
|
| 0.50 |
independent |
0/2 |
2025 |
Protocol to analyze deep-learning-predicted functional scores for noncoding de novo variants and their correlation with complex brain traits
score:
bench +0.5
words: comparison
|
| 0.50 |
independent |
0/46 |
2026 |
AlphaGenome Atlas: in silico mutagenesis of the entire human genome improves prioritization and interpretation of non-coding variants
score:
bench +0.5
words: benchmark
|
| 0.50 |
independent |
0/4 |
2025 |
Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning
score:
bench +0.5
words: systematic
|
| 0.50 |
partial |
2/20 |
2025 |
Decoding Chromatin Dynamics in Cardiac Organoids Reveals Genetic Drivers of Human Heart Development and Disease
score:
bench +0.5
words: systematic
shared authors:
Anshul Bharat Kundaje, William James Greenleaf
|
| 0.50 |
independent |
0/21 |
2026 |
Integrating multi-omic QTLs and predictive models reveals regulatory architectures at immune related GWAS loci in CD4+ T cells
score:
bench +0.5
words: systematic
|
| 0.50 |
independent |
0/16 |
2025 |
Expanding the DNA Motif Lexicon of the Transcriptional Regulatory Code
score:
bench +0.5
words: comparative
|
| 0.50 |
partial |
1/21 |
2025 |
The nascent transcriptome delineates the regulatory landscape in human health and disease
score:
bench +0.5
words: systematic
shared authors:
Anshul Bharat Kundaje
|
| 0.50 |
partial |
1/14 |
2026 |
Massively multiplex multimodal chemical screens at single-cell resolution
score:
bench +0.5
words: systematic
shared authors:
Anshul Bharat Kundaje
|
| 0.50 |
independent |
0/6 |
2026 |
Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles
score:
bench +0.5
words: baseline
|
| 0.50 |
independent |
0/1 |
2026 |
The Encyclopedia of DNA Elements
score:
bench +0.5
words: systematic
|
| 0.50 |
independent |
0/7 |
2026 |
Sequence-based modeling of plant epigenomes reveals cell-type-specific cis -regulatory grammar
score:
bench +0.5
words: evaluating
|
| 0.50 |
independent |
0/9 |
2025 |
Machine Learning-Based Prediction of Cell-type Resolved Brain eQTLs Enhances Discovery of Variants Explaining Alzheimer’s Disease Heritability
score:
bench +0.5
words: compare
|
| 0.50 |
independent |
0/2 |
2025 |
The Algorithm for Reversible Jump Inference of Motifs
score:
bench +0.5
words: comparative
|
| 0.50 |
independent |
0/5 |
2026 |
Adaptive loss of function accelerated the evolution of ancient and modern human cognition
score:
bench +0.5
words: compare
|
| 0.50 |
independent |
0/4 |
2026 |
Mapping Genetic Risk Associations to Cellular Contexts via Deep Learning and Biological Ontologies
score:
bench +0.5
words: evaluate
|
| 0.50 |
independent |
0/5 |
2026 |
An empirical Bayes framework for burden and dispersion association tests helps prioritize rare variants associated with Alzheimer’s disease
score:
bench +0.5
words: systematic
|
| 0.50 |
independent |
0/4 |
2026 |
Identifying severe COVID-19 risk variants modulating enhancer reporter activity in lung cells
score:
bench +0.5
words: evaluating
|
| 0.50 |
independent |
0/48 |
2026 |
A multi-tissue epigenomic atlas links the sheep non-coding genome to domestication and complex traits
score:
bench +0.5
words: comparative
|
| 0.50 |
independent |
0/3 |
2026 |
Leveraging human-trained neural networks for cross-species chromatin regulation annotations
score:
bench +0.5
words: assess
|
| 0.50 |
partial |
1/21 |
2026 |
Mapping and rewiring the MYBPC3 promoter for rescue of haploinsufficiency driven hypertrophic cardiomyopathy
score:
bench +0.5
words: systematic
shared authors:
Anshul Bharat Kundaje
|
| 0.50 |
independent |
0/9 |
2026 |
Genome-Wide Evolution of Lineage-Specific Chromatin Accessibility Links Regulatory Changes to Cichlid Phenotypic Diversity
score:
bench +0.5
words: comparative
|
| 0.50 |
independent |
0/7 |
2026 |
Controlling for DNA dosage with whole-genome sequencing improves ATAC-seq peak calling
score:
bench +0.5
words: compare
|
| 0.50 |
independent |
0/7 |
2026 |
High-throughput identification of chromatin-opening transcription factors
score:
bench +0.5
words: assess
|
| 0.50 |
independent |
0/8 |
2026 |
Reconstructing human gene regulatory evolution using deep learning
score:
bench +0.5
words: comparison
|
| 0.50 |
partial |
1/17 |
2026 |
Integrating sequence-to-omics predictions and personal multi-omics for rare variant prioritization
score:
bench +0.5
words: compare
shared authors:
Anshul Bharat Kundaje
|
| 0.50 |
partial |
1/6 |
2026 |
SMFNet reveals principles of combinatorial transcription factor assembly
score:
bench +0.5
words: systematic
shared authors:
Anshul Bharat Kundaje
|
| 0.50 |
partial |
1/26 |
2026 |
Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling
score:
bench +0.5
words: systematic
shared authors:
Anshul Bharat Kundaje
|