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ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

2024 · https://doi.org/10.1101/2024.12.25.630221

13 authors: Anusri Pampari, Anna Shcherbina, Evgeny Z. Kvon, Michael Kosicki, Surag Nair, Soumya Kundu, Arwa S. Kathiria, Viviana I. Risca, Kristiina Kuningas, Kaur Alasoo, William James Greenleaf, Len A. Pennacchio, Anshul Bharat Kundaje

Resource name scored: ChromBPNet

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Code

GitHub detects MIT License (MIT) in kundajelab/chrombpnet, on 2026-11-10.

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Weights

The Zenodo record declares cc-by-4.0 for zenodo.7443683, on 2026-11-10.

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172 citing works in OpenAlex on 2026-11-10, 172 read.

independentpartialsame-groupunknown
1442611

Author overlap with the primary paper, as a share of each citing work's authors: none is independent, under half is partial, half or more is same-group, and unknown means an author list is missing on one side. 0 of the partial and same-group works share only authors marked weak.

What this cannot see, and how it was computed

A work OpenAlex holds no reference list for cites nothing there, so it cannot appear below however squarely it evaluates this paper. Share of 2020-2025 works with no reference list, of all works / of works cited 5+ times (OpenAlex, measured 2026-11-02): journal 34% / 3%; repository (preprints) 82% / 44%; conference 53% / 15%; no venue recorded 86% / 53%. Evaluations published only as preprints or conference papers are the likeliest to be missing.

The score counts benchmark and critique words, a title hit outweighing an abstract hit, and demotes reviews and errata. It ranks; it does not say which works are evaluations. The words are English: a paper in another language scores zero, and that zero means unknown.

Authors are matched on surname + first initial, accent- and case-folded. This is lossy: two different people who share both count as overlap, and a name written surname-first ("Xu T") does not match the same name written given-first ("Tam Xu"). A shared author marked weak matched on an initial alone, on a surname of two letters or fewer, or with forenames or middle initials that differ; the overlap counts it either way.

Scored above zero: 94

Ranked by how much each reads like a benchmark or a critique. The order is for reading; it does not say which works are evaluations.

scoreoverlapsharedyearciting work
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

Scored above zero on the title alone: 1

OpenAlex has no abstract for these, so they are ranked apart rather than below everything that has one.

scoreoverlapsharedyearciting work
4.00 independent 0/1 2026 eLife Assessment: Sequential and coordinated control of human plasma cell differentiation by IRF4 and BLIMP1 utilizing a discriminating ISRE/EICE motif lexicon
score: bench +4
words: assess, assessment

Scored zero or below: 77

22 of these have no abstract and were read on the title alone. Zero means no evaluation words were found, not that the work is not an evaluation.

List them
scoreoverlapsharedyearciting work
0.00 independent 0/62 2026 Genome modelling and design across all domains of life with Evo 2
0.00 partial 1/36 2025 Predicting expression-altering promoter mutations with deep learning
shared authors: Anshul Bharat Kundaje
0.00 partial 2/20 2023 Rewriting regulatory DNA to dissect and reprogram gene expression
shared authors: Anusri Pampari, Anshul Bharat Kundaje
0.00 independent 0/27 2025 Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion
0.00 partial 4/21 2026 Multiomics and deep learning dissect regulatory syntax in human development
shared authors: Michael Kosicki, Len A. Pennacchio, Anshul Bharat Kundaje, William James Greenleaf
0.00 independent 0/1 2026 Tangermeme: a toolkit for understanding cis-regulatory logic using deep learning models
0.00 independent 0/18 2025 Modeling the vertebrate regulatory sequence landscape by UUATAC-seq and deep learning
0.00 independent 0/11 2026 Gene regulatory landscape dissected by single-cell four-omics sequencing
0.00 partial 2/7 2025 Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage
shared authors: Anusri Pampari, Anshul Bharat Kundaje
0.00 independent 0/22 2025 Recent evolution of the developing human intestine affects metabolic and barrier functions
0.00 partial 2/19 2026 Decoding common and rare noncoding variant effects across cellular and developmental contexts
shared authors: Soumya Kundu, Anshul Bharat Kundaje
0.00 partial 4/20 2025 In vivo mapping of mutagenesis sensitivity of human enhancers
shared authors: Michael Kosicki, Anusri Pampari, Anshul Bharat Kundaje, Len A. Pennacchio
0.00 independent 0/7 2025 Motif-based models accurately predict cell type-specific distal regulatory elements
0.00 independent 0/3 2025 Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity
0.00 independent 0/7 2025 Decoding cnidarian cell type gene regulation
0.00 independent 0/7 2026 Cooperativity enables widespread role of low-affinity motifs in chromatin accessibility and increases regulatory potential
0.00 partial 2/8 2026 Flexible use of conserved motifs constrains genome access in cell type evolution
shared authors: Anusri Pampari, Anshul Bharat Kundaje
0.00 partial 1/10 2026 Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo
shared authors: Evgeny Z. Kvon
0.00 independent 0/3 2025 Predicting the regulatory genome
0.00 independent 0/8 2026 Interpretable biophysical neural networks of transcriptional activation domains separate roles of protein abundance and coactivator binding
0.00 independent 0/2 2025 Missing regulatory effects on complex traits: Contribution of distal variants
0.00 independent 0/18 2025 Sensitive Transcriptomics and Genotyping reveals function of genetic variants in immunity
0.00 independent 0/17 2025 MYOD represses gene expression from non-E-box motifs
0.00 independent 0/6 2025 Programming human cell type-specific gene expression via an atlas of AI-designed enhancers
0.00 independent 0/18 2025 Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation
0.00 independent 0/39 2025 An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome
0.00 independent 0/10 2025 Decoding the gene regulatory landscape through multimodal learning of protein-DNA interactions
0.00 independent 0/6 2025 PRISM: ancestry-aware integration of tissue-specific genomic annotations enhances the transferability of polygenic scores
0.00 independent 0/11 2025 Comprehensive molecular impact mapping of common and rare variants at GWAS loci
0.00 independent 0/3 2025 C.La.P.: Enhancing transformer-based genomic signal modeling by integrating DNA sequences and chromatin accessibility data
0.00 independent 0/7 2025 3D Epigenome Evolution Underlies Divergent Gene Regulatory Programs in Primate Neural Development
0.00 independent 0/27 2026 An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain
0.00 independent 0/8 2026 Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers
0.00 independent 0/11 2026 Enhancer Tuning by Sequence-Specific Repressors
0.00 independent 0/5 2026 “Frustratingly Easy” Domain Adaptation for Cross-Species Transcription Factor Binding Prediction
0.00 partial 1/9 2025 Chromatin and gene-regulatory dynamics of human pulmogenesis by single cell multiomic sequencing
shared authors: William James Greenleaf
0.00 partial 2/6 2025 Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells
shared authors: Anshul Bharat Kundaje, William James Greenleaf
0.00 independent 0/39 2025 An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome
0.00 independent 0/4 2026 GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles
0.00 same-group 1/2 2026 ARSENAL: Learning Transferable Regulatory DNA Representations with Targeted Short-Context Language Models
shared authors: Anshul Bharat Kundaje
0.00 independent 0/11 2026 Genome-wide maps of transcription factor footprints identify noncoding variants rewiring gene regulatory networks
0.00 independent 0/2 2026 A toolkit for modeling cis-regulatory logic of enhancers at large scale
0.00 independent 0/14 2026 BLIMP1 shapes germinal center B cell clonal diversity by gating chromatin accessibility during light-to-dark zone transition
0.00 independent 0/10 2026 In vivo measurement and prediction of cell-type-resolved non-coding variant effects in human immunity
0.00 independent 0/9 2026 PanACRpred: Predicting Accessible Chromatin Regions in Pangenomes Using Motif Chaining
0.00 independent 0/5 2026 Sequential and coordinated control of human plasma cell differentiation by IRF4 and BLIMP1 associated with a discriminating ISRE/EICE motif lexicon
0.00 unknown – 2026 Non-coding variant prioritization based on cell type, developmental stage and evolutionary constraint
0.00 independent 0/15 2026 Targeting DNMT1 augments anti-tumor CD8⁺ T cell function
0.00 partial 1/7 2026 Architectural chromatin interactions provide a framework for context-dependent gene regulation
shared authors: Anshul Bharat Kundaje
0.00 independent 0/1 2026 DeepGeSeq: deep learning library for genomic sequence modeling and analysis
0.00 independent 0/5 2026 Author response: Sequential and coordinated control of human plasma cell differentiation by IRF4 and BLIMP1 utilizing a discriminating ISRE/EICE motif lexicon
0.00 independent 0/1 2026 Multi-omics and machine learning approaches for complex diseases
0.00 independent 0/1 2026 Ancient vocabulary for evolving cells
0.00 independent 0/20 2026 Estrogen interactions with breast cancer risk variants in regulatory DNA
0.00 independent 0/20 2026 Reconstructing sequence-grammar trajectories enables interpretable and tunable cis-regulatory element design
0.00 independent 0/8 2026 Pathway to Independence: the next generation of developmental biology
0.00 independent 0/10 2026 Few-shot regulatory sequence design with a genomic language model
0.00 independent 0/5 2026 ChAI-Net learns a regulatory code for chromatin co-accessibility
-0.25 independent 0/4 2025 A comprehensive survey of genome language models in bioinformatics
score: bench +2, crit +0.75, demote_type -3
words: assess, assessing, benchmark, evaluation, limitation
-1.00 independent 0/3 2026 Bridging precision agriculture and human medicine through comparative genetics
score: bench +2, demote_type -3
words: comparative
-2.50 independent 0/8 2026 AI-driven discovery in protein science for immunology and infectious disease research
score: bench +0.5, demote_type -3
words: benchmark
-2.50 independent 0/3 2026 Unlocking the Regulatory Genome: Interpreting the Clinical Impact of Noncoding Variants in Genetic Cardiomyopathies
score: bench +0.5, demote_type -3
words: systematic
-3.00 independent 0/3 2025 Modelling and design of transcriptional enhancers
score: demote_type -3
-3.00 independent 0/3 2026 Leveraging genomic deep learning models for the prediction of noncoding variant effects
score: demote_type -3
-3.00 independent 0/4 2026 Toward generalizable and interpretable AI in regulatory genomics
score: demote_type -3
-3.00 independent 0/4 2025 Bridging the variant-to-function gap in type 2 diabetes: advances and challenges
score: demote_type -3
-3.00 independent 0/2 2025 Machine learning approaches enable the discovery of therapeutics across domains
score: demote_type -3
-3.00 independent 0/2 2025 Molecular circuits for genomic recording of cellular events
score: demote_type -3
-3.00 partial 1/7 2026 A practical guide to studying genome function using single-molecule genomics
score: demote_type -3
shared authors: William James Greenleaf
-3.00 independent 0/2 2025 Non-coding variation in dementias: mechanisms, insights, and challenges
score: demote_type -3
-3.00 independent 0/9 2026 Harnessing Deep Learning Models for Guide RNA Optimization and Off‐Target Prediction in CRISPR Systems
score: demote_type -3
-3.00 independent 0/5 2026 Single-Cell Studies Advance Understanding of the Genetic and Molecular Basis of Atherosclerosis
score: demote_type -3
-3.00 independent 0/2 2026 How WRKY transcription factors fine-tune specificity in plant stress responses: from W-box to regulatory code
score: demote_type -3
-3.00 independent 0/2 2026 Mendelian disorders of the epigenetic machinery: a decade of insights into the molecular basis
score: demote_type -3
-3.00 independent 0/4 2026 Mechanisms underlying disease-causing variants in promoters and enhancers
score: demote_type -3
-3.00 independent 0/4 2026 Machine learning and statistical methods for molecular quantitative trait loci
score: demote_type -3
-4.25 independent 0/8 2024 Perspective on recent developments and challenges in regulatory and systems genomics
score: bench +1, crit +0.75, demote_title -3, demote_type -3
words: benchmark, benchmarking, limitation