Gregory Andrews

Inferring binding specificities of human transcription factors with the wisdom of crowds

The paper benchmarks methods for inferring transcription factor binding specificities using a large community challenge and finds deep learning models outperform traditional methods, though positional weight matrices are competitive.

BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era

Bidirectional Mamba2 plant genomic language models (318M to 3.2B parameters) trained on 320 land-plant genomes top a 22-task frozen-model aggregate; a small variant reaches 131,072 bp context.

Architectural chromatin interactions provide a framework for context-dependent gene regulation

The paper develops an integrative framework to classify and interpret promoter-centric chromatin interactions by combining Hi-C, ChIA-PET, and functional genomic data, identifying a distinct class of architectural promoter-enhancer interactions with context-dependent regulatory roles.

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

Integrating gene annotation with orthology inference at scale

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

Evolutionary constraint and innovation across hundreds of placental mammals

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites

The paper updates Factorbook, a TF-centric database, by expanding its motif catalog and integrating it with ENCODE data to annotate candidate regulatory sites and provide tools for variant and disease analysis.