Genetics & Genomics · Life Sciences
Genomics
The newest papers in Genomics that ReadSearch has read, newest first. Each links to its own page, with its authors, date, where it was published and the original.
57 papers, from 31 August 2026 to 6 November 2026: 44 arXiv preprints, 8 bioRxiv preprints and 5 OpenAlex records.
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Newest papers, page 3
AmbiModBench: Benchmarking Gene Perturbation Prediction Beyond Shared Responses
Predicting cellular responses to genetic perturbations helps prioritize experiments in single-cell genomics, where exhaustive measurement is infeasible.BarcodeMAE+: Rethinking Masked Pretraining and Global Representations for DNA Barcode Foundation Models
Many DNA foundation models are pretrained by masking parts of a sequence and asking the model to reconstruct them.BaseCamp --- An Agentic AI Framework for Automating DNA Sequencing Data Pipelines
DNA sequencing pipelines, spanning quality control, alignment, variant calling, and annotation, are now reliably executed by workflow management systems that orchestrate established bioinformatics…Large Language Model Agents for Evidence Based Genetic Disease Severity Classification
Disease severity classification for genetic conditions is subjective and labor-intensive, creating bottlenecks in genomic screening, where commercial panels vary widely in size and overlap.HPOQuest: A Rare-Disease Diagnostic Agent Using Active Phenotype Acquisition
More than 300 million people worldwide are affected by one of over 7,000 known rare diseases, yet diagnosis remains difficult because patients initially present with incomplete and heterogeneous…PlainMap: a lightweight, restartable mapping pipeline for ancient and modern DNA
Mapping sequencing reads to a reference genome requires preprocessing and alignment choices that can vary with library type, fragment length, sequencing platform, and reference genome.HyCoSeq: Contextual Hyperbolic Representation Learning for Genomic Sequences
Hyperbolic geometry provides a natural inductive bias for genomic representation learning, but existing hyperbolic genomic models primarily use Lorentz convolutions to learn local sequence…Towards a knowledge-enhanced single-cell foundation model
Single-cell foundation models (scFMs) increasingly rely on large-scale transcriptomic pretraining, yet expanding pretraining data can yield diminishing gains while substantially increasing…Democratizing Clinical Tumor Whole Genome Sequencing: 18-hour End-to-end Analysis via Trillion-parameter Large Language Models Locally Deployed on Consumer-grade Hardware
Whole genome sequencing (WGS) is essential for precision oncology, yet its clinical adoption remains limited by prohibitive computational costs and multi-day turnaround times.Structure is not mechanism: high-gain gated-FFN rows across text and genomic foundation models
A small number of unusually high-gain parameters can exert disproportionate effects in transformer language models, but whether analogous structures recur in genomic foundation models and whether…Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens
Many biological discovery problems require experiments to be selected sequentially under constrained budgets.A Transformer-Based Delta Expression Encoder for Psilocybin Transcriptional Response: Architecture, Representations, and Biological Validation
Understanding why individuals respond differently to psilocybin requires modeling the drug's transcriptional perturbation signature at the cell-type level.Human mutation field reveals an equilibrium-like structure with irreversible circulation
The evolution of DNA sequences can be viewed as stochastic dynamics on a high-dimensional discrete space, but it is unclear when empirical transition biases reduce to an effective energy landscape…Mutation--selection balance on an infinite trait space: confinement, drift and equilibrium
We study a trait-structured population model incorporating mutation, selection and density-dependent regulation on a countably infinite trait space.BME-like Quartet Weights for Phylogenetic Trees
Like pairwise distances, quartets can be highly redundant and correlated on a phylogenetic tree, and their number grows on the order of n^4 rather than n^2.Modeling microbiome dynamics on social networks: how between-host transmission shapes within-host evolution
A social network perspective on the human microbiome is crucial for understanding how the interplay between within-host microbial dynamics and between-host transmission influences microbial…Genetic association testing with multivariate survival phenotypes under interval censoring
Set-based genetic association tests provide a powerful framework for detecting genetic effects on complex traits by jointly analyzing multiple genetic variants.