Genomics Papers

New Genomics papers from DNA sequencing and assembly, gene finding, RNA editing. Thank you to arXiv for use of its open access interoperability.

[Genomics Papers @KNM]

Annotation-Informed Block-Sparse Bayesian Modeling for cis-Expression Prediction

Lei Huang, Hui Shen, Kuan-Jui Su, Chuan Qiu, Martha Isabel Gonzalez-Ramirez, Anqi Liu, Zhe Luo, Yun Gong, Yipu Zhang, Dawei Li, Chaoyang Zhang, …
https://t.co/iIFnyd8I7u [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶]

[Genomics Papers @KNM]

Meta-analysis of scRNA-seq data for choroidal endothelial cells in dry Age-related Macular Degeneration

Kyle M. Veksler, Levi Dong, Timothy A. Blenkinsop, Aurelian Radu
https://t.co/58yIlSyWm0 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

[Emerging Technologies Papers @ETN]

Whole-Blood Boundary Analysis of BioFET-Based ctDNA Detection for Intravascular Sensing in Intrabody Nanonetworks

Ida Kleger-Rudomin, Filip Lemic, Sergi Abadal, Eduard Alarcon, Ethungshan Shitiri
https://t.co/51eETfbc6f [𝚌𝚜.𝙴𝚃]
💬Accepted to ACM NanoCom 2026

[Genomics Papers @KNM]

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation

Cameron Dufault, Scott Xu, Alan M. Moses
https://t.co/WZeeiWj6oV [𝚚-𝚋𝚒𝚘.𝙶𝙽]

[Genomics Papers @KNM]

AnnotateMissense: a genome-wide annotation and benchmarking framework for missense pathogenicity prediction

Muhammad Muneeb, David B. Ascher
https://t.co/duTTuneSou [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶]

[Genomics Papers @KNM]

WTKO-CNN: Deep Learning Reveals Sequence Motifs Distinguishing Wild-Type and Knockout ATAC-seq Peaks

Lopamudra Dey
https://t.co/RUqVO25Gox [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸]

[Genomics Papers @KNM]

Population-Specific Genetic and Non-Genetic Influences on Sleep Traits and Health Outcomes

Jiheum Park, Stephanie Y. Shue, Rocio Barragan, Jeong Yun Yang, Tian Gu, Chin Hur, Marie-Pierre St-Onge
https://t.co/FSNgSi4UxK [𝚚-𝚋𝚒𝚘.𝙶𝙽]

[Genomics Papers @KNM]

bioETH-PRS: Confidential Polygenic Risk Scoring without a Trusted Evaluator via Fully Homomorphic Encryption on a Programmable Blockchain

Kimon Antonios Provatas, Christos Galanopoulos, Ilias Georgakopoulos-Soares
https://t.co/tbIjvBc6s8 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

[Genomics Papers @KNM]

Multi-Modal Machine Learning for Population- and Subject-Specific lncRNA-Type 2 Diabetes Association Analysis

Ashwani Siwach, Sanjeev Narayan Sharma, Sunil Datt Sharma
https://t.co/JWi5KpfQxp [𝚚-𝚋𝚒𝚘.𝙶𝙽]

[Genomics Papers @KNM]

Informational blueprints reveal condition-dependent gene regulatory architectures

Doruk Efe Gökmen, Rosalind Wenshan Pan, Tom Röschinger, Stephen Quake, Hernan Garcia, …
https://t.co/FURTHR0BX0 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚘𝚗𝚍-𝚖𝚊𝚝.𝚜𝚝𝚊𝚝-𝚖𝚎𝚌𝚑 𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚚-𝚋𝚒𝚘.𝚀𝙼]

[Genomics Papers @KNM]

PACE: Geometry-Aware Bridge Transport for Single-Cell Trajectory Inference

Chenglei Yu*, Chuanrui Wang*, Bangyan Liao, Tailin Wu
https://t.co/JuFgx780eL [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶]

[Genomics Papers @KNM]

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction

Peiting Shi, Ningfeng Que, Xianzhe Huang, Xiaofei Wang, Jianzhong Jeff Xi
https://t.co/sTOrvfcm3B [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚚-𝚋𝚒𝚘.𝚀𝙼]

[Genomics Papers @KNM]

Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction

Younhun Kim, Georg K. Gerber, Travis E. Gibson
https://t.co/ZPMP4eZOjc [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸]

[Genomics Papers @KNM]

SCOPE: Siamese Contrastive Operon Pair Embeddings for Functional Sequence Representation and Classification

Akarsh Gupta, Kenneth Rodrigues, Sagnik Chatterjee
https://t.co/fhWB4FmuwO [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸 𝚌𝚜.𝙴𝚃 𝚌𝚜.𝙻𝙶]

[Genomics Papers @KNM]

A Linear-Transformer Hybrid for SNP-Based Genotype-to-Phenotype Prediction in Grapevine

Yibin Wang, Murukarthick Jayakodi, Silvas Kirubakaran, Ambika Chandra, Azlan Zahid
https://t.co/fhLATHz0dC [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸]

[Genomics Papers @KNM]

OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning

Maciej Sypetkowski, Joanna Krawczyk, Łukasz Smoliński, Remigiusz Kinas, Przemysław Pietrzak, Tomasz Jetka, Rafał Powalski
https://t.co/uhfwS9ZBvF [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸 𝚚-𝚋𝚒𝚘.𝙲𝙱]

[Genomics Papers @KNM]

EFGPP: Exploratory framework for genotype-phenotype prediction

Muhammad Muneeb, David B. Ascher
https://t.co/li5gfGOd7q [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶]
💬Code: https://t.co/ng9WKpoElI

[Genomics Papers @KNM]

ORBIT: Learning Gene Program Co-Activation Structure for Cell-Type-Stratified Pathway Rewiring Analysis in Single-Cell Transcriptomics

Yuechen Wang, Lina Jia, Qinglong Wang, Feng Tian
https://t.co/vQBmDulH7y [𝚚-𝚋𝚒𝚘.𝙶𝙽]

[Genomics Papers @KNM]

PhenotypeToGeneDownloaderR: automated multi-source retrieval and validation of phenotype-associated genes

Muhammad Muneeb, David B. Ascher
https://t.co/Xsbe2ZIydP [𝚚-𝚋𝚒𝚘.𝙶𝙽]
💬Code: https://t.co/DsAwxkgw3D

[Genomics Papers @KNM]

CellxPert: Inference-Time MCMC Steering of a Multi-Omics Single-Cell Foundation Model for In-Silico Perturbation

Andac Demir, Erik W. Anderson, Jeremy L. Jenkins, Srayanta Mukherjee
https://t.co/8noOGhCzJT [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸]