Genomics

Authors and titles for recent submissions

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Total of 10 entries

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[1] arXiv:2411.08073 [pdf, html, other]: Title: LoRA-BERT: a Natural Language Processing Model for Robust and Accurate Prediction of long non-coding RNAs

Nicholas Jeon, Xiaoning Qian, Lamin SaidyKhan, Paul de Figueiredo, Byung-Jun Yoon

Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[2] arXiv:2411.08072 (cross-list from q-bio.QM) [pdf, html, other]: Title: Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+

Ethan Weinberger, Ryan Conrad, Tal Ashuach

Comments: 15 pages, 4 figures, will be included in the AIDrugX workshop in Neurips 2024

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Genomics (q-bio.GN); Machine Learning (stat.ML)

No updates for this time period.

[3] arXiv:2411.06798 [pdf, other]: Title: LA4SR: illuminating the dark proteome with generative AI

David R. Nelson, Ashish Kumar Jaiswal, Noha Ismail, Alexandra Mystikou, Kourosh Salehi-Ashtiani

Subjects: Genomics (q-bio.GN); Artificial Intelligence (cs.AI); Computation and Language (cs.CL); Quantitative Methods (q-bio.QM)
[4] arXiv:2411.06785 (cross-list from cs.LG) [pdf, html, other]: Title: White-Box Diffusion Transformer for single-cell RNA-seq generation

Zhuorui Cui, Shengze Dong, Ding Liu

Comments: 11pages, 3 figures

Subjects: Machine Learning (cs.LG); Genomics (q-bio.GN)
[5] arXiv:2411.06635 (cross-list from cs.LG) [pdf, other]: Title: Mixed Effects Deep Learning Autoencoder for interpretable analysis of single cell RNA Sequencing data

Aixa X. Andrade, Son Nguyen, Albert Montillo

Comments: Main manuscript: 29 pages, including 10 figures and 8 tables. Supplemental material: 17 pages

Subjects: Machine Learning (cs.LG); Genomics (q-bio.GN)

[6] arXiv:2411.05266 [pdf, html, other]: Title: Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering

Stephanie Young, Jerome Gilles

Journal-ref: Journal of Theoretical Biology, Vol.596, 111972, 2025

Subjects: Genomics (q-bio.GN)
[7] arXiv:2411.05055 [pdf, html, other]: Title: Integrating Large Language Models for Genetic Variant Classification

Youssef Boulaimen, Gabriele Fossi, Leila Outemzabet, Nathalie Jeanray, Oleksandr Levenets, Stephane Gerart, Sebastien Vachenc, Salvatore Raieli, Joanna Giemza

Comments: 21 pages, 7 figures

Subjects: Genomics (q-bio.GN); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[8] arXiv:2411.03871 (cross-list from cs.DS) [pdf, html, other]: Title: Safe Paths and Sequences for Scalable ILPs in RNA Transcript Assembly Problems

Francisco Sena, Alexandru I. Tomescu

Subjects: Data Structures and Algorithms (cs.DS); Optimization and Control (math.OC); Genomics (q-bio.GN)

[9] arXiv:2411.04363 [pdf, other]: Title: Perspective on recent developments and challenges in regulatory and systems genomics

Julia Zeiltinger, Sushmita Roy, Ferhat Ay, Anthony Mathelier, Alejandra Medina-Rivera, Shaun Mahony, Saurabh Sinha, Jason Ernst

Subjects: Genomics (q-bio.GN)
[10] arXiv:2411.04148 [pdf, other]: Title: Upcycling Human Excrement: The Gut Microbiome to Soil Microbiome Axis

Jeff Meilander, Chloe Herman, Andrew Manley, Georgia Augustine, Dawn Birdsell, Evan Bolyen, Kimberly R. Celona, Hayden Coffey, Jill Cocking, Teddy Donoghue, Alexis Draves, Daryn Erickson, Marissa Foley, Liz Gehret, Johannah Hagen, Crystal Hepp, Parker Ingram, David John, Katarina Kadar, Paul Keim, Victoria Lloyd, Christina Osterink, Victoria Queeney, Diego Ramirez, Antonio Romero, Megan C. Ruby, Jason W. Sahl, Sydni Soloway, Nathan E. Stone, Shannon Trottier, Kaleb Van Orden, Alexis Painter, Sam Wallace, Larissa Wilcox, Colin V. Wood, Jaiden Yancey, J. Gregory Caporaso

Comments: Main text: 9 pages, 2 figures; Extended data: 10 figures; Supplemental Text: 32 pages, 8 figures, 2 tables

Subjects: Genomics (q-bio.GN)

Total of 10 entries

Showing up to 50 entries per page: fewer | more | all