Genomic analysis on viruses such as SARS-CoV-2 variants: Beta, Gamma, Delta, and Omicron is heavily dominated by classical bioinformatics methods, including Sequence Alignment, Phylogenetic Analysis,...
arXiv:2609.14882v1 Announce Type: cross
Abstract: Nucleotide sequence analysis is central to problems spanning regulatory genomics, evolutionary biology, and phenotype prediction. Classical bioinform...
By Evgeny S. Saveliev, Krzysztof Kacprzyk, Charlotte Capitanchik, Neelanjan Mukherjee, Kate Matlin, Ryan Sheridan, Srinivas Ramachandran, Jernej Ule, David L. Bentley, Mihaela van der Schaar
The paper introduces Murmur2Vec, a lightweight, alignment‑free embedding that uses k‑mer counts hashed with MurmurHash to create a compact representation for biological sequences. It provides a full theoretical analysis, including bias/variance formulas, a Johnson–Lindenstrauss‑style concentration bound, and an excess‑risk bound that clarifies the trade‑off between hash‑table size and classifier performance. Empirically, Murmur2Vec matches or surpasses a fine‑tuned 650M‑parameter ESM‑2 protein language model across several classification tasks, including SARS‑CoV‑2 spike lineage and HIV‑1 Env subtype identification.
By Sarwan Ali, Taslim Murad, Imdadullah Khan, Safi Faizullah
arXiv:2608. 11269v1 Announce Type: cross Abstract: Omics datasets, particularly single-cell RNA sequencing data, are high-dimensional, sparse, noisy, and dominated by zero values, making faithful low-dimensional representation challenging.
By Fenosoa Randrianjatovo, Maya Saleh, Simon Girard, Amadou Barry
arXiv:2607. 01627v1 Announce Type: cross Abstract: Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development.
By Wenbo Zhang
arXiv:2503. 22939v4 Announce Type: replace Abstract: The integration of heterogeneous multi-omics datasets at a systems level remains a central challenge for developing analytical and computational models in precision cancer diagnostics.
By Fadi Alharbi, Nishant Budhiraja, Aleksandar Vakanski, Boyu Zhang, Murtada K. Elbashir, Harshith Guduru, Mohanad Mohammed