bioRxiv Subject Collection: Genomics Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics"
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Combinatorial docking and molecular generation to navigate over 100-billion molecules for prospective ligand discovery
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https://www.biorxiv.org/content/10.64898/2026.06.07.730716v1?rss=1
20-fold computational cost reductions. Docking-predicted poses of the best VAChT-binding compounds were confirmed by cryo-EM structures. These methods provide exhaustive and generative paths for navigating the trillion-molecule frontier of drug discovery.
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HoloCell: A Generative Foundation Model for Holistic Cellular Modeling
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https://www.biorxiv.org/content/10.64898/2026.06.07.730684v1?rss=1
2026-06-11doi:10.64898/2026.06.07.730684Cold Spring Harbor Laboratory2026-06-11
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Liquidity of gene co-expression trajectories across the lifespan highlights delayed maturation and the perinatal GABA switch in schizophrenia risk
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https://www.biorxiv.org/content/10.64898/2026.06.10.731457v1?rss=1
2026-06-11doi:10.64898/2026.06.10.731457Cold Spring Harbor Laboratory2026-06-11
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Sequence-Based Therapeutic Peptide Classification with Augmented Negative Sampling
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https://www.biorxiv.org/content/10.64898/2026.06.07.730473v1?rss=1
2026-06-11doi:10.64898/2026.06.07.730473Cold Spring Harbor Laboratory2026-06-11
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Robust semi-supervised scRNA-seq integration from virtual adversarial learning
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https://www.biorxiv.org/content/10.64898/2026.06.07.730754v1?rss=1
2026-06-11doi:10.64898/2026.06.07.730754Cold Spring Harbor Laboratory2026-06-11
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HOMED enables hierarchical and multimodal optimization of DNA methylation deconvolution across tissues
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https://www.biorxiv.org/content/10.64898/2026.06.08.730896v1?rss=1
2026-06-10doi:10.64898/2026.06.08.730896Cold Spring Harbor Laboratory2026-06-10
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Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins
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https://www.biorxiv.org/content/10.64898/2026.06.09.728211v1?rss=1
2026-06-10doi:10.64898/2026.06.09.728211Cold Spring Harbor Laboratory2026-06-10
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Pseudoperplexity Probes Memorization in Protein Language Models
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https://www.biorxiv.org/content/10.64898/2026.06.08.730685v1?rss=1
2026-06-10doi:10.64898/2026.06.08.730685Cold Spring Harbor Laboratory2026-06-10
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Interspecies variation of 45S ribosomal DNA in vertebrates
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https://www.biorxiv.org/content/10.64898/2026.06.09.731232v1?rss=1
2026-06-10doi:10.64898/2026.06.09.731232Cold Spring Harbor Laboratory2026-06-10
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A scalable MNase-seq framework for reproducible nucleosome profiling across pluripotent stem cell and cardiomyocyte models
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https://www.biorxiv.org/content/10.64898/2026.06.08.731013v1?rss=1
2026-06-10doi:10.64898/2026.06.08.731013Cold Spring Harbor Laboratory2026-06-10
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Metagenomic prediction of methane emissions in sheep using single- and multi-matrix BLUP models with taxonomic and functional microbial features
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https://www.biorxiv.org/content/10.64898/2026.06.10.731298v1?rss=1
2026-06-10doi:10.64898/2026.06.10.731298Cold Spring Harbor Laboratory2026-06-10
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GEOAgent: An AI-driven Autonomous Framework for Intelligent GEO Data Retrieval and Standardized Preprocessing
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https://www.biorxiv.org/content/10.64898/2026.06.06.730646v1?rss=1
2026-06-10doi:10.64898/2026.06.06.730646Cold Spring Harbor Laboratory2026-06-10
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Promera: a unified model for biomolecular structure prediction, filtering, and design
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https://www.biorxiv.org/content/10.64898/2026.06.07.729267v1?rss=1
2026-06-10doi:10.64898/2026.06.07.729267Cold Spring Harbor Laboratory2026-06-10
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When batch correction corrupts gene expression: uncovering distortions in correlation structures
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https://www.biorxiv.org/content/10.64898/2026.06.06.729466v1?rss=1
2026-06-10doi:10.64898/2026.06.06.729466Cold Spring Harbor Laboratory2026-06-10
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A Unified Spatial AI Framework for Cross-Domain Tissue-State Analysis in Trauma, Oral, and Cardiovascular Pathology
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https://www.biorxiv.org/content/10.64898/2026.06.07.730662v1?rss=1
2026-06-10doi:10.64898/2026.06.07.730662Cold Spring Harbor Laboratory2026-06-10
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APOSM: Pairwise preference learning improves generative small-molecule design
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https://www.biorxiv.org/content/10.64898/2026.06.06.730554v1?rss=1
2026-06-10doi:10.64898/2026.06.06.730554Cold Spring Harbor Laboratory2026-06-10
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RERconverge Update: Runtime Reduction and Analysis Function Overhaul
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https://www.biorxiv.org/content/10.64898/2026.06.06.730612v1?rss=1
2026-06-10doi:10.64898/2026.06.06.730612Cold Spring Harbor Laboratory2026-06-10
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FIND: a software tool for identifying population-enriched pathogenic variants in gnomAD
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https://www.biorxiv.org/content/10.64898/2026.06.05.730273v1?rss=1
0.00008 in one ancestry group and at least tenfold higher than in all others (after zeroing populations with four or fewer observed alleles). Testing FIND on the genes FLNC, TMEM127, MYH7, and BRCA2 confirmed its utility and functionality by identifying nine well-known founder mutations and seven candidate founders. Candidates enriched in African American and admixed American populations were validated with the All of Us database, highlighting the utility of this approach for populations historically underrepresented in genetic studies. Source code is freely available at https://github.com/aacoder105/FIND under an MIT license, with a web interface at https://ethnic-variant-mutation-finder.onrender.com/.
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Long-read cross-platform validation reveals novel repeat features in myotonic dystrophy type 2
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https://www.biorxiv.org/content/10.64898/2026.06.06.730578v1?rss=1
2026-06-10doi:10.64898/2026.06.06.730578Cold Spring Harbor Laboratory2026-06-10
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Is level-1 blob reconstruction under the network multispecies coalescent easy?
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https://www.biorxiv.org/content/10.64898/2026.06.06.730607v1?rss=1
2026-06-10doi:10.64898/2026.06.06.730607Cold Spring Harbor Laboratory2026-06-10
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SPARQ-MI leverages end-to-end spatial single-cell analysis of the tumor microenvironment
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https://www.biorxiv.org/content/10.64898/2026.06.06.730569v1?rss=1
2026-06-10doi:10.64898/2026.06.06.730569Cold Spring Harbor Laboratory2026-06-10
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Gene loss under constant cold reveals "natural knockout" loci in Antarctic notothenioid fishes
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https://www.biorxiv.org/content/10.64898/2026.06.06.730616v1?rss=1
2026-06-10doi:10.64898/2026.06.06.730616Cold Spring Harbor Laboratory2026-06-10
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Bias-mitigated microbiome inference refines coronary artery disease signature
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https://www.biorxiv.org/content/10.64898/2026.06.04.730260v1?rss=1
70% zeros) and correlation structure of real 16S amplicon data, BootDA achieved the highest sensitivity among tested methods, including ANCOM-BC2, LinDA, MaAsLin 3, and Wilcoxon tests, while controlling the false discovery rate. Performance was retained in low biomass settings when contamination contributed ~50% of counts, and without negative controls, indicating de novo decontamination capability. Applied to a coronary artery disease cohort, BootDA refined the original signature to two co-enriched genera, Klebsiella and Gemmiger, and excluded likely contaminants. BootDA is available as an R package and could generalise to other sparse, high dimensional biological data.
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ECMME: an atlas of selection pressures on the mammalian extracellular matrix reveals contrasting evolutionary dynamics
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https://www.biorxiv.org/content/10.64898/2026.06.08.730821v1?rss=1
2026-06-10doi:10.64898/2026.06.08.730821Cold Spring Harbor Laboratory2026-06-10
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Whole genome sequencing and variant discovery in 344 global grasspea (Lathyrus sativus L.) lines
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https://www.biorxiv.org/content/10.64898/2026.06.05.730453v1?rss=1
2026-06-09doi:10.64898/2026.06.05.730453Cold Spring Harbor Laboratory2026-06-09
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Deciphering the limitations of immortalized hepatocyte cell lines for the study of liver cis-regulatory elements
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https://www.biorxiv.org/content/10.64898/2026.06.05.730479v1?rss=1
2026-06-09doi:10.64898/2026.06.05.730479Cold Spring Harbor Laboratory2026-06-09
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Enhancer-gene regulatory interactions in colorectal cancer revealed through genome-wide CRISPRi perturbations
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https://www.biorxiv.org/content/10.64898/2026.06.05.730086v1?rss=1
2026-06-09doi:10.64898/2026.06.05.730086Cold Spring Harbor Laboratory2026-06-09
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Quantifying annotation-stratified pleiotropy and co-polygenicity between complex traits
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https://www.biorxiv.org/content/10.64898/2026.06.04.730246v1?rss=1
2026-06-09doi:10.64898/2026.06.04.730246Cold Spring Harbor Laboratory2026-06-09
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Imputed graph-genotyped structural variants identify regulatory haplotypes associated with gene expression in Atlantic salmon
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https://www.biorxiv.org/content/10.64898/2026.06.03.729980v1?rss=1
2026-06-09doi:10.64898/2026.06.03.729980Cold Spring Harbor Laboratory2026-06-09
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PanKbase Integrated Single-Cell Map: A Comprehensive Atlas of Human Pancreatic Islets
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https://www.biorxiv.org/content/10.64898/2026.06.02.729719v1?rss=1
2026-06-09doi:10.64898/2026.06.02.729719Cold Spring Harbor Laboratory2026-06-09