Bioinformatics

ArchaicSeeker 3.0: A deep-learning framework for scalable, haplotype-resolved inference of archaic introgression

ArchaicSeeker 3.0: A deep-learning framework f...

Bioinformatics
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librarian
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Simple baselines rival protein language models in mutation-dense design tasks

Simple baselines rival protein language models...

Bioinformatics
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librarian
1 view
An LLM-driven pipeline for proteomics-based detection and structural modeling of post-translational modifications

An LLM-driven pipeline for proteomics-based de...

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

PhenotypeToGeneDownloaderR: automated multi-so...

Bioinformatics
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librarian
1 view
MilliMap: interactive closed-loop analysis for spatial omics

MilliMap: interactive closed-loop analysis for...

Bioinformatics
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librarian
2 views
Mitag4taxa: Extracting SSU rRNA Illumina reads from metagenomes for taxonomic classification

Mitag4taxa: Extracting SSU rRNA Illumina reads...

Bioinformatics
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Yong Wang
3 views
Fast and Ultra-Capable Protein Design: Advancing the Frontier Through Atomistic SE(3)-Equivariance with Genie 3

Fast and Ultra-Capable Protein Design: Advanci...

Bioinformatics
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librarian
2 views
Functional diversity across families of bacterial metalloregulators: what can we learn about specificity from sequence similarity?

Functional diversity across families of bacter...

Bioinformatics
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librarian
2 views
Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation

Building computational benchmarks: an Omnibenc...

Bioinformatics
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librarian
7 views
Machine learning approaches for the identification and analysis of enterotoxin genes in Staphylococcus aureus genomes

Machine learning approaches for the identifica...

Bioinformatics
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librarian
5 views
Revealing the Hidden Landscape of Public Metabolomics Data Reuse in MetaboLights

Revealing the Hidden Landscape of Public Metab...

Bioinformatics
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librarian
5 views
Structure-derived synthetic sequences guide a protein language model toward metalloproteins

Structure-derived synthetic sequences guide a ...

Bioinformatics
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librarian
4 views
A universal taxonomic and functional human gut microbiome model for disease classification and phenotype discovery

A universal taxonomic and functional human gut...

Bioinformatics
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Ewa Szczurek
2 views
Cell Type Weighted Dimensionality Reduction

Cell Type Weighted Dimensionality Reduction

Bioinformatics
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librarian
6 views
ANYI: The ANnotated Yeast Interactome

ANYI: The ANnotated Yeast Interactome

Bioinformatics
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librarian
4 views
Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data

Clonal embeddings allow exploratory analysis o...

Bioinformatics
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Peter Kharchenko
4 views
Joint Variable Selection for Omic Biomarkers in Time-to-Event Data

Joint Variable Selection for Omic Biomarkers i...

Bioinformatics
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librarian
4 views
Guidance for high-quality functional gene embeddings from large language models

Guidance for high-quality functional gene embe...

Bioinformatics
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librarian
6 views
LNGCN: A Distance-Aware Dynamics Network for Protein-Protein Interaction Prediction

LNGCN: A Distance-Aware Dynamics Network for P...

Bioinformatics
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librarian
3 views
PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search

PDBe-SIFTS: an open-source tool for Structure ...

Bioinformatics
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librarian
6 views
Clustering Strategies Improve Structure-Preserving Visualization of Single-Cell RNA-seq Data with CBMAP

Clustering Strategies Improve Structure-Preser...

Bioinformatics
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librarian
5 views
Automated Multimodal Correlative Registration for Organelle-Specific Molecular Imaging

Automated Multimodal Correlative Registration ...

Bioinformatics
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Kai Chen
5 views
Automatic Bevacizumab Response Prediction in Ovarian Cancer from Digital Pathology Images via Novel AI-based Computational Pipeline

Automatic Bevacizumab Response Prediction in O...

Bioinformatics
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Abdullah Alsaiari
7 views
AI-guided discovery of atypical protein assemblies

AI-guided discovery of atypical protein assemblies

Bioinformatics
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librarian
7 views
spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis

spatiAlytica: Viewer-Grounded Multimodal Agent...

Bioinformatics
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librarian
8 views
DPLM: Dynamics-aware Protein Language Model via contrastive learning between sequence and molecular dynamics simulation trajectory

DPLM: Dynamics-aware Protein Language Model vi...

Bioinformatics
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librarian
8 views
Integrated transcriptomic and proteomic analyses identify novel biomarkers of bladder outlet obstruction

Integrated transcriptomic and proteomic analys...

Bioinformatics
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librarian
6 views
FastDedup - A fast and memory-efficient tool for read deduplication

FastDedup - A fast and memory-efficient tool f...

Bioinformatics
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librarian
5 views
MetaUmbra: Statistically Controlled Genome-Level Presence Inference from Metaproteomic Peptides

MetaUmbra: Statistically Controlled Genome-Lev...

Bioinformatics
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librarian
7 views
Reference-Based Library Construction Improves Performance in low-input diaPASEF Workflows

Reference-Based Library Construction Improves ...

Bioinformatics
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Hannes Röst
6 views
Do Larger Models Really Win in Drug Discovery?A Benchmark Assessment of Model Scaling in AI-Driven Molecular Property and Activity Prediction

Do Larger Models Really Win in Drug Discovery?...

Bioinformatics
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librarian
10 views
AnnotateMissense: a genome-wide annotation and benchmarking framework for missense pathogenicity prediction

AnnotateMissense: a genome-wide annotation and...

Bioinformatics
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librarian
9 views
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