Bioinformatics

Integrating suboptimal secondary structures, AI-assisted genomic synteny, and evolutionary conservation to identify bacterial ncRNA homologs beyond sequence similarity

Integrating suboptimal secondary structures, A...

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Josef Pánek
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SHINE: Decoding transcriptional-metabolic microenvironments through higher-order spatial integration

SHINE: Decoding transcriptional-metabolic micr...

Bioinformatics
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librarian
1 view
Reference Regulatory Element-Guided Gene Expression Analysis for Mechanistic Inference of Gene Regulatory Networks

Reference Regulatory Element-Guided Gene Expre...

Bioinformatics
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librarian
1 view
CurateMake: an auditable workflow for multi-source ITS reference database harmonisation and phylogenetic validation

CurateMake: an auditable workflow for multi-so...

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Auguste Gardette
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Differential multi-omics analysis of pulmonary arterial hypertension microvascular endothelial cells for differential drug response

Differential multi-omics analysis of pulmonary...

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librarian
1 view
Evaluating the use of non-linear models in data-driven rescoring of peptide-spectrum matches

Evaluating the use of non-linear models in dat...

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librarian
1 view
Biological Continued Pretraining Reshapes the Capability Profile of a Foundation Model Without Catastrophic Forgetting

Biological Continued Pretraining Reshapes the ...

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librarian
1 view
FUSED: A Functional Representation for Joint Structural and Elemental Analysis of Protein Ligand Binding Sites

FUSED: A Functional Representation for Joint S...

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librarian
1 view
Unraveling the Comedone Switch through Single-Cell Resolution of Human Acne Lesions

Unraveling the Comedone Switch through Single-...

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Tolga Düz
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MSstatsBioNet: Integrating Statistical Analyses with Prior Knowledge Biomolecular Networks for Quantitative Proteomics and Phosphoproteomics

MSstatsBioNet: Integrating Statistical Analyse...

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librarian
1 view
Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes

Phylogenize2: robust phylogenetic methods link...

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librarian
1 view
Spatial Topology Reveals Biologically Distinct Recurrent Motifs in Colorectal Cancer

Spatial Topology Reveals Biologically Distinct...

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librarian
1 view
A robust, sensitive phylogenetic method enables gene-level metagenomic analyses

A robust, sensitive phylogenetic method enable...

Bioinformatics
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librarian
2 views
Single-cell gene networks nominate IKZF1 as an Alzheimer's microglial regulator

Single-cell gene networks nominate IKZF1 as an...

Bioinformatics
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librarian
7 views
Reproducible-by-design: Romics Processor, a FAIR ecosystem for multi-omics and spatial-omics analysis

Reproducible-by-design: Romics Processor, a FA...

Bioinformatics
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librarian
5 views
Reliability-weighted target prioritization in CD4+ T-cell Perturb-seq: a generalizability-theory decomposition

Reliability-weighted target prioritization in ...

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Che Cheng
5 views
Integrative computational toxicology reveals PFOS and PFHxS associated inflammatory keratinocyte niches in psoriasis through exposure transcriptomics, single-cell spatial mapping and token-aware virtual perturbation

Integrative computational toxicology reveals P...

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Qianying Yu
3 views
Computational design of a multi-epitope vaccine against M. tuberculosis

Computational design of a multi-epitope vaccin...

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Hameed Ayobami
3 views
A Multi-Omics Framework Reveals Phosphorylation-Dependent Control of Protein Interactions

A Multi-Omics Framework Reveals Phosphorylatio...

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Kosuke Ogata
2 views
Evidence for lanthanide and PQQ dependent dehydrogenases in Eukarya

Evidence for lanthanide and PQQ dependent dehy...

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librarian
2 views
De novo design of ligand binding and sensing with a physics based generative approach

De novo design of ligand binding and sensing w...

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librarian
4 views
elDORS: An elevated Database Of RNA Sequences

elDORS: An elevated Database Of RNA Sequences

Bioinformatics
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Nivedita Dutta
6 views
Frozen Protein Foundation-Model Embeddings Improve Antibody-Antigen ΔΔG Ranking

Frozen Protein Foundation-Model Embeddings Imp...

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librarian
5 views
AI-enabled reconstruction of 3D spatial multi-omics at single-cell resolution

AI-enabled reconstruction of 3D spatial multi-...

Bioinformatics
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librarian
4 views
Integrative single-nucleus multi-omics profiling identifies candidate regulators and signaling axes in Alzheimer's disease lipid-processing microglia

Integrative single-nucleus multi-omics profili...

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Li Shen
5 views
MolMAE: A Surface-Centric Multimodal Masked Autoencoder for Molecular Representation Learning

MolMAE: A Surface-Centric Multimodal Masked Au...

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Jiaqing Li
5 views
Asymmetric Structural Transfer Between Natural Language and Biological Foundation Models

Asymmetric Structural Transfer Between Natural...

Bioinformatics
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librarian
6 views
Capabilities, specificity gaps and training-data dependence of AlphaFold3 across diverse application areas

Capabilities, specificity gaps and training-da...

Bioinformatics
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librarian
11 views
TEDlm: domain-centric protein language models with optional structural pre-training

TEDlm: domain-centric protein language models ...

Bioinformatics
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librarian
9 views
EcoXAI: Autonomous Agentic Ecosystem for Explainable Artificial Intelligence and Biomedical Discovery

EcoXAI: Autonomous Agentic Ecosystem for Expla...

Bioinformatics
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Jason Moore
11 views
TOPAS: phosphoproteome data analysis and decision support platform for molecular tumor boards

TOPAS: phosphoproteome data analysis and decis...

Bioinformatics
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Matthew The
11 views
Quantum Encoding Strategies for Drug Response Prediction: An Exhaustive Benchmark on a 20-Qubit Superconducting QPU

Quantum Encoding Strategies for Drug Response ...

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librarian
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