Bioinformatics

Understanding the bias of compositional microbiome differential abundance estimation

Understanding the bias of compositional microb...

Bioinformatics
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librarian
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Physics-inspired computational methods for spatial transcriptomics reveal a dysplasia-restricted premalignant basin and a density-asymmetric autocrine niche in oral mucosal carcinogenesis

Physics-inspired computational methods for spa...

Bioinformatics
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librarian
5 views
Deterministic retrieval recovers biomedical associations lost by language models

Deterministic retrieval recovers biomedical as...

Bioinformatics
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Abhishek Halder
4 views
PixelDeck: A local-first media library manager for biomedical imaging

PixelDeck: A local-first media library manager...

Bioinformatics
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librarian
3 views
Topological attention asymmetry in ESM-2 attention implicitly encodes the allosteric hierarchy of the adenosine A2A receptor

Topological attention asymmetry in ESM-2 atten...

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librarian
4 views
Protein Function Prediction with Pretrained ProtT5 Embeddings and Gradient Boosting

Protein Function Prediction with Pretrained Pr...

Bioinformatics
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librarian
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A transcriptomic-driven segmentation and cell simulation framework for high-resolution spatial transcriptomics and cell-cell communication

A transcriptomic-driven segmentation and cell ...

Bioinformatics
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Intawat Nookaew
14 views
A Multi-modal LLM-Knowledge Fusion Framework for Predicting Single-cell Genetic Perturbation Effects

A Multi-modal LLM-Knowledge Fusion Framework f...

Bioinformatics
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Ying Zhou
14 views
Learning dynamics of unsupervised deep learning reveal epoch-specific genetic architectures of brain morphology

Learning dynamics of unsupervised deep learnin...

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Degui Zhi
8 views
ActSeekN: A Structural-Motif-Based Pipeline for Interpretable Enzyme Function Annotation

ActSeekN: A Structural-Motif-Based Pipeline fo...

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Sandra Castillo
9 views
Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

Accurate ab initio gene prediction in eukaryot...

Bioinformatics
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librarian
11 views
UshEffect-3D: Structure-informed Classification of USH2A Missense Variants for Inherited Retinal Disease

UshEffect-3D: Structure-informed Classificatio...

Bioinformatics
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librarian
6 views
MOSAIC: a longitudinal phenotypic clock to dissect organismal aging trajectories in C. elegans

MOSAIC: a longitudinal phenotypic clock to dis...

Bioinformatics
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Florence Solari
8 views
Unraveling protein conformational plasticity with PROTEUS

Unraveling protein conformational plasticity w...

Bioinformatics
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librarian
7 views
SynCom101: A web-based platform for the standardized design of functionally tailored synthetic microbial communities

SynCom101: A web-based platform for the standa...

Bioinformatics
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librarian
5 views
Controlling for DNA dosage with Whole Genome Sequencing improves ATAC-seq peak calling

Controlling for DNA dosage with Whole Genome S...

Bioinformatics
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librarian
8 views
A Systematic Approach Toward Implementing Machine Learning Techniques to Analyze Gut Microbiome Data

A Systematic Approach Toward Implementing Mach...

Bioinformatics
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Sahar Jahanikia
10 views
AlphaUnfold: Probing Potential Unfolding and Structural Fragility in AlphaFold3 Models via Short-Time High-Pressure MD

AlphaUnfold: Probing Potential Unfolding and S...

Bioinformatics
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Fabio Pegado
11 views
Cross-Species Adaptation of RETFound for Rodent OCT Age Estimation Reveals Strong CNN Baselines in Data-Scarce Space Biology

Cross-Species Adaptation of RETFound for Roden...

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Lauren Sanders
8 views
Integrative Clinical-Molecular Modeling Identifies LRRN4CL as a Determinant of Structural and Functional Myocardial Improvement

Integrative Clinical-Molecular Modeling Identi...

Bioinformatics
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librarian
7 views
Multi-Modal Deep Learning Integrates Spatial Topologies and Sequential Motifs to Identify Class I HDAC Inhibitors as Pan-Cancer Therapeutics

Multi-Modal Deep Learning Integrates Spatial T...

Bioinformatics
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Siyuan Tong
14 views
PP-MAPS: dynamic pharmacophore signatures of protein-peptide interfaces from molecular dynamics trajectories

PP-MAPS: dynamic pharmacophore signatures of p...

Bioinformatics
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librarian
13 views
Graph Neural Networks (GNNs) for Protein-Ligand Interaction Prediction

Graph Neural Networks (GNNs) for Protein-Ligan...

Bioinformatics
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librarian
12 views
MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes

MVCBench: A Multimodal Benchmark for Drug-indu...

Bioinformatics
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librarian
9 views
MSAgent: An Evidence Grounded Agentic Framework for LLM-driven Scientific Exploration in Mass Spectrometry-based Metabolomics

MSAgent: An Evidence Grounded Agentic Framewor...

Bioinformatics
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Jun Xia
6 views
CellPulse: A Foundation Model of Coordinated Gene Dynamics Simulating Viral Infectious Diseases

CellPulse: A Foundation Model of Coordinated G...

Bioinformatics
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librarian
5 views
Probabilistic coupling of cellular and microenvironmental heterogeneity by masked self-supervised learning

Probabilistic coupling of cellular and microen...

Bioinformatics
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librarian
8 views
Efficient and scalable modelling of cotranscriptional RNA folding with deterministic and iterative RNA structure sampling

Efficient and scalable modelling of cotranscri...

Bioinformatics
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librarian
6 views
Genomic dialects: How amino acid properties and the second codon base shape the informational accents of life

Genomic dialects: How amino acid properties an...

Bioinformatics
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librarian
5 views
scConcept enables concept-level exploration of single-cell transcriptomic data

scConcept enables concept-level exploration of...

Bioinformatics
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librarian
8 views
Quantifying data reuse in proteomics using PRIDE downloads statistics and a semi-supervised LLM-based framework

Quantifying data reuse in proteomics using PRI...

Bioinformatics
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librarian
12 views
Hierarchical Breakdown of RNA Structure Prediction in CASP16: From Reliable Local Features to Speculative Multimer Assembly

Hierarchical Breakdown of RNA Structure Predic...

Bioinformatics
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librarian
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