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Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images

Bioinformatics, 2022-03, Vol.38 (6), p.1700-1707

2022

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metID: an R package for automatable compound annotation for LC−MS-based data

Bioinformatics, 2022-01, Vol.38 (2), p.568-569

2022

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massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation

Bioinformatics, 2022-03, Vol.38 (7), p.2015-2021

2022

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AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge

Bioinformatics (Oxford, England), 2022-01, Vol.38 (3), p.849-852

2022

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Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model

Bioinformatics (Oxford, England), 2022-01, Vol.38 (3), p.818-826

2022

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MACA: marker-based automatic cell-type annotation for single-cell expression data

Bioinformatics, 2022-03, Vol.38 (6), p.1756-1760

2022

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Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides

Bioinformatics (Oxford, England), 2022-02, Vol.38 (5), p.1470-1472

2022

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Deep learning for survival analysis in breast cancer with whole slide image data

Bioinformatics (Oxford, England), 2022-07, Vol.38 (14), p.3629-3637

2022

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Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

Bioinformatics (Oxford, England), 2021-11, Vol.37 (21), p.3974-3975

2021

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MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities

Bioinformatics (Oxford, England), 2022-06, Vol.38 (13), p.3429-3437

2022

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ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath

Bioinformatics, 2022-03, Vol.38 (7), p.1930-1937

2022

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Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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Increasing confidence in proteomic spectral deconvolution through mass defect

Bioinformatics (Oxford, England), 2022-11, Vol.38 (22), p.5119-5120

2022

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Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores

Bioinformatics, 2021-12, Vol.37 (23), p.4399-4404

2021

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MobilityTransformR: an R package for effective mobility transformation of CE-MS data

Bioinformatics, 2022-08, Vol.38 (16), p.4044-4045

2022

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scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction

Bioinformatics (Oxford, England), 2022-10, Vol.38 (20), p.4745-4753

2022

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FastMix: a versatile data integration pipeline for cell type-specific biomarker inference

Bioinformatics (Oxford, England), 2022-10, Vol.38 (20), p.4735-4744

2022

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FBA: feature barcoding analysis for single cell RNA-Seq

Bioinformatics (Oxford, England), 2021-11, Vol.37 (22), p.4266-4268

2021

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ADViSELipidomics: a workflow for analyzing lipidomics data

Bioinformatics (Oxford, England), 2022-12, Vol.38 (24), p.5460-5462

2022

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BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations

Bioinformatics, 2022-03, Vol.38 (6), p.1692-1699

2022

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Identify connectome between genotypes and brain network phenotypes via deep self-reconstruction sparse canonical correlation analysis

Bioinformatics (Oxford, England), 2022-04, Vol.38 (8), p.2323-2332

2022

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benchdamic: benchmarking of differential abundance methods for microbiome data

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons

Bioinformatics, 2022-01, Vol.38 (2), p.503-512

2022

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Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES

Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images

metID: an R package for automatable compound annotation for LC−MS-based data

massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation

AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge

Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model

MACA: marker-based automatic cell-type annotation for single-cell expression data

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides

Deep learning for survival analysis in breast cancer with whole slide image data

Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities

ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

Increasing confidence in proteomic spectral deconvolution through mass defect

Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores

MobilityTransformR: an R package for effective mobility transformation of CE-MS data

scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction

FastMix: a versatile data integration pipeline for cell type-specific biomarker inference

FBA: feature barcoding analysis for single cell RNA-Seq

ADViSELipidomics: a workflow for analyzing lipidomics data

BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations

Identify connectome between genotypes and brain network phenotypes via deep self-reconstruction sparse canonical correlation analysis

benchdamic: benchmarking of differential abundance methods for microbiome data

Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons

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