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Response to ‘comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing’ by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M

Briefings in bioinformatics, 2023-09, Vol.24 (6)

2023

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Estimation of alternative splicing isoform frequencies from RNA-Seq data

Algorithms for molecular biology, 2011-04, Vol.6 (1), p.9-9, Article 9

2011

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Inferring viral quasispecies spectra from 454 pyrosequencing reads

BMC bioinformatics, 2011-07, Vol.12 Suppl 6 (S6), p.S1-S1, Article S1

2011

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A comprehensive benchmarking of WGS-based deletion structural variant callers

Briefings in bioinformatics, 2022-07, Vol.23 (4)

2022

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VISTA: an integrated framework for structural variant discovery

Briefings in bioinformatics, 2024-07, Vol.25 (5)

2024

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Accurate viral population assembly from ultra-deep sequencing data

Bioinformatics (Oxford, England), 2014-06, Vol.30 (12), p.i329-i337

2014

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Estimating Enzyme Expression and Metabolic Pathway Activity in Borreliella -Infected and Uninfected Mice

Journal of computational biology, 2024-06

2024

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Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants

Journal of computational biology, 2017-06, Vol.24 (6), p.558-570

2017

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Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples

Briefings in bioinformatics, 2021-11, Vol.22 (6)

2021

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Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes

Research in Computational Molecular Biology, 2024, Vol.14758, p.356-359

2024

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Fusing Label Relations for Chinese EMR Named Entity Recognition with Machine Reading Comprehension

Bioinformatics Research and Applications, 2023, Vol.13760, p.41-51

2023

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NIDN: Medical Code Assignment via Note-Code Interaction Denoising Network

Bioinformatics Research and Applications, 2023, Vol.13760, p.62-74

2023

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MPCDDI: A Secure Multiparty Computation-Based Deep Learning Framework for Drug-Drug Interaction Predictions

Bioinformatics Research and Applications, 2023, Vol.13760, p.263-274

2023

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EMRShareChain: A Privacy-Preserving EMR Sharing System Model Based on the Consortium Blockchain

Bioinformatics Research and Applications, 2023, Vol.13760, p.343-355

2023

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GNN-Dom: An Unsupervised Method for Protein Domain Partition via Protein Contact Map

Bioinformatics Research and Applications, 2023, Vol.13760, p.286-294

2023

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A Multimodal Data Fusion-Based Deep Learning Approach for Drug-Drug Interaction Prediction

Bioinformatics Research and Applications, 2023, Vol.13760, p.275-285

2023

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Distance Profiles of Optimal RNA Foldings

Bioinformatics Research and Applications, 2023, Vol.13760, p.315-329

2023

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ARGLRR: An Adjusted Random Walk Graph Regularization Sparse Low-Rank Representation Method for Single-Cell RNA-Sequencing Data Clustering

Bioinformatics Research and Applications, 2023, Vol.13760, p.126-137

2023

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An SMT-Based Framework for Reasoning About Discrete Biological Models

Bioinformatics Research and Applications, 2023, Vol.13760, p.114-125

2023

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Deep Learning-Enhanced MHC-II Presentation Prediction and Peptidome Deconvolution

Bioinformatics Research and Applications, 2023, Vol.13760, p.180-191

2023

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Heterogeneous PPI Network Representation Learning for Protein Complex Identification

Bioinformatics Research and Applications, 2023, Vol.13760, p.217-228

2023

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A Clonal Evolution Simulator for Planning Somatic Evolution Studies

Bioinformatics Research and Applications, 2023, Vol.13760, p.229-242

2023

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Transposition Distance Considering Intergenic Regions for Unbalanced Genomes

Bioinformatics Research and Applications, 2023, Vol.13760, p.100-113

2023

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Entropy Based Clustering of Viral Sequences

Bioinformatics Research and Applications, 2023, Vol.13760, p.369-380

2023

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Prediction of Drug-Disease Relationship on Heterogeneous Networks Based on Graph Convolution

Bioinformatics Research and Applications, 2023, Vol.13760, p.243-254

2023

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Response to ‘comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing’ by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M

Estimation of alternative splicing isoform frequencies from RNA-Seq data

Inferring viral quasispecies spectra from 454 pyrosequencing reads

A comprehensive benchmarking of WGS-based deletion structural variant callers

VISTA: an integrated framework for structural variant discovery

Accurate viral population assembly from ultra-deep sequencing data

Estimating Enzyme Expression and Metabolic Pathway Activity in Borreliella -Infected and Uninfected Mice

Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants

Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples

Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes

Fusing Label Relations for Chinese EMR Named Entity Recognition with Machine Reading Comprehension

NIDN: Medical Code Assignment via Note-Code Interaction Denoising Network

MPCDDI: A Secure Multiparty Computation-Based Deep Learning Framework for Drug-Drug Interaction Predictions

EMRShareChain: A Privacy-Preserving EMR Sharing System Model Based on the Consortium Blockchain

GNN-Dom: An Unsupervised Method for Protein Domain Partition via Protein Contact Map

A Multimodal Data Fusion-Based Deep Learning Approach for Drug-Drug Interaction Prediction

Distance Profiles of Optimal RNA Foldings

ARGLRR: An Adjusted Random Walk Graph Regularization Sparse Low-Rank Representation Method for Single-Cell RNA-Sequencing Data Clustering

An SMT-Based Framework for Reasoning About Discrete Biological Models

Deep Learning-Enhanced MHC-II Presentation Prediction and Peptidome Deconvolution

Heterogeneous PPI Network Representation Learning for Protein Complex Identification

A Clonal Evolution Simulator for Planning Somatic Evolution Studies

Transposition Distance Considering Intergenic Regions for Unbalanced Genomes

Entropy Based Clustering of Viral Sequences

Prediction of Drug-Disease Relationship on Heterogeneous Networks Based on Graph Convolution

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