11 Result(s)
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Ngoc Hieu Tran
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Open AccessAuthor Correction: Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics
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Open AccessGlycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics
Here we present GlycanFinder, a database search and de novo sequencing tool for the analysis of intact glycopeptides from mass spectrometry data. GlycanFinder integrates peptide-based and glycan-based search s...
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Open AccessDeep neural network for detecting arbitrary precision peptide features through attention based segmentation
A promising technique of discovering disease biomarkers is to measure the relative protein abundance in multiple biofluid samples through liquid chromatography with tandem mass spectrometry (LC-MS/MS) based qu...
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Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices
De novo peptide sequencing is the key technology for finding novel peptides from mass spectra. The overall quality of sequencing results depends on the de novo peptide sequencing algorithm as well as the quali...
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Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines
Tumour-specific neoantigens play a major role for develo** personal vaccines in cancer immunotherapy. We propose a personalized de novo peptide sequencing workflow to identify HLA-I and HLA-II neoantigens di...
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Open AccessGenetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data
The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Co...
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Open AccessDeepIso: A Deep Learning Model for Peptide Feature Detection from LC-MS map
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based quantitative proteomics provides the relative different protein abundance in healthy and disease-afflicted patients, which offers the inform...
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Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry
We present DeepNovo-DIA, a de novo peptide-sequencing method for data-independent acquisition (DIA) mass spectrometry data. We use neural networks to capture precursor and fragment ions across m/z, retention-time...
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Open AccessComplete De Novo Assembly of Monoclonal Antibody Sequences
De novo protein sequencing is one of the key problems in mass spectrometry-based proteomics, especially for novel proteins such as monoclonal antibodies for which genome information is often limited or not availa...
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Open AccessComparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction
Enormous volumes of short read data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly a...
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Open AccessCounting motifs in the human interactome
Small over-represented motifs in biological networks often form essential functional units of biological processes. A natural question is to gauge whether a motif occurs abundantly or rarely in a biological ne...
