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MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms

Bioinformatics (Oxford, England), 2015-06, Vol.31 (12), p.i106-i115

2015

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MpoxRadar: a worldwide MPXV genomic surveillance dashboard

Nucleic acids research, 2023-07, Vol.51 (W1), p.W331-W337

2023

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Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation

PLoS computational biology, 2019-07, Vol.15 (7), p.e1007208-e1007208

2019

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Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters

PLoS computational biology, 2019-12, Vol.15 (12), p.e1007527-e1007527

2019

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DUDes: a top-down taxonomic profiler for metagenomics

Bioinformatics (Oxford, England), 2016-08, Vol.32 (15), p.2272-2280

2016

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Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2

BMC bioinformatics, 2024-07, Vol.25 (1), p.228-13, Article 228

2024

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seq-seq-pan: building a computational pan-genome data structure on whole genome alignment

BMC genomics, 2018-01, Vol.19 (1), p.47-47, Article 47

2018

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The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components

PLoS pathogens, 2015-06, Vol.11 (6), p.e1004883-e1004883

2015

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Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation

Frontiers in immunology, 2018-10, Vol.9, p.2282-2282

2018

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iPiG: integrating peptide spectrum matches into genome browser visualizations

PloS one, 2012-12, Vol.7 (12), p.e50246-e50246

2012

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Metagenomic profiling of known and unknown microbes with microbeGPS

PloS one, 2015-02, Vol.10 (2), p.e0117711-e0117711

2015

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Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?

Briefings in bioinformatics, 2018-09, Vol.19 (5), p.954-970

2018

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MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling

Microbiome, 2017-08, Vol.5 (1), p.101-101, Article 101

2017

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LazyFox: fast and parallelized overlapping community detection in large graphs

PeerJ. Computer science, 2023-04, Vol.9, p.e1291-e1291, Article e1291

2023

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Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters

Genome research, 2024-06, Vol.34 (6), p.914-924

2024

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Life Cycle Stage-resolved Proteomic Analysis of the Excretome/Secretome from Strongyloides ratti—Identification of Stage-specific Proteases

Molecular & cellular proteomics, 2011-12, Vol.10 (12), p.M111.010157-M111.010157, Article M111.010157

2011

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The three-year evolution of Germany's Digital Therapeutics reimbursement program and its path forward

NPJ digital medicine, 2024-05, Vol.7 (1), p.139-139, Article 139

2024

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RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data

PloS one, 2015-09, Vol.10 (9), p.e0137896-e0137896

2015

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ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing

Bioinformatics, 2022-06, Vol.38 (Supplement_1), p.i153-i160

2022

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Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development

Frontiers in immunology, 2018-08, Vol.9, p.1868-1868

2018

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Concise Representation of Mass Spectrometry Images by Probabilistic Latent Semantic Analysis

Analytical chemistry (Washington), 2008-12, Vol.80 (24), p.9649-9658

2008

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The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis

Gut pathogens, 2024-05, Vol.16 (1), p.27-27, Article 27

2024

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FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data

eLife, 2020-12, Vol.9

2020

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Quantitative comparison of a human cancer cell surface proteome between interphase and mitosis

The EMBO journal, 2015-01, Vol.34 (2), p.251-265

2015

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Docking small peptides remains a great challenge: an assessment using AutoDock Vina

Briefings in bioinformatics, 2015-11, Vol.16 (6), p.1045-1056

2015

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MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms

MpoxRadar: a worldwide MPXV genomic surveillance dashboard

Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation

Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters

DUDes: a top-down taxonomic profiler for metagenomics

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2

seq-seq-pan: building a computational pan-genome data structure on whole genome alignment

The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components

Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation

iPiG: integrating peptide spectrum matches into genome browser visualizations

Metagenomic profiling of known and unknown microbes with microbeGPS

Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling

LazyFox: fast and parallelized overlapping community detection in large graphs

Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters

Life Cycle Stage-resolved Proteomic Analysis of the Excretome/Secretome from Strongyloides ratti—Identification of Stage-specific Proteases

The three-year evolution of Germany's Digital Therapeutics reimbursement program and its path forward

RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data

ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing

Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development

Concise Representation of Mass Spectrometry Images by Probabilistic Latent Semantic Analysis

The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis

FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data

Quantitative comparison of a human cancer cell surface proteome between interphase and mitosis

Docking small peptides remains a great challenge: an assessment using AutoDock Vina

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