List of works - Bernhard Y Renard

Abundance estimation and differential testing on strain level in metagenomics data.

scientific article published on July 2017

Active learning for convenient annotation and classification of secondary ion mass spectrometry images.

scientific article published on 13 December 2012

Addition to "Phosphoproteomic Analysis of Aurora Kinase Inhibition in Monopolar Cytokinesis".

scientific article published on 11 November 2015

An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples

scientific article published on 25 October 2019

Analyzing genome coverage profiles with applications to quality control in metagenomics.

scientific article published on 14 April 2013

Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition.

scientific article

Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zaïre Lineage

scientific article

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

scientific article published on 09 December 2019

Computational protein profile similarity screening for quantitative mass spectrometry experiments

scientific article published on 27 October 2009

Confidence-based somatic mutation evaluation and prioritization

scientific article

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

scientific article published on 15 December 2021

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

article

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017

Critical Assessment of Metagenome Interpretation: the second round of challenges

scientific article published in April 2022

DUDes: a top-down taxonomic profiler for metagenomics.

scientific article published on 24 March 2016

Detecting horizontal gene transfer by mapping sequencing reads across species boundaries.

scientific article

Detection of Unknown Amino Acid Substitutions Using Error-Tolerant Database Search

scientific article published on January 2016

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

scientific article published on 21 April 2015

Estimating the computational limits of detection of microbial non-model organisms

scientific article

Estimating the confidence of peptide identifications without decoy databases

scientific article published on 01 June 2010

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

scientific article

First Draft Genome Sequence of Balamuthia mandrillaris, the Causative Agent of Amoebic Encephalitis.

scientific article published on 24 September 2015

GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads

scientific article

HiLive: real-time mapping of illumina reads while sequencing.

scientific article published on 29 October 2016

IPred - integrating ab initio and evidence based gene predictions to improve prediction accuracy

scientific article published on 26 February 2015

Interpretable detection of novel human viruses from genome sequencing data

scientific article published on 31 January 2020

Interpretable detection of novel human viruses from genome sequencing data

scientific article published on 01 February 2021

Life cycle stage-resolved proteomic analysis of the excretome/secretome from Strongyloides ratti--identification of stage-specific proteases

scientific article published on 30 September 2011

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

scientific article published on June 2015

Metagenomic abundance estimation and diagnostic testing on species level.

scientific article published on 31 August 2012

Metagenomic profiling of known and unknown microbes with microbeGPS.

scientific article

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics

scientific article

NITPICK: peak identification for mass spectrometry data

scientific article

Overcoming species boundaries in peptide identification with Bayesian information criterion-driven error-tolerant peptide search (BICEPS).

scientific article

PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data

scientific article

PathoLive - Real time pathogen identification from metagenomic Illumina datasets

scientific article published on 31 August 2018

Phosphoproteomic Analysis of Aurora Kinase Inhibition in Monopolar Cytokinesis.

scientific article published on 13 August 2015

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics.

scientific article published on June 2014

Pre- and post-processing workflow for affinity purification mass spectrometry data.

scientific article

Proteomic analysis of protein carbonylation: a useful tool to unravel nanoparticle toxicity mechanisms

scientific article

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

scientific article

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

scientific article

Reliable variant calling during runtime of Illumina sequencing

scientific article published on 11 November 2019

SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists ⬇️

scientific article published on February 3, 2011

SLIMM: species level identification of microorganisms from metagenomes

scientific article

Serum-free freezing media support high cell quality and excellent ELISPOT assay performance across a wide variety of different assay protocols.

scientific article published on 9 November 2012

Specificity control for read alignments using an artificial reference genome-guided false discovery rate.

scientific article published on 17 May 2013

SuRankCo: supervised ranking of contigs in de novo assemblies

scientific article published on 30 July 2015

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

scientific article published on 4 June 2015

Toward digital staining using imaging mass spectrometry and random forests.

scientific article published on July 2009

When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification

scientific article

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

scientific article published on 23 July 2019

gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms

scientific article published on 05 August 2020

iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification.

scientific article published on 20 November 2015

iPiG: integrating peptide spectrum matches into genome browser visualizations

scientific article

rapmad: Robust analysis of peptide microarray data.

scientific article

List of works by Bernhard Y Renard

Abundance estimation and differential testing on strain level in metagenomics data.

Active learning for convenient annotation and classification of secondary ion mass spectrometry images.

Addition to "Phosphoproteomic Analysis of Aurora Kinase Inhibition in Monopolar Cytokinesis".

An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples

Analyzing genome coverage profiles with applications to quality control in metagenomics.

Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition.

Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zaïre Lineage

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

Computational protein profile similarity screening for quantitative mass spectrometry experiments

Confidence-based somatic mutation evaluation and prioritization

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Critical Assessment of Metagenome Interpretation: the second round of challenges

DUDes: a top-down taxonomic profiler for metagenomics.

Detecting horizontal gene transfer by mapping sequencing reads across species boundaries.

Detection of Unknown Amino Acid Substitutions Using Error-Tolerant Database Search

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

Estimating the computational limits of detection of microbial non-model organisms

Estimating the confidence of peptide identifications without decoy databases

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

First Draft Genome Sequence of Balamuthia mandrillaris, the Causative Agent of Amoebic Encephalitis.

GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads

HiLive: real-time mapping of illumina reads while sequencing.

IPred - integrating ab initio and evidence based gene predictions to improve prediction accuracy

Interpretable detection of novel human viruses from genome sequencing data

Interpretable detection of novel human viruses from genome sequencing data

Life cycle stage-resolved proteomic analysis of the excretome/secretome from Strongyloides ratti--identification of stage-specific proteases

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

Metagenomic abundance estimation and diagnostic testing on species level.

Metagenomic profiling of known and unknown microbes with microbeGPS.

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics

NITPICK: peak identification for mass spectrometry data

Overcoming species boundaries in peptide identification with Bayesian information criterion-driven error-tolerant peptide search (BICEPS).

PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data

PathoLive - Real time pathogen identification from metagenomic Illumina datasets

Phosphoproteomic Analysis of Aurora Kinase Inhibition in Monopolar Cytokinesis.

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics.

Pre- and post-processing workflow for affinity purification mass spectrometry data.

Proteomic analysis of protein carbonylation: a useful tool to unravel nanoparticle toxicity mechanisms

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

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

Reliable variant calling during runtime of Illumina sequencing

SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists ⬇️

SLIMM: species level identification of microorganisms from metagenomes

Serum-free freezing media support high cell quality and excellent ELISPOT assay performance across a wide variety of different assay protocols.

Specificity control for read alignments using an artificial reference genome-guided false discovery rate.

SuRankCo: supervised ranking of contigs in de novo assemblies

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

Toward digital staining using imaging mass spectrometry and random forests.

When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification

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

gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms

iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification.

iPiG: integrating peptide spectrum matches into genome browser visualizations

rapmad: Robust analysis of peptide microarray data.