Lista de obras - Bernhard Y Renard - Dominio Público Uruguay

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

artículo científico publicado en 2017

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

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2019

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

artículo científico publicado en 2013

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

artículo científico publicado en 2009

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

artículo científico publicado en 2014

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

artículo científico publicado en 2019

Computational protein profile similarity screening for quantitative mass spectrometry experiments

artículo científico publicado en 2009

Confidence-based somatic mutation evaluation and prioritization

artículo científico publicado en 2012

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

artículo científico publicado en 2021

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

article

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

artículo científico publicado en 2017

Critical Assessment of Metagenome Interpretation: the second round of challenges

artículo científico publicado en 2022

DUDes: a top-down taxonomic profiler for metagenomics.

artículo científico publicado en 2016

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

artículo científico publicado en 2016

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

Estimating the confidence of peptide identifications without decoy databases

artículo científico publicado en 2010

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2013

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

Interpretable detection of novel human viruses from genome sequencing data

artículo científico publicado en 2020

Interpretable detection of novel human viruses from genome sequencing data

artículo científico publicado en 2021

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

artículo científico publicado en 2011

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

artículo científico publicado en 2015

Metagenomic abundance estimation and diagnostic testing on species level.

artículo científico publicado en 2012

Metagenomic profiling of known and unknown microbes with microbeGPS.

artículo científico publicado en 2015

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

artículo científico publicado en 2016

NITPICK: peak identification for mass spectrometry data

artículo científico publicado en 2008

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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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.

artículo científico publicado en 2015

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

Reliable variant calling during runtime of Illumina sequencing

artículo científico publicado en 2019

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

artículo científico publicado el 3 de febrero de 2011

SLIMM: species level identification of microorganisms from metagenomes

artículo científico publicado en 2017

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

artículo científico publicado en 2012

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

artículo científico publicado en 2013

SuRankCo: supervised ranking of contigs in de novo assemblies

artículo científico publicado en 2015

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

artículo científico publicado en 2015

Toward digital staining using imaging mass spectrometry and random forests.

artículo científico publicado en 2009

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

artículo científico publicado en 2009

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

artículo científico publicado en 2020

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

artículo científico publicado en 2015

iPiG: integrating peptide spectrum matches into genome browser visualizations

artículo científico publicado en 2012

rapmad: Robust analysis of peptide microarray data.

artículo científico publicado en 2011

Lista de obras de 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.