Thomas Bürger
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View article: How omics biology research can leverage generative artificial intelligence while avoiding the pitfalls of hallucinations?
How omics biology research can leverage generative artificial intelligence while avoiding the pitfalls of hallucinations? Open
Generative artificial intelligence can be used to create realistic new data, even for complex real-word processes which cannot be exhaustively modelled: the model is simply learnt from pre-existing data. Generative artificial intelligence …
View article: Penalized likelihood optimization for censored missing value imputation in proteomics
Penalized likelihood optimization for censored missing value imputation in proteomics Open
SUMMARY Label-free bottom-up proteomics using mass spectrometry and liquid chromatography has long been established as one of the most popular high-throughput analysis workflows for proteome characterization. However, it produces data hind…
View article: Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes
Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes Open
Phosphorylation is a major post-translation modification (PTM) of proteins which is finely tuned by the activity of several hundred kinases and phosphatases. It controls most if not all cellular pathways including anti-viral responses. Acc…
View article: Plasma ALS and Gal-3BP differentiate early from advanced liver fibrosis in MASLD patients
Plasma ALS and Gal-3BP differentiate early from advanced liver fibrosis in MASLD patients Open
View article: Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes
Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes Open
Phosphorylation is a major post-translation modification (PTM) of proteins which is finely tuned by the activity of several hundred kinases and phosphatases. It controls most if not all cellular pathways including anti-viral responses. Acc…
View article: Fudging the volcano-plot without dredging the data
Fudging the volcano-plot without dredging the data Open
View article: Penalized likelihood optimization for censored missing value imputation in proteomics
Penalized likelihood optimization for censored missing value imputation in proteomics Open
Label-free bottom-up proteomics using mass spectrometry and liquid chromatography has long been established as one of the most popular high-throughput analysis workflows for proteome characterization. However, it produces data hindered by …
View article: Pulse-SILAC and Interactomics Reveal Distinct DDB1-CUL4–Associated Factors, Cellular Functions, and Protein Substrates
Pulse-SILAC and Interactomics Reveal Distinct DDB1-CUL4–Associated Factors, Cellular Functions, and Protein Substrates Open
View article: Controlling for false discoveries subsequently to large scale one‐way ANOVA testing in proteomics: Practical considerations
Controlling for false discoveries subsequently to large scale one‐way ANOVA testing in proteomics: Practical considerations Open
In discovery proteomics, as well as many other “omic” approaches, the possibility to test for the differential abundance of hundreds (or of thousands) of features simultaneously is appealing, despite requiring specific statistical safeguar…
View article: Calibrating Control-Bounded ADCs
Calibrating Control-Bounded ADCs Open
The paper considers the calibration of control-bounded analog-to-digital converters. It is demonstrated that variations of the analog frontend can be addressed by calibrating the digital estimation filter. In simulations (both behavioral a…
View article: Challenging Targets or Describing Mismatches? A Comment on Common Decoy Distribution by Madej et al.
Challenging Targets or Describing Mismatches? A Comment on Common Decoy Distribution by Madej et al. Open
In their recent article, Madej et al. (Madej, D.; Wu, L.; Lam, H.Common Decoy Distributions Simplify False Discovery Rate Estimation in Shotgun Proteomics. J. Proteome Res.2022, 21 (2), 339-348) proposed an original way to solve the…
View article: Challenging targets or describing mismatches? A comment on Common Decoy Distribution by Madej et al
Challenging targets or describing mismatches? A comment on Common Decoy Distribution by Madej et al Open
In their recent article, Madej et al. 1 proposed an original way to solve the recurrent issue of controlling for the false discovery rate (FDR) in peptide-spectrum-match (PSM) validation. Briefly, they proposed to derive a single precise d…
View article: Controlling for false discoveries subsequently to large scale one-way ANOVA testing in proteomics: practical considerations
Controlling for false discoveries subsequently to large scale one-way ANOVA testing in proteomics: practical considerations Open
In discovery proteomics, as well as many other “omic” approaches, the possibility to test for the differential abundance of hundreds (or of thousands) of features simultaneously is appealing, despite requiring specific statistical safeguar…
View article: An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics
An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics Open
Background Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic d…
View article: Can Omics Biology Go Subjective because of Artificial Intelligence? A Comment on “Challenges and Opportunities for Bayesian Statistics in Proteomics” by Crook et al.
Can Omics Biology Go Subjective because of Artificial Intelligence? A Comment on “Challenges and Opportunities for Bayesian Statistics in Proteomics” by Crook et al. Open
In their recent review ( J. Proteome Res. 2022, 21 (4), 849-864), Crook et al. diligently discuss the basics (and less basics) of Bayesian modeling, survey its various applications to proteomics, and highlight its potential for the …
View article: Erstellung von Basensättigungskarten für Waldböden mit Vegetationsaufnahmen. Vollständiges Literaturverzeichnis online
Erstellung von Basensättigungskarten für Waldböden mit Vegetationsaufnahmen. Vollständiges Literaturverzeichnis online Open
Die Nährstoffausstattung des Oberbodens ist für die Vitalität und das Wachstum der Waldbäume entscheidend. Die seit Jahrzehnten hohen Stickstoffeinträge in die Wälder führen zu Eutrophierung. Gleichzeitig verarmt der Boden an wichtigen Näh…
View article: Additional file 1 of An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics
Additional file 1 of An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics Open
Additional file 1: Table S1. Detailed sample description. For each sample it is reported the depths of their proteome and transcriptome datasets, the technology used to generate them, data availability on public repositories and the refere…
View article: ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis
ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis Open
View article: Transcriptome-informed reduction of protein databases: an analysis of how and when proteogenomics enhances eukaryotic proteomics
Transcriptome-informed reduction of protein databases: an analysis of how and when proteogenomics enhances eukaryotic proteomics Open
Background Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic d…
View article: Statistical Analysis of Quantitative Peptidomics and Peptide-Level Proteomics Data with Prostar
Statistical Analysis of Quantitative Peptidomics and Peptide-Level Proteomics Data with Prostar Open
View article: Sketched Stochastic Dictionary Learning for large‐scale data and application to high‐throughput mass spectrometry
Sketched Stochastic Dictionary Learning for large‐scale data and application to high‐throughput mass spectrometry Open
Factorization of large data corpora has emerged as an essential technique to extract dictionaries (sets of patterns that are meaningful for sparse encoding). Following this line, we present a novel algorithm based on compressive learning t…
View article: Unveiling the links between peptide identification and differential analysis FDR controls by means of a practical introduction to knockoff filters
Unveiling the links between peptide identification and differential analysis FDR controls by means of a practical introduction to knockoff filters Open
In proteomic differential analysis, FDR control is often performed through a multiple test correction ( i . e ., the adjustment of the original p-values). In this protocol, we apply a recent and alternative method, based on so-called knock…
View article: Introduction de l'ingénierie ontologique dans la méthodologie de développement des progiciels de gestion des collectivités territoriales
Introduction de l'ingénierie ontologique dans la méthodologie de développement des progiciels de gestion des collectivités territoriales Open
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View article: Cued Speech hand gestures recognition tool
Cued Speech hand gestures recognition tool Open
Automatic real-time translation of gestured languages for hearing-impaired would be a major advance on disabled integration path. In this paper, we present a demonstrator on Cued Speech hand gesture recognition. Cued Speech is a specific v…
View article: Classification supervisée avec second étage optionnel pour variables de covariance conditionnelle hétérogène
Classification supervisée avec second étage optionnel pour variables de covariance conditionnelle hétérogène Open
En informatique, il est fréquent qu'un problème de classification fasse intervenir des variables de nature hétérogène, dont les différentes covariances (conditionnellement `a la classe) n'ont pas le mˆeme ordre de grandeur. Si la procédure…
View article: Conception d'un système domotique pour l'assistance aux personnes dépendantes
Conception d'un système domotique pour l'assistance aux personnes dépendantes Open
Les personnes en situation de handicap éprouvent parfois de réelles difficultés, voire une incapacité physique totale, à effectuer les activités de la vie quotidienne de manière autonome. De nombreuses initiatives ont introduit la domotiqu…
View article: Modèle de supervision d'interaction non-intrusif basé sur les ontologies
Modèle de supervision d'interaction non-intrusif basé sur les ontologies Open
L'automatisationetlasupervisiondessystèmespervasifsestàl'heure actuelle principalement basée sur l'utilisation massive de capteurs distribués dans l'environnement. Dans cet article, nous proposons un modèle de super- vision d'interactions …
View article: Defining new approximations of belief function by means of Dempster's combination
Defining new approximations of belief function by means of Dempster's combination Open
Approximating a belief function (with a probability distribution or with another belief function with a restricted number of focal elements) is an important issue in Dempster-Shafer Theory. The reason is that such approximations are really…
View article: Ambient Assisted Living with Linux
Ambient Assisted Living with Linux Open
Population ageing is set to affect European countries over the coming decades, increasing the number of dependent people. In this context, Ambient Assisted Living (AAL) is one solution to enable these people to stay in their preferred envi…
View article: Aide à la conception d'un système domotique pour l'assistance aux personnes à mobilité réduite
Aide à la conception d'un système domotique pour l'assistance aux personnes à mobilité réduite Open
People with limited mobility have considerable difficulties or even physical incapacities to perform daily tasks independently. The use of home automation is one way to overcome these motor disabilities. Many works have shown the dynamics …