How (not) to generate a highly predictive biomarker panel using machine learning

H Desaire - Journal of proteome research, 2022 - ACS Publications
This review “teaches” researchers how to make their lackluster proteomics data look really
impressive, by applying an inappropriate but pervasive strategy that selects features in a …

Model population analysis for variable selection

HD Li, YZ Liang, QS Xu, DS Cao - Journal of Chemometrics, 2010 - Wiley Online Library
To build a credible model for given chemical or biological or clinical data, it may be helpful to
first get somewhat better insight into the data itself before modeling and then to present the …

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery

H López-Fernández, HM Santos, JL Capelo… - BMC …, 2015 - Springer
Background Mass spectrometry is one of the most important techniques in the field of
proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due …

Advances, obstacles, and opportunities for machine learning in proteomics

H Desaire, EP Go, D Hua - Cell Reports Physical Science, 2022 - cell.com
The fields of proteomics and machine learning are both large disciplines, each producing
well over 5,000 publications per year. However, studies combining both fields are still …

Advances in current diabetes proteomics: from the perspectives of label-free quantification and biomarker selection

J Fu, Y Luo, M Mou, H Zhang, J Tang… - Current Drug …, 2020 - ingentaconnect.com
Background: Due to its prevalence and negative impacts on both the economy and society,
the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label …

Identification of Bacillus strains by MALDI TOF MS using geometric approach

KV Starostin, EA Demidov, AV Bryanskaya… - Scientific Reports, 2015 - nature.com
Microorganism identification by MALDI TOF mass-spectrometry is based on the comparison
of the mass spectrum of the studied organism with those of reference strains. It is a rapid and …

Machine learning in mass spectrometry: a MALDI-TOF MS approach to phenotypic antibacterial screening

LN van Oosten, CD Klein - Journal of medicinal chemistry, 2020 - ACS Publications
Machine learning techniques can be applied to MALDI-TOF mass spectral data of drug-
treated cells to obtain classification models which assign the mechanism of action of drugs …

High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics

MQ Yang, BD Athey, HR Arabnia, AH Sung, Q Liu… - BMC genomics, 2009 - Springer
The advent of high-throughput next generation sequencing technologies have fostered
enormous potential applications of supercomputing techniques in genome sequencing, epi …

Evaluation of peak-picking algorithms for protein mass spectrometry

C Bauer, R Cramer, J Schuchhardt - Data Mining in Proteomics: From …, 2010 - Springer
Peak picking is an early key step in MS data analysis. We compare three commonly used
approaches to peak picking and discuss their merits by means of statistical analysis …

Evaluating feature selection strategies for high dimensional, small sample size datasets

A Golugula, G Lee… - 2011 Annual International …, 2011 - ieeexplore.ieee.org
In this work, we analyze and evaluate different strategies for comparing Feature Selection
(FS) schemes on High Dimensional (HD) biomedical datasets (eg gene and protein …