Integrating machine learning and multiscale modeling—perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences
Fueled by breakthrough technology developments, the biological, biomedical, and
behavioral sciences are now collecting more data than ever before. There is a critical need …
behavioral sciences are now collecting more data than ever before. There is a critical need …
[PDF][PDF] Machine learning in bioinformatics
This article reviews machine learning methods for bioinformatics. It presents modelling
methods, such as supervised classification, clustering and probabilistic graphical models for …
methods, such as supervised classification, clustering and probabilistic graphical models for …
De novo peptide sequencing by deep learning
De novo peptide sequencing from tandem MS data is the key technology in proteomics for
the characterization of proteins, especially for new sequences, such as mAbs. In this study …
the characterization of proteins, especially for new sequences, such as mAbs. In this study …
[HTML][HTML] ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity
ProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and
protein sequence databases has been developed. This algorithm uses a three tier scoring …
protein sequence databases has been developed. This algorithm uses a three tier scoring …
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
A number of different approaches have been described to identify proteins from tandem
mass spectrometry (MS/MS) data. The most common approaches rely on the available …
mass spectrometry (MS/MS) data. The most common approaches rely on the available …
Advances in structure elucidation of small molecules using mass spectrometry
The structural elucidation of small molecules using mass spectrometry plays an important
role in modern life sciences and bioanalytical approaches. This review covers different soft …
role in modern life sciences and bioanalytical approaches. This review covers different soft …
PepNovo: de novo peptide sequencing via probabilistic network modeling
A Frank, P Pevzner - Analytical chemistry, 2005 - ACS Publications
We present a novel scoring method for de novo interpretation of peptides from tandem mass
spectrometry data. Our scoring method uses a probabilistic network whose structure reflects …
spectrometry data. Our scoring method uses a probabilistic network whose structure reflects …
Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
A key problem in computational proteomics is distinguishing between correct and false
peptide identifications. We argue that evaluating the error rates of peptide identifications is …
peptide identifications. We argue that evaluating the error rates of peptide identifications is …
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
S Tanner, H Shu, A Frank, LC Wang, E Zandi… - Analytical …, 2005 - ACS Publications
Reliable identification of posttranslational modifications is key to understanding various
cellular regulatory processes. We describe a tool, InsPecT, to identify posttranslational …
cellular regulatory processes. We describe a tool, InsPecT, to identify posttranslational …
Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model
Novel protein discovery and immunopeptidomics depend on highly sensitive de novo
peptide sequencing with tandem mass spectrometry. Despite notable improvement using …
peptide sequencing with tandem mass spectrometry. Despite notable improvement using …