A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction
Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility
complex (MHC) class I loci in humans. The binding and interaction between HLA-I …
complex (MHC) class I loci in humans. The binding and interaction between HLA-I …
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework
As a newly discovered post-translational modification (PTM), lysine malonylation (Kmal)
regulates a myriad of cellular processes from prokaryotes to eukaryotes and has important …
regulates a myriad of cellular processes from prokaryotes to eukaryotes and has important …
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods
The roles of proteolytic cleavage have been intensively investigated and discussed during
the past two decades. This irreversible chemical process has been frequently reported to …
the past two decades. This irreversible chemical process has been frequently reported to …
A tunable synthetic mammalian oscillator
M Tigges, TT Marquez-Lago, J Stelling, M Fussenegger - Nature, 2009 - nature.com
Autonomous and self-sustained oscillator circuits mediating the periodic induction of specific
target genes are minimal genetic time-keeping devices found in the central and peripheral …
target genes are minimal genetic time-keeping devices found in the central and peripheral …
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences
Structural and physiochemical descriptors extracted from sequence data have been widely
used to represent sequences and predict structural, functional, expression and interaction …
used to represent sequences and predict structural, functional, expression and interaction …
iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data
Z Chen, P Zhao, F Li, TT Marquez-Lago… - Briefings in …, 2020 - academic.oup.com
With the explosive growth of biological sequences generated in the post-genomic era, one
of the most challenging problems in bioinformatics and computational biology is to …
of the most challenging problems in bioinformatics and computational biology is to …
Dynamic regulation of T follicular regulatory cell responses by interleukin 2 during influenza infection
D Botta, MJ Fuller, TT Marquez-Lago, H Bachus… - Nature …, 2017 - nature.com
Abstract Interleukin 2 (IL-2) promotes Foxp3+ regulatory T (Treg) cell responses, but inhibits
T follicular helper (TFH) cell development. However, it is not clear how IL-2 affects T follicular …
T follicular helper (TFH) cell development. However, it is not clear how IL-2 affects T follicular …
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles
Evolutionary information in the form of a Position-Specific Scoring Matrix (PSSM) is a widely
used and highly informative representation of protein sequences. Accordingly, PSSM-based …
used and highly informative representation of protein sequences. Accordingly, PSSM-based …
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome
Motivation Kinase-regulated phosphorylation is a ubiquitous type of post-translational
modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays …
modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays …
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy
Proteases are enzymes that specifically cleave the peptide backbone of their target proteins.
As an important type of irreversible post-translational modification, protein cleavage …
As an important type of irreversible post-translational modification, protein cleavage …