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Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a...

Published in Journal of Integrative Bioinformatics

When inferring the evolution of a gene/gene family, it is advisable to use all available coding sequences (CDS) from as many species genomes as possible in order to infer and date all gene duplications and losses. Nowadays, this means using hundreds or even thousands of CDSs, which makes the inferred phylogenetic trees difficult to visualize and in...

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024

Published in Journal of Integrative Bioinformatics

Detecting outliers in case-control cohorts for improving deep learning networks on Schizophrenia prediction

Published in Journal of Integrative Bioinformatics

This study delves into the intricate genetic and clinical aspects of Schizophrenia, a complex mental disorder with uncertain etiology. Deep Learning (DL) holds promise for analyzing large genomic datasets to uncover new risk factors. However, based on reports of non-negligible misdiagnosis rates for SCZ, case-control cohorts may contain outlying ge...

Transformers meets neoantigen detection: a systematic literature review

Published in Journal of Integrative Bioinformatics

Cancer immunology offers a new alternative to traditional cancer treatments, such as radiotherapy and chemotherapy. One notable alternative is the development of personalized vaccines based on cancer neoantigens. Moreover, Transformers are considered a revolutionary development in artificial intelligence with a significant impact on natural languag...

MakeSBML: a tool for converting between Antimony and SBML

Published in Journal of Integrative Bioinformatics

We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web application that translates models expressed in human-readable Antimony to the System Biology Markup Language...

SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem

Published in Journal of Integrative Bioinformatics

Julia is a general purpose programming language that was designed for simplifying and accelerating numerical analysis and computational science. In particular the Scientific Machine Learning (SciML) ecosystem of Julia packages includes frameworks for high-performance symbolic-numeric computations. It allows users to automatically enhance high-level...

Unlocking the power of AI models: exploring protein folding prediction through comparative analysis

Published in Journal of Integrative Bioinformatics

Protein structure determination has made progress with the aid of deep learning models, enabling the prediction of protein folding from protein sequences. However, obtaining accurate predictions becomes essential in certain cases where the protein structure remains undescribed. This is particularly challenging when dealing with rare, diverse struct...

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

Published in Journal of Integrative Bioinformatics

Modern biological research is increasingly informed by computational simulation experiments, which necessitate the development of methods for annotating, archiving, sharing, and reproducing the conducted experiments. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Informati...

Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences,...

Published in Journal of Integrative Bioinformatics

The vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprec...

MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps

Published in Journal of Integrative Bioinformatics

Molecular interaction maps (MIMs) are static graphical representations depicting complex biochemical networks that can be formalized using one of the Systems Biology Graphical Notation languages. Regardless of their extensive coverage of various biological processes, they are limited in terms of dynamic insights. However, MIMs can serve as template...