Biology subjects

Malik Sheriff, R. S.

Publications and source records attributed to Malik Sheriff, R. S..

5 recordsLinked to original sources

bioRxiv2025

FAIRification of computational models in biology

Computational models are essential for studying complex systems which, particularly in clinical settings, need to be quality-approved and transparent. To enhance the communication of a models features and capabilities, we propose an adaptation of the Findability, Accessibility, Interoperability and Reusability (FAIR) indicators published by the Research Data Alliance to assess models encoded in domain-specific standards, such as those established by COMBINE. The assessments guide FAIRification and add value to models.

systems biology↗

bioRxiv2025

Talk2Biomodels: AI agent-based open-source LLM initiative for kinetic biological models

In this study, we present Talk2Biomodels (T2B), an open-source1, user-friendly, large language model-based agentic AI platform designed to democratize access to computational models of biological interactions and promote the FAIRification (Findability, Accessibility, Interoperability, and Reusability) of these models. T2B enables users to explore and analyse mathematical models of biological systems using natural language. It eschews the traditional graphical user interface (GUI) and minimally adaptable workflow in favour of a modern agentic framework to provide a dynamic and immersive experience to explore mathematical models of biological interactions through conversations in natural language. T2B supports models encoded in the open-source community format Systems Biology Markup Language (SBML) and is integrated with the BioModels database (https://www.ebi.ac.uk/biomodels/), enabling seamless exploration, simulation, and analysis of curated systems biology models. Use cases in precision medicine, epidemiology, and emergent systems properties of biological networks are presented to demonstrate how experts and non-experts in computational biology can benefit from T2B.

systems biology↗

bioRxiv2023

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse

Machine learning (ML) models are widely used in life sciences and medicine; however, they are scattered across various platforms and there are several challenges that hinder their accessibility, reproducibility and reuse. In this manuscript, we present the formalisation and pilot implementation of community protocol to enable FAIReR (Findable, Accessible, Interoperable, Reusable, and Reproducible) sharing of ML models. The protocol consists of eight steps, including sharing model training code, dataset information, reproduced figures, model evaluation metrics, trained models, Dockerfiles, model metadata, and FAIR dissemination. Applying these measures we aim to build and share a comprehensive public collection of FAIR ML models in the BioModels repository through incentivized community curation. In a pilot implementation, we curated diverse ML models to demonstrate the feasibility of our approach and we discussed the current challenges. Building a FAIReR collection of ML models will directly enhance the reproducibility and reusability of ML models, minimising the effort needed to reimplement models, maximising the impact on the application and significantly accelerating the advancement in the field of life science and medicine.

bioinformatics↗

bioRxiv2020

A FGF2-mediated incoherent feedforward loop inducesErk inhibition and promotes naive pluripotency

Naive pluripotency is a transient state during mammalian development that can be recapitulated indefinitely in vitro by inhibition of the mitogen-activated protein kinase (MAPK/Erk) signalling and activation of STAT and Wnt pathways. How Erk is inhibited in vivo to promote naive pluripotency remains largely unknown. By combining live cell imaging and quantitative proteomics we found that FGF2, a known Erk activator and pro-differentiation cue, induces instead long-term Erk inhibition in both ES cells and mouse embryos. We show that Erk inhibition results from a FGF2-induced incoherent feedforward loop. Importantly, we see that FGF2 induces up-regulation of naive pluripotency factors, down-regulation of DNA methylation by suppression of de novo DNA methylases thereby helping maintain naive pluripotency. We show that FGF2 is expressed maternally and propose that integration of signals from the embryos niche may contribute to the generation of embryonic lineages with the right cell proportions. We suggest that feedforward regulation may play a role driving transient, reversible developmental transitions.

developmental biology↗

bioRxiv2020

Reproducibility in systems biology modelling

The reproducibility crisis has emerged as an important concern across many fields of science including life science, since many published results failed to reproduce. Systems biology modelling, which involves mathematical representation of biological processes to study complex system behaviour, was expected to be least affected by this crisis. While lack of reproducibility of experimental results and computational analysis could be a repercussion of several compounded factors, it was not fully understood why systems biology models with well-defined mathematical expressions fail to reproduce and how prevalent it is. Hence, we systematically attempted to reproduce 455 kinetic models of biological processes published in peer-reviewed research articles from 152 journals; which is collectively a work of about 1400 scientists from 49 countries. Our investigation revealed that about half (49%) of the models could not be reproduced using the information provided in the published manuscripts. With further effort, an additional 12% of the models could be reproduced either by empirical correction or support from authors. The other 37% remained non-reproducible models due to missing parameter values, missing initial concentration, inconsistent model structure, or a combination of these factors. Among the corresponding authors of the non-reproducible model we contacted, less than 30% responded. Our analysis revealed that models published in journals across several fields of life science failed to reproduce, revealing a common problem in the peer-review process. Hence, we propose an 8-point reproducibility scorecard that can be used by authors, reviewers and journal editors to assess each model and address the reproducibility crisis.

systems biology↗