Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science.

Łukasz Huminiecki

doi:10.3390/e24010017

Abstract

Mendel proposed an experimentally verifiable paradigm of particle-based heredity that has been influential for over 150 years. The historical arguments have been reflected in the near past as Mendel’s concept has been diversified by new types of omics data. As an effect of the accumulation of omics data, a virtual gene concept forms, giving rise to genetical data science. The concept integrates genetical, functional, and molecular features of the Mendelian paradigm. I argue that the virtual gene concept should be deployed pragmatically. Indeed, the concept has already inspired a practical research program related to systems genetics. The program includes questions about functionality of structural and categorical gene variants, about regulation of gene expression, and about roles of epigenetic modifications. The methodology of the program includes bioinformatics, machine learning, and deep learning. Education, funding, careers, standards, benchmarks, and tools to monitor research progress should be provided to support the research program.

Highlights

I start by underlining the long-term significance of the Mendelian gene concept
There is a group of practitioners who are interested in such theories or can apply them for practical purposes. The aim of this opinionated review is to argue for the support, funding, formalization of goals and achievements, benchmarking, and methodological development of the research program that is focused on the virtual gene concept
The Virtual Gene Concept Is Helpful in Genetics Education, in Computational Biology Research, and as a Focus of Data Integration

Summary

Introduction

I start by underlining the long-term significance of the Mendelian gene concept. I argue that genetics is transformed into an interdisciplinary data science. I argue that the virtual gene concept can shape a vibrant research program if applied pragmatically. In his seminal 1866 paper [2], Gregor Mendel proposed a paradigm of intra-cellular, discrete, and particulate differentiating element mediating heredity (differirenden Zellelemente in German). There is a group of practitioners who are interested in such theories or can apply them for practical purposes The aim of this opinionated review is to argue for the support, funding, formalization of goals and achievements, benchmarking, and methodological development of the research program that is focused on the virtual gene concept

Integrating Genomics Data Gives Rise to the Virtual Gene Concept

Goals of the Research Program

Recent Examples

Potential Weaknesses of the Research Program

Findings

Related Research Programs