In recent years, artificial intelligence (AI)/machine learning has emerged as a plausible alternative to systems biology for the elucidation of biological phenomena and in attaining specified design ... Brief Bioinform. 2022 Nov; 23(6): bbac436. Published online 2022 Sep 30. doi: 10.1093/bib/bbac436 PMCID: PMC9677488 PMID: 36184188 Machine learning alternative to systems biology
Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the ... annotations, reproducibility, systems biology, community standards Introduction Scientists from different systems biology fields have long been developing community-driven guidelines and best practices for
Here, we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML) into ... al., 2014). The penetration of the hybrid modeling technique in systems biology is however lagging behind. We have previously published hybrid metabolic flux analysis techniques that combine metabolic
Precision medicine relies on molecular and systems biology methods as well as bidirectional association studies of phenotypes and (high-throughput) genomic data. However, the integrated use of such ... and environmental factors. Determining their cause, optimal therapies and prognosis requires matching clinical phenotypes with underlying biomolecular mechanisms [1]. Using molecular and systems biology
Over the last decades, image processing and analysis have become one of the key technologies in systems biology and medicine. The quantification of anatomical structures and dynamic processes in ... images in the training set, or that can be tuned using transfer learning thereby reducing the amount of training data needed. However, the range of imaging systems and segmentation targets in the
The desire to understand genomic functions and the behavior of complex gene regulatory networks has recently been a major research focus in systems biology. As a result, a plethora of computational ... material available at 10.1186/s12859-021-04361-8. Keywords: Boolean networks, Factor graph, Network perturbation, Systems biology Background In biological networks, the temporal evolution of gene or
To develop mechanistic dynamic models in systems biology, one often needs to identify all (or minimal) representations of the biological processes that are consistent with experimental data, out of a ... identification in systems biology Mikołaj Rybiński,1,2 Simon Möller,1 Mikael Sunnåker,1 Claude Lormeau,1,3 and Jörg Stelling1 Mikołaj Rybiński 1Department of Biosystems Science and Engineering and SIB Swiss
In systems biology, it is important to reconstruct regulatory networks from quantitative molecular profiles. Gaussian graphical models (GGMs) are one of the most popular methods to this end. A GGM ... -bio.sourceforge.net/recount/ExpressionSets/bottomly_eset.RData and from original publication with PubMed Identifier 21455293 (M. musculus dataset). Abstract Background In systems biology, it is important to
Many systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL ... ] [CrossRef] [Google Scholar] 8. Altaf-Ul-Amin M, et al. Systems biology in the context of big data and networks. Biomed Res Int. 2014;2014:428570. [PMC free article] [PubMed] [Google Scholar] 9. Lysenko A
2018;118:919–88. [PMC free article] [PubMed] [Google Scholar] 20. Yıldız SY. Systems glycobiology: past, present, and future. In: Behzadi P, Bernabò N (eds). Computational Biology and Chemistry [Internet ... ] [Google Scholar] 22. Aoki-Kinoshita KF. Glycome informatics: using systems biology to gain mechanistic insights into glycan biosynthesis. Curr Opin Chem Eng 2021;32:100683. [Google Scholar] 23. Marx V
Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or molecule of origin. Accurate data interpretation ... Abu Dhabi (NYUAD) Research Institute to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) and by other research funding from NYUAD to KCG. Availability of data and materials Synthetic
Prediction of protein complexes from protein–protein interaction (PPI) networks is an important problem in systems biology, as they control different cellular functions. The existing solutions employ ... Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany btaa1089-aff2 Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology
The universal expressibility assumption of Deep Neural Networks (DNNs) is the key motivation behind recent worksin the systems biology community to employDNNs to solve important problems in ... and Systems Biology, University of Chicago, Chicago, IL 60637, USA Find articles by Yi Liu Kenneth Barr b2 Department of Human Genetics, Ecology and Evolution, Molecular Genetics & Cell Biology
drug response Eliot Y. Zhu1,2,3,4 and Adam J. Dupuy1,2 Eliot Y. Zhu 1Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA USA 2Holden Comprehensive Cancer Center, The ... University of Iowa, Iowa City, IA USA 3Cancer Biology Graduate Program, The University of Iowa, Iowa City, IA USA 4The Medical Scientist Training Program, The University of Iowa, Iowa City, IA USA Find
systems pharmacology perspective Qiao Liu,1 Bohyun Lee,2 and Lei Xie1,2,3,4 Qiao Liu 1Department of Computer Science, Hunter College, The City University of New York, New York, NY USA Find articles by ... City University of New York, New York, NY USA 2Ph.D. Program in Computer Science, The City University of New York, New York, NY USA 3Ph.D. Program in Biochemistry and Biology, The City University of
The evolution of bacterial drug resistance and other features in biology, the progression of cancer and other diseases and a wide range of broader questions can often be viewed as the sequential ... by Marcus T Moen Iain G Johnston Department of Mathematics, University of Bergen, Bergen, Vestland, Norway Computational Biology Unit, University of Bergen, Bergen, Vestland, Norway CAMRIA
Motivation: Model selection is a fundamental part of the scientific process in systems biology. Given a set of competing hypotheses, we routinely wish to choose the one that best explains the ... should be regarded as Joint First Authors. the biological community and includes an SBML (Systems Biology Markup Language, Rodriguez et al., 2007) parser so that models can be specified according to
Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from ... perturbations [26–28]. Steady-state simulations are commonly used in systems biology to perform forward simulations of directed networks in order to predict the behaviour of a network and its associated
Motivation: Many problems of interest in dynamic modeling and control of biological systems can be posed as non-linear optimization problems subject to algebraic and dynamic constraints. In the ... . Biol ., 4 , 11 . Banga , J. ( 2008 ) Optimization in computational systems biology . BMC Syst. Biol ., 2 , 47 - 53 . de Hijas-Liste , G. et al. ( 2014 ) Global dynamic optimization approach to predict
Biological processes are complex systems with distinct behaviour. Despite the growing amount of available data, knowledge is sparse and often insufficient to investigate the complex regulatory ... Medical Systems Biology, Ulm University, Ulm, Baden-Wuerttemberg 89081, Germany Find articles by Christoph Müssel Nensi Ikonomi Institute of Medical Systems Biology, Ulm University, Ulm, Baden
