Herbert M Sauro
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Explore the profile of Herbert M Sauro including associated specialties, affiliations and a list of published articles.
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Recent Articles
1.
Sauro H, Agmon E, Blinov M, Gennari J, Hellerstein J, Heydarabadipour A, et al.
ArXiv
. 2025 Mar;
PMID: 40034129
Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data...
2.
Smith L, Malik-Sheriff R, Nguyen T, Hermjakob H, Karr J, Shaikh B, et al.
bioRxiv
. 2025 Feb;
PMID: 39896466
The BioModels Repository contains over 1000 manually curated mechanistic models drawn from published literature, most of which are encoded in the Systems Biology Markup Language (SBML). This community-based standard formally...
3.
Bruggeman F, Remeijer M, Droste M, Salinas L, Wortel M, Planque R, et al.
Biosystems
. 2024 Nov;
:105067.
PMID: 39492480
Since its conception some fifty years ago, metabolic control analysis (MCA) aims to understand how cells control their metabolism by adjusting the activity of their enzymes. Here we extend its...
4.
Cardiff R, Carothers J, Zalatan J, Sauro H
ACS Synth Biol
. 2024 Aug;
13(9):2643-2652.
PMID: 39119666
The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in...
5.
Xu J, Wiley H, Sauro H
J Theor Biol
. 2024 Jul;
593:111901.
PMID: 39004118
Predictive models of signaling pathways have proven to be difficult to develop. Traditional approaches to developing mechanistic models rely on collecting experimental data and fitting a single model to that...
6.
Sauro H
ArXiv
. 2024 Jul;
PMID: 38947916
In this paper, a set of Python methods is described that can be used to compute the frequency response of an arbitrary biochemical network given any input and output. Models...
7.
Jardine B, Smith L, Sauro H
J Integr Bioinform
. 2024 Jun;
21(1).
PMID: 38860571
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...
8.
Smith L, Sauro H
ArXiv
. 2024 Jun;
PMID: 38827452
Antimony is a high-level, human-readable text-based language designed for defining and sharing models in the systems biology community. It enables scientists to describe biochemical networks and systems using a simple...
9.
Andrews S, Kochen M, Smith L, Feng S, Wiley H, Sauro H
bioRxiv
. 2024 May;
PMID: 38746178
Biochemical reaction networks perform a variety of signal processing functions, one of which is computing the integrals of signal values. This is often used in integral feedback control, where it...
10.
Jakubowski H, Agnew H, Jardine B, Sauro H
Biochem Mol Biol Educ
. 2024 Mar;
52(4):426-435.
PMID: 38516799
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their...