27 papers · ranked by Valyu relevance
Nasem Badreldin, Xiaodong Cheng, Ali Youssef, Jianguo Liu
This review highlights the critical role of software sensors in advancing biosystem monitoring and control by addressing the unique challenges biological systems pose. Biosystems-from cellular interactions to ecological dynamics-are characterized by intrinsic nonlinearity, temporal variability, and uncertainty, posing…
Sandra Garcia-Rey, Eva Gil-Hernandez, Lourdes Basabe-Desmonts, Fernando Benito-Lopez + 1 more
'Fernando Benito-Lopez' 'Haw-Ming Huang'] Glucose is an analyte of great importance, both in the clinical and sports fields. Since blood is the gold standard biofluid used for the analytical determination of glucose, there is high interest in finding alternative non-invasive biofluids, such as sweat, for its…
Yuxiang Yao, Dong Liu, Zheting Zhang, Chengchen Zhao + 1 more
Complex biosystems exhibit ordered, functional, self-organized features. How-ever, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R package, designed for analyzing properties of biosystems. We demonstrate its…
Andrei Khrennikov
The aim of this review is to highlight the possibility to apply the mathematical formalism and methodology of quantum theory to model behaviour of complex biosystems, from genomes and proteins to animals, humans, ecological and social systems. Such models are known as quantum-like and they should be distinguished from…
Ezio Bartocci, Pietro Lió, Marta Zofia Kwiatkowska
As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable…
Tjeerd V. olde Scheper
The representation of arbitrary data in a biological system is one of the most elusive elements of biological information processing. The often logarithmic nature of information in amplitude and frequency presented to biosystems prevents simple encapsulation of the information contained in the input. Criticality…
Abhishek Dey, Shaunak Sen
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of analytical and computational approaches, we adapt and develop the method of…
Duncan Ayers, Philip J. Day
The exponential development of highly advanced scientific and medical research technologies throughout the past 30 years has arrived to the point where the high number of characterized molecular agents related to pathogenesis cannot be readily integrated or processed by conventional analytical approaches. Indeed, the…
Harold Duruflé, Merwann Selmani, Philippe Ranocha, Elisabeth Jamet + 2 more
The high-throughput data generated by new biotechnologies used in biological studies require specific and adapted statistical treatments. In this work, we propose a novel and powerful framework to manage and analyse multi-omics heterogeneous data to carry out an integrative analysis. We illustrate it using the package…
Felix Tretter, Olaf Wolkenhauer, Michael Meyer-Hermann, Johannes W. Dietrich + 3 more
'Johannes W. Dietrich' 'Sara Green' 'James Marcum' 'Wolfram Weckwerth'] Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular…
Vincent J. Henry, Anne Goelzer, Arnaud Ferré, Stephan Fischer + 4 more
'Marc Dinh' 'Valentin Loux' 'Christine Froidevaux' 'Vincent Fromion'] Background High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires integrative tools and methods…
Lingxia Qiao, Ali Khalilimeybodi, Nathaniel J. Linden, Padmini Rangamani
'Padmini Rangamani'] Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing biochemical regulatory mechanisms. Building on experiments…
Suguru Fujita, Yasuaki Karasawa, Ken-ichi Hironaka, Y-h. Taguchi + 1 more
High-throughput omics technologies have enabled the profiling of entire biological systems. For the biological interpretation of such omics data, two analyses, hypothesis- and data-driven analyses including tensor decomposition, have been used. Both analyses have their own advantages and disadvantages and are mutually…
Amrit Singh, Scott J. Tebbutt, Bruce M. McManus
High-throughput technologies produce complex high-dimensional datasets which are analyzed using a variety of ever-evolving bioinformatics tools. Well-designed web frameworks enable more intuitive and efficient analysis such that less time is spent on coding and more time is spent on interpretation of results and…
Authors not listed
Global food security and environmental sustainability are closely linked to positive plant-soil feedback, for example through reduced dependence on synthetic agrochemicals. Beyond their nutritional value as protein- and lipid-rich crops, legumes have an essential ecological function by enhancing soil fertility and…
Denise Slenter, M. Kutmon, Chris T. Evelo, Egon L. Willighagen
Metabolomics data analysis for phenotype identification commonly reveals only a small set of biochemical markers, often containing overlapping metabolites for individual phenotypes. Differentiation between distinctive sample groups requires understanding the underlying causes of metabolic changes. However, combining…
Bob Eisenberg
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long time. Physiologists have successfully analyzed a broad range of biological systems…
Khalid Raza
In recent years, rapid developments in genomics and proteomics have generated a large amount of biological data. Drawing conclusions from these data requires sophisticated computational analyses. Bioinformatics, or computational biology, is the interdisciplinary science of interpreting biological data using information…
Anna Matuszyńska, Oliver Ebenhöh, Matias D. Zurbriggen, Daniel C. Ducat + 1 more
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It…
Sara da Silva Nascimento, Pierre Teodósio Félix
Biosensors are small devices that use biological reactions to detect target analytes. Such devices combine a biological component with a physical transducer, which converts bio-recognition processes into measurable signals. Its use brings a number of advantages, as they are highly sensitive and selective, relatively…
Zongqi Guo, Nikolas Zuchowicz, Jessica Bouwmeester, Amey S. Joshi + 9 more
'Amanda L. Neisch' 'Kieran Smith' 'Jonathan Daly' 'Michael L. Etheridge' 'Erik B. Finger' 'Suhasa B. Kodandaramaiah' 'Thomas S. Hays' 'Mary Hagedorn' 'John C. Bischof'] Title: Abstract Vitrification-based cryopreservation is a promising approach to achieving long-term storage of biological systems for maintaining…
Xiaosun Lu, J. S. Marron, Perry D. Haaland
Object oriented data analysis (OODA) aims at statistically analyzing populations of complicated objects. This paper is motivated by a study of cell images in cell culture biology, which highlights a common critical issue: choice of data objects. Instead of conventionally treating either the individual cells or the…
R. Sajulga, C. Easterly, M. Riffle, B. Mesuere + 12 more
To gain a fuller appreciation of microbiome dynamics, researchers characterize the functional role of expressed microbial genes/proteins. This can be accomplished through metaproteomics, which characterizes the protein complement of the microbiome. Several software tools exist for analyzing microbiomes at the…
Adarsh Arun, Jana Weber, Zhen Guo, Alexei Lapkin
As the chemical sector looks to decarbonize, one promising solution is the utilization of bio-feedstocks and biowaste to produce functional molecules. There is, therefore, great interest in understanding how and where to integrate these resources within chemical supply chains. To assist such efforts, screening…
Authors not listed
This study outlines a process simulation for producing biodiesel from waste cooking oil (WCO) using Aspen HYSYS V11. A two-stage Continuous Stirred-Tank Reactor (CSTR) system was designed to operate at 65 °C and 1 atm, with a methanol-to-oil molar ratio used is 6:1 along with 2 wt% KOH as a catalyst. The simulation…
Authors not listed
Introduction: Blood microsampling (BµS) devices collect less than 100 µL of blood, offering a less invasive and more cost-effective alternative to venipuncture. However, its metabolomic comparability to conventional samples remains unclear, and standardized BµS metabolomic workflows are lacking. Objectives: This study…
Sebastián Leavy, Gabriela Allegretti, Elen Presotto, Marco Antônio Montoya + 1 more
concepts, methods, data, indicators and their limitations Authors: ['Sebastián Leavy' 'Gabriela Allegretti' 'Elen Presotto' 'Marco Antônio Montoya' 'Edson Talamini'] Despite its relevance, measuring the contributions of the bioeconomy to national economies remains an arduous task that faces limitations. Part of the…