scholarly journals Padlock and Proximity Probes forIn Situand Array-Based Analyses: Tools for the Post-Genomic Era

2003 ◽  
Vol 4 (5) ◽  
pp. 525-530 ◽  
Author(s):  
Ulf Landegren ◽  
Fredrik Dahl ◽  
Mats Nilsson ◽  
Simon Fredriksson ◽  
Johan Banér ◽  
...  
Keyword(s):  
Full Advantage ◽  
High Throughput ◽  
General Problem ◽  
Genetic Information ◽  
Biological Systems ◽  
Biological Information ◽  
Dna Ligation ◽  
Health And Disease ◽  
Macromolecular Composition ◽  
Detection Specificity

Highly specific high-throughput assays will be required to take full advantage of the accumulating information about the macromolecular composition of cells and tissues, in order to characterize biological systems in health and disease. We discuss the general problem of detection specificity and present the approach our group has taken, involving the reformatting of analogue biological information to digital reporter segments of genetic information via a series of DNA ligation assays. The assays enable extensive, coordinated analyses of the numbers and locations of genes, transcripts and protein.

Bioinformatics as Emerging Tool and Pipeline Frameworks

2021 ◽  
Vol 1 (4) ◽  
pp. 411-415
Author(s):  
Tinatin Mshvidobadze ◽  
Keyword(s):  
Health Care ◽  
Human Health ◽  
Health Care System ◽  
High Throughput ◽  
Biological Information ◽  
Forensic Sciences ◽  
Process Sequence ◽  
Human Genomes ◽  
Growing Network ◽  
Care System

In this article, we will discuss the areas of origin of bioinformatics in the human health care system. Due to the growing network of biological information databases such as human genomes, transcriptomics and proteomics, bioinformatics has become the approach of choosing forensic sciences. High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Here we survey and compare the design philosophies of several current pipeline frameworks.

scholarly journals PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Juan Xie ◽  
Jinfang Zheng ◽  
Xu Hong ◽  
Xiaoxue Tong ◽  
Shiyong Liu
Keyword(s):  
Full Advantage ◽  
High Throughput ◽  
Binding Sites ◽  
High Throughput Sequencing ◽  
Secondary Structures ◽  
Biological Processes ◽  
Genome Wide ◽  
Rna Interaction ◽  
Rna Complexes ◽  
Better Than

AbstractProtein-RNA interaction participates in many biological processes. So, studying protein–RNA interaction can help us to understand the function of protein and RNA. Although the protein–RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can’t be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein–RNA interaction. PRIME-3D2D is almost as good as PRIME at modeling protein–RNA complexes. PRIME-3D2D can be used to predict binding sites on PDB data (MCC = 0.75/0.70 for binding sites in protein/RNA) and transcription-wide (MCC = 0.285 for binding sites in RNA). Testing on PDB and yeast transcription-wide data show that PRIME-3D2D performs better than other binding sites predictor. So, PRIME-3D2D can be used to predict the binding sites both on PDB and genome-wide, and it’s freely available.

scholarly journals Biological information

2020 ◽  
Vol 139 (4) ◽  
pp. 361-370
Author(s):  
Jürgen Jost
Keyword(s):  
Computer Science ◽  
Genetic Information ◽  
Spatial Organization ◽  
Environmental Information ◽  
External Factors ◽  
Biological Information ◽  
Cellular Processes ◽  
Theory Of Information ◽  
Concept Of Information

AbstractIn computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology. Nevertheless, I argue that Shannon’s concept of information is useful in biology, although its application is not as straightforward as many people think. In fact, the recently developed theory of information decomposition can shed much light on the complementarity between coding and regulatory, or internal and environmental information. The key challenge that we formulate in this contribution is to understand how genetic information and external factors combine to create an organism, and conversely how the genome has learned in the course of evolution how to harness the environment, and analogously how coding, regulation and spatial organization interact in cellular processes.

scholarly journals Defining Microbiome Health through a Host Lens

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Sean M. Gibbons
Keyword(s):  
Complex System ◽  
Gut Microbiota ◽  
High Throughput ◽  
Mental State ◽  
Human Disease ◽  
Evolutionary Dynamics ◽  
Systems Approach ◽  
Commensal Microbiota ◽  
Ecosystem Level ◽  
Health And Disease

ABSTRACT We are walking ecosystems, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. The physiology of our commensal microbiota is intertwined with our metabolism, immune function, and mental state. The specifics of this entanglement remain largely unknown and are somewhat unique to individuals, and when any one piece of this complex system breaks, our health can suffer. There appear to be many ways to build a healthy, functional microbiome and several distinct ways in which it can break. Despite the hundreds of associations with human disease, there are only a handful of cases where the exact contribution of the microbiome to the etiology of disease is known. Our laboratory takes a systems approach, integrating dynamic high-throughput host phenotyping with eco-evolutionary dynamics and metabolism of gut microbiota to better define health and disease for each individual at the ecosystem level.

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

2006 ◽  
Vol 9 (5) ◽  
pp. 365-380 ◽  
Author(s):  
Jens Sobek ◽  
Kerstin Bartscherer ◽  
Anette Jacob ◽  
Jvrg Hoheisel ◽  
Philipp Angenendt
Keyword(s):  
High Throughput ◽  
Biological Systems ◽  
Microarray Technology ◽  
High Throughput Analysis ◽  
Throughput Analysis

Function-based, biologically inspired concept generation

2010 ◽  
Vol 24 (4) ◽  
pp. 521-535 ◽  
Author(s):  
Jacquelyn K.S. Nagel ◽  
Robert L. Nagel ◽  
Robert B. Stone ◽  
Daniel A. McAdams
Keyword(s):  
Engineering Design ◽  
Biological Systems ◽  
Natural World ◽  
Biological Information ◽  
Biological Knowledge ◽  
Concept Generation ◽  
Biologically Inspired ◽  
Modeling Methodology ◽  
Functional Representation ◽  
Engineering Designs

AbstractThe natural world provides numerous cases for inspiration in engineering design. Biological organisms, phenomena, and strategies, which we refer to as biological systems, provide a rich set of analogies. These systems provide insight into sustainable and adaptable design and offer engineers billions of years of valuable experience, which can be used to inspire engineering innovation. This research presents a general method for functionally representing biological systems through systematic design techniques, leading to the conceptualization of biologically inspired engineering designs. Functional representation and abstraction techniques are used to translate biological systems into an engineering context. The goal is to make the biological information accessible to engineering designers who possess varying levels of biological knowledge but have a common understanding of engineering design. Creative or novel engineering designs may then be discovered through connections made between biology and engineering. To assist with making connections between the two domains concept generation techniques that use biological information, engineering knowledge, and automatic concept generation software are employed. Two concept generation approaches are presented that use a biological model to discover corresponding engineering components that mimic the biological system and use a repository of engineering and biological information to discover which biological components inspire functional solutions to fulfill engineering requirements. Discussion includes general guidelines for modeling biological systems at varying levels of fidelity, advantages, limitations, and applications of this research. The modeling methodology and the first approach for concept generation are illustrated by a continuous example of lichen.

scholarly journals Disentangling the biological information encoded in disordered mitochondrial morphology through its rapid elicitation by iCMM

2020 ◽  
Author(s):  
Takafumi Miyamoto ◽  
Hideki Uosaki ◽  
Yuhei Mizunoe ◽  
Satoi Goto ◽  
Daisuke Yamanaka ◽  
...  
Keyword(s):  
Genetic Engineering ◽  
Morphological Changes ◽  
Biological Significance ◽  
Biological Information ◽  
Mitochondrial Morphology ◽  
Cellular Functions ◽  
Health And Disease ◽  
Novel Method ◽  
Morphological Patterns

AbstractMitochondrial morphology is dynamically changed in conjunction with spatiotemporal functionality. Although considerable efforts have been made to understand why abnormal mitochondrial morphology occurs in various diseases, the biological significance of mitochondrial morphology in states of health and disease remains to be elucidated owing to technical limitations. In the present study, we developed a novel method, termed inducible Counter Mitochondrial Morphology (iCMM), to purposely manipulate mitochondrial morphological patterns on a minutes timescale, using a chemically inducible dimerization system. Using iCMM, we showed that mitochondrial morphological changes rapidly lead to the characteristic reconstitution of various biological information, which is difficult to investigate by conventional genetic engineering. The manipulation of mitochondrial morphology using iCMM can improve our understanding of the interplay between mitochondrial morphology and cellular functions.

Sign in / Sign up

Export Citation Format

Share Document