Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Computational Epigenetics: the new scientific paradigm.

ABSTRACT: Epigenetics has recently emerged as a critical field for studying how non-gene factors can influence the traits and functions of an organism. At the core of this new wave of research is the use of computational tools that play critical roles not only in directing the selection of key experiments, but also in formulating new testable hypotheses through detailed analysis of complex genomic information that is not achievable using traditional approaches alone. Epigenomics, which combines traditional genomics with computer science, mathematics, chemistry, biochemistry and proteomics for the large-scale analysis of heritable changes in phenotype, gene function or gene expression that are not dependent on gene sequence, offers new opportunities to further our understanding of transcriptional regulation, nuclear organization, development and disease. This article examines existing computational strategies for the study of epigenetic factors. The most important databases and bioinformatic tools in this rapidly growing field have been reviewed.

SUBMITTER: Lim SJ

PROVIDER: S-EPMC2957762 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Computational Epigenetics: the new scientific paradigm.

Lim Shen Jean SJ Tan Tin Wee TW Tong Joo Chuan JC

Bioinformation 20100123 7

Epigenetics has recently emerged as a critical field for studying how non-gene factors can influence the traits and functions of an organism. At the core of this new wave of research is the use of computational tools that play critical roles not only in directing the selection of key experiments, but also in formulating new testable hypotheses through detailed analysis of complex genomic information that is not achievable using traditional approaches alone. Epigenomics, which combines traditiona ...[more]

PMID: 20978607

Similar Datasets

A new paradigm for the scientific enterprise: nurturing the ecosystem.

Project description:The institutions of science are in a state of flux. Declining public funding for basic science, the increasingly corporatized administration of universities, increasing "adjunctification" of the professoriate and poor academic career prospects for postdoctoral scientists indicate a significant mismatch between the reality of the market economy and expectations in higher education for science. Solutions to these issues typically revolve around the idea of fixing the career "pipeline", which is envisioned as being a pathway from higher-education training to a coveted permanent position, and then up a career ladder until retirement. In this paper, we propose and describe the term "ecosystem" as a more appropriate way to conceptualize today's scientific training and the professional landscape of the scientific enterprise. First, we highlight the issues around the concept of "fixing the pipeline". Then, we articulate our ecosystem metaphor by describing a series of concrete design patterns that draw on peer-to-peer, decentralized, cooperative, and commons-based approaches for creating a new dynamic scientific enterprise.

| S-EPMC6171719 | biostudies-literature

Pandemics, policy, and the power of paradigm: will COVID-19 lead to a new scientific revolution?

Project description:Critical historical analysis of the 19th-century cholera and 21st-century coronavirus-19 (COVID-19) pandemics suggests that in conflicts over pandemic-mitigation policies, the professional backgrounds of principal opponents reveal dominant and minority scientific paradigms, presaging possible epistemological shifts. Epistemic conflict over cholera helped spur biomedical expertise as the dominant paradigm for U.S. public health science and policy beginning in the 20th century. This paradigm was reflected in federal government reliance on infectious disease physicians as the primary scientific decision makers in the COVID-19 pandemic. Similarly, epistemic conflict over challenges to behavioral and social well-being in 2020 may highlight discordance between the dominant biomedical paradigm used in making federal policy and the inherently holistic impact of that policy on population health, suggesting need for a new paradigm of multidisciplinary scientific engagement. Because population-wide public health initiatives affect many aspects of health-physiological, psychological, behavioral, and social-that are best measured and interpreted by experts in these respective fields, multidisciplinary scientific engagement would facilitate optimal, holistic evaluation of policy benefits and harms. This multidisciplinary approach, analogous to that currently recommended in medical management of chronic disease, would advance epidemiological research to inform evidence-based policy for public health crises in which U.S. population-wide interventions are contemplated.

| S-EPMC8882036 | biostudies-literature

Epigenetics: a promising paradigm for better understanding and managing pain.

Project description:UnlabelledEpigenetic regulation of gene expression is a rapidly growing area of research. Considering the longevity and plasticity of neurons, the studies on epigenetic pathways in the nervous system should be of special interest for both epigeneticists and neuroscientists. Activation or inactivation of different epigenetic pathways becomes more pronounced when the cells experience rapid changes in their environment, and such changes can be easily caused by injury and inflammation, resulting in pain perception or distortion of pain perception (eg, hyperalgesia). Therefore, in this regard, the field of pain is at an advantage to study the epigenetic pathways. More importantly, understanding pain from an epigenetics point of view would provide a new paradigm for developing drugs or strategies for pain management. In this review, we introduce basic concepts of epigenetics, including chromatin dynamics, histone modifications, DNA methylation, and RNA-induced gene silencing. In addition, we provide evidence from published studies suggesting wide implication of different epigenetic pathways within pain pathways.PerspectiveThis article provides a brief overview of epigenetic pathways for gene regulation and highlights their involvement in pain. Our goal is to expose the readers to these concepts so that pain-related phenotypes can be investigated from the epigenetic point of view.

| S-EPMC3672350 | biostudies-literature

Molecular Crowding: The History and Development of a Scientific Paradigm.

Project description:It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.

| S-EPMC10979406 | biostudies-literature

Epigenetics and chromatin dynamics: a review and a paradigm for functional disorders.

Project description:Motility and functional gastrointestinal disorders have high prevalence in the community, cause significant morbidity, and represent a major health care burden. Despite major advances in our understanding of the cellular and molecular basis of gastrointestinal neuromuscular functions, many of these diseases still defy mechanistic explanations. The biopsychosocial model underlying the current classification of functional gastrointestinal disorders recognizes and integrates the pathogenetic role of genetic, environmental, and psychosocial factors but has not been associated with specific molecular mechanisms.Here, we propose that this integrative function is encoded in the chromatin, composed of the DNA and associated histone and non-histone proteins and non-coding RNA. By establishing epigenetically heritable 'molecular memories' of past stimuli including environmental challenges, the chromatin determines an individual's responses to future insults and translates them into high-order outputs such as symptoms and illness behavior. Thus, surveying epigenetic signatures throughout the genome of affected cells in individual patients may make it possible to better understand and ultimately control the phenomena described by the biopsychosocial model. In this review, we provide a high-level but comprehensive description of the concepts and mechanisms underlying epigenetics and chromatin dynamics, describe the mechanisms whereby the environment can alter the epigenome and identify aspects of functional gastrointestinal and motility disorders where epigenetic mechanisms are most likely to play important roles.

| S-EPMC3607505 | biostudies-literature

Cancer epigenetics: new therapies and new challenges.

Project description:Cancer is nowadays considered to be both a genetic and an epigenetic disease. The most well studied epigenetic modification in humans is DNA methylation; however it becomes increasingly acknowledged that DNA methylation does not work alone, but rather is linked to other modifications, such as histone modifications. Epigenetic abnormalities are reversible and as a result novel therapies that work by reversing epigenetic effects are being increasingly explored. The biggest clinical impact of epigenetic modifying agents in neoplastic disorders thus far has been in haematological malignancies, and the efficacy of DNMT inhibitors and HDAC inhibitors in blood cancers clearly attests to the principle that therapeutic modification of the cancer cell epigenome can produce clinical benefit. This paper will discuss the most well studied epigenetic modifications and how these are linked to cancer, will give a brief overview of the clinical use of epigenetics as biomarkers, and will focus in more detail on epigenetic drugs and their use in solid and blood cancers.

| S-EPMC3600296 | biostudies-literature

The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.

Project description:The Seven Bridges Cancer Genomics Cloud (CGC; www.cancergenomicscloud.org) enables researchers to rapidly access and collaborate on massive public cancer genomic datasets, including The Cancer Genome Atlas. It provides secure on-demand access to data, analysis tools, and computing resources. Researchers from diverse backgrounds can easily visualize, query, and explore cancer genomic datasets visually or programmatically. Data of interest can be immediately analyzed in the cloud using more than 200 preinstalled, curated bioinformatics tools and workflows. Researchers can also extend the functionality of the platform by adding their own data and tools via an intuitive software development kit. By colocalizing these resources in the cloud, the CGC enables scalable, reproducible analyses. Researchers worldwide can use the CGC to investigate key questions in cancer genomics. Cancer Res; 77(21); e3-6. ©2017 AACR.

| S-EPMC5832960 | biostudies-literature

Internal replication of computational workflows in scientific research.

Project description:Failures to reproduce research findings across scientific disciplines from psychology to physics have garnered increasing attention in recent years. External replication of published findings by outside investigators has emerged as a method to detect errors and bias in the published literature. However, some studies influence policy and practice before external replication efforts can confirm or challenge the original contributions. Uncovering and resolving errors before publication would increase the efficiency of the scientific process by increasing the accuracy of published evidence. Here we summarize the rationale and best practices for internal replication, a process in which multiple independent data analysts replicate an analysis and correct errors prior to publication. We explain how internal replication should reduce errors and bias that arise during data analyses and argue that it will be most effective when coupled with pre-specified hypotheses and analysis plans and performed with data analysts masked to experimental group assignments. By improving the reproducibility of published evidence, internal replication should contribute to more rapid scientific advances.

| S-EPMC7403855 | biostudies-literature

A new structural paradigm in copper resistance in a human pathogen

Project description:Copper is essential for both innate and adaptive immune function and copper resistance has emerged as an important determinant of virulence of microbial pathogens. In the human pathogen Streptococcus pneumoniae (Spn), cytoplasmic copper resistance is mediated by an operon encoding the copper-responsive repressor CopY, CupA, of unknown function, and CopA, a copper effluxing P1B-type ATPase. We show that CupA is a novel cell membrane-anchored Cu(I) chaperone for CopA, and that a Cu(I)-binding competent, membrane-localized CupA, like CopA, is obligatory for copper resistance.

2013-05-24 | GSE39176 | GEO

Gene knockdown suggests a new paradigm for transcription factor TFIIB functionality

Project description:Experimental and bioinformatic studies of transcription initiation by RNA polymerase II (RNAP2) have revealed a mechanism of RNAP2 transcription initiation less uniform across gene promoters than initially thought. However, the general transcription factor TFIIB is presumed to be universally required for RNAP2 transcription initiation. Based on bioinformatic analysis of data, TFIIB knockdown in primary and transformed cell lines, and in vitro transcription experiments, we report that TFIIB is dispensable for transcription of most human promoters, but is essential for HSV-1 gene transcription and replication. We report a novel cell cycle TFIIB regulation and involvement of the acetylated TFIIB variant in chromosomal condensation. Taken together, these results establish a new paradigm for TFIIB functionality as a determinant of the human transcriptome, which when downregulated has potent anti-viral effects.

2014-12-31 | GSE48847 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data