24 papers · ranked by Valyu relevance
Panni Simona, Kalpana Panneerselvam, Pablo Porras, Margaret Duesbury + 4 more
In recent years, a huge amount of data on ncRNA interactions has been described in scientific papers and databases. Although considerable effort has been made to annotate the available knowledge in public repositories, there are still significant discrepancies in how different resources capture and interpret data on…
Thomas G Minchington, Sam Griffiths-Jones, Nancy Papalopulu
The dynamics of gene expression is implicated in an increasing number of fundamental biological processes, including cell fate decisions, inflammation and stem cell heterogeneity. However, the prevalence of the underlying network structures which drive dynamical behaviour, such as bistability, robusteness and noise…
Alexandra Drakaki, Dimitrios Iliopoulos
MicroRNAs are small non-coding RNAs that regulate gene expression at the transcriptional or posttranscriptional level. They are involved in cellular development, differentiation, proliferation and apoptosis and play a significant role in cancer. Examination of tumor-specific microRNA expression profiles has revealed…
Jun-ichi Satoh, Hiroko Tabunoki
Background MicroRNAs (miRNAs) mediate posttranscriptional regulation of protein-coding genes by binding to the 3' untranslated region of target mRNAs, leading to translational inhibition, mRNA destabilization or degradation, depending on the degree of sequence complementarity. In general, a single miRNA concurrently…
Ricky Bhajun, Laurent Guyon, Amandine Pitaval, Eric Sulpice + 6 more
'Stéphanie Combe' 'Patricia Obeid' 'Vincent Haguet' 'Itebeddine Ghorbel' 'Christian Lajaunie' 'Xavier Gidrol'] MiRNAs are key regulators of gene expression. By binding to many genes, they create a complex network of gene co-regulation. Here, using a network-based approach, we identified miRNA hub groups by their close…
Elsi Ferro, Chiara Enrico Bena, Silvia Grigolon, Carla Bosia
MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation. Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular…
Joseph J Nalluri, Bhanu K Kamapantula, Debmalya Barh, Neha Jain + 6 more
Background MicroRNAs (miRNAs) have increasingly been found to regulate diseases at a significant level. The interaction of miRNA and diseases is a complex web of multilevel interactions, given the fact that a miRNA regulates upto 50 or more diseases and miRNAs/diseases work in clusters. The clear patterns of miRNA…
Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush + 1 more
Conventional methods to analyze genomic data do not make use of the interplay between multiple factors, such as between microRNAs (miRNAs) and the mRNA transcripts they regulate, and thereby often fail to identify the cellular processes that are unique to specific tissues. We developed PUMA (PANDA Using MicroRNA…
Mahashweta Basu, Nitai P. Bhattacharyya, P. K. Mohanty
MicroRNAs (miRNAs) are small non-coding RNAs which regulate gene expression by binding to the 3′ UTR of the corresponding messenger RNAs. We construct miRNA co-target networks for 22 different species using a target prediction database, MicroCosm Tagets. The miRNA pairs of individual species having one or more common…
Ziynet Nesibe Kesimoglu, Serdar Bozdag
To understand driving biological factors for complex diseases like cancer, regulatory circuity of genes needs to be discovered. Recently, a new gene regulation mechanism called competing endogenous RNA (ceRNA) interactions has been discovered. Certain genes targeted by common microRNAs (miRNAs) “compete” for these…
Jun-ichi Satoh
MicroRNAs (miRNAs), a class of endogenous small noncoding RNAs, mediate posttranscriptional regulation of protein-coding genes by binding chiefly to the 3’ untranslated region of target mRNAs, leading to translational inhibition, mRNA destabilization or degradation. A single miRNA concurrently downregulates hundreds of…
Asha A. Nair, Xiaojia Tang, Kevin J. Thompson, Krishna R. Kalari + 1 more
Complex interactions between mRNAs and microRNAs influence cellular functions. The interactions between mRNA and microRNAs also determine the post-transcriptional availability of free mRNAs and unbound microRNAs. The microRNAs bind to one or more microRNA Response Elements (MREs) predominantly located on the…
Olga Plotnikova, Ancha Baranova, Mikhail Skoblov
MicroRNAs play a key role in the regulation of gene expression. A majority of microRNA-mRNA interactions remain unidentified. Despite extensive research, our ability to predict human microRNA-mRNA interactions using computational algorithms remains limited by a complexity of the models for non-canonical interactions…
Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino + 2 more
'Michele Caselle' 'Xianghong Jasmine Zhou'] It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a Transcription Factor (TF) which regulates the…
Mahashweta Basu, Nitai P. Bhattacharyya, P. K. Mohanty
In a recent work [arXiv:1307.1382] it was pointed out that the link-weight distribution of microRNA (miRNA) co-target network of a wide class of species are universal up to scaling. The number cell types, widely accepted as a measure of complexity, turns out to be proportional to these scale-factor. In this article we…
Carla Bosia, Matteo Osella, Mariama El Baroudi, Davide Corà + 1 more
'Michele Caselle'] 1 Human Genetic Foundation, Molecular Biotechnology Center, University of Torino, V. Nizza 52 a, I-10126, Torino, Italy. 2 Center for Complex Systems in Molecular Biology and Medicine, University of Torino, V. Accademia Albertina 13, I-10100 Torino, Italy. 3 Genomic Physics Group, FRE 3214 CNRS…
Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino + 1 more
'Michele Caselle'] It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a Transcription Factor (TF) which regulates the other targets. This…
Laura Cantini, Enzo Médico, Santo Fortunato, Michele Caselle
We propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multinetworks that we consider combine transcription factor co-targeting, microRNA co-targeting, protein-protein interaction and gene co-expression…
Dimpal A. Nyayanit, Chetan Gadgil
MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused directly by the components of the biogenesis pathway or indirectly by other…
Xiao‐Jun Tian, Hang Zhang, Jingyu Zhang, Jianhua Xing
miRNAs serve as crucial post-transcriptional regulators in various essential cell fate decision. However, the contribution of the mRNA-miRNA mutual regulation to bistability is not fully understood. Here, we built a set of mathematical models of mRNA-miRNA interactions and systematically analyzed the sensitivity of…
Hirotake Udono, Minzhi Fan, Yoko Saito, Hirohisa Ohno + 4 more
Programmable droplets, artificial liquid-like condensates of nucleic acids, are intelligent out-of-equilibrium systems that allow the critical aspects of their biological counterparts to be harnessed programmably, such as molecular sensing and phase-state change. While DNA has been central to the previous efforts, less…
Authors not listed
Active assembly of matter is a defining trait of living systems, enabling the creation of far-from-equilibrium materials essential for the functionality of life. This is achieved through energy-dissipative, multi-step processes facilitated by various biomolecular agents for chemical and mechanical assembly of matter.…
Aarav Arora, Igor Tsigelny, Valentina Kouznetsova
Purpose Laryngeal cancer (LC) is the most common head and neck cancer, which often goes undiagnosed due to the expensiveness and inaccessible nature of current diagnosis methods. Many recent studies have shown that microRNAs (miRNAs) are crucial biomarkers for a variety of cancers. Methods In this study, we create a…
Authors not listed
Background and Objectives: Major Depressive Disorder (MDD) is a mental disorder characterized by persistent feelings of sadness, loss of interest, and agitation. MDD is the leading cause of disability worldwide, yet it is still largely underdiagnosed due to misinterpretation of behavioral symptoms. Despite growing…