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Total 21 results found since Jan 2013.

Machine learning for small interfering RNAs: a concise review of recent developments
The advent of machine learning and its subsequent integration into small interfering RNA (siRNA) research heralds a new epoch in the field of RNA interference (RNAi). This review emphasizes the urgency and relevance of assimilating the plethora of contributions and advancements in this domain, particularly focusing on the period of 2019–2023. Given the rapid progression of deep learning technologies, our synthesis of recent research is paramount to staying apprised of the state-of-the-art methods being utilized. It not only offers a comprehensive insight into the confluence of machine learning and siRNA but also serves a...
Source: Frontiers in Genetics - July 13, 2023 Category: Genetics & Stem Cells Source Type: research

Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL
Genomics Proteomics Bioinformatics. 2023 Feb 10:S1672-0229(23)00032-3. doi: 10.1016/j.gpb.2023.01.006. Online ahead of print.ABSTRACTPrediction of the response of cancer patients to different treatments and identification of biomarkers of drug response are two major goals of individualized medicine. Here, we developed a deep learning framework called TINDL, completely trained on preclinical cancer cell lines (CCLs), to predict the response of cancer patients to different treatments. TINDL utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the statistical disc...
Source: Genomics Proteomics ... - February 12, 2023 Category: Genetics & Stem Cells Authors: David Earl Hostallero Lixuan Wei Liewei Wang Junmei Cairns Amin Emad Source Type: research

Electroacupuncture at Zusanli ameliorates the autistic-like behaviors of rats through activating the Nrf2-mediated antioxidant responses
CONCLUSION: These data suggested that electroacupuncture at ST36 protected nerve function in ASD rats through Nrf2 activation and the antioxidant response.PMID:35339642 | DOI:10.1016/j.gene.2022.146440
Source: Gene - March 27, 2022 Category: Genetics & Stem Cells Authors: Yong-Hong Zhao Hong-Guang Fu Hui Cheng Rui-Juan Zheng Guo Wang Sheng Li En-Yao Li Li-Guo Li Source Type: research

Genes, Vol. 13, Pages 319: The siRNA Off-Target Effect Is Determined by Base-Pairing Stabilities of Two Different Regions with Opposite Effects
In this study, we investigated the most responsible region for the off-target effect by conducting a comprehensive analysis of the thermodynamic properties of all possible siRNA subregions that involved a machine learning technique using a random sampling procedure. As a result, the thermodynamic stability of nucleotides 2–5 showed the highest positive correlation with the off-target effect, and nucleotides 8–14 showed the most negative correlation. Thus, it is revealed that the siRNA off-target effect is determined by the base-pairing stabilities of two different subregions with opposite effects.
Source: Genes - February 9, 2022 Category: Genetics & Stem Cells Authors: Yoshiaki Kobayashi Shen Tian Kumiko Ui-Tei Tags: Article Source Type: research

GSE180248 Transcriptomic analysis of HDAC6-selective and broad HDAC inhibitors in human WT iPSC cardiomyocytes
Contributors : Jin Yang ; Francis Grafton ; Ana Budan ; Sara Ranjbarvaziri ; Farshad Farshidfar ; Marie Cho ; Emma Xu ; Jaclyn Ho ; Mahnaz Maddah ; Kevin E Loewke ; Julio Medina ; David Sperandio ; Snahel Patel ; Tim Hoey ; Mohammad A MandegarSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDilated cardiomyopathy (DCM) is characterized by reduced cardiac output, as well as thinning and enlargement of left ventricular chambers. These characteristics eventually lead to heart failure. Current standards of care do not target the underlying molecular mechanisms associated with genetic forms...
Source: GEO: Gene Expression Omnibus - December 31, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE179656 Phenotypic Screening  with Deep Learning Identifies HDAC6 Inhibitors as Cardioprotective Agents in Mouse Models of Dilated Cardiomyopathy 
Contributors : Jin Yang ; Francis Grafton ; Ana Budan ; Sara Ranjbarvaziri ; Farshad Farshidfar ; Marie Cho ; Emma Xu ; Jaclyn Ho ; Mahnaz Maddah ; Kevin E Loewke ; Julio Medina ; David Sperandio ; Snahel Patel ; Tim Hoey ; Mohammad A MandegarSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDilated cardiomyopathy (DCM) is characterized by reduced cardiac output, as well as thinning and enlargement of left ventricular chambers. These characteristics eventually lead to heart failure. Current standards of care do not target the underlying molecular mechanisms associated with genetic forms...
Source: GEO: Gene Expression Omnibus - December 31, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE136193 Characterizing epigenetic effects of HISTONE DEACETYLASE 6 on DNA methylation, siRNA biogenesis and nucleosome positioning using two hda6 alleles in ros1 background
Contributors : Shoudong Zhang ; Huan Zhong ; Qianwen WangSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Arabidopsis thalianaDNA cytosine methylation is a hallmark of epigenetic gene silencing. DNA demethylation requires ROS1, a bifunctional  DNA glycosylase/lyases and open chromatin status mediated by IDM1. HDA6 is a RDP3-like histone deacetylase and was confirmed to mediate DNA methylation. In previous screening for ros1 suppressor, we identified two hda6 mutants revert...
Source: GEO: Gene Expression Omnibus - July 7, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Methylation profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE154232 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (srHC-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : OtherOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome by inducing ectopic transcription factors (TFs...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE154214 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (ChIP-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partia...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE154148 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (RNA-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome b...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

An Ensemble Strategy to Predict Prognosis in Ovarian Cancer Based on Gene Modules
Conclusion Considering the heterogeneity and complexity of ovarian cancer, we demonstrated a new method to predict the prognosis of ovarian cancer based on the clustering information and gene co-expression network in each subtype of cancer patients. We divided the ovarian cancer data into three subtypes by clustering analysis and we found that the survival risks in these three subtypes were significantly different. We mined the important communities based on the co-expression networks in each subtype. There are 50, 73, and 92 communities in the first, second and third subtype, respectively. Next, we constructed a new ense...
Source: Frontiers in Genetics - April 23, 2019 Category: Genetics & Stem Cells Source Type: research

The Functions of Non-coding RNAs in rRNA Regulation
Qi Yan1, Chengming Zhu1, Shouhong Guang1,2* and Xuezhu Feng1* 1Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China 2CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, China Ribosomes are ribonucleoprotein machines that decode the genetic information embedded in mRNAs into polypeptides. Ribosome biogenesis is tightly coordinated and controlled from the transcription of pre-rRNAs to the assembly of ribosomes. Defects or disorders in rRNA production result in a number of human ri...
Source: Frontiers in Genetics - April 4, 2019 Category: Genetics & Stem Cells Source Type: research