keyword
https://read.qxmd.com/read/38520499/identification-of-potential-hub-genes-related-to-acute-pancreatitis-and-chronic-pancreatitis-via-integrated-bioinformatics-analysis-and-in-vitro-analysis
#1
JOURNAL ARTICLE
Lu Yuan, Yiyuan Liu, Lingyan Fan, Cai Sun, Sha Ran, Kuilong Huang, Yan Shen
Acute pancreatitis (AP) and chronic pancreatitis (CP) are considered to be two separate pancreatic diseases in most studies, but some clinical retrospective analyses in recent years have found some degree of correlation between the two in actual treatment, however, the exact association is not clear. In this study, bioinformatics analysis was utilized to examine microarray sequencing data in mice, with the aim of elucidating the critical signaling pathways and genes involved in the progression from AP to CP...
March 23, 2024: Molecular Biotechnology
https://read.qxmd.com/read/38475691/credo-a-friendly-customizable-reproducible-docker-file-generator-for-bioinformatics-applications
#2
JOURNAL ARTICLE
Simone Alessandri, Maria L Ratto, Sergio Rabellino, Gabriele Piacenti, Sandro Gepiro Contaldo, Simone Pernice, Marco Beccuti, Raffaele A Calogero, Luca Alessandri
BACKGROUND: The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the analysis process. These issues can lead to discrepancies in results, undermining the credibility and impact of bioinformatics research and creating mistrust in the scientific process. To address these challenges, open science practices such as sharing data, code, and methods have been encouraged...
March 12, 2024: BMC Bioinformatics
https://read.qxmd.com/read/38444759/cold-exposure-impacts-dna-methylation-patterns-in-cattle-sperm
#3
JOURNAL ARTICLE
Md Nazmul Hossain, Yao Gao, Michael J Hatfield, Jeanene M de Avila, Matthew C McClure, Min Du
DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS)...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38436559/exploring-mirna-target-gene-pair-detection-in-disease-with-cormit
#4
JOURNAL ARTICLE
Jose Cordoba-Caballero, James R Perkins, Federico García-Criado, Diana Gallego, Alicia Navarro-Sánchez, Mireia Moreno-Estellés, Concepción Garcés, Fernando Bonet, Carlos Romá-Mateo, Rocio Toro, Belén Perez, Pascual Sanz, Matthias Kohl, Elena Rojano, Pedro Seoane, Juan A G Ranea
A wide range of approaches can be used to detect micro RNA (miRNA)-target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology...
January 22, 2024: Briefings in Bioinformatics
https://read.qxmd.com/read/38435719/investigating-the-overlap-of-machine-learning-algorithms-in-the-final-results-of-rna-seq-analysis-on-gene-expression-estimation
#5
JOURNAL ARTICLE
Kalliopi-Maria Stathopoulou, Spiros Georgakopoulos, Sotiris Tasoulis, Vassilis P Plagianakos
Advances in computer science in combination with the next-generation sequencing have introduced a new era in biology, enabling advanced state-of-the-art analysis of complex biological data. Bioinformatics is evolving as a union field between computer Science and biology, enabling the representation, storage, management, analysis and exploration of many types of data with a plethora of machine learning algorithms and computing tools. In this study, we used machine learning algorithms to detect differentially expressed genes between different types of cancer and showing the existence overlap to final results from RNA-sequencing analysis...
December 2024: Health Information Science and Systems
https://read.qxmd.com/read/38422042/sexual-dimorphic-mirna-mediated-response-of-bovine-elongated-embryos-to-the-maternal-microenvironment
#6
JOURNAL ARTICLE
Dessie Salilew-Wondim, Michael Hoelker, Eva Held-Hoelker, Franca Rings, Ernst Tholen, Christine Große-Brinkhaus, Karl Shellander, Carina Blaschka, Urban Besenfelder, Vita Havlicek, Dawit Tesfaye
A skewed male-to-female ratio in cattle is believed to be due to the biased embryo losses during pregnancy. The changes in biochemical secretion such as miRNAs by the embryo due to altered maternal environment could cause a sex biased selective implantation resulting in a skewed male to female ratio at birth. Nevertheless, it is still not clear whether the male and female embryos could modify their miRNA expression patterns differently in response to altered physiological developmental conditions. Therefore, this study was focused on identifying sex specific miRNA expression patterns induced in the embryo during the elongation period in response to the maternal environment...
2024: PloS One
https://read.qxmd.com/read/38412294/biscuit-an-efficient-standards-compliant-tool-suite-for-simultaneous-genetic-and-epigenetic-inference-in-bulk-and-single-cell-studies
#7
JOURNAL ARTICLE
Wanding Zhou, Benjamin K Johnson, Jacob Morrison, Ian Beddows, James Eapen, Efrat Katsman, Ayush Semwal, Walid Abi Habib, Lyong Heo, Peter W Laird, Benjamin P Berman, Timothy J Triche, Hui Shen
Data from both bulk and single-cell whole-genome DNA methylation experiments are under-utilized in many ways. This is attributable to inefficient mapping of methylation sequencing reads, routinely discarded genetic information, and neglected read-level epigenetic and genetic linkage information. We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, for simultaneous extraction of genetic and epigenetic information from bulk and single-cell DNA methylation sequencing...
February 27, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38407991/cam3-0-determining-cell-type-composition-and-expression-from-bulk-tissues-with-fully-unsupervised-deconvolution
#8
JOURNAL ARTICLE
Chiung-Ting Wu, Dongping Du, Lulu Chen, Rujia Dai, Chunyu Liu, Guoqiang Yu, Saurabh Bhardwaj, Sarah J Parker, Zhen Zhang, Robert Clarke, David M Herrington, Yue Wang
MOTIVATION: Complex tissues are dynamic eco-systems consisting of molecularly distinct yet interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell type compositions and cell-specific expressions. With few exceptions, most existing deconvolution tools exploit supervised approaches requiring various types of references that may be unreliable or even unavailable for specific tissue microenvironments. RESULTS: We previously developed a fully unsupervised deconvolution method-Convex Analysis of Mixtures (CAM), that enables estimation of cell type composition and expression from bulk tissues...
February 26, 2024: Bioinformatics
https://read.qxmd.com/read/38404557/the-effect-of-astragali-radix-radix-angelica-sinensis-on-acute-kidney-injury-a-network-pharmacology-and-molecular-docking-study
#9
JOURNAL ARTICLE
Qin Wang, Wenrui Zhen, Giuseppe Lippi, Qi Liu
BACKGROUND: Acute kidney injury (AKI) is a devastating clinical syndrome with high mortality rate attributed to lack of effective treatment. The herbal pair of Astragali Radix (AR) and Radix Angelica Sinensis (RAS) is a commonly prescribed herbal formula or is added to other traditional Chinese medicine (TCM) prescriptions for the treatment of kidney diseases. AR-RAS has certain protective effects on AKI in experiments, but the relevant mechanisms have yet to be clear. So this study aims to explore the mechanism of action of AR-RAS in AKI by combining network pharmacology and molecular docking methods...
January 31, 2024: Translational Andrology and Urology
https://read.qxmd.com/read/38393017/metabcombiner-2-0-disparate-multi-dataset-feature-alignment-for-lc-ms-metabolomics
#10
JOURNAL ARTICLE
Hani Habra, Jennifer L Meijer, Tong Shen, Oliver Fiehn, David A Gaul, Facundo M Fernández, Kaitlin R Rempfert, Thomas O Metz, Karen E Peterson, Charles R Evans, Alla Karnovsky
Liquid chromatography-high-resolution mass spectrometry (LC-HRMS), as applied to untargeted metabolomics, enables the simultaneous detection of thousands of small molecules, generating complex datasets. Alignment is a crucial step in data processing pipelines, whereby LC-MS features derived from common ions are assembled into a unified matrix amenable to further analysis. Variability in the analytical factors that influence liquid chromatography separations complicates data alignment. This is prominent when aligning data acquired in different laboratories, generated using non-identical instruments, or between batches from large-scale studies...
February 15, 2024: Metabolites
https://read.qxmd.com/read/38378440/cytopipeline-and-cytopipelinegui-a-bioconductor-r-package-suite-for-building-and-visualizing-automated-pre-processing-pipelines-for-flow-cytometry-data
#11
JOURNAL ARTICLE
Philippe Hauchamps, Babak Bayat, Simon Delandre, Mehdi Hamrouni, Marie Toussaint, Stephane Temmerman, Dan Lin, Laurent Gatto
BACKGROUND: With the increase of the dimensionality in flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data analysis pipelines. A crucial part of these pipelines consists of pre-processing and applying quality control filtering to the raw data, in order to use high quality events in the downstream analyses. This part can in turn be split into a number of elementary steps: signal compensation or unmixing, scale transformation, debris, doublets and dead cells removal, batch effect correction, etc...
February 20, 2024: BMC Bioinformatics
https://read.qxmd.com/read/38374087/transomics2cytoscape-an-automated-software-for-interpretable-2-5-dimensional-visualization-of-trans-omic-networks
#12
JOURNAL ARTICLE
Kozo Nishida, Junichi Maruyama, Kazunari Kaizu, Koichi Takahashi, Katsuyuki Yugi
Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2.5 dimension (2.5D visualization), which is an isometric view of stacked X-Y planes, is a convenient way to interpret multi-omics/trans-omics data in the context of the conventional layouts of biochemical networks drawn on each of the stacked omics layers...
February 19, 2024: NPJ Systems Biology and Applications
https://read.qxmd.com/read/38343804/abnormal-expression-profile-of-plasma-exosomal-micrornas-in-exclusive-electronic-cigarette-adult-users
#13
Dongmei Li, Zidian Xie, Sadiya Bi Shaikh, Irfan Rahman
Background Exposure to electronic cigarette (e-cigarette) aerosol has been linked to several health concerns, including DNA damage, elevated oxidative stress, the release of inflammatory cytokine, and dysfunctions in epithelial barriers. However, little is known about the effect of exclusive e-cigarette use on expression profiles of exosomal miRNAs, which play critical regulatory roles in many inflammatory responses and disease processes including cancer. We aim to compare the exosomal microRNA expression profile between exclusive e-cigarette users and normal controls without any tobacco product use (non-users)...
January 24, 2024: Research Square
https://read.qxmd.com/read/38326539/exploring-the-mechanism-of-action-of-sparganii-rhizoma-curcumae-rhizoma-for-in-treating-castration-resistant-prostate-cancer-a-network-based-pharmacology-and-experimental-validation-study
#14
JOURNAL ARTICLE
Litong Wu, Yan Long, Junfeng Qiu, Xinjun Dai, Xujun You, Tiantian Li, Haijun Chen
Sparganii Rhizoma-Curcumae Rhizoma (SR-CR) is a classic drug pair for the treatment of castration-resistant prostate cancer (CRPC), but its mechanism has not been clarified. The study aims to elucidate the potential mechanism of SR-CR in the management of CRPC. The present study employed the TCMSP as well as the SwissTargetPrediction platform to retrieve the chemical composition and targets of SR-CR. The therapeutic targets of CRPC were identified through screening the GeneCards, Disgenet, and OMIM databases...
February 7, 2024: Scientific Reports
https://read.qxmd.com/read/38316789/orchestrating-chromosome-conformation-capture-analysis-with-bioconductor
#15
JOURNAL ARTICLE
Jacques Serizay, Cyril Matthey-Doret, Amaury Bignaud, Lyam Baudry, Romain Koszul
Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book ( https://bioconductor.org/books/OHCA/ ) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data...
February 5, 2024: Nature Communications
https://read.qxmd.com/read/38312938/spatialheatmap-visualizing-spatial-bulk-and-single-cell-assays-in-anatomical-images
#16
JOURNAL ARTICLE
Jianhai Zhang, Le Zhang, Brendan Gongol, Jordan Hayes, Alexander T Borowsky, Julia Bailey-Serres, Thomas Girke
Visualizing spatial assay data in anatomical images is vital for understanding biological processes in cell, tissue, and organ organizations. Technologies requiring this functionality include traditional one-at-a-time assays, and bulk and single-cell omics experiments, including RNA-seq and proteomics. The spatialHeatmap software provides a series of powerful new methods for these needs, and allows users to work with adequately formatted anatomical images from public collections or custom images. It colors the spatial features (e...
March 2024: NAR genomics and bioinformatics
https://read.qxmd.com/read/38283191/systems-biology-approach-to-identify-biomarkers-and-therapeutic-targets-for-colorectal-cancer
#17
JOURNAL ARTICLE
Niloufar Sadat Kalaki, Mozhgan Ahmadzadeh, Mohammad Najafi, Meysam Mobasheri, Hossein Ajdarkosh, Mohammad Hadi Karbalaie Niya
BACKGROUND: Colorectal cancer (CRC), is the third most prevalent cancer across the globe, and is often detected at advanced stage. Late diagnosis of CRC, leave the chemotherapy and radiotherapy as the main options for the possible treatment of the disease which are associated with severe side effects. In the present study, we seek to explore CRC gene expression data using a systems biology framework to identify potential biomarkers and therapeutic targets for earlier diagnosis and treatment of the disease...
March 2024: Biochemistry and Biophysics Reports
https://read.qxmd.com/read/38278964/mapping-protein-rna-binding-in-plants-with-individual-nucleotide-resolution-uv-cross-linking-and-immunoprecipitation-plant-iclip2
#18
REVIEW
Martin Lewinski, Mirko Brüggemann, Tino Köster, Marlene Reichel, Thorsten Bergelt, Katja Meyer, Julian König, Kathi Zarnack, Dorothee Staiger
Despite crucial roles of RNA-binding proteins (RBPs) in plant physiology and development, methods for determining their transcriptome-wide binding landscape are less developed than those used in other model organisms. Cross-linking and immunoprecipitation (CLIP) methods (based on UV-mediated generation of covalent bonds between RNAs and cognate RBPs in vivo, purification of the cross-linked complexes and identification of the co-purified RNAs by high-throughput sequencing) have been applied mainly in mammalian cells growing in monolayers or in translucent tissue...
January 26, 2024: Nature Protocols
https://read.qxmd.com/read/38271482/epidecoder-a-functional-exploration-tool-for-epigenetic-and-epitranscriptomic-regulation
#19
JOURNAL ARTICLE
Kandarp Joshi, Dan O Wang
Recent technological advances in sequencing DNA and RNA modifications using high-throughput platforms have generated vast epigenomic and epitranscriptomic datasets whose power in transforming life science is yet fully unleashed. Currently available in silico methods have facilitated the identification, positioning and quantitative comparisons of individual modification sites. However, the essential challenge to link specific 'epi-marks' to gene expression in the particular context of cellular and biological processes is unmet...
January 22, 2024: Briefings in Bioinformatics
https://read.qxmd.com/read/38243704/despace-spatially-variable-gene-detection-via-differential-expression-testing-of-spatial-clusters
#20
JOURNAL ARTICLE
Peiying Cai, Mark D Robinson, Simone Tiberi
MOTIVATION: Spatially resolved transcriptomics (SRT) enables scientists to investigate spatial context of mRNA abundance, including identifying spatially variable genes (SVGs), i.e., genes whose expression varies across the tissue. Although several methods have been proposed for this task, native SVG tools cannot jointly model biological replicates, or identify the key areas of the tissue affected by spatial variability. RESULTS: Here, we introduce DESpace, a framework, based on an original application of existing methods, to discover SVGs...
January 18, 2024: Bioinformatics
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