Article
Mathematics
Nor Hamizah Miswan, Ismat Mohd Sulaiman, Chee Seng Chan, Chong Guan Ng
Summary: This study used association rule mining algorithms to discover the correlation between readmission factors and basic demographic variables, which can help in reducing patient readmissions by aiding in resource preparation and decision-making.
Article
Biochemical Research Methods
Trevor Manz, Sehi L'Yi, Nils Gehlenborg
Summary: Gos is a Python library that allows for the creation of interactive visualizations of genomics and epigenomics data. It simplifies the process by providing a consistent interface and hiding technical complexities. It seamlessly integrates with computational notebooks for interactive analysis workflows.
Article
Computer Science, Artificial Intelligence
Balu Bhasuran, Jeyakumar Natarajan
Summary: This study used advanced experimental methods such as next-generation sequencing to identify potential genetic biomarkers and gene variants related to diseases. To extract meaningful information from the scientific literature, sophisticated text mining-based knowledge-driven frameworks were utilized.
KNOWLEDGE AND INFORMATION SYSTEMS
(2023)
Article
Biochemistry & Molecular Biology
Veronique Geoffroy, Jean-Baptiste Lamouche, Thomas Guignard, Samuel Nicaise, Arnaud Kress, Sophie Scheidecker, Antony Le Bechec, Jean Muller
Summary: Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity to use different technologies (array CGH, SNP array, Karyotype, Optical Genome Mapping horizontal ellipsis ) to detect each category of SV or to get an appropriate resolution (Whole Genome Sequencing). The AnnotSV webserver aims at being an efficient tool to annotate and interpret SV potential pathogenicity in the context of human diseases, recognize potential false positive variants from all the SV identified, and visualize the patient variants repertoire. The most recent developments in the AnnotSV webserver include updated annotations sources and ranking, three novel output formats for diverse utilization, and two novel user interfaces including an interactive circos view.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Daria Kostiniuk, Hely Tamminen, Pashupati P. Mishra, Saara Marttila, Emma Raitoharju
Summary: The nc886 locus is not polymorphically imprinted in non-human primates and guinea pigs, unlike in humans, suggesting that animal models are not applicable for nc886 research. The data obtained suggests that the nc886 region may be classically imprinted in great apes and potentially also in Old World monkeys.
Article
Biochemical Research Methods
Benjamin Hepp, Violette Da Cunha, Florence Lorieux, Jacques Oberto
Summary: BAGET 2.0 is an updated web service that allows access to the sequence and synteny of any gene from completely sequenced bacteria and archaea in just three mouse clicks, and it can also process user-provided annotated genomes.
Article
Plant Sciences
Yang Lv, Jie Ma, Yueying Wang, Quan Wang, Xueli Lu, Haitao Hu, Qian Qian, Longbiao Guo, Lianguang Shang
Summary: This study measured and analyzed the growth response traits of 225 rice varieties under normal and low nitrogen environments, revealing the genetic control of LNGR and identifying candidate genes and haplotypes related to LN and NUE in rice. Our findings provide new insights into the genetic regulation of LNGR and offer important clues for further exploration of candidate genes and haplotypes related to LN and NUE in rice.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Computer Science, Interdisciplinary Applications
Ali Yavari, Amir Rajabzadeh, Fardin Abdali-Mohammadi
Summary: Existing data mining solutions for identifying risk factors associated with diseases have limitations due to the use of crisp partitions for numerical features and lack of patient-specific profiles. This paper introduces a profile-based fuzzy association rule mining approach to accurately assess risk factors correlated with diseases. The proposed method shows higher partitioning accuracy and reasonable execution time compared to other methods.
JOURNAL OF BIOMEDICAL INFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Andrew J. Modzelewski, Wanqing Shao, Jingqi Chen, Angus Lee, Xin Qi, Mackenzie Noon, Kristy Tjokro, Gabriele Sales, Anne Biton, Aparna Anand, Terence P. Speed, Zhenyu Xuan, Ting Wang, Davide Risso, Lin He
Summary: Retrotransposons play a crucial role in gene regulation during mammalian preimplantation development, with species-specific transposon promoters generating alternative protein isoforms that impact cell proliferation. The unique expression of Cdk2ap1(Delta N) in preimplantation embryos of each mammalian species correlates with the duration of preimplantation development.
Article
Biochemistry & Molecular Biology
Yoonbee Kim, Jong-Hoon Park, Young-Rae Cho
Summary: Network-based computational approaches are used for efficient disease-gene association prediction. This survey provides an overview of network-based disease-gene association prediction methods and shows that integrative methods perform better.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Jianmei Zhao, Fengcui Qian, Xuecang Li, Zhengmin Yu, Jiang Zhu, Rui Yu, Yue Zhao, Ke Ding, Yanyu Li, Yongsan Yang, Qi Pan, Jiaxin Chen, Chao Song, Qiuyu Wang, Jian Zhang, Guohua Wang, Chunquan Li
Summary: This study developed a database called CanMethdb for annotating the upstream and downstream regulatory elements of CpG genes in cancer. It includes annotations for cis-regulatory elements, TF binding sites, and functional annotations for target genes based on DNA methylation and gene expression profiles in diverse cancers. CanMethdb can facilitate in-depth studies of target gene regulations in cancer based on DNA methylation.
Article
Geriatrics & Gerontology
Bo-Hyun Kim, Hyunwoo Lee, Hongki Ham, Hee Jin Kim, Hyemin Jang, Jun Pyo Kim, Yu Hyun Park, Mansu Kim, Sang Won Seo
Summary: This study aimed to identify genes related to A beta uptake and investigate their effects on clinical outcomes. The findings revealed six genes significantly associated with A beta uptake and their SNPs were associated with decreased hippocampal volume and cognitive scores.
FRONTIERS IN AGING NEUROSCIENCE
(2023)
Review
Computer Science, Artificial Intelligence
Iztok Fister Jr, Iztok Fister, Dusan Fister, Vili Podgorelec, Sancho Salcedo-Sanz
Summary: Association rule mining aims to search for relationships between attributes in transaction databases. The process involves pre-processing techniques, rule mining, and post-processing with visualization. This review paper provides a literature review and analysis of techniques, applications, and future research directions in association rule mining and visualization.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Biochemical Research Methods
Teresa De Jesus Martinez, Elliot A. Hershberg, Emma Guo, Garrett J. Stevens, Colin Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes
Summary: JBrowse Jupyter is a package that aims to bridge the gap between Python programming and genomic visualization. It provides a Python interface to quickly set up, launch and customize JBrowse views in Jupyter notebooks. Users can also share their data through Google's Colab notebooks, ensuring reproducible interactive views.
Article
Computer Science, Artificial Intelligence
Xubo Du, Fusheng Yu
Summary: The study proposes a fast algorithm based on the anti-monotonicity of support for mining temporal associations in multi-attributed graph sequences. Experiments show that the algorithm is more effective and efficient in terms of efficiency and accuracy compared to other existing algorithms.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
