Výsledky vyhledávání - "Journal of bioinformatics and computational biology"

Application of t-SNE to human genetic data Autor Li, Wentian, Cerise, Jane E, Yang, Yaning, Han, Henry

“…The t-distributed stochastic neighbor embedding t-SNE is a new dimension reduction and visualization technique for high-dimensional data. t-SNE is rarely…”
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DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning Autor Barukab, Omar, Ali, Farman, Khan, Sher Afzal

“…DNA-binding proteins (DBPs) perform an influential role in diverse biological activities like DNA replication, slicing, repair, and transcription. Some DBPs…”
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PDB-2-PBv3.0: An updated protein block database Autor Karuppasamy, Muthuvel Prasath, Venkateswaran, Suresh, Subbiah, Parthasarathy

“…Our protein block (PB) sequence database PDB-2-PBv1.0 provides PB sequences and dihedral angles for 74,297 protein structures comprising of 103,252 protein…”
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Fractal dimensionality of a coiled helical coil Autor Kak, Subhash

“…The helical coil is ubiquitous in biological and natural systems, and it is often the basic form in complex structures. This paper considers the question of…”
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Modelling and optimizing combination therapeutic strategies for KRAS- and EGFR-mutant lung cancer Autor Wu, Lanqi, Yu, Ruocheng, Yao, Minghui, Rahaman, Md Matiur, Fang, Zhaoyuan

“…Non-small cell lung carcinoma (NSCLC) is well-known for its high incidence (about 80% of lung cancer) and genetic heterogeneity. Personalized driver mutations…”
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The novel design of a multi-epitope vaccine candidate against the dengue virus using advanced immunoinformatics and structural analysis Autor Fath, Mohsen Karami

“…Dengue virus (DENV) remains a major public health challenge with limited vaccine options, and current licensed vaccines exhibit restricted efficacy and safety…”
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COLDLNA: Enhancing long-range node features extraction to improve robust generalization ability of drug-target binding affinity prediction in cold-start scenarios Autor Xu, Ting, Jiang, Shaohua, Ding, Weibin, Wang, Peng

“…Recent advances in deep learning have driven significant progress in drug-target affinity (DTA) prediction. However, many models do not effectively utilize…”
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Cancer classification and functional pathway discovery using TCGA transcriptomic profiles: A matched case-control framework Autor Wang, Jie-Huei, Guo, Tzung-Ying, Pai, Yen-Yi, Hou, Po-Lin, Kumari, Himani, Chan, Michael W Y

“…Leveraging high-dimensional transcriptomic data from The Cancer Genome Atlas (TCGA) for cancer classification holds critical significance for advancing…”
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Editorial: Guidelines for Credible Machine Learning in Computational Biology Autor Wong, Limsoon

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Volcano plots in analyzing differential expressions with mRNA microarrays Autor Li, Wentian

“…A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the…”
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Parameter estimation analysis of the glioblastoma immune model Autor Liu, Biao, Shen, Mengru, Zhao, Meiling

“…In exploring optimal strategies for immunotherapy in glioblastoma (GBM), one of the main challenges is enhancing treatment response. To better understand the…”
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NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency Autor Grigoryeva, Maria A, Khrenova, Maria G, Zvereva, Maria I

“…In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for…”
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Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM Autor Qian, Yan, Xiao, Lei, Zhou, Yiding, Deng, Li

“…Current metagenomic classification methods are limited by short -mer lengths and database dependency, resulting in insufficient taxonomic resolution at the…”
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Visual-SELEX: A technology ensemble for evaluating aptamer structural similarity via 3D visual spatial conformational analysis Autor Wang, Nijia

“…To date, the study of single-stranded DNA (ssDNA) similarity has focused mainly on the similarity of bases in the same position in the nucleic acid sequence…”
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Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases Autor Irankhah, Leili, Khorsand, Babak, Naghibzadeh, Mahmoud, Savadi, Abdorreza

“…Accurate knowledge of the genome, virus and bacteria that have invaded our bodies is crucial for diagnosing many human diseases. The field of bioinformatics…”
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A brief review and comparative analysis of RNA secondary structure prediction tools Autor Ballaney, Pranav, Saha, Gourav, Kulshrestha, Vaibhav, Thaker, Poojan Hasmukhray, Hasija, Prakhar, Talukdar, Indrani, Aduri, Raviprasad

“…Ribonucleic acid (RNA) lies at the heart of the central dogma. It spans the breadth of biological functions, from information storage to gene regulation and…”
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An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra Autor Han, Fang, Zhang, Kaizhong

“…Shotgun proteomics coupled with high-performance liquid chromatography and mass spectrometry has been instrumental in identifying proteins in complex mixtures…”
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Deep learning inference of miRNA expression from bulk and single-cell mRNA expression Autor Ripan, Rony Chowdhury, Athaya, Tasbiraha, Li, Xiaoman, Hu, Haiyan

“…Studying miRNA activity at the single-cell level presents a significant challenge due to the limitations of existing single-cell technologies in capturing…”
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Analysis of clonal evolution in cancer: A computational perspective Autor Ribeiro, Paulo Henrique, Simao, Adenilso

“…Cancer is a complex disease that progresses through Darwinian evolution in cells with genetic mutations, leading to the development of multiple distinct cell…”
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Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation Autor Zhao, Na, Liu, Haihong, Yan, Fang

“…Bacillus subtilis (B. subtilis), a bacterium known to enter a competent state spontaneously, has garnered significant attention due to its intricate internal…”
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