Noisecut: a python package for noise-tolerant classification of binary data using prior knowledge integration and max-cut solutions
BMC Bioinformatics
by Moein E. Samadi, Hedieh Mirzaieazar, Alexander Mitsos and Andreas Schuppert
2d ago
Classification of binary data arises naturally in many clinical applications, such as patient risk stratification through ICD codes. One of the key practical challenges in data classification using machine lea ..read more
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A protein network refinement method based on module discovery and biological information
BMC Bioinformatics
by Li Pan, Haoyue Wang, Bo Yang and Wenbin Li
2d ago
The identification of essential proteins can help in understanding the minimum requirements for cell survival and development to discover drug targets and prevent disease. Nowadays, node ranking methods are a ..read more
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Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning
BMC Bioinformatics
by Xin Zeng, Guang-Peng Su, Shu-Juan Li, Shuang-Qing Lv, Meng-Liang Wen and Yi Li
2d ago
Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Alt ..read more
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MMGAT: a graph attention network framework for ATAC-seq motifs finding
BMC Bioinformatics
by Xiaotian Wu, Wenju Hou, Ziqi Zhao, Lan Huang, Nan Sheng, Qixing Yang, Shuangquan Zhang and Yan Wang
2d ago
Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene ..read more
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TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing
BMC Bioinformatics
by Jianqiao Hu, Sai Luo, Ming Tian and Adam Yongxin Ye
4d ago
High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, ‘N’s. PCR duplicates introduced i ..read more
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Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed)
BMC Bioinformatics
by Claus Vogl, Mariia Karapetiants, Burçin Yıldırım, Hrönn Kjartansdóttir, Carolin Kosiol, Juraj Bergman, Michal Majka and Lynette Caitlin Mikula
4d ago
Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying along chromosomes. Evolutionary, biological, and biomedical analyses aim t ..read more
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Biomedical semantic text summarizer
BMC Bioinformatics
by Mahira Kirmani, Gagandeep Kour, Mudasir Mohd, Nasrullah Sheikh, Dawood Ashraf Khan, Zahid Maqbool, Mohsin Altaf Wani and Abid Hussain Wani
4d ago
Text summarization is a challenging problem in Natural Language Processing, which involves condensing the content of textual documents without losing their overall meaning and information content, In the domai ..read more
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MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
BMC Bioinformatics
by Rafael Peres da Silva, Chayaporn Suphavilai and Niranjan Nagarajan
4d ago
With the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of ..read more
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Designing and delivering bioinformatics project-based learning in East Africa
BMC Bioinformatics
by Caleb K. Kibet, Jean-Baka Domelevo Entfellner, Daudi Jjingo, Etienne Pierre de Villiers, Santie de Villiers, Karen Wambui, Sam Kinyanjui and Daniel Masiga
1w ago
The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its go ..read more
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MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach
BMC Bioinformatics
by Jorge F. Beltrán, Lisandra Herrera-Belén, Fernanda Parraguez-Contreras, Jorge G. Farías, Jorge Machuca-Sepúlveda and Stefania Short
1w ago
Protein toxins are defense mechanisms and adaptations found in various organisms and microorganisms, and their use in scientific research as therapeutic candidates is gaining relevance due to their effectivene ..read more
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