Kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R
BMC Bioinformatics
by Louis J. M. Aslett and Ryan R. Christ
2d ago
Approximating the recent phylogeny of N phased haplotypes at a set of variants along the genome is a core problem in modern population genomics and central to performing genome-wide screens for association, selec ..read more
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Protein embedding based alignment
BMC Bioinformatics
by Benjamin Giovanni Iovino and Yuzhen Ye
2d ago
Despite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20–35% pairwise identity (so called "twilight zone") remains a difficult problem. Many alignment algor ..read more
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HormoNet: a deep learning approach for hormone-drug interaction prediction
BMC Bioinformatics
by Neda Emami and Reza Ferdousi
2d ago
Several experimental evidences have shown that the human endogenous hormones can interact with drugs in many ways and affect drug efficacy. The hormone drug interactions (HDI) are essential for drug treatment ..read more
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GPAD: a natural language processing-based application to extract the gene-disease association discovery information from OMIM
BMC Bioinformatics
by K. M. Tahsin Hassan Rahit, Vladimir Avramovic, Jessica X. Chong and Maja Tarailo-Graovac
3d ago
Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) databa ..read more
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Correction: Modifying the false discovery rate procedure based on the information theory under arbitrary correlation structure and its performance in high-dimensional genomic data
BMC Bioinformatics
by Sedighe Rastaghi, Azadeh Saki and Hamed Tabesh
1w ago
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PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes
BMC Bioinformatics
by Katelyn McNair, Peter Salamon, Robert A. Edwards and Anca M. Segall
1w ago
One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery se ..read more
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SNVstory: inferring genetic ancestry from genome sequencing data
BMC Bioinformatics
by Audrey E. Bollas, Andrei Rajkovic, Defne Ceyhan, Jeffrey B. Gaither, Elaine R. Mardis and Peter White
1w ago
Genetic ancestry, inferred from genomic data, is a quantifiable biological parameter. While much of the human genome is identical across populations, it is estimated that as much as 0.4% of the genome can diff ..read more
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A novel microbe-drug association prediction model based on graph attention networks and bilayer random forest
BMC Bioinformatics
by Haiyue Kuang, Zhen Zhang, Bin Zeng, Xin Liu, Hao Zuo, Xingye Xu and Lei Wang
1w ago
In recent years, the extensive use of drugs and antibiotics has led to increasing microbial resistance. Therefore, it becomes crucial to explore deep connections between drugs and microbes. However, traditiona ..read more
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CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data
BMC Bioinformatics
by Philippe Hauchamps, Babak Bayat, Simon Delandre, Mehdi Hamrouni, Marie Toussaint, Stephane Temmerman, Dan Lin and Laurent Gatto
1w ago
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 a ..read more
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Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences
BMC Bioinformatics
by Il-Youp Kwak, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Daniel J. Garry, Jianyi Zhang and Wuming Gong
1w ago
The breakthrough high-throughput measurement of the cis-regulatory activity of millions of randomly generated promoters provides an unprecedented opportunity to systematically decode the cis-regulatory logic t ..read more
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