Search Results - "BMC bioinformatics"

CellProfiler 4: improvements in speed, utility and usability by Stirling, David R, Swain-Bowden, Madison J, Lucas, Alice M, Carpenter, Anne E, Cimini, Beth A, Goodman, Allen

“…Abstract Background Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput…”
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ImageJ2: ImageJ for the next generation of scientific image data by Rueden, Curtis T, Schindelin, Johannes, Hiner, Mark C, DeZonia, Barry E, Walter, Alison E, Arena, Ellen T, Eliceiri, Kevin W

“…ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible…”
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HH-suite3 for fast remote homology detection and deep protein annotation by Steinegger, Martin, Meier, Markus, Mirdita, Milot, Vöhringer, Harald, Haunsberger, Stephan J, Söding, Johannes

“…Abstract Background HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based…”
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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees by Zhang, Chao, Rabiee, Maryam, Sayyari, Erfan, Mirarab, Siavash

“…Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one…”
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iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data by Ge, Steven Xijin, Son, Eun Wo, Yao, Runan

“…RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for…”
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Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies by Roach, Michael J, Schmidt, Simon A, Borneman, Anthony R

“…Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies…”
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Modeling aspects of the language of life through transfer-learning protein sequences by Heinzinger, Michael, Elnaggar, Ahmed, Wang, Yu, Dallago, Christian, Nechaev, Dmitrii, Matthes, Florian, Rost, Burkhard

“…Predicting protein function and structure from sequence is one important challenge for computational biology. For 26 years, most state-of-the-art approaches…”
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Random forest versus logistic regression: a large-scale benchmark experiment by Couronné, Raphael, Probst, Philipp, Boulesteix, Anne-Laure

“…The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown…”
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Rapid and precise alignment of raw reads against redundant databases with KMA by Clausen, Philip T L C, Aarestrup, Frank M, Lund, Ole

“…As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing…”
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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads by Uliano-Silva, Marcela, Ferreira, João Gabriel R N, Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W, Durbin, Richard, Blaxter, Mark, McCarthy, Shane A

“… PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised…”
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Statistical power for cluster analysis by Dalmaijer, Edwin S, Nord, Camilla L, Astle, Duncan E

“…Cluster algorithms are gaining in popularity in biomedical research due to their compelling ability to identify discrete subgroups in data, and their…”
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InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams by Heberle, Henry, Meirelles, Gabriela Vaz, da Silva, Felipe R, Telles, Guilherme P, Minghim, Rosane

“…Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for…”
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SVM-RFE: selection and visualization of the most relevant features through non-linear kernels by Sanz, Hector, Valim, Clarissa, Vegas, Esteban, Oller, Josep M, Reverter, Ferran

“…Support vector machines (SVM) are a powerful tool to analyze data with a number of predictors approximately equal or larger than the number of observations…”
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metaX: a flexible and comprehensive software for processing metabolomics data by Wen, Bo, Mei, Zhanlong, Zeng, Chunwei, Liu, Siqi

“…Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data…”
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Reactome pathway analysis: a high-performance in-memory approach by Fabregat, Antonio, Sidiropoulos, Konstantinos, Viteri, Guilherme, Forner, Oscar, Marin-Garcia, Pablo, Arnau, Vicente, D'Eustachio, Peter, Stein, Lincoln, Hermjakob, Henning

“…Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis,…”
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So you think you can PLS-DA? by Ruiz-Perez, Daniel, Guan, Haibin, Madhivanan, Purnima, Mathee, Kalai, Narasimhan, Giri

“…Partial Least-Squares Discriminant Analysis (PLS-DA) is a popular machine learning tool that is gaining increasing attention as a useful feature selector and…”
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MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis by Licursi, Valerio, Conte, Federica, Fiscon, Giulia, Paci, Paola

“…miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than…”
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ANGSD: Analysis of Next Generation Sequencing Data by Korneliussen, Thorfinn Sand, Albrechtsen, Anders, Nielsen, Rasmus

“…High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to…”
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MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction by Han, Changhee, Rundo, Leonardo, Murao, Kohei, Noguchi, Tomoyuki, Shimahara, Yuki, Milacski, Zoltán Ádám, Koshino, Saori, Sala, Evis, Nakayama, Hideki, Satoh, Shin'ichi

“…Unsupervised learning can discover various unseen abnormalities, relying on large-scale unannotated medical images of healthy subjects. Towards this,…”
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Single sample scoring of molecular phenotypes by Foroutan, Momeneh, Bhuva, Dharmesh D, Lyu, Ruqian, Horan, Kristy, Cursons, Joseph, Davis, Melissa J

“…Gene set scoring provides a useful approach for quantifying concordance between sample transcriptomes and selected molecular signatures. Most methods use…”
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