New Articles From BMC Bioinformatics

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BMC Bioinformatics

The following new articles have just been published in BMC Bioinformatics SOFTWARE penalizedclr: an R package for penalized conditional logistic regression for integration of multiple omics layers Vera Djordjilović, Erica Ponzi … Magne Thoresen BMC Bioinformatics 2024, 25:226 | Published on: 27 June 2024 Full Text | PDF RESEARCH Can large language models understand molecules? Shaghayegh Sadeghi, Alan Bui … Alioune Ngom BMC Bioinformatics 2024, 25:225 | Published on: 26 June 2024 Full Text | PDF CORRECTION Correction: Improving somatic exome sequencing performance by biological replicates Yunus Emre Cebeci, Rumeysa Aslihan Erturk … Mehmet Baysan BMC Bioinformatics 2024, 25:223 | Published on: 25 June 2024 Full Text | PDF RESEARCH iProL: identifying DNA promoters from sequence information based on Longformer pre-trained model Binchao Peng, Guicong Sun and Yongxian Fan BMC Bioinformatics 2024, 25:224 | Published on: 25 June 2024 Full Text | PDF SOFTWARE Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling Worakorn Phumiphanjarphak and Pakorn Aiewsakun BMC Bioinformatics 2024, 25:222 | Published on: 24 June 2024 Full Text | PDF RESEARCH Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs Yuto Takemoto, Daisuke Ito … Masahiro Nakatochi BMC Bioinformatics 2024, 25:221 | Published on: 20 June 2024 Full Text | PDF SOFTWARE PxBLAT: an efficient python binding library for BLAT Yangyang Li and Rendong Yang BMC Bioinformatics 2024, 25:219 | Published on: 19 June 2024 Full Text | PDF SOFTWARE iGenSig-Rx: an integral genomic signature based white-box tool for modeling cancer therapeutic responses using multi-omics data Sanghoon Lee, Min Sun … Xiao-Song Wang BMC Bioinformatics 2024, 25:220 | Published on: 19 June 2024 Full Text | PDF RESEARCH Leveraging permutation testing to assess confidence in positive-unlabeled learning applied to high-dimensional biological datasets Shiwei Xu and Margaret E. Ackerman BMC Bioinformatics 2024, 25:218 | Published on: 19 June 2024 Full Text | PDF SOFTWARE SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions Carlos Willian Dias Dantas, Sebastião Rodrigues da Costa Neto … Rommel Thiago Jucá Ramos BMC Bioinformatics 2024, 25:217 | Published on: 18 June 2024 Full Text | PDF RESEARCH EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction Fatma S. Ahmed, Saleh Aly and Xiangrong Liu BMC Bioinformatics 2024, 25:216 | Published on: 18 June 2024 Full Text | PDF RESEARCH CPMI: comprehensive neighborhood-based perturbed mutual information for identifying critical states of complex biological processes Jing Ren, Peiluan Li and Jinling Yan BMC Bioinformatics 2024, 25:215 | Published on: 15 June 2024 Full Text | PDF RESEARCH A deep learning framework for predicting disease-gene associations with functional modules and graph augmentation Xianghu Jia, Weiwen Luo … Xiaoquan Su BMC Bioinformatics 2024, 25:214 | Published on: 14 June 2024 Full Text | PDF SOFTWARE PyMulSim: a method for computing node similarities between multilayer networks via graph isomorphism networks Pietro Cinaglia BMC Bioinformatics 2024, 25:211 | Published on: 13 June 2024 Full Text | PDF RESEARCH CAraCAl: CAMML with the integration of chromatin accessibility Courtney Schiebout and H. Robert Frost BMC Bioinformatics 2024, 25:212 | Published on: 13 June 2024 Full Text | PDF RESEARCH Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique Ilya Tyagin and Ilya Safro BMC Bioinformatics 2024, 25:213 | Published on: 13 June 2024 Full Text | PDF SOFTWARE StatiCAL: an interactive tool for statistical analysis of biomedical data and scientific valorization Tanguy Pace-Loscos, Jocelyn Gal … Dorian Culié BMC Bioinformatics 2024, 25:210 | Published on: 12 June 2024 Full Text | PDF RESEARCH Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data Khong-Loon Tiong, Dmytro Luzhbin and Chen-Hsiang Yeang BMC Bioinformatics 2024, 25:209 | Published on: 12 June 2024 Full Text | PDF RESEARCH Integrating transformers and many-objective optimization for drug design Nicholas Aksamit, Jinqiang Hou … Beatrice Ombuki-Berman BMC Bioinformatics 2024, 25:208 | Published on: 8 June 2024 Full Text | PDF SOFTWARE dgfr: an R package to assess sequence diversity of gene families Laila Viana Almeida, João Luís Reis-Cunha and Daniella C. Bartholomeu BMC Bioinformatics 2024, 25:207 | Published on: 6 June 2024