BMC Bioinform.

Publications

volume 25, number 1, 2024

Bingjun Li, Sheida Nabavi
A multimodal graph neural network framework for cancer molecular subtype classification. BMC Bioinform. 25 (1) (2024)
Xu Zhang, Ya Su, Andrew N. Lane, Arnold J. Stromberg, Teresa W.-M. Fan, Chi Wang
Correction: Bayesian kinetic modeling for tracer-based metabolomic data. BMC Bioinform. 25 (1) (2024)
Tay Xin Hui, Shahreen Kasim, Izzatdin Abdul Aziz, Mohd Farhan Md Fudzee, Nazleeni Samiha Haron, Tole Sutikno, Rohayanti Hassan, Hairulnizam Mahdin, Seah Choon Sen
Robustness evaluations of pathway activity inference methods on gene expression data. BMC Bioinform. 25 (1) (2024)
Clémence Joseph, Haris Zafeiropoulos, Kristel Bernaerts, Karoline Faust
Predicting microbial interactions with approaches based on flux balance analysis: an evaluation. BMC Bioinform. 25 (1) (2024)
Xue-Qin Chen, Jie Ma, Di Xu, Zuo-Lin Xiang
Correction: Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma. BMC Bioinform. 25 (1) (2024)
Benedikt Venn, Thomas Leifeld, Ping Zhang, Timo Mühlhaus
Temporal classification of short time series data. BMC Bioinform. 25 (1) (2024)
Sahar Mohseni-Takalloo, Hadis Mohseni, Hassan Mozaffari-Khosravi, Masoud Mirzaei, Mahdieh Hosseinzadeh
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest. BMC Bioinform. 25 (1) (2024)
Jamshaid A. Shahir, Natalie Stanley, Jeremy E. Purvis
Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks. BMC Bioinform. 25 (1) (2024)
Madiha Shabbir, Aziz Mithani
Roast: a tool for reference-free optimization of supertranscriptome assemblies. BMC Bioinform. 25 (1) (2024)
Kimberly To, Judy Strickland, Emily Reinke, Alexandre Borrel, Jim Truax, Heather Maldonado, David G. Allen, Nicole C. Kleinstreuer
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App. BMC Bioinform. 25 (1) (2024)
Xiaoping Min, Chongzhou Yang, Jun Xie, Yang Huang, Nan Liu, Xiaocheng Jin, Tianshu Wang, Zhibo Kong, Xiaoli Lu, Shengxiang Ge, Jun Zhang, Ningshao Xia
Tpgen: a language model for stable protein design with a specific topology structure. BMC Bioinform. 25 (1) (2024)
Dengju Yao, Bailin Li, Xiaojuan Zhan, Xiaorong Zhan, Liyang Yu
GCNFORMER: graph convolutional network and transformer for predicting lncRNA-disease associations. BMC Bioinform. 25 (1) (2024)
David Rojas-Velazquez, Sarah Kidwai, Aletta D. Kraneveld, Alberto Tonda, Daniel L. Oberski, Johan Garssen, Alejandro Lopez Rincon
Methodology for biomarker discovery with reproducibility in microbiome data using machine learning. BMC Bioinform. 25 (1) (2024)
Honglei Wang, Tao Huang, Dong Wang, Wenliang Zeng, Yanjing Sun, Lin Zhang
MSCAN: multi-scale self- and cross-attention network for RNA methylation site prediction. BMC Bioinform. 25 (1) (2024)
Jamshaid A. Shahir, Natalie Stanley, Jeremy E. Purvis
Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks. BMC Bioinform. 25 (1) (2024)
Yiran Huang, Fuhao Chen, Hongtao Sun, Cheng Zhong
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation. BMC Bioinform. 25 (1) (2024)
Rukundo Prince, Zhendong Niu, Zahid Younas Khan, Masabo Emmanuel, Niyishaka Patrick
COVID-19 detection from chest X-ray images using CLAHE-YCrCb, LBP, and machine learning algorithms. BMC Bioinform. 25 (1) (2024)
Ali Hakem Alsaeedi, Haider Hameed R. Al-Mahmood, Zainab Fahad Alnaseri, Mohammad R. Aziz, Dhiah Al-Shammary, Ayman Ibaida, Khandakar Ahmed
Fractal feature selection model for enhancing high-dimensional biological problems. BMC Bioinform. 25 (1) (2024)
Yifan Li, Qianying Li, Lvying Wu, Haiyan Wang, Hui Shi, Chenhui Yang, Yiqun Gu, Jianyuan Li, Zhiliang Ji
SperMD: the expression atlas of sperm maturation. BMC Bioinform. 25 (1) (2024)
Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori
DiCleave: a deep learning model for predicting human Dicer cleavage sites. BMC Bioinform. 25 (1) (2024)
Josip Maric, Kresimir Krizanovic, Sylvain Riondet, Niranjan Nagarajan, Mile Sikic
Comparative analysis of metagenomic classifiers for long-read sequencing datasets. BMC Bioinform. 25 (1) (2024)
Pedro A. Saa, Sebastian Zapararte, Christopher C. Drovandi, Lars K. Nielsen
LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models. BMC Bioinform. 25 (1) (2024)
Clayton Carter, Aaron Saporito, Stephen M. Douglass
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots. BMC Bioinform. 25 (1) (2024)
Yongjian Guan, Chang-Qing Yu, Li-Ping Li, Zhu-Hong You, Weixiao Meng, Xin-Fei Wang, Chen Yang, Lu-Xiang Guo
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules. BMC Bioinform. 25 (1) (2024)
Eli J. Draizen, John Readey, Cameron Mura, Philip E. Bourne
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data. BMC Bioinform. 25 (1) (2024)
Naghme Nazer, Mohammad Hossein Sepehri, Hoda Mohammadzade, Mahya Mehrmohamadi
A novel approach toward optimal workflow selection for DNA methylation biomarker discovery. BMC Bioinform. 25 (1) (2024)
Lasse Meyer, Nils Eling, Bernd Bodenmiller
cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data. BMC Bioinform. 25 (1) (2024)
Jing Zhu, Chao Che, Hao Jiang, Jian Xu, Jiajun Yin, Zhaoqian Zhong
SSF-DDI: a deep learning method utilizing drug sequence and substructure features for drug-drug interaction prediction. BMC Bioinform. 25 (1) (2024)
Tianhua Yao, Xicheng Chen, Haojia Wang, Chengcheng Gao, Jia Chen, Dali Yi, Zeliang Wei, Ning Yao, Yang Li, Dong Yi, Yazhou Wu
Deep evolutionary fusion neural network: a new prediction standard for infectious disease incidence rates. BMC Bioinform. 25 (1) (2024)
Patrick E. Gelbach, Handan Cetin, Stacey D. Finley
Flux sampling in genome-scale metabolic modeling of microbial communities. BMC Bioinform. 25 (1) (2024)
Lifei Wang, Rui Nie, Xuexia Miao, Yankai Cai, Anqi Wang, Hanwen Zhang, Jiang Zhang, Jun Cai
InClust+: the deep generative framework with mask modules for multimodal data integration, imputation, and cross-modal generation. BMC Bioinform. 25 (1) (2024)
Wei Han, Sanguo Zhang, Hailong Gao, Deliang Bu
Clustering on hierarchical heterogeneous data with prior pairwise relationships. BMC Bioinform. 25 (1) (2024)
Thi-Hau Nguyen, Ha-Nam Nguyen, Trung-Nghia Vu
CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs. BMC Bioinform. 25 (1) (2024)
Tim U. H. Baumeister, Eivind Aadland, Roger G. Linington, Olav M. Kvalheim
Multivariate pattern analysis: a method and software to reveal, quantify, and visualize predictive association patterns in multicollinear data. BMC Bioinform. 25 (1) (2024)
Morteza Rakhshaninejad, Mohammad Fathian, Reza Shirkoohi, Farnaz Barzinpour, Amir H. Gandomi
Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach. BMC Bioinform. 25 (1) (2024)
Georg Hahn, Sharon Marie Lutz, Julian Hecker, Dmitry Prokopenko, Michael H. Cho, Edwin K. Silverman, Scott T. Weiss, Christoph Lange
Fast computation of the eigensystem of genomic similarity matrices. BMC Bioinform. 25 (1) (2024)
Haiyang Chang, Daniel A. Ashlock, Steffen P. Graether, Stefan M. Keller
Anchor Clustering for million-scale immune repertoire sequencing data. BMC Bioinform. 25 (1) (2024)
Yuke Xie, Xueqing Peng, Peiluan Li
MIWE: detecting the critical states of complex biological systems by the mutual information weighted entropy. BMC Bioinform. 25 (1) (2024)
Joel Nulsen, Nosheen Hussain, Aws Al-Deka, Jason Yap, Khalil Uddin, Christopher Yau, Ahmed Ashour Ahmed
Correction: Completing a genomic characterisation of microscopic tumour samples with copy number. BMC Bioinform. 25 (1) (2024)
Zachary L. Maas, Robin D. Dowell
Internal and external normalization of nascent RNA sequencing run-on experiments. BMC Bioinform. 25 (1) (2024)
Mahmoud Gamal, Marwa A. Ibrahim
% method: a reliable and accurate approach for qPCR analysis. BMC Bioinform. 25 (1) (2024)
Andrew D. McCall
Colocalization by cross-correlation, a new method of colocalization suited for super-resolution microscopy. BMC Bioinform. 25 (1) (2024)
Eduardo N. Castanho, João Lobo, Rui Henriques, Sara C. Madeira
Correction: G-bic: generating synthetic benchmarks for biclustering. BMC Bioinform. 25 (1) (2024)
Yu Han, Qiong Zhou, Leibo Liu, Jianwei Li, Yuan Zhou
DNI-MDCAP: improvement of causal MiRNA-disease association prediction based on deep network imputation. BMC Bioinform. 25 (1) (2024)
Lei Chen, Chenyu Zhang, Jing Xu
PredictEFC: a fast and efficient multi-label classifier for predicting enzyme family classes. BMC Bioinform. 25 (1) (2024)
Dengju Yao, Yuexiao Deng, Xiaojuan Zhan, Xiaorong Zhan
Predicting lncRNA-disease associations using multiple metapaths in hierarchical graph attention networks. BMC Bioinform. 25 (1) (2024)
Emma E. Kim, Chloe Soohyun Jang, Hakin Kim, Buhm Han
PASTRY: achieving balanced power for detecting risk and protective minor alleles in meta-analysis of association studies with overlapping subjects. BMC Bioinform. 25 (1) (2024)
Qian Liu, Qiang Hu, Song Liu, Alan Hutson, Martin Morgan
ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management. BMC Bioinform. 25 (1) (2024)
Edwin Alvarez-Mamani, Reinhard Dechant, César Armando Beltrán Castañón, Alfredo J. Ibáñez
Graph embedding on mass spectrometry- and sequencing-based biomedical data. BMC Bioinform. 25 (1) (2024)
Jiahao Wei, Linzhang Lu, Tie Shen
Predicting drug-protein interactions by preserving the graph information of multi source data. BMC Bioinform. 25 (1) (2024)