Works in BMC Bioinformatics, 2024, Vol 25, Issue 1

Results: 381

Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05664-2

By:

Zhuang, Yongwen;
Kim, Na Yeon;
Fritsche, Lars G.;
Mukherjee, Bhramar;
Lee, Seunggeun

Publication type:

Article

vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05676-y

By:

Bhuva, Dharmesh D.;
Tan, Chin Wee;
Liu, Ning;
Whitfield, Holly J.;
Papachristos, Nicholas;
Lee, Samuel C.;
Kharbanda, Malvika;
Mohamed, Ahmed;
Davis, Melissa J.

Publication type:

Article

Enabling personalised disease diagnosis by combining a patient's time-specific gene expression profile with a biomedical knowledge base.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05674-0

By:

Verma, Ghanshyam;
Rebholz-Schuhmann, Dietrich;
Madden, Michael G.

Publication type:

Article

Correction: Multiple imputation and direct estimation for qPCR data with non-detects.

Published in:

2024

By:

Sherina, Valeriia;
McMurray, Helene R.;
Powers, Winslow;
Land, Harmut;
Love, Tanzy M. T.;
McCall, Matthew N.

Publication type:

Correction Notice

MRMPro: a web-based tool to improve the speed of manual calibration for multiple reaction monitoring data analysis by mass spectrometry.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05685-x

By:

Wang, Ruimin;
Jiang, Hengxuan;
Lu, Miaoshan;
Tong, Junjie;
An, Shaowei;
Wang, Jinyin;
Yu, Changbin

Publication type:

Article

Modifying the false discovery rate procedure based on the information theory under arbitrary correlation structure and its performance in high-dimensional genomic data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05678-w

By:

Rastahi, Sedighe;
Saki, Azadeh;
Tabesh, Hamed

Publication type:

Article

A new approach to describe the taxonomic structure of microbiome and its application to assess the relationship between microbial niches.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05575-8

By:

Pappalardo, Vincent Y.;
Azarang, Leyla;
Zaura, Egija;
Brandt, Bernd W.;
de Menezes, Renée X.

Publication type:

Article

Evaluation of penalized and machine learning methods for asthma disease prediction in the Korean Genome and Epidemiology Study (KoGES).

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05677-x

By:

Choi, Yongjun;
Cha, Junho;
Choi, Sungkyoung

Publication type:

Article

Colocalization by cross-correlation, a new method of colocalization suited for super-resolution microscopy.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05675-z

By:

McCall, Andrew D.

Publication type:

Article

ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05663-3

By:

Westrin, Karl Johan;
Kretzschmar, Warren W.;
Emanuelsson, Olof

Publication type:

Article

Multi-label classification with XGBoost for metabolic pathway prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05666-0

By:

Joe, Hyunwhan;
Kim, Hong-Gee

Publication type:

Article

Multivariate pattern analysis: a method and software to reveal, quantify, and visualize predictive association patterns in multicollinear data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05660-6

By:

Baumeister, Tim U. H.;
Aadland, Eivind;
Linington, Roger G.;
Kvalheim, Olav M.

Publication type:

Article

CCL-DTI: contributing the contrastive loss in drug–target interaction prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05671-3

By:

Dehghan, Alireza;
Abbasi, Karim;
Razzaghi, Parvin;
Banadkuki, Hossein;
Gharaghani, Sajjad

Publication type:

Article

PredictEFC: a fast and efficient multi-label classifier for predicting enzyme family classes.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05665-1

By:

Chen, Lei;
Zhang, Chenyu;
Xu, Jing

Publication type:

Article

Learning self-supervised molecular representations for drug–drug interaction prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05643-7

By:

Kpanou, Rogia;
Dallaire, Patrick;
Rousseau, Elsa;
Corbeil, Jacques

Publication type:

Article

PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05640-w

By:

Glascock, Abigail;
Waltari, Eric;
Dudas, Gytis;
Wong, Joan;
Ahyong, Vida

Publication type:

Article

Predicting lncRNA-disease associations using multiple metapaths in hierarchical graph attention networks.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05672-2

By:

Yao, Dengju;
Deng, Yuexiao;
Zhan, Xiaojuan;
Zhan, Xiaorong

Publication type:

Article

Flux sampling in genome-scale metabolic modeling of microbial communities.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05655-3

By:

Gelbach, Patrick E.;
Cetin, Handan;
Finley, Stacey D.

Publication type:

Article

MIWE: detecting the critical states of complex biological systems by the mutual information weighted entropy.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05667-z

By:

Xie, Yuke;
Peng, Xueqing;
Li, Peiluan

Publication type:

Article

Anchor Clustering for million-scale immune repertoire sequencing data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05659-z

By:

Chang, Haiyang;
Ashlock, Daniel A.;
Graether, Steffen P.;
Keller, Stefan M.

Publication type:

Article

Fast computation of the eigensystem of genomic similarity matrices.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05650-8

By:

Hahn, Georg;
Lutz, Sharon M.;
Hecker, Julian;
Prokopenko, Dmitry;
Cho, Michael H.;
Silverman, Edwin K.;
Weiss, Scott T.;
Lange, Christoph

Publication type:

Article

InClust+: the deep generative framework with mask modules for multimodal data integration, imputation, and cross-modal generation.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05656-2

By:

Wang, Lifei;
Nie, Rui;
Miao, Xuexia;
Cai, Yankai;
Wang, Anqi;
Zhang, Hanwen;
Zhang, Jiang;
Cai, Jun

Publication type:

Article

A novel approach toward optimal workflow selection for DNA methylation biomarker discovery.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05658-0

By:

Nazer, Naghme;
Sepehri, Mohammad Hossein;
Mohammadzade, Hoda;
Mehrmohamadi, Mahya

Publication type:

Article

SSF-DDI: a deep learning method utilizing drug sequence and substructure features for drug–drug interaction prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05654-4

By:

Zhu, Jing;
Che, Chao;
Jiang, Hao;
Xu, Jian;
Yin, Jiajun;
Zhong, Zhaoqian

Publication type:

Article

Clustering on hierarchical heterogeneous data with prior pairwise relationships.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05652-6

By:

Han, Wei;
Zhang, Sanguo;
Gao, Hailong;
Bu, Deliang

Publication type:

Article

Predicting microbial interactions with approaches based on flux balance analysis: an evaluation.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05651-7

By:

Joseph, Clémence;
Zafeiropoulos, Haris;
Bernaerts, Kristel;
Faust, Karoline

Publication type:

Article

Deep evolutionary fusion neural network: a new prediction standard for infectious disease incidence rates.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05621-5

By:

Yao, Tianhua;
Chen, Xicheng;
Wang, Haojia;
Gao, Chengcheng;
Chen, Jia;
Yi, Dali;
Wei, Zeliang;
Yao, Ning;
Li, Yang;
Yi, Dong;
Wu, Yazhou

Publication type:

Article

Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05662-4

By:

Huang, Yiran;
Chen, Fuhao;
Sun, Hongtao;
Zhong, Cheng

Publication type:

Article

Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05657-1

By:

Rakhshaninejad, Morteza;
Fathian, Mohammad;
Shirkoohi, Reza;
Barzinpour, Farnaz;
Gandomi, Amir H.

Publication type:

Article

Tpgen: a language model for stable protein design with a specific topology structure.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05637-5

By:

Min, Xiaoping;
Yang, Chongzhou;
Xie, Jun;
Huang, Yang;
Liu, Nan;
Jin, Xiaocheng;
Wang, Tianshu;
Kong, Zhibo;
Lu, Xiaoli;
Ge, Shengxiang;
Zhang, Jun;
Xia, Ningshao

Publication type:

Article

MSCAN: multi-scale self- and cross-attention network for RNA methylation site prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05649-1

By:

Wang, Honglei;
Huang, Tao;
Wang, Dong;
Zeng, Wenliang;
Sun, Yanjing;
Zhang, Lin

Publication type:

Article

CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05646-4

By:

Nguyen, Thi-Hau;
Nguyen, Ha-Nam;
Vu, Trung Nghia

Publication type:

Article

Temporal classification of short time series data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05636-6

By:

Venn, Benedikt;
Leifeld, Thomas;
Zhang, Ping;
Mühlhaus, Timo

Publication type:

Article

SperMD: the expression atlas of sperm maturation.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05631-x

By:

Li, Yifan;
Li, Qianying;
Wu, Lvying;
Wang, Haiyan;
Shi, Hui;
Yang, Chenhui;
Gu, Yiqun;
Li, Jianyuan;
Ji, Zhiliang

Publication type:

Article

COVID-19 detection from chest X-ray images using CLAHE-YCrCb, LBP, and machine learning algorithms.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05427-5

By:

Prince, Rukundo;
Niu, Zhendong;
Khan, Zahid Younas;
Emmanuel, Masabo;
Patrick, Niyishaka

Publication type:

Article

Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05641-9

By:

Shahir, Jamshaid A.;
Stanley, Natalie;
Purvis, Jeremy E.

Publication type:

Article

Methodology for biomarker discovery with reproducibility in microbiome data using machine learning.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05639-3

By:

Rojas-Velazquez, David;
Kidwai, Sarah;
Kraneveld, Aletta D.;
Tonda, Alberto;
Oberski, Daniel;
Garssen, Johan;
Lopez-Rincon, Alejandro

Publication type:

Article

A multimodal graph neural network framework for cancer molecular subtype classification.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05622-4

By:

Li, Bingjun;
Nabavi, Sheida

Publication type:

Article

MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05647-3

By:

Carter, Clayton;
Saporito, Aaron;
Douglass, Stephen M.

Publication type:

Article

DNI-MDCAP: improvement of causal MiRNA-disease association prediction based on deep network imputation.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05644-6

By:

Han, Yu;
Zhou, Qiong;
Liu, Leibo;
Li, Jianwei;
Zhou, Yuan

Publication type:

Article

Correction: Completing a genomic characterisation of microscopic tumour samples with copy number.

Published in:

2024

By:

Nulsen, Joel;
Hussain, Nosheen;
Al-Deka, Aws;
Yap, Jason;
Uddin, Khalil;
Yau, Christopher;
Ahmed, Ahmed Ashour

Publication type:

Correction Notice

Robustness evaluations of pathway activity inference methods on gene expression data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05632-w

By:

Hui, Tay Xin;
Kasim, Shahreen;
Aziz, Izzatdin Abdul;
Fudzee, Mohd Farhan Md;
Haron, Nazleeni Samiha;
Sutikno, Tole;
Hassan, Rohayanti;
Mahdin, Hairulnizam;
Sen, Seah Choon

Publication type:

Article

PASTRY: achieving balanced power for detecting risk and protective minor alleles in meta-analysis of association studies with overlapping subjects.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05627-z

By:

Kim, Emma E.;
Jang, Chloe Soohyun;
Kim, Hakin;
Han, Buhm

Publication type:

Article

Internal and external normalization of nascent RNA sequencing run-on experiments.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05607-3

By:

Maas, Zachary L.;
Dowell, Robin D.

Publication type:

Article

Comparative analysis of metagenomic classifiers for long-read sequencing datasets.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05634-8

By:

Marić, Josip;
Križanović, Krešimir;
Riondet, Sylvain;
Nagarajan, Niranjan;
Šikić, Mile

Publication type:

Article

The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05633-9

By:

Mohseni-Takalloo, Sahar;
Mohseni, Hadis;
Mozaffari-Khosravi, Hassan;
Mirzaei, Masoud;
Hosseinzadeh, Mahdieh

Publication type:

Article

Introducing the f<sub>0</sub>% method: a reliable and accurate approach for qPCR analysis.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05630-y

By:

Gamal, Mahmoud;
Ibrahim, Marwa A.

Publication type:

Article

Correction: G-bic: generating synthetic benchmarks for biclustering.

Published in:

2024

By:

Castanho, Eduardo N.;
Lobo, João P.;
Henriques, Rui;
Madeira, Sara C.

Publication type:

Correction Notice

DiCleave: a deep learning model for predicting human Dicer cleavage sites.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05638-4

By:

Mu, Lixuan;
Song, Jiangning;
Akutsu, Tatsuya;
Mori, Tomoya

Publication type:

Article

Fractal feature selection model for enhancing high-dimensional biological problems.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05619-z

By:

Alsaeedi, Ali Hakem;
Al-Mahmood, Haider Hameed R.;
Alnaseri, Zainab Fahad;
Aziz, Mohammad R.;
Al-Shammary, Dhiah;
Ibaida, Ayman;
Ahmed, Khandakar

Publication type:

Article