Works in BioData Mining, 2025, Vol 18, Issue 1

Results: 48

The ethics of data mining in healthcare: challenges, frameworks, and future directions.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00461-w

By:

Ahmed, Mohamed Mustaf;
Okesanya, Olalekan John;
Oweidat, Majd;
Othman, Zhinya Kawa;
Musa, Shuaibu Saidu;
Lucero-Prisno III, Don Eliseo

Publication type:

Article

Vibe coding: a new paradigm for biomedical software development.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00462-9

By:

Moore, Jason H.;
Tatonetti, Nicholas

Publication type:

Article

subMG automates data submission for metagenomics studies.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00453-w

By:

Tubbesing, Tom;
Schlüter, Andreas;
Sczyrba, Alexander

Publication type:

Article

Recent advances in deep learning for protein-protein interaction: a review.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00457-6

By:

Cui, Jiafu;
Yang, Siqi;
Yi, Litai;
Xi, Qilemuge;
Yang, Dezhi;
Zuo, Yongchun

Publication type:

Article

Heart rate transition patterns reveal autonomic dysfunction in heart failure with renal function decline: a symbolic and Markov model approach.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00460-x

By:

Widatalla, Namareq;
Younis, Sona Al;
Khandoker, Ahsan

Publication type:

Article

A compact encoding of the genome suitable for machine learning prediction of traits and genetic risk scores.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00459-4

By:

Fatapour, Yasaman;
Brody, James P.

Publication type:

Article

Network-based analyses of multiomics data in biomedicine.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00452-x

By:

Kumar, Rachit;
Romano, Joseph D.;
Ritchie, Marylyn D.

Publication type:

Article

DBSCAN and DBCV application to open medical records heterogeneous data for identifying clinically significant clusters of patients with neuroblastoma.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00455-8

By:

Chicco, Davide;
Oneto, Luca;
Cangelosi, Davide

Publication type:

Article

A probabilistic approach for building disease phenotypes across electronic health records.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00454-9

By:

Vidmar, David;
De Freitas, Jessica;
Thompson, Will;
Pfeifer, John M.;
Fornwalt, Brandon K.;
Zimmerman, Noah;
Miotto, Riccardo;
Chen, Ruijun

Publication type:

Article

Correction: Learning the therapeutic targets of acute myeloid leukemia through multiscale human interactome network and community analysis.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00451-y

By:

Sivanathan, Suruthy;
Hu, Ting

Publication type:

Article

Enhancing hepatopathy clinical trial efficiency: a secure, large language model-powered pre-screening pipeline.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00458-5

By:

Gui, Xiongbin;
Lv, Hanlin;
Wang, Xiao;
Lv, Longting;
Xiao, Yi;
Wang, Lei

Publication type:

Article

Geospatial analysis of short sleep duration and cognitive disability in US adults: a multi-state study using machine learning techniques.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00456-7

By:

Te, Tue T.;
Bui, Alex A. T.;
Fung, Constance H.;
Boland, Mary Regina

Publication type:

Article

Joint models in big data: simulation-based guidelines for required data quality in longitudinal electronic health records.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00450-z

By:

Hunsdieck, Berit;
Bender, Christian;
Ickstadt, Katja;
Mielke, Johanna

Publication type:

Article

Correction: Motif clustering and digital biomarker extraction for free-living physical activity analysis.

Published in:

2025

By:

Liang, Ya-Ting;
Wang, Charlotte

Publication type:

Correction Notice

Motif clustering and digital biomarker extraction for free-living physical activity analysis.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00424-1

By:

Liang, Ya-Ting;
Wang, Charlotte

Publication type:

Article

Revisiting the approaches to DNA damage detection in genetic toxicology: insights and regulatory implications.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00447-8

By:

Alnasser, Sulaiman Mohammed

Publication type:

Article

Learning the therapeutic targets of acute myeloid leukemia through multiscale human interactome network and community analysis.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00444-x

By:

Sivanathan, Suruthy;
Hu, Ting

Publication type:

Article

Inter-organ correlation based multi-task deep learning model for dynamically predicting functional deterioration in multiple organ systems of ICU patients.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00445-w

By:

Zeng, Zhixuan;
Liu, Yang;
Yao, Shuo;
Lin, Minjie;
Cai, Xu;
Nan, Wenbin;
Xie, Yiyang;
Gong, Xun

Publication type:

Article

Enhancing clinical outcome predictions through effective sample size evaluation in graph-based digital twin modeling.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00446-9

By:

Li, Xi;
Chang, Jui-Hsuan;
Venkatesan, Mythreye;
Wang, Zhiping Paul;
Moore, Jason H.

Publication type:

Article

Towards precision oncology: a multi-level cancer classification system integrating liquid biopsy and machine learning.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00439-8

By:

Eledkawy, Amr;
Hamza, Taher;
El-Metwally, Sara

Publication type:

Article

Few-shot biomedical NER empowered by LLMs-assisted data augmentation and multi-scale feature extraction.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00443-y

By:

Zhao, Di;
Mu, Wenxuan;
Jia, Xiangxing;
Liu, Shuang;
Chu, Yonghe;
Meng, Jiana;
Lin, Hongfei

Publication type:

Article

Network-based multi-omics integrative analysis methods in drug discovery: a systematic review.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00442-z

By:

Jiang, Wei;
Ye, Weicai;
Tan, Xiaoming;
Bao, Yun-Juan

Publication type:

Article

Inferring protein from transcript abundances using convolutional neural networks.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00434-z

By:

Schwehn, Patrick Maximilian;
Falter-Braun, Pascal

Publication type:

Article

AI as an accelerator for defining new problems that transcends boundaries.

Published in:

2025

By:

Obafemi-Ajayi, Tayo;
Jennings, Steven F.;
Zhang, Yu;
Liu, Kara Li;
Peckham, Joan;
Moore, Jason H.

Publication type:

Literature Review

Machine learning models for reinjury risk prediction using cardiopulmonary exercise testing (CPET) data: optimizing athlete recovery.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00431-2

By:

Abasi, Arezoo;
Nazari, Ahmad;
Moezy, Azar;
Fatemi Aghda, Seyed Ali

Publication type:

Article

Feature graphs for interpretable unsupervised tree ensembles: centrality, interaction, and application in disease subtyping.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00430-3

By:

Sirocchi, Christel;
Urschler, Martin;
Pfeifer, Bastian

Publication type:

Article

Agenda setting for health equity assessment through the lenses of social determinants of health using machine learning approach: a framework and preliminary pilot study.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00428-x

By:

Ramezani, Maryam;
Mobinizadeh, Mohammadreza;
Bakhtiari, Ahad;
Rabiee, Hamid R.;
Mostafavi, Hakimeh;
Olyaeemanesh, Alireza;
Fazaeli, Ali Akbar;
Atashi, Alireza;
Sazgarnejad, Saharnaz;
Mohamadi, Efat;
Takian, Amirhossein

Publication type:

Article

Multivariate longitudinal clustering reveals neuropsychological factors as dementia predictors in an Alzheimer's disease progression study.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00441-0

By:

Ribino, Patrizia;
Di Napoli, Claudia;
Paragliola, Giovanni;
Chicco, Davide;
Gasparini, Francesca

Publication type:

Article

Advancing preeclampsia prediction: a tailored machine learning pipeline integrating resampling and ensemble models for handling imbalanced medical data.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00440-1

By:

Ma, Yinyao;
Lv, Hanlin;
Ma, Yanhua;
Wang, Xiao;
Lv, Longting;
Liang, Xuxia;
Wang, Lei

Publication type:

Article

High-dimensional mediation analysis reveals the mediating role of physical activity patterns in genetic pathways leading to AD-like brain atrophy.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00432-1

By:

Xu, Hanxiang;
Mu, Shizhuo;
Bao, Jingxuan;
Davatzikos, Christos;
Shou, Haochang;
Shen, Li

Publication type:

Article

Automatic detection and extraction of key resources from tables in biomedical papers.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00438-9

By:

Ozyurt, Ibrahim Burak;
Bandrowski, Anita

Publication type:

Article

Leveraging mixed-effects regression trees for the analysis of high-dimensional longitudinal data to identify the low and high-risk subgroups: simulation study with application to genetic study.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00437-w

By:

Jahangiri, Mina;
Kazemnejad, Anoshirvan;
Goldfeld, Keith S.;
Daneshpour, Maryam S.;
Momen, Mehdi;
Mostafaei, Shayan;
Khalili, Davood;
Akbarzadeh, Mahdi

Publication type:

Article

Unsupervised clustering based coronary artery segmentation.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00435-y

By:

Serrano-Antón, Belén;
Insúa Villa, Manuel;
Pendón-Minguillón, Santiago;
Paramés-Estévez, Santiago;
Otero-Cacho, Alberto;
López-Otero, Diego;
Díaz-Fernández, Brais;
Bastos-Fernández, María;
González-Juanatey, José R.;
P. Muñuzuri, Alberto

Publication type:

Article

EnSCAN: ENsemble Scoring for prioritizing CAusative variaNts across multiplatform GWASs for late-onset alzheimer's disease.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00436-x

By:

Erdogan, Onur;
Iyigun, Cem;
Aydın Son, Yeşim

Publication type:

Article

Analysis of global trends and hotspots of skin microbiome in acne: a bibliometric perspective.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00433-0

By:

Zhang, Lanfang;
Cai, Yuan;
Li, Lin;
Hu, Jie;
Jia, Changsha;
Kuang, Xu;
Zhou, Yi;
Lan, Zhiai;
Liu, Chunyan;
Jiang, Feng;
Sun, Nana;
Zeng, Ni

Publication type:

Article

Immune cell profiles and predictive modeling in osteoporotic vertebral fractures using XGBoost machine learning algorithms.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00427-y

By:

Chen, Yi-Chou;
Su, Hui-Chen;
Huang, Shih-Ming;
Yu, Ching-Hsiao;
Chang, Jen-Huei;
Chiu, Yi-Lin

Publication type:

Article

XGBoost-enhanced ensemble model using discriminative hybrid features for the prediction of sumoylation sites.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-024-00415-8

By:

Khan, Salman;
Noor, Sumaiya;
Javed, Tahir;
Naseem, Afshan;
Aslam, Fahad;
AlQahtani, Salman A.;
Ahmad, Nijad

Publication type:

Article

A deep learning approach for classifying and predicting children's nutritional status in Ethiopia using LSTM-FC neural networks.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00425-0

By:

Begashaw, Getnet Bogale;
Zewotir, Temesgen;
Fenta, Haile Mekonnen

Publication type:

Article

MiCML: a causal machine learning cloud platform for the analysis of treatment effects using microbiome profiles.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00422-3

By:

Koh, Hyunwook;
Kim, Jihun;
Jang, Hyojung

Publication type:

Article

A generative deep neural network for pan-digestive tract cancer survival analysis.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00426-z

By:

Xu, Lekai;
Lan, Tianjun;
Huang, Yiqian;
Wang, Liansheng;
Lin, Junqi;
Song, Xinpeng;
Tang, Hui;
Cao, Haotian;
Chai, Hua

Publication type:

Article

Motif clustering and digital biomarker extraction for free-living physical activity analysis.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-025-00424-1

By:

Liang, Ya-Ting;
Wang, Charlotte

Publication type:

Article

An ensemble machine learning-based performance evaluation identifies top In-Silico pathogenicity prediction methods that best classify driver mutations in cancer.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-024-00420-x

By:

Das, Subrata;
Patel, Vatsal;
Chakravarty, Shouvik;
Ghosh, Arnab;
Mukhopadhyay, Anirban;
Biswas, Nidhan K.

Publication type:

Article

Correction: Predictive modeling of ALS progression: an XGBoost approach using clinical features.

Published in:

2025

By:

Gupta, Richa;
Bhandari, Mansi;
Grover, Anhad;
Al-shehari, Taher;
Kadrie, Mohammed;
Alfakih, Taha;
Alsalman, Hussain

Publication type:

Correction Notice

Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-024-00418-5

By:

Fitzsimmons, Lane;
Acosta, Maria T.;
Adams, David R.;
Afzali, Ben;
Al-Beshri, Ali;
Allenspach, Eric;
Allworth, Aimee;
Alvarez, Raquel L.;
Alvey, Justin;
Andrews, Ashley;
Ashley, Euan A.;
Bacino, Carlos A.;
Bademci, Guney;
Balasubramanyam, Ashok;
Baldridge, Dustin;
Baldwin, Erin;
Bale, Jim;
Bamshad, Michael;
Barbouth, Deborah;
Bayrak-Toydemir, Pinar

Publication type:

Article

MultiChem: predicting chemical properties using multi-view graph attention network.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-024-00419-4

By:

Moon, Heesang;
Rho, Mina

Publication type:

Article

Genome-wide association studies are enriched for interacting genes.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-024-00421-w

By:

Nguyen, Peter T.;
Coetzee, Simon G.;
Silacheva, Irina;
Hazelett, Dennis J.

Publication type:

Article

The Venus score for the assessment of the quality and trustworthiness of biomedical datasets.

Published in:

BioData Mining, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13040-024-00412-x

By:

Chicco, Davide;
Fabris, Alessandro;
Jurman, Giuseppe

Publication type:

Article

Open challenges and opportunities in federated foundation models towards biomedical healthcare.

Published in:

2025

By:

Li, Xingyu;
Peng, Lu;
Wang, Yu-Ping;
Zhang, Weihua

Publication type:

Literature Review