Briefings in bioinformatics

Keyphrases

Publications

volume 25, number 5, 2024

Xinze Liu, Jingxuan Shi, Yuanyuan Jiao, Jiaqi An, Jingwei Tian, Yue Yang, Li Zhuo
Integrated multi-omics with machine learning to uncover the intricacies of kidney disease. Briefings in bioinformatics 25 (5) (2024)
Wentao Cui, Qingqing Long, Meng Xiao, Xuezhi Wang, Guihai Feng, Xin Li, Pengfei Wang, Yuanchun Zhou
Refining computational inference of gene regulatory networks: integrating knockout data within a multi-task framework. Briefings in bioinformatics 25 (5) (2024)
Liang Liu, Peiqing Sun, Wei Zhang
A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics. Briefings in bioinformatics 25 (5) (2024)
Yang Li, Anjun Ma, Yizhong Wang, Qi Guo, Cankun Wang, Hongjun Fu, Bingqiang Liu, Qin Ma
Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. Briefings in bioinformatics 25 (5) (2024)
Keyun Zhu, Mengting Huang, Yimeng Wang, Yaxin Gu, Weihua Li, Guixia Liu, Yun Tang
MetaPredictor: in silico prediction of drug metabolites based on deep language models with prompt engineering. Briefings in bioinformatics 25 (5) (2024)
Feng Li, Jingwen Wang, Mengyue Li, Xiaomeng Zhang, Yongjuan Tang, Xinyu Song, Yifang Zhang, Liying Pei, Jiaqi Liu, Chunlong Zhang, Xia Li, Yanjun Xu, Yunpeng Zhang
Identifying cell type-specific transcription factor-mediated activity immune modules reveal implications for immunotherapy and molecular classification of pan-cancer. Briefings in bioinformatics 25 (5) (2024)
Zeyu Lu, Xue Xiao, Qiang Zheng, Xinlei Wang, Lin Xu
Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets. Briefings in bioinformatics 25 (5) (2024)
Yinyin Wang, Yihang Sui, Jiaqi Yao, Hong Jiang, Qimeng Tian, Yun Tang, Yongyu Ou, Jing Tang, Ninghua Tan
Herb-CMap: a multimodal fusion framework for deciphering the mechanisms of action in traditional Chinese medicine using Suhuang antitussive capsule as a case study. Briefings in bioinformatics 25 (5) (2024)
Weining Lu, Yin Tang, Yu Liu, Shiyi Lin, Qifan Shuai, Bin Liang, Rongqing Zhang, Yu Cheng, Dong Fang
CatLearning: highly accurate gene expression prediction from histone mark. Briefings in bioinformatics 25 (5) (2024)
Noura Aherrahrou, Hamid Tairi, Zouhair Aherrahrou
Genomic privacy preservation in genome-wide association studies: taxonomy, limitations, challenges, and vision. Briefings in bioinformatics 25 (5) (2024)
Chang Dou, Yijie Yang, Fei Zhu, BingZhi Li, Yuping Duan
Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints. Briefings in bioinformatics 25 (5) (2024)
Xinhao Yi, Siwei Liu, Yu Wu, Douglas McCloskey, Zaiqiao Meng
BPP: a platform for automatic biochemical pathway prediction. Briefings in bioinformatics 25 (5) (2024)
Vijini G Mallawaarachchi, Anuradha Wickramarachchi, Hansheng Xue, Bhavya Papudeshi, Susanna R Grigson, George Spyro Bouras, Rosa E Prahl, Anubhav Kaphle, Andrey Verich, Berenice Talamantes-Becerra, Elizabeth A Dinsdale, Robert A Edwards
Solving genomic puzzles: computational methods for metagenomic binning. Briefings in bioinformatics 25 (5) (2024)
Yiran Huang, Yufu Lin, Wei Lan, Cuiyu Huang, Cheng Zhong
GloEC: a hierarchical-aware global model for predicting enzyme function. Briefings in bioinformatics 25 (5) (2024)
Yuefan Lin, Zixiang Pan, Yuansong Zeng, Yuedong Yang, Zhiming Dai
Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation. Briefings in bioinformatics 25 (5) (2024)
Yiran Huang, Yufu Lin, Wei Lan, Cuiyu Huang, Cheng Zhong
GloEC: a hierarchical-aware global model for predicting enzyme function. Briefings in bioinformatics 25 (5) (2024)
Yinyin Wang, Yihang Sui, Jiaqi Yao, Hong Jiang, Qimeng Tian, Yun Tang, Yongyu Ou, Jing Tang, Ninghua Tan
Herb-CMap: a multimodal fusion framework for deciphering the mechanisms of action in traditional Chinese medicine using Suhuang antitussive capsule as a case study. Briefings in bioinformatics 25 (5) (2024)
Yuefan Lin, Zixiang Pan, Yuansong Zeng, Yuedong Yang, Zhiming Dai
Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation. Briefings in bioinformatics 25 (5) (2024)
Yiran Huang, Yufu Lin, Wei Lan, Cuiyu Huang, Cheng Zhong
GloEC: a hierarchical-aware global model for predicting enzyme function. Briefings in bioinformatics 25 (5) (2024)
Chang Dou, Yijie Yang, Fei Zhu, BingZhi Li, Yuping Duan
Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints. Briefings in bioinformatics 25 (5) (2024)
Noura Aherrahrou, Hamid Tairi, Zouhair Aherrahrou
Genomic privacy preservation in genome-wide association studies: taxonomy, limitations, challenges, and vision. Briefings in bioinformatics 25 (5) (2024)
Yinyin Wang, Yihang Sui, Jiaqi Yao, Hong Jiang, Qimeng Tian, Yun Tang, Yongyu Ou, Jing Tang, Ninghua Tan
Herb-CMap: a multimodal fusion framework for deciphering the mechanisms of action in traditional Chinese medicine using Suhuang antitussive capsule as a case study. Briefings in bioinformatics 25 (5) (2024)
Chang Dou, Yijie Yang, Fei Zhu, BingZhi Li, Yuping Duan
Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints. Briefings in bioinformatics 25 (5) (2024)
Liang Liu, Peiqing Sun, Wei Zhang
A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics. Briefings in bioinformatics 25 (5) (2024)
Weining Lu, Yin Tang, Yu Liu, Shiyi Lin, Qifan Shuai, Bin Liang, Rongqing Zhang, Yu Cheng, Dong Fang
CatLearning: highly accurate gene expression prediction from histone mark. Briefings in bioinformatics 25 (5) (2024)
Weining Lu, Yin Tang, Yu Liu, Shiyi Lin, Qifan Shuai, Bin Liang, Rongqing Zhang, Yu Cheng, Dong Fang
CatLearning: highly accurate gene expression prediction from histone mark. Briefings in bioinformatics 25 (5) (2024)

volume 25, number 6, 2024

Aliaa E Ali, Li-Li Li, Michael J Courtney, Olli T Pentikäinen, Pekka A Postila
Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1. Briefings in bioinformatics 25 (6) (2024)
Yabin Kuang, Minzhu Xie
DrugDoctor: enhancing drug recommendation in cold-start scenario via visit-level representation learning and training. Briefings in bioinformatics 25 (6) (2024)
Musaddiq K Lodi, Anna Chernikov, Preetam Ghosh
COFFEE: consensus single cell-type specific inference for gene regulatory networks. Briefings in bioinformatics 25 (6) (2024)

volume 25, number Supplement_1, 2024

Nathan A Ruprecht, Joshua D Kennedy, Benu Bansal, Sonalika Singhal, Donald Sens, Angela Maggio, Valena Doe, Dale Hawkins, Ross Campbel, Kyle O'Connell, Jappreet Singh Gill, Kalli Schaefer, Sandeep K Singhal
Transcriptomics and epigenetic data integration learning module on Google Cloud. Briefings in bioinformatics 25 (Supplement_1) (2024)
Christopher L Hemme, Laura Beaudry, Zelaikha Yosufzai, Allen Kim, Daniel Pan, Ross Campbell, Marcia Price, Bongsup P Cho
A cloud-based learning module for biomarker discovery. Briefings in bioinformatics 25 (Supplement_1) (2024)
Owen M Wilkins, Ross Campbell, Zelaikha Yosufzai, Valena Doe, Shannon M Soucy
Cloud-based introduction to BASH programming for biologists. Briefings in bioinformatics 25 (Supplement_1) (2024)
Christopher L Hemme, Laura Beaudry, Zelaikha Yosufzai, Allen Kim, Daniel Pan, Ross Campbell, Marcia Price, Bongsup P Cho
A cloud-based learning module for biomarker discovery. Briefings in bioinformatics 25 (Supplement_1) (2024)
Ha Nguyen, Van-Dung Pham, Hung Nguyen, Bang Tran, Juli Petereit, Tin Nguyen
CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome. Briefings in bioinformatics 25 (Supplement_1) (2024)
Nathan A Ruprecht, Joshua D Kennedy, Benu Bansal, Sonalika Singhal, Donald Sens, Angela Maggio, Valena Doe, Dale Hawkins, Ross Campbel, Kyle O'Connell, Jappreet Singh Gill, Kalli Schaefer, Sandeep K Singhal
Transcriptomics and epigenetic data integration learning module on Google Cloud. Briefings in bioinformatics 25 (Supplement_1) (2024)
Alan E Woessner, Usman Anjum, Hadi Salman, Jacob Lear, Jeffrey T Turner, Ross Campbell, Laura Beaudry, Justin Zhan, Lawrence E Cornett, Susan Gauch, Kyle P Quinn
Identifying and training deep learning neural networks on biomedical-related datasets. Briefings in bioinformatics 25 (Supplement_1) (2024)
Owen M Wilkins, Ross Campbell, Zelaikha Yosufzai, Valena Doe, Shannon M Soucy
Cloud-based introduction to BASH programming for biologists. Briefings in bioinformatics 25 (Supplement_1) (2024)
Kyle A O'Connell, Benjamin Kopchick, Thad Carlson, David Belardo, Stephanie D Byrum
Understanding proteome quantification in an interactive learning module on Google Cloud Platform. Briefings in bioinformatics 25 (Supplement_1) (2024)
Owen M Wilkins, Ross Campbell, Zelaikha Yosufzai, Valena Doe, Shannon M Soucy
Cloud-based introduction to BASH programming for biologists. Briefings in bioinformatics 25 (Supplement_1) (2024)
Kyle A O'Connell, Benjamin Kopchick, Thad Carlson, David Belardo, Stephanie D Byrum
Understanding proteome quantification in an interactive learning module on Google Cloud Platform. Briefings in bioinformatics 25 (Supplement_1) (2024)
Ha Nguyen, Van-Dung Pham, Hung Nguyen, Bang Tran, Juli Petereit, Tin Nguyen
CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome. Briefings in bioinformatics 25 (Supplement_1) (2024)
Yujia Qin, Angela Maggio, Dale Hawkins, Laura Beaudry, Allen Kim, Daniel Pan, Ting Gong, Yuanyuan Fu, Hua Yang, Youping Deng
Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform. Briefings in bioinformatics 25 (Supplement_1) (2024)
Nathan A Ruprecht, Joshua D Kennedy, Benu Bansal, Sonalika Singhal, Donald Sens, Angela Maggio, Valena Doe, Dale Hawkins, Ross Campbel, Kyle O'Connell, Jappreet Singh Gill, Kalli Schaefer, Sandeep K Singhal
Transcriptomics and epigenetic data integration learning module on Google Cloud. Briefings in bioinformatics 25 (Supplement_1) (2024)
Christopher L Hemme, Laura Beaudry, Zelaikha Yosufzai, Allen Kim, Daniel Pan, Ross Campbell, Marcia Price, Bongsup P Cho
A cloud-based learning module for biomarker discovery. Briefings in bioinformatics 25 (Supplement_1) (2024)
Avinash M Veerappa, M Jordan Rowley, Angela Maggio, Laura Beaudry, Dale Hawkins, Allen Kim, Sahil Sethi, Paul L Sorgen, Chittibabu Guda
CloudATAC: a cloud-based framework for ATAC-Seq data analysis. Briefings in bioinformatics 25 (Supplement_1) (2024)
Yujia Qin, Angela Maggio, Dale Hawkins, Laura Beaudry, Allen Kim, Daniel Pan, Ting Gong, Yuanyuan Fu, Hua Yang, Youping Deng
Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform. Briefings in bioinformatics 25 (Supplement_1) (2024)
Etienne Gnimpieba Z, Timothy W Hartman, Tuyen Do, Jessica L S Zylla, Shiva Aryal, Samuel J Haas, Diing D M Agany, Bichar Dip Shrestha Gurung, Valena Doe, Zelaikha Yosufzai, Daniel Pan, Ross Campbell, Victor C Huber, Rajesh Kumar Sani, Venkataramana R Gadhamshetty, Carol Lushbough
Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities. Briefings in bioinformatics 25 (Supplement_1) (2024)
Avinash M Veerappa, M Jordan Rowley, Angela Maggio, Laura Beaudry, Dale Hawkins, Allen Kim, Sahil Sethi, Paul L Sorgen, Chittibabu Guda
CloudATAC: a cloud-based framework for ATAC-Seq data analysis. Briefings in bioinformatics 25 (Supplement_1) (2024)
Alan E Woessner, Usman Anjum, Hadi Salman, Jacob Lear, Jeffrey T Turner, Ross Campbell, Laura Beaudry, Justin Zhan, Lawrence E Cornett, Susan Gauch, Kyle P Quinn
Identifying and training deep learning neural networks on biomedical-related datasets. Briefings in bioinformatics 25 (Supplement_1) (2024)
Avinash M Veerappa, M Jordan Rowley, Angela Maggio, Laura Beaudry, Dale Hawkins, Allen Kim, Sahil Sethi, Paul L Sorgen, Chittibabu Guda
CloudATAC: a cloud-based framework for ATAC-Seq data analysis. Briefings in bioinformatics 25 (Supplement_1) (2024)