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ORCIDBioinformatics, Volume 41
Volume 41, Number 1, 2025
- Daniel Mechtersheimer
, Wenze Ding, Xiangnan Xu, Sanghyun Kim, Carolyn Sue, Yue Cao, Jean Y. H. Yang:
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits.
Volume 41, Number 3, 2025
- Rawan Shraim, Brian Mooney, Karina L. Conkrite, Amber K. Hamilton, Gregg B. Morin, Poul H. Sorensen, John M. Maris, Sharon J. Diskin, Ahmet Sacan:
ImmunoTar - integrative prioritization of cell surface targets for cancer immunotherapy.
Volume 41, Number 4, 2025
- Zhuoyu Wei, Yongqi Shen, Xiang Tang, Jian Wen, Youyi Song, Mingqiang Wei, Jing Cheng, Xiaolei Zhu:
AVPpred-BWR: antiviral peptides prediction via biological words representation.
Volume 41, Number 7, 2025
- Sicen Liu, Shutao Chen, Tao Bai, Bin Liu:
FusionEncoder: identification of intrinsically disordered regions based on multi-feature fusion. - Meiling Liu, Shuangshuang Wang, Zeyu Luo, Guohua Wang, Yuming Zhao:
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction.
Volume 41, Number 9, 2025
- Asato Yoshinaga, Osamu Maruyama:
CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning. - Tianci Wang, Xin Lai, Shenjie Wang, Yuqian Liu, Xiaoyan Zhu, Jiayin Wang:
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples. - Tong Wang, Zhi-Ping Liu:
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection. - Helena García-Cebollada, Alfonso López, Vladimir Espinosa Angarica, Juan José Galano-Frutos, Javier Sancho:
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins. - Carl M. Kobel, Velma T. E. Aho, Ove Øyås, Niels Nørskov-Lauritsen, Ben J. Woodcroft, Phillip B. Pope:
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. - Shuang Wang, Tianle Ma, Kaiyu Dong, Peifu Han, Xue Li, Junteng Ma, Mao Li, Tao Song:
MVSO-PPIS: a structured objective learning model for protein-protein interaction sites prediction via multi-view graph information integration. - Joseph L. Hellerstein, Lucian P. Smith, Lillian T. Tatka, Steven S. Andrews, Michael A Kochen, Herbert M. Sauro:
Discovering subnetworks in SBML models. - Ryan R. Wick, Benjamin P. Howden, Timothy P. Stinear:
Autocycler: long-read consensus assembly for bacterial genomes. - Johannes Hingerl, Alexander Karollus, Julien Gagneur:
Flashzoi: an enhanced Borzoi for accelerated genomic analysis. - Ke Yan, Shutao Chen, Bin Liu, Hao Wu:
Accurate prediction of toxicity peptide and its function using multi-view tensor learning and latent semantic learning framework. - Xiang Liu, Yi-Han Tang, James Blachly, Stephen Edge, Yasminka A Jakubek, Martin McCarter, Abdul Rafeh Naqash, Kenneth G. Nepple, Afaf Osman, Matthew J. Reilley, Gregory Riedlinger, Bodour Salhia, Bryan P. Schneider, Craig Shriver, Michelle L. Churchman, Robert J. Rounbehler, Jamie K. Teer, Nancy Gillis, Mingxiang Teng:
qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics. - Sebastian Persson, Fabian Fröhlich, Stephan Grein, Torkel Loman, Damiano Ognissanti, Viktor Hasselgren, Jan Hasenauer, Marija Cvijovic:
PEtab.jl: advancing the efficiency and utility of dynamic modelling. - Seokjun On, Yujin Jeong, Eun-Sol Kim:
Structure-guided sequence representation learning for generalizable protein function prediction.
Volume 41, Number 10, 2025
- Armin Rauschenberger, Petr V. Nazarov, Enrico Glaab:
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation. - Marcos Lopez-De-Castro, Alberto García-Galindo, José González-Gomariz, Rubén Armañanzas:
Conformal inference for reliable single cell RNA-seq annotation. - Daniel Kim, Carissa Chen, Lijia Yu, Jean Yee Hwa Yang, Pengyi Yang:
CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data. - Wouter Duverger, Georg Ramer, Nikolaos N. Louros, Joost Schymkowitz, Frederic Rousseau:
AXZ viewer: a web application to visualize unprocessed AFM-IR data. - L. Moritz Blumer, Jeffrey M. Good, Richard Durbin:
WinPCA: a package for windowed principal component analysis. - Chunfeng He, Yue Xu, Yuan Zhou, Jiayao Fan, Chunxiao Cheng, Ran Meng, Lang Wu, Ruiyuan Pan, Ravi V. Shah, Eric R. Gamazon, Dan Zhou:
Integrating population-level and cell-based signatures for drug repositioning. - Qicheng Zhao, Anji Deng, Qihuang Zhang:
DiSTect: a Bayesian model for disease-associated gene discovery and prediction in spatial transcriptomics. - Cem Ata Baykara, Ali Burak Ünal, Nico Pfeifer, Mete Akgün:
Privacy-preserving federated unsupervised domain adaptation with application to age prediction from DNA methylation data. - Austin M. Marcus, Jordan C. Rozum, Herbert Sizek, Luis M. Rocha:
CANA v1.0.0: efficient quantification of canalization in automata networks. - Shengli Zhang, Jingyi Ren, Yunyun Liang:
An innovative peptide toxicity prediction model based on multi-scale convolutional neural network and residual connection. - Hongxin Xiang, Mingquan Liu, Linlin Hou, Shuting Jin, Jianmin Wang, Jun Xia, Wenjie Du, Sisi Yuan, Xiangzheng Fu, Xinyu Yang, Li Zeng, Lei Xu:
An image-based protein-ligand binding representation learning framework via multi-level flexible dynamics trajectory pre-training. - Xinyu Zhou, Yi Yan, Kevin Hu, Haixu Tang, Yijie Wang, Lu Wang, Chi Zhang, Sha Cao:
Predicting the trend of SARS-CoV-2 mutation frequencies using historical data. - Elias Dohmen, Margaux Aubel, Lars A Eicholt, Paul Roginski, Victor Luria, Amir Karger, Anna Grandchamp:
DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation. - Güliz Akkaya, Nesli Erdogmus, Mete Akgün:
PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption. - Hung-Ching Chang, Yusi Fang, Michael T. Gorczyca, Kayhan Batmanghelich, George C. Tseng:
High-dimensional causal mediation analysis by partial sum statistic and sample splitting strategy in imaging genetics application. - Hukam C. Rawal, Qi Chen, Tong Zhou:
FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs. - Trevor Schneggenburger, Jaroslaw Zola:
SKiM: accurately classifying metagenomic ONT reads in limited memory.
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