Bioinformatics (Oxford, England)

Keyphrases

Publications

volume 40, number Supplement_1, 2024

Noa Ecker, Dorothée Huchon, Yishay Mansour, Itay Mayrose, Tal Pupko
A machine-learning-based alternative to phylogenetic bootstrap. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Fernando Zhapa-Camacho, Zhenwei Tang, Maxat Kulmanov, Hoehndorf Robert
Predicting protein functions using positive-unlabeled ranking with ontology-based priors. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Kayvon Mazooji, Ilan Shomorony
Fast multiple sequence alignment via multi-armed bandits. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Michael F Adamer, Sarah Catharina Brüningk, Dexiong Chen, Karsten M Borgwardt
Biomarker identification by interpretable maximum mean discrepancy. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)

volume 40, number Supplement_2, 2024

Bastian Pfeifer, Christel Sirocchi, Marcus D Bloice, Markus Kreuzthaler, Martin Urschler
Federated unsupervised random forest for privacy-preserving patient stratification. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Zhijian Huang, Ziyu Fan, Siyuan Shen, Min Wu, Lei Deng
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Yutong Li, Pedro Henrique da Costa Avelar, Xinyue Chen, Li Zhang, Min Wu, Sophia Tsoka
CLigOpt: controllable ligand design through target-specific optimization. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Zhijian Huang, Ziyu Fan, Siyuan Shen, Min Wu, Lei Deng
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Yimin Fan, Yaxuan Li, Yunhua Zhong, Liang Hong, Lei Li, Yu Li
Learning meaningful representation of single-neuron morphology via large-scale pre-training. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Tobias Pietz, Sukrit Gupta, Christoph N Schlaffner, Saima Ahmed, Hanno Steen, Bernhard Y Renard, Katharina Baum
PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Anu Kukkonen-Macchi, Sampsa Hautaniemi, Katharina F Heil, Merja Heinäniemi, Lars Juhl Jensen, Sini Junttila, Lukas Käll, Asta Laiho, Peter Maccallum, Matti Nykter, Bengt Persson, Tomi Suomi, Tim Van Den Bossche, Tommi H Nyrönen, Laura L Elo
ECCB2024: The 23rd European Conference on Computational Biology. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Zhi Yan, Zhen Cao, Luay Nakhleh
Polyphest: fast polyploid phylogeny estimation. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Teemu J Rintala, Francesco Napolitano, Vittorio Fortino
Multi-task deep latent spaces for cancer survival and drug sensitivity prediction. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith S Rodriguez, Chunyu Ma, David Koslicki
Metagenomic functional profiling: to sketch or not to sketch? Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Katerina C Nastou, Mikaela Koutrouli, Sampo Pyysalo, Lars Juhl Jensen
Improving dictionary-based named entity recognition with deep learning. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Piotr Stomma, Witold R Rudnicki
HCS-hierarchical algorithm for simulation of omics datasets. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Yutong Li, Pedro Henrique da Costa Avelar, Xinyue Chen, Li Zhang, Min Wu, Sophia Tsoka
CLigOpt: controllable ligand design through target-specific optimization. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert
Metadata-guided feature disentanglement for functional genomics. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Qi Jiang, Lin Wan
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Piotr Stomma, Witold R Rudnicki
HCS-hierarchical algorithm for simulation of omics datasets. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Yuehua Zhu, Panayiotis V Benos, Maria Chikina
A hybrid constrained continuous optimization approach for optimal causal discovery from biological data. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Zizhan Gao, Kai Cao, Lin Wan
Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Felix Becker, Felix Becker
learnMSA2: deep protein multiple alignments with large language and hidden Markov models. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Tianci Song, Eric Cosatto, Gaoyuan Wang, Rui Kuang, Mark Gerstein, Martin Renqiang Min, Jonathan Warrell
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Bastian Pfeifer, Christel Sirocchi, Marcus D Bloice, Markus Kreuzthaler, Martin Urschler
Federated unsupervised random forest for privacy-preserving patient stratification. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Rami Nasser, Leah V Schaffer, Trey Ideker, Roded Sharan
Multi-modal contrastive learning of subcellular organization using DICE. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Tobias Pietz, Sukrit Gupta, Christoph N Schlaffner, Saima Ahmed, Hanno Steen, Bernhard Y Renard, Katharina Baum
PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Sjoerd van den Belt, Hanqing Zhao, Nikolaos Alachiotis
Scalable CNN-based classification of selective sweeps using derived allele frequencies. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Jiaqi Zhang, Erica Larschan, Jeremy Bigness, Ritambhara Singh
scNODE : generative model for temporal single cell transcriptomic data prediction. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Zhi Yan, Zhen Cao, Luay Nakhleh
Polyphest: fast polyploid phylogeny estimation. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Tim Mirus, Robert Lohmayer, Clementine Döhring, Bjarni V Halldórsson, Birte Kehr
GGTyper: genotyping complex structural variants using short-read sequencing data. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Anu Kukkonen-Macchi, Sampsa Hautaniemi, Katharina F Heil, Merja Heinäniemi, Lars Juhl Jensen, Sini Junttila, Lukas Käll, Asta Laiho, Peter Maccallum, Matti Nykter, Bengt Persson, Tomi Suomi, Tim Van Den Bossche, Tommi H Nyrönen, Laura L Elo
ECCB2024: The 23rd European Conference on Computational Biology. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Soufyan Lakbir, Caterina Buranelli, Gerrit A Meijer, Zhisheng Huang, Remond J A Fijneman, Sanne Abeln
CIBRA identifies genomic alterations with a system-wide impact on tumor biology. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Srijay Deshpande, Sokratia Georgaka, Michael Haley, Robert Sellers, James Minshull, Jayakrupakar Nallala, Martin Fergie, Nicholas Stone, Nasir Rajpoot, Syed Murtuza Baker, Mudassar Iqbal, Kevin Couper, Federico Roncaroli, Fayyaz Ul Amir Afsar Minhas
Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith S Rodriguez, Chunyu Ma, David Koslicki
Metagenomic functional profiling: to sketch or not to sketch? Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Tianci Song, Eric Cosatto, Gaoyuan Wang, Rui Kuang, Mark Gerstein, Martin Renqiang Min, Jonathan Warrell
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Jiaqi Zhang, Erica Larschan, Jeremy Bigness, Ritambhara Singh
scNODE : generative model for temporal single cell transcriptomic data prediction. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Soufyan Lakbir, Caterina Buranelli, Gerrit A Meijer, Zhisheng Huang, Remond J A Fijneman, Sanne Abeln
CIBRA identifies genomic alterations with a system-wide impact on tumor biology. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Sjoerd van den Belt, Hanqing Zhao, Nikolaos Alachiotis
Scalable CNN-based classification of selective sweeps using derived allele frequencies. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Tim Mirus, Robert Lohmayer, Clementine Döhring, Bjarni V Halldórsson, Birte Kehr
GGTyper: genotyping complex structural variants using short-read sequencing data. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Xiaolei Brian Zhang, Grace Oualline, Jim Shaw, Yun William Yu
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Yimin Fan, Yaxuan Li, Yunhua Zhong, Liang Hong, Lei Li, Yu Li
Learning meaningful representation of single-neuron morphology via large-scale pre-training. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Huiying Yan, Shaojun Wang, Hancheng Liu, Hiroshi Mamitsuka, Shanfeng Zhu
GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Katerina C Nastou, Mikaela Koutrouli, Sampo Pyysalo, Lars Juhl Jensen
Improving dictionary-based named entity recognition with deep learning. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert
Metadata-guided feature disentanglement for functional genomics. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Srijay Deshpande, Sokratia Georgaka, Michael Haley, Robert Sellers, James Minshull, Jayakrupakar Nallala, Martin Fergie, Nicholas Stone, Nasir Rajpoot, Syed Murtuza Baker, Mudassar Iqbal, Kevin Couper, Federico Roncaroli, Fayyaz Ul Amir Afsar Minhas
Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Qi Jiang, Lin Wan
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Felix Becker, Felix Becker
learnMSA2: deep protein multiple alignments with large language and hidden Markov models. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Yuehua Zhu, Panayiotis V Benos, Maria Chikina
A hybrid constrained continuous optimization approach for optimal causal discovery from biological data. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Xiaolei Brian Zhang, Grace Oualline, Jim Shaw, Yun William Yu
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)