Research graph
References from NextVir: Enabling classification of tumor-causing viruses with genomic foundation models. Local targets link to admitted publications; unresolved targets remain external evidence.
Human viruses and cancer
10.3390/v6104047 · 2014 · External reference
The landscape of viral associations in human cancers
10.1038/s41588-019-0558-9 · 2020 · External reference
Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence
10.1098/rstb.2019.0041 · 2019 · External reference
The scope of viral causation of human cancers: interpreting virus density from an evolutionary perspective
10.1098/rstb.2018.0304 · 2019 · External reference
ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer
10.1093/nar/gky180 · 2018 · External reference
A deep learning approach reveals unexplored landscape of viral expression in cancer
10.1038/s41467-023-36336-z · 2023 · External reference
10.1145/3535508.3545551
10.1145/3535508.3545551 · External reference
Identifying viruses from metagenomic data using deep learning
10.1007/s40484-019-0187-4 · 2020 · External reference
Virtifier: a deep learning-based identifier for viral sequences from metagenomes
10.1093/bioinformatics/btab845 · 2022 · External reference
Interrelated oncogenic viruses and breast cancer
10.3389/fmolb.2022.781111 · 2022 · External reference
Multiple oncogenic viruses are present in human breast tissues before development of virus associated breast cancer
10.1186/s13027-017-0165-2 · 2017 · External reference
High-throughput sequencing-based investigation of viruses in human cancers by multienrichment approach
10.1093/infdis/jiz318 · 2019 · External reference
Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution
2024 · External reference
DNABERT: pre-trained bidirectional encoder representations from transformers model for DNA-language in genome
10.1093/bioinformatics/btab083 · 2021 · External reference
The nucleotide transformer: building and evaluating robust foundation models for human genomics
2023 · External reference
Unresolved reference
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10.18653/v1/d18-2012
10.18653/v1/d18-2012 · External reference
10.18653/v1/p16-1162
10.18653/v1/p16-1162 · External reference
10.18653/v1/2021.emnlp-main.467
10.18653/v1/2021.emnlp-main.467 · External reference
Unresolved reference
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A large genome center’s improvements to the Illumina sequencing system
10.1038/nmeth.1270 · 2008 · External reference
iCAV: an integrative database of cancer-associated viruses
2021 · External reference
Finishing the finished human chromosome 22 sequence
2008 · External reference
ART: a next-generation sequencing read simulator
10.1093/bioinformatics/btr708 · 2012 · External reference
aBayesQR: a Bayesian method for reconstruction of viral populations characterized by low diversity
10.1089/cmb.2017.0249 · 2018 · External reference
Viral quasispecies reconstruction via tensor factorization with successive read removal
2018 · External reference
Insertion-and-deletion mutations between the genomes of SARS-CoV, SARS-CoV-2, and bat coronavirus RaTG13
10.1128/spectrum.00716-22 · 2022 · External reference
Bacteria in cancer initiation, promotion and progression
10.1038/s41568-023-00594-2 · 2023 · External reference
MetaTransformer: deep metagenomic sequencing read classification using self-attention models
2023 · External reference
Investigation of machine learning algorithms for taxonomic classification of marine metagenomes
2023 · External reference
The human “contaminome”: bacterial, viral and computational contamination in whole genome sequences from 1000 families
10.1038/s41598-022-13269-z · 2022 · External reference
10.1101/2023.08.28.555020
10.1101/2023.08.28.555020 · External reference
Benchmarking DNA foundation models for genomic sequence classification
2024 · External reference
