Accès ouvert
2026
dataset
OpenAlex
Uri Neri, Antônio Pedro Camargo, Dimitris Karapliafis
RolyPoly data bundle Date / Bundle Version: 2026-09-03 This deposit contains the custom built and reference (3rd party) data required for all functionality of RolyPoly-tk, an RNA-Virus analysis tool kit. This includes external raw databases, bundled for convinenve, and custom, purpose built …
il, br
(code pays fourni par la source)
Accès ouvert
2026
dataset
OpenAlex
Uri Neri, Antônio Pedro Camargo, Dimitris Karapliafis
RolyPoly data bundle Date / Bundle Version: 2026-08-19 This deposit contains the custom built and reference (3rd party) data required for all functionality of RolyPoly-tk, an RNA-Virus analysis tool kit. This includes external raw databases, bundled for convinenve, and custom, purpose built …
il, br
(code pays fourni par la source)
Accès ouvert
2026
preprint
OpenAlex
Cédric Lood, Swapnil Prakash Doijad, Evelien M. Adriaenssens, Yīmíng Bào et autres
Abstract The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all fifteen ranks of the virus taxonomy. We led an open community …
gb, de, cn, pl, us, au, br, be, nl, kr, fr, hk, se, co, it, Afrique du Sud
(code pays fourni par la source)
Accès ouvert
2026
article
OpenAlex
Uri Neri, Antônio Pedro Camargo, Brian Bushnell, Rick Beeloo et autres
MOTIVATION: CRISPR spacer-protospacer matching is widely used to infer host-virus interactions in microbial and viromics studies, but the choice of sequence search or alignment tool and its reporting behavior is often under-evaluated for this specific task. RESULTS: Using synthetic, semi-synthetic, and real …
us, nl
(code pays fourni par la source)
Accès ouvert
2026
article
OpenAlex
Dimitris Karapliafis, Uri Neri, Ingrida Olendraitė, Justine Charon et autres
Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RNA viruses rely on identifying the conserved RNA-dependent RNA polymerase (RdRp) by scanning sequencing datasets with specialized profile Hidden Markov Models (pHMMs). …
nl, us, gb, fr, jp
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Accès ouvert
2026
article
OpenAlex
Alexander G. Lucaci, Hisham Shaikh, Li Chong Chong, Rachid Tahzima et autres
RNA-dependent RNA polymerase, or RdRp, remains the central molecular hallmark of RNA viruses. It serves as both a universal anchor for virus detection and a critical target for understanding the functional and evolutionary properties of RNA viruses. Since the inaugural RdRp summit …
us, be, de, it, cz, jp, fr, fi, in, nl, gb, ar, ph, kr, rs, lt, si
(code pays fourni par la source)
Accès ouvert
2026
preprint
OpenAlex
Daniel A. Villarreal, Nino Makasarashvili, Aaryan Kapoor, Max Root et autres
Metatranscriptomics has transformed our view of RNA bacteriophage diversity, revealing vast numbers of single-stranded RNA (ssRNA) phages whose protein capsids can be engineered for biotechnology applications. However, many ssRNA phages remain hidden from current detection methods, which require protein-level similarity to known …
us, il
(code pays fourni par la source)
Accès ouvert
2026
supplementary-materials
OpenAlex
Uri Neri, Antônio Pedro Camargo, Bushnell Brian, Rick Beeloo et autres
Dataset Overview Benchmark inputs, raw tool outputs, and logs for CRISPR spacer–protospacer matching benchmarks (real and simulated sets). Raw outputs and subsampled/simulated inputs are included; large intermediate tools_results.tsv tables are omitted to keep size manageable. Logs, SLURM logs, and job/bash scripts are …
nl
(code pays fourni par la source)
Accès ouvert
2026
preprint
OpenAlex
Dimitris Karapliafis, Uri Neri, Ingrida Olendraitė, Justine Charon et autres
Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RNA viruses that encode RNA-dependent RNA polymerase (RdRp) rely on identifying this conserved protein by employing profile Hidden Markov Models (pHMMs) to …
nl, us, gb, fr, jp
(code pays fourni par la source)
Accès ouvert
2026
editorial
OpenAlex
So Nakagawa, Artem Babaian, Simon Roux, Uri Neri
Following the success of the first meeting, the second RdRp Summit was held on May 11-12, 2025, 40 in Lisbon, Portugal. Two years had passed since the first meeting, and studies and projects 41 conducted during these two years were presented and …
jp, pl, ca, us
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Accès ouvert
2026
software
OpenAlex
Simon Roux, Uri Neri
polars-dovmed is a python package for text search and extraction from NCBI's PubMed Central Open Access subset. It is powered by the polars dataframe library and leverages modern file formats (parquet) to efficiently scan public literature.
us
(code pays fourni par la source)
Accès ouvert
2025
article
OpenAlex
Israela Turgeman-Grott, Noam Golan, Uri Neri, Doron Naki et autres
Extremophilic archaea can have chronic viral infections that are well-tolerated by the hosts and may potentially protect against more lethal infections. Here we show that a natural Haloferax strain (48N), is chronically infected by a lemon-shaped virus. This viral infection is not …
il
(code pays fourni par la source)