Author
Bar-Ilan University
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
8 papers
Recent·Most cited
Joon Klaps, Philippe Lemey, Magda Bletsa, nf-core community, Liana Eleni Kafetzopoulou
The paper introduces a pipeline for automated viral genome reconstruction and variant analysis from metagenomic data, validated on simulated and real datasets.
Bioinformatics · Apr 14, 2026Peer-reviewedBioinformatics
Evangelos Karatzas, Martín Beracochea, Fotis A. Baltoumas, Eleni Aplakidou, Lorna Richardson, James A. Fellows Yates, Daniel Lundin, nf-core community, Aydın Buluç, Nikos C. Kyrpides, Ilias Georgakopoulos‐Soares, Georgios A. Pavlopoulos, Robert D. Finn
The paper introduces a scalable pipeline for grouping protein sequences into families, showing it matches curated databases and scales linearly with input size.
GigaScience · Jan 1, 2026Peer-reviewedBioinformatics
Austyn Trull, nf-core community, Elizabeth A. Worthey, Lara Ianov
The paper introduces a Nextflow-based pipeline for analyzing Oxford Nanopore single-cell RNA sequencing data, enabling gene and transcript-level quantification with portability and reproducibility.
Bioinformatics · Sep 1, 2025Peer-reviewedBioinformatics
Luisa Santus, Jose Espinosa‐Carrasco, Leon Rauschning, Júlia Mir-Pedrol, Igor Trujnara, Alessio Vignoli, Leila Mansouri, Athanasios Baltzis, Evan W. Floden, Paolo Di Tommaso, Edgar Garriga Nogales, Adam Gudyś, Sebastian Deorowicz, Cameron L. M. Gilchrist, Martin Steinegger, , Cédric Notredame
The paper presents an nf-core framework for comparing multiple sequence aligners, aiming to streamline deployment and evaluation of MSA tools in HPC environments.
NAR Genomics and Bioinformatics · Jul 4, 2025Peer-reviewedBioinformatics
Gisela Gabernet, Susanna Marquez, Robert D. Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Yann Lee, Cole G. Jensen, David Ladd, Mark Polster, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus Christian Kowarik, , Steven H. Kleinstein
The paper introduces nf-core/airrflow, a Nextflow-based workflow for processing AIRR-seq data, validated on simulated and real datasets to analyze immune receptor repertoires.
PLoS Computational Biology · Jul 26, 2024Peer-reviewedBioinformatics
Friederike Hanssen, Maxime Ulysse Garcia, Lasse Folkersen, Anders Pedersen, Francesco Lescai, Susanne Jodoin, E. Miller, Matthias Seybold, Oskar Wacker, Nicholas H. Smith, nf-core community, Gisela Gabernet, Sven Nahnsen
The paper presents an optimized variant calling pipeline that reduces storage and runtime costs for DNA sequencing analysis.
NAR Genomics and Bioinformatics · Mar 23, 2024Peer-reviewedBioinformatics
Sofia Stamouli, Moritz E. Beber, Tanja Normark, Thomas A. Christensen, Lili Li, Maxime Borry, Mahwash Jamy, nf-core community, James A. Fellows Yates
The paper introduces nf-core/taxprofiler, a pipeline for automated metagenomic taxonomic classification and profiling using multiple tools and databases.
bioRxiv · Oct 20, 2023 · PreprintGenomics
Simone Carpanzano, Mariangela Santorsola, nf-core community, Francesco Lescai
hgtseq is a pipeline for analyzing horizontal gene transfer from sequencing data, showcasing its performance on mammalian exome datasets.
International Journal of Molecular Sciences · Nov 22, 2022Peer-reviewedBioinformatics