| Bioconda: sustainable and comprehensive software distribution for the life sciences B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ... Nature methods 15 (7), 475-476, 2018 | 1236 | 2018 |
| Eleven grand challenges in single-cell data science D Lähnemann, J Köster, E Szczurek, DJ McCarthy, SC Hicks, ... Genome Biology 21 (1), 1-35, 2020 | 1167 | 2020 |
| De novo assembly of viral quasispecies using overlap graphs JA Baaijens, AZ El Aabidine, E Rivals, A Schönhuth Genome research 27 (5), 835-848, 2017 | 122 | 2017 |
| A high-quality human reference panel reveals the complexity and distribution of genomic structural variants JY Hehir-Kwa, T Marschall, WP Kloosterman, LC Francioli, JA Baaijens, ... Nature communications 7 (1), 1-10, 2016 | 109 | 2016 |
| Computational graph pangenomics: a tutorial on data structures and their applications JA Baaijens, P Bonizzoni, C Boucher, G Della Vedova, Y Pirola, R Rizzi, ... Natural Computing 21 (1), 81-108, 2022 | 55 | 2022 |
| Full-length de novo viral quasispecies assembly through variation graph construction JA Baaijens, B Van der Roest, J Köster, L Stougie, A Schönhuth Bioinformatics 35 (24), 5086-5094, 2019 | 54 | 2019 |
| Strain-aware assembly of genomes from mixed samples using flow variation graphs JA Baaijens, L Stougie, A Schönhuth Research in Computational Molecular Biology: 24th Annual International …, 2020 | 44 | 2020 |
| Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification JA Baaijens, A Zulli, IM Ott, ME Petrone, T Alpert, JR Fauver, CC Kalinich, ... medRxiv, 2021 | 37 | 2021 |
| Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques JA Baaijens, A Zulli, IM Ott, I Nika, MJ van der Lugt, ME Petrone, T Alpert, ... Genome biology 23 (1), 236, 2022 | 34 | 2022 |
| Overlap graph-based generation of haplotigs for diploids and polyploids JA Baaijens, A Schönhuth Bioinformatics 35 (21), 4281-4289, 2019 | 21 | 2019 |
| On the existence of identifiable reparametrizations for linear compartment models JA Baaijens, J Draisma SIAM Journal on Applied Mathematics 76 (4), 1577-1605, 2016 | 18 | 2016 |
| Euclidean distance degrees of real algebraic groups JA Baaijens, J Draisma Linear Algebra and its Applications 467, 174-187, 2015 | 17 | 2015 |
| 12 Grand challenges in single-cell data science D Laehnemann, J Köster, E Szczurek, DJ McCarthy, SC Hicks, ... PeerJ Preprints, 2019 | 8 | 2019 |
| Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data SG Sutcliffe, SA Kraemer, I Ellmen, JJ Knapp, AK Overton, D Nash, ... Microbial Genomics 10 (5), 001249, 2024 | 4 | 2024 |
| A high-quality reference panel reveals the complexity and distribution of structural genome changes in a human population J Hehir-Kwa, T Marschall, WP Kloosterman, LC Francioli, JA Baaijens, ... BioRxiv, 036897, 2016 | 4 | 2016 |
| Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification (preprint) JA Baaijens, A Zulli, IM Ott, ME Petrone, T Alpert, JR Fauver, CC Kalinich, ... | 3 | 2021 |
| Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes J Bemmelen, DS Smyth, JA Baaijens BMC bioinformatics 25 (1), 126, 2024 | 1 | 2024 |
| Simulated reads for benchmarking SARS-CoV-2 lineage abundance estimation J van Bemmelen, JA Baaijens, DS Smyth Zenodo, 2023 | 1 | 2023 |
| ORCA: Predicting replication origins in circular prokaryotic chromosomes Z van Meel, JA Baaijens bioRxiv, 2024.03. 28.587133, 2024 | | 2024 |
| De novo approaches to haplotype-aware genome assembly JA Baaijens Utrecht University, 2019 | | 2019 |
