| Transcriptome assembly from long-read RNA-seq alignments with StringTie2 S Kovaka, AV Zimin, GM Pertea, R Razaghi, SL Salzberg, M Pertea Genome Biology 20 (1), 1-13, 2019 | 1282 | 2019 |
| Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED S Kovaka, Y Fan, B Ni, W Timp, MC Schatz Nature Biotechnology 39 (4), 431-441, 2021 | 242 | 2021 |
| Novel circular RNA NF1 acts as a molecular sponge, promoting gastric cancer by absorbing miR-16 Z Wang, K Ma, S Pitts, Y Cheng, X Liu, X Ke, S Kovaka, H Ashktorab, ... Endocrine-related cancer, 2018 | 57 | 2018 |
| Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing S Kovaka, S Ou, KM Jenike, MC Schatz Nature Methods 20 (1), 12-16, 2023 | 46 | 2023 |
| Genomics and development of Lentinus tigrinus, a white-rot wood-decaying mushroom with dimorphic fruiting bodies B Wu, Z Xu, A Knudson, A Carlson, N Chen, S Kovaka, K LaButti, ... Genome biology and evolution, 2018 | 42 | 2018 |
| Pan-genomic Matching Statistics for Targeted Nanopore Sequencing O Ahmed, M Rossi, S Kovaka, MC Schatz, T Gagie, C Boucher, ... iScience, 102696, 2021 | 24 | 2021 |
| High resolution copy number inference in cancer using short-molecule nanopore sequencing T Baslan, S Kovaka, FJ Sedlazeck, Y Zhang, R Wappel, S Tian, SW Lowe, ... Nucleic acids research 49 (21), e124-e124, 2021 | 22 | 2021 |
| Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment S Kovaka, PW Hook, KM Jenike, V Shivakumar, LB Morina, R Razaghi, ... bioRxiv, 2024.03. 05.583511, 2024 | 8 | 2024 |
| Sigmoni: classification of nanopore signal with a compressed pangenome index VS Shivakumar, OY Ahmed, S Kovaka, M Zakeri, B Langmead bioRxiv, 2023.08. 15.553308, 2023 | 7 | 2023 |
| Tracking the History of Knowledge Using Historical Editions of Encyclopedia Britannica M Gronas, A Rumshisky, A Gabrovski, S Kovaka, H Chen Adaptation of Language Resources and Tools for Processing Cultural Heritage …, 2012 | 1 | 2012 |
| MEM-based pangenome indexing for k-mer queries S Hwang, NK Brown, OY Ahmed, KM Jenike, S Kovaka, MC Schatz, ... bioRxiv, 2024.05. 20.595044, 2024 | | 2024 |
