| Current progress and open challenges for applying deep learning across the biosciences N Sapoval, A Aghazadeh, MG Nute, DA Antunes, A Balaji, R Baraniuk, ... Nature Communications 13 (1), 1728, 2022 | 197 | 2022 |
| Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ … GA Hudson, BJ Burkhart, AJ DiCaprio, CJ Schwalen, B Kille, ... Journal of the American Chemical Society 141 (20), 8228-8238, 2019 | 145 | 2019 |
| Bioinformatic expansion and discovery of thiopeptide antibiotics CJ Schwalen, GA Hudson, B Kille, DA Mitchell Journal of the American Chemical Society 140 (30), 9494-9501, 2018 | 128 | 2018 |
| Bioinformatics-guided expansion and discovery of graspetides S Ramesh, X Guo, AJ DiCaprio, AM De Lio, LA Harris, BL Kille, ... ACS chemical biology 16 (12), 2787-2797, 2021 | 33 | 2021 |
| SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning A Balaji, B Kille, AD Kappell, GD Godbold, M Diep, RAL Elworth, Z Qian, ... Genome biology 23 (1), 133, 2022 | 32 | 2022 |
| Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data Y Liu, J Kearney, M Mahmoud, B Kille, FJ Sedlazeck, TJ Treangen Nature communications 13 (1), 1321, 2022 | 26 | 2022 |
| Multiple genome alignment in the telomere-to-telomere assembly era B Kille, A Balaji, FJ Sedlazeck, M Nute, TJ Treangen Genome Biology 23 (1), 182, 2022 | 22 | 2022 |
| Fast processing and querying of 170tb of genomics data via a repeated and merged bloom filter (rambo) G Gupta, M Yan, B Coleman, B Kille, RAL Elworth, T Medini, T Treangen, ... Proceedings of the 2021 International Conference on Management of Data, 2226 …, 2021 | 20 | 2021 |
| PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment Q Wang, B Kille, TR Liu, RAL Elworth, TJ Treangen Nature communications 12 (1), 1-12, 2021 | 16 | 2021 |
| Peptidase activation by a leader peptide-bound RiPP recognition element AM Kretsch, MG Gadgil, AJ DiCaprio, SE Barrett, BL Kille, Y Si, L Zhu, ... Biochemistry 62 (4), 956-967, 2023 | 15 | 2023 |
| Ultra-high throughput mapping of genetic design space RW O’Connell, K Rai, TC Piepergerdes, Y Wang, KD Samra, JA Wilson, ... BioRxiv, 2023.03. 16.532704, 2023 | 12 | 2023 |
| Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation B Kille, E Garrison, TJ Treangen, AM Phillippy Bioinformatics 39 (9), 2023 | 9 | 2023 |
| Catalytic Site Proximity Profiling for Functional Unification of Sequence-Diverse Radical S-Adenosylmethionine Enzymes TW Precord, S Ramesh, SR Dommaraju, LA Harris, BL Kille, DA Mitchell ACS bio & med Chem Au 3 (3), 240-251, 2023 | 8 | 2023 |
| Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets B Kille, Y Liu, N Sapoval, M Nute, L Rauchwerger, N Amato, TJ Treangen 2021 IEEE International Parallel and Distributed Processing Symposium …, 2021 | 6 | 2021 |
| An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates AM Mc Cartney, M Mahmoud, M Jochum, DP Agustinho, B Zorman, ... F1000Research 10, 2021 | 5 | 2021 |
| Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens MX Wang, EG Lou, N Sapoval, E Kim, P Kalvapalle, B Kille, RAL Elworth, ... Nature Communications 15 (1), 6306, 2024 | 2* | 2024 |
| Parsnp 2.0: scalable core-genome alignment for massive microbial datasets B Kille, MG Nute, V Huang, E Kim, AM Phillippy, TJ Treangen Bioinformatics 40 (5), btae311, 2024 | 2 | 2024 |
| Complete sequencing of ape genomes DA Yoo, A Rhie, P Hebbar, F Antonacci, GA Logsdon, SJ Solar, D Antipov, ... bioRxiv, 2024.07. 31.605654, 2024 | | 2024 |
| Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet N Sapoval, Y Liu, K Curry, B Kille, W Huang, N Kokroko, MG Nute, ... bioRxiv, 2024.06. 01.596961, 2024 | | 2024 |
