Bryce Kille
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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
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
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
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
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
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
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
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
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
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
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
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
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
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
B Kille, E Garrison, TJ Treangen, AM Phillippy
Bioinformatics 39 (9), 2023
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
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
Olivar: 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, ...
bioRxiv, 2023
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
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