| Comprehensive multi-omics analysis reveals mitochondrial stress as a central biological hub for spaceflight impact WA da Silveira, H Fazelinia, SB Rosenthal, EC Laiakis, MS Kim, ... Cell 183 (5), 1185-1201. e20, 2020 | 284 | 2020 |
| 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 | 260 | 2022 |
| Advances in computational methods for phylogenetic networks in the presence of hybridization RAL Elworth, HA Ogilvie, J Zhu, L Nakhleh Bioinformatics and phylogenetics: seminal contributions of Bernard Moret …, 2019 | 101 | 2019 |
| SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission N Sapoval, M Mahmoud, MD Jochum, Y Liu, RAL Elworth, Q Wang, ... Genome research 31 (4), 635-644, 2021 | 55* | 2021 |
| The essential role of hypermutation in rapid adaptation to antibiotic stress HH Mehta, AG Prater, K Beabout, RAL Elworth, M Karavis, HS Gibbons, ... Antimicrobial agents and chemotherapy 63 (7), 10.1128/aac. 00744-19, 2019 | 54 | 2019 |
| To petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics RAL Elworth, Q Wang, PK Kota, CJ Barberan, B Coleman, A Balaji, ... Nucleic acids research 48 (10), 5217-5234, 2020 | 41 | 2020 |
| 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 | 34 | 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 | 30* | 2021 |
| Pathogenic Nocardia cyriacigeorgica and Nocardia nova evolve to resist trimethoprim-sulfamethoxazole by both expected and unexpected pathways H Mehta, J Weng, A Prater, RAL Elworth, X Han, Y Shamoo Antimicrobial agents and chemotherapy 62 (7), 10.1128/aac. 00364-18, 2018 | 29 | 2018 |
| 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), 1167, 2021 | 20 | 2021 |
| DGEN: A Test Statistic for Detection of General Introgression Scenarios RAL Elworth, C Allen, T Benedict, P Dulworth, L Nakhleh 18th International Workshop on Algorithms in Bioinformatics (WABI 2018) 113 …, 2018 | 17 | 2018 |
| De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee Y Liu, RAL Elworth, MD Jochum, KM Aagaard, TJ Treangen Nature Communications 13 (1), 6799, 2022 | 16 | 2022 |
| One-pass diversified sampling with application to terabyte-scale genomic sequence streams B Coleman, B Geordie, L Chou, RAL Elworth, T Treangen, A Shrivastava International Conference on Machine Learning, 4202-4218, 2022 | 14 | 2022 |
| Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides RAL Elworth, C Diaz, J Yang, P de Figueiredo, K Ternus, T Treangen PLoS Pathogens 16 (8), e1008649, 2020 | 14 | 2020 |
| SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest D Albin, D Nasko, RAL Elworth, J Lu, A Balaji, C Diaz, N Shah, J Selengut, ... 2019 IEEE international conference on bioinformatics and biomedicine (BIBM …, 2019 | 11 | 2019 |
| KOMB: K-core based de novo characterization of copy number variation in microbiomes A Balaji, N Sapoval, C Seto, RAL Elworth, Y Fu, MG Nute, T Savidge, ... Computational and Structural Biotechnology Journal 20, 3208-3222, 2022 | 10 | 2022 |
| Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance C McCall, RA Leo Elworth, KM Wylie, TN Wylie, K Dyson, R Doughty, ... ACS ES&T Water 3 (9), 2955-2965, 2023 | 8 | 2023 |
| Faster pan-genome construction for efficient differentiation of naturally occurring and engineered plasmids with plaster Q Wang, RA Elworth, TR Liu, TJ Treangen 19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 2019 | 7 | 2019 |
| ALPHA: A toolkit for automated local phylogenomic analyses RAL Elworth, C Allen, T Benedict, P Dulworth, L Nakhleh Bioinformatics 34 (16), 2848-2850, 2018 | 7 | 2018 |
| Diversified RACE sampling on data streams applied to metagenomic sequence analysis B Coleman, B Geordie, L Chou, RAL Elworth, TJ Treangen, A Shrivastava bioRxiv, 852889, 2019 | 4 | 2019 |