Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA MC Liu, GR Oxnard, EA Klein, C Swanton, MV Seiden, MC Liu, ... Annals of Oncology 31 (6), 745-759, 2020 | 966 | 2020 |
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage NH Putnam, BL O'Connell, JC Stites, BJ Rice, M Blanchette, R Calef, ... Genome research 26 (3), 342-350, 2016 | 717 | 2016 |
Deeply conserved synteny resolves early events in vertebrate evolution O Simakov, F Marlétaz, JX Yue, B O’Connell, J Jenkins, A Brandt, R Calef, ... Nature Ecology & Evolution 4 (6), 820-830, 2020 | 249 | 2020 |
Evaluation of cell-free DNA approaches for multi-cancer early detection A Jamshidi, MC Liu, EA Klein, O Venn, E Hubbell, JF Beausang, S Gross, ... Cancer Cell 40 (12), 1537-1549. e12, 2022 | 90 | 2022 |
Convolutional neural network systems and methods for data classification V Nicula, A Valouev, D Filippova, MH Larson, MC MAHER, ... US Patent 11,482,303, 2022 | 7 | 2022 |
Method and system for selecting, managing, and analyzing data of high dimensionality D Filippova, A Valouev, V Nicula, K Jagadeesh, MC MAHER, MH Larson, ... US Patent App. 16/352,739, 2019 | 5 | 2019 |
Model-based featurization and classification AP Fields, JF Beausang, OC Venn, A Jamshidi, MC MAHER, Q Liu, ... US Patent App. 15/931,022, 2020 | 4 | 2020 |
Systems and methods for enriching for cancer-derived fragments using fragment size D Filippova, MH Larson, MC MAHER, MP dos Santos Pimentel, ... US Patent 11,929,148, 2024 | 3 | 2024 |
The Circulating Cell-free Genome Atlas (CCGA) study: size selection of cell-free DNA (cfDNA) fragments D Filippova, MH Larson, MC Maher, R Calef, M Pimentel, Y Zhou, ... J Clin Oncol 37, 2019 | 3 | 2019 |
HPV-driven cancers show distinct methylation signatures in cell-free DNA (cfDNA) R Calef, O Venn, MC Maher, JF Beausang, E Hubbell, A Patel, AP Fields, ... Cancer Research 80 (16), 2020 | 1 | 2020 |
Identification of cancer subtypes with a ctDNA-based targeted methylation assay T Nance, T Shaver, Y Zhou, M Antonio, Y Gao, J Heiss, R Calef, J Hiatt, ... Breast 58, 21, 2024 | | 2024 |
Convolutional neural network systems and methods for data classification V Nicula, A VALOUEV, D Filippova, MH Larson, MC MAHER, ... US Patent App. 18/240,489, 2024 | | 2024 |
Systems and methods for detecting disease subtypes T Nance, J Bredno, OC Venn, RAP Calef, J Tom US Patent App. 18/362,342, 2024 | | 2024 |
Systems and methods for performing additive smoothing on low-coverage sequencing data from a nucleic acid sample RAP Calef, EM Scott, K Samuel-gama US Patent App. 18/194,250, 2023 | | 2023 |
Convolutional neural network systems and methods for data classification V Nicula, A Valouev, D Filippova, MH Larson, MC MAHER, ... US Patent 11,783,915, 2023 | | 2023 |
Systems and methods for classifying patients with respect to multiple cancer classes MC MAHER, A Valouev, D Filippova, V Nicula, K Jagadeesh, OC Venn, ... US Patent App. 18/151,197, 2023 | | 2023 |
Systems and methods for classifying patients with respect to multiple cancer classes MC MAHER, A Valouev, D Filippova, V Nicula, K Jagadeesh, OC Venn, ... US Patent 11,581,062, 2023 | | 2023 |
Systems and methods for estimating cell source fractions using methylation information J Xiang, RAP CALEF | | 2022 |
Conditional tissue of origin return for localization accuracy OC Venn, PD Freese, SS Gross, RAP Calef, A Jamshidi US Patent App. 17/714,062, 2022 | | 2022 |
Detecting cross-contamination in sequencing data O Sakarya, CJAV Yakym, PP Singh, RAP Calef, R Huang US Patent App. 17/478,856, 2022 | | 2022 |