| Assemblathon 1: a competitive assessment of de novo short read assembly methods D Earl, K Bradnam, JS John, A Darling, D Lin, J Fass, HOK Yu, V Buffalo, ... Genome research 21 (12), 2224-2241, 2011 | 654 | 2011 |
| Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers CM Blakely, TBK Watkins, W Wu, B Gini, JJ Chabon, CE McCoach, ... Nature genetics 49 (12), 1693-1704, 2017 | 580 | 2017 |
| Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, ... Science 346 (6215), 1254449, 2014 | 411 | 2014 |
| The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage J Abramyan, D Badenhorst, KK Biggar, GM Borchert, CW Botka, ... Genome Biology 14 (3), R28, 2013 | 396 | 2013 |
| Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection P Ulz, S Perakis, Q Zhou, T Moser, J Belic, I Lazzeri, A Wölfler, A Zebisch, ... Nature communications 10 (1), 4666, 2019 | 270 | 2019 |
| Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution JA Cahill, RE Green, TL Fulton, M Stiller, F Jay, N Ovsyanikov, ... PLoS genetics 9 (3), e1003345, 2013 | 218 | 2013 |
| Genome modeling and design across all domains of life with Evo 2 G Brixi, MG Durrant, J Ku, M Poli, G Brockman, D Chang, GA Gonzalez, ... BioRxiv, 2025.02. 18.638918, 2025 | 214 | 2025 |
| Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA N Wan, D Weinberg, TY Liu, K Niehaus, EA Ariazi, D Delubac, A Kannan, ... BMC cancer 19 (1), 832, 2019 | 211 | 2019 |
| Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes JA St John, EL Braun, SR Isberg, LG Miles, AY Chong, J Gongora, ... Genome Biology 13 (1), 415, 2012 | 166 | 2012 |
| Cactus graphs for genome comparisons B Paten, M Diekhans, D Earl, JS John, J Ma, B Suh, D Haussler Journal of Computational Biology 18 (3), 469-481, 2011 | 151 | 2011 |
| Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family W Gillis, J St John, B Bowerman, S Schneider BMC evolutionary biology 9 (1), 207, 2009 | 68 | 2009 |
| Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling ES Rice, S Kohno, JS John, S Pham, J Howard, LF Lareau, BL O'Connell, ... Genome research 27 (5), 686-696, 2017 | 51 | 2017 |
| Integrated systems and methods for automated processing and analysis of biological samples, clinical information processing and clinical trial matching T Matsuguchi, AF Caulin, JAS John, S Soi, EC AHMED, E Pazarentzos, ... US Patent App. 15/727,491, 2018 | 50 | 2018 |
| Oncogenic activation of the PI3-kinase p110β isoform via the tumor-derived PIK3CβD1067V kinase domain mutation E Pazarentzos, P Giannikopoulos, G Hrustanovic, J St John, VR Olivas, ... Oncogene 35 (9), 1198-1205, 2016 | 50 | 2016 |
| Integrated systems and methods for automated processing and analysis of biological samples, clinical information processing and clinical trial matching T Matsuguchi, JAS John, E Pazarentzos, W Polkinghorn, ... US Patent App. 15/727,501, 2018 | 41 | 2018 |
| Blood-based detection of early-stage colorectal cancer using multiomics and machine learning G Putcha, TY Liu, E Ariazi, M Bertin, A Drake, M Dzamba, G Hogan, ... Abstract presented at: the American Society of Clinical Oncology (ASCO) GI …, 2020 | 29 | 2020 |
| Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC W Jaratlerdsiri, J Deakin, RM Godinez, X Shan, DG Peterson, S Marthey, ... PloS one 9 (12), e114631, 2014 | 27 | 2014 |
| Cactus Graphs for Genome Comparisons B Paten, M Diekhans, D Earl, J St. John, J Ma, B Suh, D Haussler Research in Computational Molecular Biology, 410-425, 2010 | 17 | 2010 |
| BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery PS John, D Lin, P Binder, M Greaves, V Shah, JS John, A Lange, P Hsu, ... arXiv preprint arXiv:2411.10548, 2024 | 16 | 2024 |
| Evaluation of a sensitive blood test for the detection of colorectal advanced adenomas in a prospective cohort using a multiomics approach J Lin, E Ariazi, M Dzamba, TK Hsu, S Kothen-Hill, K Li, TY Liu, S Mahajan, ... J Clin Oncol 39 (3), 43, 2021 | 14 | 2021 |
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