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John St. John
John St. John
Machine Learning Scientist @ Ravel
Dirección de correo verificada de ravel.bio - Página principal
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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
6302011
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
4822017
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
3672013
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
3652014
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
1832013
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
1732019
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
1612012
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, 1-10, 2019
1362019
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
1332011
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
612009
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
452017
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
442016
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
372018
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
272018
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
262014
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
182020
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
162010
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, 43, 2021
62021
Inference of tumor cell-specific transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection of cancer
P Ulz, S Perakis, Q Zhou, T Moser, J Belic, I Lazzeri, A Wlfler, A Zebisch, ...
bioRxiv, 2019
62019
Methods for Predicting EGFR Tyrosine Kinase Inhibitor Efficacy
P Giannikopoulos, JS John, J Parker, T Bivona
US Patent App. 14/671,213, 2016
52016
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Artículos 1–20