John St. John
John St. John
Computational Biologist - Modeling, Freenome
Verified email at freenome.com - Homepage
TitleCited byYear
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
4872011
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
2432013
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
1832014
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
1272013
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
1262012
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, 2017
1102017
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
752011
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
392009
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, 2016
272016
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
192017
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
132014
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
92010
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
52019
INTEGRATED GENOMIC ANALYSIS BY WHOLE EXOME AND TRANSCRIPTOME SEQUENCING OF TUMOR SAMPLES FROM EGFR-MUTANT NON-SMALL-CELL LUNG CANCER (NSCLC) PATIENTS WITH ACQUIRED RESISTANCE …
T Bivona, P Gianikopoulos, C Costa, N Karachaliou, J St John, ...
JOURNAL OF THORACIC ONCOLOGY 8, S386-S386, 2013
22013
Inference of tumor cell-specific transcription factor binding from cell-free DNA
P Ulz, S Perakis, Q Zhou, T Moser, J Belic, A Wölfler, A Zebisch, A Gerger, ...
BioRxiv, 456681, 2018
12018
Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers
CM Blakely, TBK Watkins, W Wu, B Gini, JJ Chabon, CE McCoach, ...
bioRxiv, 117291, 2017
12017
Integrated genomic analysis of EGFR-mutant non-small cell lung cancer immediately following erlotinib initiation in patients.
TG Bivona, P Giannikopoulos, C Costa, N Karachaliou, S Viteri, ...
Journal of Clinical Oncology 31 (15_suppl), 11067-11067, 2013
12013
Integrated genomic analysis by whole exome and transcriptome sequencing of tumor samples from EGFR-mutant non-small-cell lung cancer (NSCLC) patients (p) with acquired …
JS Weissman, P Giannikopoulos, J St. John, AV Uzilov, C Costa, ...
Journal of Clinical Oncology 31 (15_suppl), 11010-11010, 2013
12013
Predicting gene expression from plasma cell-free DNA using both the fragment length and fragment position
JA St John, E Gafni, B White, A Kannan, L Hansen, A Jaroszewicz, ...
Cancer Research 79 (13 Supplement), 4349-4349, 2019
2019
Su1658–Machine Learning Enables Detection of Early-Stage Colorectal Cancer by Whole-Genome Sequencing of Plasma Cell-Free Dna
N Wan, D Weinberg, T Liu, K Niehaus, D Delubac, A Kannan, B White, ...
Gastroenterology 156 (6), S-600-S-601, 2019
2019
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