|Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer|
JS Duncan, MC Whittle, K Nakamura, AN Abell, AA Midland, ...
Cell 149 (2), 307-321, 2012
|Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas|
P Wang, Q Dong, C Zhang, PF Kuan, Y Liu, WR Jeck, JB Andersen, ...
Oncogene 32 (25), 3091-3100, 2013
|Inhibition of lapatinib-induced kinome reprogramming in ERBB2-positive breast cancer by targeting BET family bromodomains|
TJ Stuhlmiller, SM Miller, JS Zawistowski, K Nakamura, AS Beltran, ...
Cell reports 11 (3), 390-404, 2015
|Rho directs widespread termination of intragenic and stable RNA transcription|
JM Peters, RA Mooney, PF Kuan, JL Rowland, S Keleş, R Landick
Proceedings of the National Academy of Sciences 106 (36), 15406-15411, 2009
|Median absolute deviation to improve hit selection for genome-scale RNAi screens|
N Chung, XD Zhang, A Kreamer, L Locco, PF Kuan, S Bartz, PS Linsley, ...
Journal of biomolecular screening 13 (2), 149-158, 2008
|DiffSplice: the genome-wide detection of differential splicing events with RNA-seq|
Y Hu, Y Huang, Y Du, CF Orellana, D Singh, AR Johnson, A Monroy, ...
Nucleic acids research 41 (2), e39-e39, 2013
|Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects|
JM Simon, KE Hacker, D Singh, AR Brannon, JS Parker, M Weiser, TH Ho, ...
Genome research 24 (2), 241-250, 2014
|HIF1α and HIF2α independently activate SRC to promote melanoma metastases|
SC Hanna, B Krishnan, ST Bailey, SJ Moschos, PF Kuan, T Shimamura, ...
The Journal of clinical investigation 123 (5), 2078-2093, 2013
|A statistical framework for the analysis of ChIP-Seq data|
PF Kuan, D Chung, G Pan, JA Thomson, R Stewart, S Keleş
Journal of the American Statistical Association 106 (495), 891-903, 2011
|MERTK receptor tyrosine kinase is a therapeutic target in melanoma|
J Schlegel, MJ Sambade, S Sather, SJ Moschos, AC Tan, A Winges, ...
The Journal of clinical investigation 123 (5), 2257-2267, 2013
|Metabolomic profiling reveals mitochondrial-derived lipid biomarkers that drive obesity-associated inflammation|
BP Sampey, AJ Freemerman, J Zhang, PF Kuan, JA Galanko, ...
PloS one 7 (6), e38812, 2012
|A statistical framework for Illumina DNA methylation arrays|
PF Kuan, S Wang, X Zhou, H Chu
Bioinformatics 26 (22), 2849-2855, 2010
|Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data|
D Chung, PF Kuan, B Li, R Sanalkumar, K Liang, EH Bresnick, C Dewey, ...
PLoS Comput Biol 7 (7), e1002111, 2011
|DNA methylation profiling in the Carolina Breast Cancer Study defines cancer subclasses differing in clinicopathologic characteristics and survival|
K Conway, SN Edmiston, R May, PF Kuan, H Chu, C Bryant, CK Tse, ...
Breast cancer research 16 (5), 1-18, 2014
|DNA‐methylation profiling distinguishes malignant melanomas from benign nevi|
K Conway, SN Edmiston, ZS Khondker, PA Groben, X Zhou, H Chu, ...
Pigment cell & melanoma research 24 (2), 352-360, 2011
|The role of Ect2 nuclear RhoGEF activity in ovarian cancer cell transformation|
LP Huff, MJ DeCristo, D Trembath, PF Kuan, M Yim, J Liu, DR Cook, ...
Genes & cancer 4 (11-12), 460-475, 2013
|Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators|
DJ Huebert, PF Kuan, S Keleş, AP Gasch
Molecular and cellular biology 32 (9), 1645-1653, 2012
|A systematic assessment of normalization approaches for the Infinium 450K methylation platform|
MC Wu, BR Joubert, P Kuan, SE Håberg, W Nystad, SD Peddada, ...
Epigenetics 9 (2), 318-329, 2014
|Application of multiplexed kinase inhibitor beads to study kinome adaptations in drug-resistant leukemia|
MJ Cooper, NJ Cox, EI Zimmerman, BJ Dewar, JS Duncan, MC Whittle, ...
PloS one 8 (6), e66755, 2013
|Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile|
W Tang, DR Morgan, MO Meyers, RL Dominguez, E Martinez, K Kakudo, ...
Infectious agents and cancer 7 (1), 1-15, 2012