Andrew D Smith
Andrew D Smith
Professor of Biological Sciences, University of Southern California
Verified email at - Homepage
Cited by
Cited by
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
TH Kim, ZK Abdullaev, AD Smith, KA Ching, DI Loukinov, RD Green, ...
Cell 128 (6), 1231-1245, 2007
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia
Y Benita, H Kikuchi, AD Smith, MQ Zhang, DC Chung, RJ Xavier
Nucleic acids research 37 (14), 4587-4602, 2009
Using quality scores and longer reads improves accuracy of Solexa read mapping
AD Smith, Z Xuan, MQ Zhang
BMC bioinformatics 9 (1), 1-8, 2008
Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
A Molaro, E Hodges, F Fang, Q Song, WR McCombie, GJ Hannon, ...
Cell 146 (6), 1029-1041, 2011
A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis
E Wagenblast, M Soto, S Gutiérrez-Angel, CA Hartl, AL Gable, AR Maceli, ...
Nature 520 (7547), 358-362, 2015
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment
E Hodges, A Molaro, CO Dos Santos, P Thekkat, Q Song, PJ Uren, J Park, ...
Molecular cell 44 (1), 17-28, 2011
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
E Hodges, AD Smith, J Kendall, Z Xuan, K Ravi, M Rooks, MQ Zhang, ...
Genome research 19 (9), 1593-1605, 2009
A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics
Q Song, B Decato, EE Hong, M Zhou, F Fang, J Qu, T Garvin, M Kessler, ...
PloS one 8 (12), e81148, 2013
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
M Regulski, Z Lu, J Kendall, MTA Donoghue, J Reinders, V Llaca, ...
Genome research 23 (10), 1651-1662, 2013
Site identification in high-throughput RNA–protein interaction data
PJ Uren, E Bahrami-Samani, SC Burns, M Qiao, FV Karginov, E Hodges, ...
Bioinformatics 28 (23), 3013-3020, 2012
Before it gets started: regulating translation at the 5′ UTR
PR Araujo, K Yoon, D Ko, AD Smith, M Qiao, U Suresh, SC Burns, ...
Comparative and functional genomics 2012, 2012
Predicting the molecular complexity of sequencing libraries
T Daley, AD Smith
Nature methods 10 (4), 325-327, 2013
Updates to the RMAP short-read mapping software
AD Smith, WY Chung, E Hodges, J Kendall, G Hannon, J Hicks, Z Xuan, ...
Bioinformatics 25 (21), 2841-2842, 2009
Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases
FV Karginov, S Cheloufi, MMW Chong, A Stark, AD Smith, GJ Hannon
Molecular cell 38 (6), 781-788, 2010
Identifying tissue-selective transcription factor binding sites in vertebrate promoters
AD Smith, P Sumazin, MQ Zhang
Proceedings of the National Academy of Sciences 102 (5), 1560-1565, 2005
Identifying dispersed epigenomic domains from ChIP-Seq data
Q Song, AD Smith
Bioinformatics 27 (6), 870-871, 2011
A transition probability model for amino acid substitutions from blocks
S Veerassamy, A Smith, ERM Tillier
Journal of Computational Biology 10 (6), 997-1010, 2003
Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments
E Dolzhenko, AD Smith
BMC bioinformatics 15 (1), 1-8, 2014
Aberrant sperm DNA methylation predicts male fertility status and embryo quality
KI Aston, PJ Uren, TG Jenkins, A Horsager, BR Cairns, AD Smith, ...
Fertility and sterility 104 (6), 1388-1397. e5, 2015
Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA
EE Hong, CY Okitsu, AD Smith, CL Hsieh
Molecular and cellular biology 33 (14), 2683-2690, 2013
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