| Year |
Citation |
Score |
| 2014 |
Dolzhenko E, Smith AD. Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments. Bmc Bioinformatics. 15: 215. PMID 24962134 DOI: 10.1186/1471-2105-15-215 |
0.346 |
|
| 2013 |
Song Q, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. Plos One. 8: e81148. PMID 24324667 DOI: 10.1371/Journal.Pone.0081148 |
0.347 |
|
| 2013 |
Regulski M, Lu Z, Kendall J, Donoghue MT, Reinders J, Llaca V, Deschamps S, Smith A, Levy D, McCombie WR, Tingey S, Rafalski A, Hicks J, Ware D, Martienssen RA. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research. 23: 1651-62. PMID 23739895 DOI: 10.1101/Gr.153510.112 |
0.319 |
|
| 2012 |
Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD. Site identification in high-throughput RNA-protein interaction data. Bioinformatics (Oxford, England). 28: 3013-20. PMID 23024010 DOI: 10.1093/Bioinformatics/Bts569 |
0.31 |
|
| 2012 |
Araujo PR, Yoon K, Ko D, Smith AD, Qiao M, Suresh U, Burns SC, Penalva LO. Before It Gets Started: Regulating Translation at the 5' UTR. Comparative and Functional Genomics. 2012: 475731. PMID 22693426 DOI: 10.1155/2012/475731 |
0.328 |
|
| 2011 |
Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell. 146: 1029-41. PMID 21925323 DOI: 10.1016/J.Cell.2011.08.016 |
0.306 |
|
| 2011 |
Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Molecular Cell. 44: 17-28. PMID 21924933 DOI: 10.1016/J.Molcel.2011.08.026 |
0.354 |
|
| 2011 |
Song Q, Smith AD. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics (Oxford, England). 27: 870-1. PMID 21325299 DOI: 10.1093/Bioinformatics/Btr030 |
0.307 |
|
| 2010 |
Zhang MQ, Smith AD. Challenges in Understanding Genome-Wide DNA Methylation Journal of Computer Science and Technology. 25: 26-34. DOI: 10.1007/S11390-010-9302-8 |
0.414 |
|
| 2009 |
Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ. Updates to the RMAP short-read mapping software. Bioinformatics (Oxford, England). 25: 2841-2. PMID 19736251 DOI: 10.1093/Bioinformatics/Btp533 |
0.619 |
|
| 2009 |
Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research. 19: 1593-605. PMID 19581485 DOI: 10.1101/Gr.095190.109 |
0.651 |
|
| 2009 |
Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ. An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Research. 37: 4587-602. PMID 19491311 DOI: 10.1093/Nar/Gkp425 |
0.414 |
|
| 2009 |
Niida A, Smith AD, Imoto S, Aburatani H, Zhang MQ, Akiyama T. Gene set-based module discovery in the breast cancer transcriptome. Bmc Bioinformatics. 10: 71. PMID 19243633 DOI: 10.1186/1471-2105-10-71 |
0.463 |
|
| 2008 |
Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T. Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. Bmc Bioinformatics. 9: 404. PMID 18823535 DOI: 10.1186/1471-2105-9-404 |
0.366 |
|
| 2008 |
Smith AD, Xuan Z, Zhang MQ. Using quality scores and longer reads improves accuracy of Solexa read mapping. Bmc Bioinformatics. 9: 128. PMID 18307793 DOI: 10.1186/1471-2105-9-128 |
0.621 |
|
| 2008 |
Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Research. 18: 46-59. PMID 18042645 DOI: 10.1101/Gr.6654808 |
0.532 |
|
| 2007 |
Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 128: 1231-45. PMID 17382889 DOI: 10.1016/J.Cell.2006.12.048 |
0.525 |
|
| 2007 |
Schones DE, Smith AD, Zhang MQ. Statistical significance of cis-regulatory modules. Bmc Bioinformatics. 8: 19. PMID 17241466 DOI: 10.1186/1471-2105-8-19 |
0.662 |
|
| 2007 |
Smith AD, Sumazin P, Zhang MQ. Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology. 3: 73. PMID 17224917 DOI: 10.1038/Msb4100114 |
0.528 |
|
| 2006 |
Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS. Computational prediction of novel components of lung transcriptional networks. Bioinformatics (Oxford, England). 23: 21-9. PMID 17050569 DOI: 10.1093/Bioinformatics/Btl531 |
0.45 |
|
| 2006 |
Smith AD, Sumazin P, Xuan Z, Zhang MQ. DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proceedings of the National Academy of Sciences of the United States of America. 103: 6275-80. PMID 16606849 DOI: 10.1073/Pnas.0508169103 |
0.66 |
|
| 2005 |
Smith AD, Sumazin P, Das D, Zhang MQ. Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (Oxford, England). 21: i403-12. PMID 15961485 DOI: 10.1093/Bioinformatics/Bti1043 |
0.502 |
|
| 2005 |
Smith AD, Sumazin P, Zhang MQ. Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proceedings of the National Academy of Sciences of the United States of America. 102: 1560-5. PMID 15668401 DOI: 10.1073/Pnas.0406123102 |
0.502 |
|
| 2005 |
Sumazin P, Chen G, Hata N, Smith AD, Zhang T, Zhang MQ. DWE: discriminating word enumerator. Bioinformatics (Oxford, England). 21: 31-8. PMID 15333453 DOI: 10.1093/Bioinformatics/Bth471 |
0.49 |
|
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