| Year |
Citation |
Score |
| 2013 |
Aow JS, Xue X, Run JQ, Lim GF, Goh WS, Clarke ND. Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal. Nucleic Acids Research. 41: 4877-87. PMID 23558744 DOI: 10.1093/Nar/Gkt210 |
0.396 |
|
| 2012 |
Orlov Y, Xu H, Afonnikov D, Lim B, Heng JC, Yuan P, Chen M, Yan J, Clarke N, Orlova N, Huss M, Gunbin K, Podkolodnyy N, Ng HH. Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell. Journal of Integrative Bioinformatics. 9: 211. PMID 22987856 DOI: 10.2390/Biecoll-Jib-2012-211 |
0.387 |
|
| 2011 |
Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, ... ... Clarke ND, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research. 21: 1757-67. PMID 21750106 DOI: 10.1101/Gr.121541.111 |
0.416 |
|
| 2010 |
Joseph R, Orlov YL, Huss M, Sun W, Kong SL, Ukil L, Pan YF, Li G, Lim M, Thomsen JS, Ruan Y, Clarke ND, Prabhakar S, Cheung E, Liu ET. Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Molecular Systems Biology. 6: 456. PMID 21179027 DOI: 10.1038/Msb.2010.109 |
0.417 |
|
| 2010 |
Chia NY, Chan YS, Feng B, Lu X, Orlov YL, Moreau D, Kumar P, Yang L, Jiang J, Lau MS, Huss M, Soh BS, Kraus P, Li P, Lufkin T, ... ... Clarke ND, et al. A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature. 468: 316-20. PMID 20953172 DOI: 10.1038/Nature09531 |
0.316 |
|
| 2010 |
Goh WS, Orlov Y, Li J, Clarke ND. Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. Plos Computational Biology. 6: e1000649. PMID 20098497 DOI: 10.1371/Journal.Pcbi.1000649 |
0.465 |
|
| 2009 |
Vega VB, Woo XY, Hamidi H, Yeo HC, Yeo ZX, Bourque G, Clarke ND. Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge. Annals of the New York Academy of Sciences. 1158: 215-23. PMID 19348643 DOI: 10.1111/J.1749-6632.2008.03759.X |
0.332 |
|
| 2009 |
Yeo ZX, Yeo HC, Yeo JK, Yeo AL, Li Y, Clarke ND. Inferring transcription factor targets from gene expression changes and predicted promoter occupancy. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 357-68. PMID 19193152 DOI: 10.1089/Cmb.2008.19Tt |
0.346 |
|
| 2009 |
Liu X, Clarke ND. Transcription factor binding probabilities in orthologous promoters: An alignment-free approach to the inference of functional regulatory targets Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5817: 229-240. DOI: 10.1007/978-3-642-04744-2_19 |
0.322 |
|
| 2008 |
Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, ... ... Clarke ND, et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Molecular Cell. 32: 878-87. PMID 19111667 DOI: 10.1016/J.Molcel.2008.11.020 |
0.519 |
|
| 2008 |
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, ... ... Clarke ND, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 133: 1106-17. PMID 18555785 DOI: 10.1016/J.Cell.2008.04.043 |
0.382 |
|
| 2007 |
Clarke ND, Ezkurdia I, Kopp J, Read RJ, Schwede T, Tress M. Domain definition and target classification for CASP7. Proteins. 69: 10-8. PMID 17654725 DOI: 10.1002/Prot.21686 |
0.3 |
|
| 2006 |
Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Research. 16: 1517-28. PMID 17053089 DOI: 10.1101/Gr.5655606 |
0.744 |
|
| 2005 |
Lieb JD, Clarke ND. Control of transcription through intragenic patterns of nucleosome composition. Cell. 123: 1187-90. PMID 16377560 DOI: 10.1016/J.Cell.2005.12.010 |
0.366 |
|
| 2005 |
Granek JA, Clarke ND. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biology. 6: R87. PMID 16207358 DOI: 10.1186/Gb-2005-6-10-R87 |
0.709 |
|
| 2005 |
Liu X, Noll DM, Lieb JD, Clarke ND. DIP-chip: rapid and accurate determination of DNA-binding specificity. Genome Research. 15: 421-7. PMID 15710749 DOI: 10.1101/Gr.3256505 |
0.518 |
|
| 2004 |
Carroll KL, Pradhan DA, Granek JA, Clarke ND, Corden JL. Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Molecular and Cellular Biology. 24: 6241-52. PMID 15226427 DOI: 10.1128/Mcb.24.14.6241-6252.2004 |
0.71 |
|
| 2004 |
Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA. DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nature Structural & Molecular Biology. 11: 714-20. PMID 15221026 DOI: 10.1038/Nsmb791 |
0.467 |
|
| 2003 |
Clarke ND, Granek JA. Rank order metrics for quantifying the association of sequence features with gene regulation. Bioinformatics (Oxford, England). 19: 212-8. PMID 12538241 DOI: 10.1093/Bioinformatics/19.2.212 |
0.693 |
|
| 2002 |
Liu X, Clarke ND. Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. Journal of Molecular Biology. 323: 1-8. PMID 12368093 DOI: 10.1016/S0022-2836(02)00894-X |
0.439 |
|
| 2001 |
Noll DM, Clarke ND. Covalent capture of a human O6-alkylguanine alkyltransferase-DNA complex using N1,O6-ethanoxanthosine, a mechanism-based crosslinker Nucleic Acids Research. 29: 4025-4034. PMID 11574685 DOI: 10.1093/Nar/29.19.4025 |
0.344 |
|
| 2000 |
Gogos A, Jantz D, Sentürker S, Richardson D, Dizdaroglu M, Clarke ND. Assignment of enzyme substrate specificity by principal component analysis of aligned protein sequences: an experimental test using DNA glycosylase homologs. Proteins. 40: 98-105. PMID 10813834 DOI: 10.1002/(Sici)1097-0134(20000701)40:1<98::Aid-Prot110>3.0.Co;2-S |
0.667 |
|
| 2000 |
Brown LR, Deng J, Clarke ND. Dominant sensitization variants of human O(6)-methylguanine-DNA-methyltransferase obtained by a mutational screen of surface residues. Mutation Research. 459: 81-7. PMID 10677686 DOI: 10.1016/S0921-8777(99)00062-2 |
0.425 |
|
| 1999 |
Gogos A, Clarke ND. Characterization of an 8-oxoguanine DNA glycosylase from Methanococcus jannaschii. The Journal of Biological Chemistry. 274: 30447-50. PMID 10521423 DOI: 10.1074/Jbc.274.43.30447 |
0.675 |
|
| 1999 |
Noll DM, Gogos A, Granek JA, Clarke ND. The C-terminal domain of the adenine-DNA glycosylase MutY confers specificity for 8-oxoguanine.adenine mispairs and may have evolved from MutT, an 8-oxo-dGTPase. Biochemistry. 38: 6374-9. PMID 10350454 DOI: 10.1021/Bi990335X |
0.717 |
|
| 1998 |
Clarke ND, Berg JM. Zinc fingers in Caenorhabditis elegans: Finding families and probing pathways Science. 282: 2018-2022. PMID 9851917 DOI: 10.1126/Science.282.5396.2018 |
0.507 |
|
| 1998 |
Yuan SM, Clarke ND. A hybrid sequence approach to the paracelsus challenge Proteins: Structure, Function and Genetics. 30: 136-143. PMID 9489921 DOI: 10.1002/(Sici)1097-0134(19980201)30:2<136::Aid-Prot3>3.0.Co;2-L |
0.364 |
|
| 1997 |
Paalman SR, Sung C, Clarke ND. Specificity of DNA repair methyltransferases determined by competitive inactivation with oligonucleotide substrates: Evidence that Escherichia coli ada repairs O6-methylguanine and O4-methylthymine with similar efficiency Biochemistry. 36: 11118-11124. PMID 9287154 DOI: 10.1021/Bi970740T |
0.347 |
|
| 1997 |
Brown LR, Deng J, Noll DM, Mori N, Clarke ND. Construction and overexpression of a synthetic gene for human DNA methylguanine methyltransferase: renaturation and rapid purification of the protein. Protein Expression and Purification. 9: 337-45. PMID 9126605 DOI: 10.1006/Prep.1996.0719 |
0.413 |
|
| 1997 |
Paalman SR, Noll DM, Clarke ND. Formation of a covalent complex between methylguanine methyltransferase and DNA via disulfide bond formation between the active site cysteine and a thiol-containing analog of guanine Nucleic Acids Research. 25: 1795-1801. PMID 9108163 DOI: 10.1093/Nar/25.9.1795 |
0.391 |
|
| 1996 |
Gogos A, Cillo J, Clarke ND, Lu AL. Specific recognition of A/G and A/7,8-dihydro-8-oxoguanine (8-oxoG) mismatches by Escherichia coli MutY: removal of the C-terminal domain preferentially affects A/8-oxoG recognition. Biochemistry. 35: 16665-71. PMID 8988002 DOI: 10.1021/Bi960843W |
0.682 |
|
| 1995 |
Clarke ND. Covariation of residues in the homeodomain sequence family Protein Science. 4: 2269-2278. PMID 8563623 DOI: 10.1002/Pro.5560041104 |
0.461 |
|
| 1995 |
Klemba M, Gardner KH, Marino S, Clarke ND, Regan L. Novel metal-binding proteins by design. Nature Structural Biology. 2: 368-73. PMID 7664093 DOI: 10.1038/Nsb0595-368 |
0.364 |
|
| 1995 |
Clarke ND. Sequence 'minimization': exploring the sequence landscape with simplified sequences Current Opinion in Biotechnology. 6: 467-472. PMID 7579658 DOI: 10.1016/0958-1669(95)80077-8 |
0.376 |
|
| 1994 |
Clarke ND, Kissinger CR, Desjarlais J, Gilliland GL, Pabo CO. Structural studies of the engrailed homeodomain. Protein Science : a Publication of the Protein Society. 3: 1779-87. PMID 7849596 DOI: 10.1002/Pro.5560031018 |
0.402 |
|
| 1991 |
Clarke ND, Beamer LJ, Goldberg HR, Berkower C, Pabo CO. The DNA binding arm of lambda repressor: critical contacts from a flexible region. Science (New York, N.Y.). 254: 267-70. PMID 1833818 DOI: 10.1126/Science.1833818 |
0.418 |
|
| 1990 |
Regan L, Clarke ND. A tetrahedral Zinc(II)-binding site introduced into a designed protein Biochemistry. 29: 10878-10883. PMID 2271687 DOI: 10.1021/Bi00501A003 |
0.357 |
|
| 1990 |
Bowie JU, Clarke ND, Pabo CO, Sauer RT. Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins. 7: 257-64. PMID 2163535 DOI: 10.1002/Prot.340070307 |
0.35 |
|
| 1984 |
Clarke ND, Kvaal M, Seeberg E. Cloning of Escherichia coli genes encoding 3-methyladenine DNA glycosylases I and II Mgg Molecular &Amp; General Genetics. 197: 368-372. PMID 6098799 DOI: 10.1007/BF00329931 |
0.303 |
|
| 1981 |
Sancar A, Clarke ND, Griswold J, Kennedy WJ, Rupp WD. Identification of the uvrB gene product. Journal of Molecular Biology. 148: 63-76. PMID 6273578 DOI: 10.1016/0022-2836(81)90235-7 |
0.33 |
|
| 1981 |
Sancar A, Wharton RP, Seltzer S, Kacinski BM, Clarke ND, Rupp WD. Identification of the uvrA gene product. Journal of Molecular Biology. 148: 45-62. PMID 6273577 DOI: 10.1016/0022-2836(81)90234-5 |
0.41 |
|
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