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*  Systematic Identification, Evolution and Expression Analysis of the Zea mays PHT1 Gene Family Reveals Several New Members...
RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res. 2015;43:W50-W56. doi: 10.1093/nar/gkv362. [PMC free article] ... Nucleic Acids Res. 2012;40:D1178-D1186. doi: 10.1093/nar/gkr944. [PMC free article] [PubMed] [Cross Ref] ... Nucleic Acids Res. 2015;43:D662-D669. doi: 10.1093/nar/gku1010. [PMC free article] [PubMed] [Cross Ref] ... Nucleic Acids Res. 2009;37:W202-W208. doi: 10.1093/nar/gkp335. [PMC free article] [PubMed] [Cross Ref] ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC4926463/
*  Cyclin-dependent kinase directly regulates initiation of meiotic recombination
Nucleic Acids Res. 2003;31:4085-4090. [PMC free article] [PubMed]. *Nandabalan K, Roeder GS. Binding of a cell-type-specific ... RNA splicing factor to its target regulatory sequence. Mol Cell Biol. 1995;15:1953-1960. [PMC free article] [PubMed] ... The consensus CDK target is the sequence T/S-P-x-K/R where x is any amino acid, although CDK targets can also be phosphorylated ... amino acid sequence identity (Supplemental Figure 1A and 1B).. An intriguing feature of MER2 is its meiosis-specific regulation ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC1950680/?lang=en-ca
*  Destabilization of tRNA3Lys from the primer-binding site of HIV-1 genome by anti-A loop polyamide nucleotide analog
We observed that polyamide nucleic acid targeted to the A-loop sequence (PNAal) exhibits high binding specificity for its ... These regulatory sequences in the 5′ non-translated region are averse to mutational changes and, therefore, can be potential ... Bastide L., Boehmer,P.E., Villani,G. and Lebleu,B. (1999) Inhibition of a DNA-helicase by peptide nucleic acids. Nucleic Acids ... Nucleic Acids Res., 26, 1198-1204. [PMC free article] [PubMed]. 38. Zhang Z., Kang,S.M., Li,Y. and Morrow,C.D. (1998) Genetic ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC97570/
*  A FOXO3/IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses
Nucleic Acids Res. 2011;39:D561-D568. [PMC free article] [PubMed]. 10. Khan N, et al. Determination of the class and isoform ... For ChIP-Seq, immunoprecipitated DNA samples were sequenced on a Illumina HiSeq 2000 sequencing system and aligned using the ... Nucleic Acids Res. 2007;35:D747-D750. [PubMed]. 28. Chiang DY, Brown PO, Eisen MB. Visualizing associations between genome ... Nucleic Acid Recognition by the Innate Immune System. Annu Rev Immunol. 2011;29:185-214. [PubMed] ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3556990/?lang=en-ca
*  Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic acids research. ... GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010;28:495-501. [PMC free article] [PubMed ... Nucleic Acids Res. 2008;36:D773-779. [PMC free article] [PubMed]. 38. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, ... Nucleic acids research. 2011;39:D876-882. [PMC free article] [PubMed]. 50. Wang HQ, Tuominen LK, Tsai CJ. SLIM: a sliding ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3380828/?lang=en-ca
*  Analysis of gene expression in prostate cancer epithelial and interstitial stromal cells using laser capture microdissection
We have recently identified potential WT1 binding sites in the regulatory sequences of genes expressed in prostate cancer ... belongs to the family of transcription factors with four Krüppel-like zinc fingers in the C-terminus that aid in nucleic acid ... Global gene expression profiling in Escherichia coli K12 The effects of leucine-responsive regulatory protein. J Biol Chem. ... Samples were amplified using the ABI 7000 thermocycler and Ct values were measured by the ABI Prism 7000 sequence detection ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC2876079/
*  amdSYM, a new dominant recyclable marker cassette for Saccharomyces cerevisiae
Shuster JR, Moyer D, Irvine B. Sequence of the Kluyveromyces lactis URA3 gene. Nucleic Acids Res. 1987;15:8573. [PMC free ... Yeast proteins can activate expression through regulatory sequences of the amdS gene of Aspergillus nidulans. Mol Gen Genet. ... Nucleic Acids Res. 2005;33:W526-W531. [PMC free article] [PubMed]. *Guldener U, Heck S, Fiedler T, Beinhauer J, Hegemann JH. A ... Nucleic Acids Res. 1996;24:2519-2524. [PMC free article] [PubMed]. *Guldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH. A ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3563226/?lang=en-ca
*  Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae
Nucleic Acids Res. 2004;32:D138-D141. doi: 10.1093/nar/gkh121. [PMC free article] [PubMed] [Cross Ref] ... Sequence alignment and phylogenetic analysis. Multiple sequence alignments and phylogenetic trees of HKs and RRs were ... Nucleic Acids Res. 1997;25:3389-3402. doi: 10.1093/nar/25.17.3389. [PMC free article] [PubMed] [Cross Ref] ... Nucleic Acids Res. 1994;22:4673-4680. doi: 10.1093/nar/22.22.4673. [PMC free article] [PubMed] [Cross Ref] ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC2222644/?lang=en-ca
*  Immunological Response to Peptide Nucleic Acid and its Peptide Conjugate Targeted to Transactivation Response (TAR) Region of...
The peptide nucleic acid targeted to a regulatory sequence of the translocated c-myc oncogene in Burkitt's lymphoma lacks ... Nucleic Acids Res. 2001;29:1852-1863. [PMC free article] [PubMed]. *NIELSEN P.E. EGHOLM M. BERG R.H. BUCHARDT O. Sequence- ... Anti-HIV-1 activity of anti-TAR polyamide nucleic acid conjugated with various membrane transducing peptides. Nucleic Acids Res ... and display higher affinity to complementary nucleic acid sequences than do normal oligo DNA or RNA. PNAs are constituted by an ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC2948452/
*  Deep sequencing and expression of microRNAs from early honeybee (Apis mellifera) embryos reveals a role in regulating early...
Nucleic Acids Res. 2009;37:5665-5677. doi: 10.1093/nar/gkp619. [PMC free article] [PubMed] [Cross Ref] ... This indicates the importance that changes to gene-regulatory sequences contribute to the evolution of developmental pathways ... Sequence and expression of Ame-mir-0005/mir-92b. (A) Sequence of the novel mir-0005 precursor, with the sequence reads aligned ... A) Sequence of the mir-0007 precursor with aligned sequence reads and read counts. Highlighted in red is the sequence with the ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3562263/?lang=en-ca
*  Complicated behavior of G-quadruplexes and evaluating G-quadruplexes' ligands in various systems mimicking cellular circumstance
Nucleic Acids Res. 2010;38:327-338. [PubMed]. 14. Xue Y., Kan Z.Y., Wang Q., Yao Y., Liu J., Hao Y.H., Tan Z. Human telomeric ... these sequences may play very important regulatory roles in telomere length maintenance, gene replication, transcription, and ... Nucleic Acids Res. 2006;34:2723-2735. [PubMed]. 9. Kan Z.Y., Yao Y., Wang P., Li X.H., Hao Y.H., Tan Z. Molecular crowding ... Nucleic Acids Res. 1999;27:537-542. [PubMed]. 30. Thakur R.K., Kumar P., Halder K., Verma A., Kar A., Parent J.L., Basundra R ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC5600415/
*  Nucleotide sequence of the plasminogen activator gene of Yersinia pestis: relationship to ompT of Escherichia coli and gene E...
Complete nucleotide sequence and deduced amino acid sequence of the ompT gene of Escherichia coli K-12. Nucleic Acids Res. 1988 ... Rosenberg M, Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979 ... This reading frame encodes a 312-amino-acid protein of 34.6 kilodaltons and containing a putative 20-amino-acid signal sequence ... The deduced amino acid sequence of Pla revealed that it possesses a high degree of homology to the products of gene E of ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC313308/?lang=en-ca
*  Functional annotation of novel lineage-specific genes using co-expression and promoter analysis
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 2005;33:W389-92. doi: 10.1093/nar/ ... CRSD: a comprehensive web server for composite regulatory signature discovery. Nucleic Acids Res. 2006;34:W571-7. doi: 10.1093/ ... A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 2003;31:3576-9. doi: 10.1093/nar/ ... Nucleic Acids Res. 1997;25:3389-402. doi: 10.1093/nar/25.17.3389. [PMC free article] [PubMed] [Cross Ref] ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC2848242/
*  A G-quadruplex structure at the 5′ end of the H19 coding region regulates H19 transcription
Rhodes D. & Lipps H. J. G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 43, 8627-8637 (2015). [PMC ... Burge S., Parkinson G. N., Hazel P., Todd A. K. & Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res ... Nucleic Acids Res. 39, 936-948 (2011). [PMC free article] [PubMed]. *Siddiqui-Jain A., Grand C. L., Bearss D. J. & Hurley L. H ... Nucleic Acids Res. 28, 1221-1227 (2000). [PMC free article] [PubMed]. *Cai X. & Cullen B. R. The imprinted H19 noncoding RNA is ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC5377947/
*  Characterization of an Entamoeba histolytica High-Mobility-Group Box Protein Induced during Intestinal Infection
Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference. Nucleic Acids ... Fig.4).4). The double mutant, as expected, did not enhance the binding of p53 to its target sequence. Interestingly, the Δ-Acid ... Nucleic Acids Res. 231019-1029. [PMC free article] [PubMed]. 8. Beck, D. L., D. R. Boettner, B. Dragulev, K. Ready, T. Nozaki, ... Nucleic Acid Res. Mol. Biol. 5435-100. [PubMed]. 17. Clark, C. G., U. C. M. Alsmark, M. Tazreiter, Y. Saito-Nakano, V. Ali, S. ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC2547075/?lang=en-ca
*  Identification of small molecule inhibitors of Zcchc11 TUTase activity
Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature 2014; 510:537-41; PMID:24847876; ... Nucleic Acids Res 2014; 42:11777-91; PMID:25223788; http://dx.doi.org/10.1093/nar/gku805 [PMC free article] [PubMed] [Cross Ref ... Nucleic acids research 2012; 40:9815-24; PMID:22885303; http://dx.doi.org/10.1093/nar/gks740 [PMC free article] [PubMed] [Cross ... 1A).25 We therefore subcloned the cDNA encoding this minimal region of Zcchc11 with a FLAG tag epitope sequence at the 3′ end ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC4615740/
*  R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data
... a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35:D61-D65. [PubMed] ... The cellular transcriptome is the complete set of protein-coding mRNAs, non-coding RNAs and other regulatory RNAs present in a ... Nucleic Acids Res. 2004;32:D493-D496. [PMC free article] [PubMed]. 27. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark ... Nucleic Acids Res. 2011;39:D876-D882. [PMC free article] [PubMed]. 26. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3351179/?lang=en-ca
*  Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome
Nucleic Acids Res. 2008;36:D102-D106. [PMC free article] [PubMed]. *Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman ... Core transcriptional regulatory circuitry in human embryonic stem cells. Cell. 2005;122:947-956. [PMC free article] [PubMed] ... OSKM DNA libraries were sequenced using an Illumina GA2 Sequencer and aligned to the human genome (NCBI v36 assembly) using ... Nucleic Acids Res. 2007;35:D88-D92. [PubMed]. *Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3508134/?lang=en-ca
*  Creating Protein Affinity Reagents by Combining Peptide Ligands on Synthetic DNA Scaffolds
The peptide sequence at each position in the array was generated randomly, selecting one of the eight amino acids, Gly, Thr, ... nucleic acid aptamers, and some small molecule ligands7-14. While these protein affinity reagents are often easier to construct ... of 4,000 unique 12-mer peptides was screened to identify sequences that bind to non-overlapping sites on the yeast regulatory ... Individual sequences were chosen from eight natural amino acids (Gly, Thr, Glu, Lys, Ser, Trp, Leu, Arg) using a random ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC2796340/
*  Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes
... effect of mRNA target sequence and chimera design. Nucleic Acids Res., 30, 5160-5167. [PMC free article] [PubMed] ... Ke X.-S., Liu,C.-M., Liu,D.-P. and Liang,C.-C. (2003) MicroRNAs: key participants in gene regulatory networks. Curr. Opin. Chem ... locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res., 31, 3758-3762. [PMC free ... fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection. Nucleic Acids Res., 30, e91. [ ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC545470/?lang=en-ca
*  Promoter propagation in prokaryotes
Nucleic Acids Res. 2006;34:D32-D36. [PMC free article] [PubMed]. 31. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of ... We term hereafter such recruited regulatory sequences as Putative Mobile Promoters (PMPs) and we hypothesize they have a large ... Nucleic Acids Res. 1997;25:3389-3402. [PMC free article] [PubMed]. 27. Kuzniar A, Dhir S, Nijveen H, Pongor S, Leunissen JA. ... Nucleic Acids Res. 2009;37:D136-D140. [PMC free article] [PubMed]. 30. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3488235/?lang=en-ca
*  lncRNAdb: a reference database for long noncoding RNAs
... a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35:D61-D65. [PubMed] ... However, some lncRNAs that are host genes for small RNA species (35,36), but may also have roles as regulatory lncRNAs, have ... Nucleic Acids Res. 2008;36:D173-D177. [PMC free article] [PubMed]. 23. Xie J, Zhang M, Zhou T, Hua X, Tang L, Wu W. Sno/ ... Nucleic Acids Res. 2009;37:D122-D126. [PMC free article] [PubMed]. 31. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3013714/
*  Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome
Nucleic Acids Res 37: D755-D761. [PMC free article] [PubMed]. 71. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. ( ... Stone JR, Wray GA (2001) Rapid evolution of cis-regulatory sequences via local point mutations. Mol Biol Evol 18: 1764-1770. [ ... The percentages of sequence identity are calculated using the pair-wise sequence alignments of the 201 bp flanking sequences of ... Nucleic Acids Res 22: 3138-3146. [PMC free article] [PubMed]. 34. Mohan M, Bartkuhn M, Herold M, Philippen A, Heinl N, et al. ( ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC3491045/?lang=en-ca
*  The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation
Nucleic Acids Res. 38:D428-432. [PMC free article] [PubMed]. 66. Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA ... Our sequencing runs yielded 29-136 million 50-base sequence reads per sample, which were subsequently aligned to a filter ... Core transcriptional regulatory circuitry in human embryonic stem cells. Cell. 2005;122:947-956. [PMC free article] [PubMed] ... Nucleic Acids Res. 2008;36:W197-201. [PMC free article] [PubMed]. 48. Zhang Y. I-TASSER: fully automated protein structure ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC2924316/?lang=en-ca
*  The serpin gene family in Anopheles gambiae
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-1797. [PMC free ... Gubb D, Robertson A, Dafforn T, Troxler L, Reichhart J. Drosophila serpins: regulatory cascades in innate immunity and ... cDNAs of the serpins were cloned, sequenced, and complete coding sequences were generated. The amino acid sequences, were ... A multiple sequence alignment of amino acid sequences of A. gambiae serpins, human alpha-1 antitrypsin (HsA1AT), and Manduca ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC2716094/