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Volume 38, Issue 22, 1 December 2010
Editorial: NAR Awards 2010
EDITORIAL: NAR AWARDS 2010
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7871–7875, https://doi.org/10.1093/nar/gkq1263
Survey and Summary
On the power and limits of evolutionary conservation—unraveling bacterial gene regulatory networks
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7877–7884, https://doi.org/10.1093/nar/gkq699
Archaeal/Eukaryal RNase P: subunits, functions and RNA diversification
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7885–7894, https://doi.org/10.1093/nar/gkq701
Computational Biology
Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7895–7907, https://doi.org/10.1093/nar/gkq679
SEWAL: an open-source platform for next-generation sequence analysis and visualization
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7908–7915, https://doi.org/10.1093/nar/gkq661
A network of conserved co-occurring motifs for the regulation of alternative splicing
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7916–7926, https://doi.org/10.1093/nar/gkq705
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7927–7942, https://doi.org/10.1093/nar/gkq714
Gene Regulation, Chromatin and Epigenetics
ChIPing the cistrome of PXR in mouse liver
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7943–7963, https://doi.org/10.1093/nar/gkq654
Identification of functional clock-controlled elements involved in differential timing of Per1 and Per2 transcription
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7964–7973, https://doi.org/10.1093/nar/gkq678
Coordinated allele-specific histone acetylation at the differentially methylated regions of imprinted genes
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7974–7990, https://doi.org/10.1093/nar/gkq680
Design of a minimal silencer for the silent mating-type locus HML of Saccharomyces cerevisiae
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 7991–8000, https://doi.org/10.1093/nar/gkq689
Heterogeneous ribonucleoprotein C displays a repressor activity mediated by T-cell intracellular antigen-1-related/like protein to modulate Fas exon 6 splicing through a mechanism involving Hu antigen R
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8001–8014, https://doi.org/10.1093/nar/gkq698
A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8015–8026, https://doi.org/10.1093/nar/gkq703
Foxm1 transcription factor is required for maintenance of pluripotency of P19 embryonal carcinoma cells
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8027–8038, https://doi.org/10.1093/nar/gkq715
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8039–8050, https://doi.org/10.1093/nar/gkq686
Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8051–8060, https://doi.org/10.1093/nar/gkq712
AUF1 p42 isoform selectively controls both steady-state and PGE2-induced FGF9 mRNA decay
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8061–8071, https://doi.org/10.1093/nar/gkq717
Gene repression by minimal lac loops in vivo
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8072–8082, https://doi.org/10.1093/nar/gkq755
Genome Integrity, Repair and Replication
Localization of xeroderma pigmentosum group A protein and replication protein A on damaged DNA in nucleotide excision repair
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8083–8094, https://doi.org/10.1093/nar/gkq649
Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8095–8104, https://doi.org/10.1093/nar/gkq685
Homeotic proteins participate in the function of human-DNA replication origins
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8105–8119, https://doi.org/10.1093/nar/gkq688
Incorporation of dUTP does not mediate mutation of A:T base pairs in Ig genes in vivo
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8120–8130, https://doi.org/10.1093/nar/gkq682
RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8131–8140, https://doi.org/10.1093/nar/gkq697
Genomics
Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8141–8148, https://doi.org/10.1093/nar/gkq729
RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8149–8163, https://doi.org/10.1093/nar/gkq804
Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8164–8177, https://doi.org/10.1093/nar/gkq955
Molecular Biology
O6-Methylguanine induces altered proteins at the level of transcription in human cells
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8178–8187, https://doi.org/10.1093/nar/gkq706
Codon reassignment in the Escherichia coli genetic code
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8188–8195, https://doi.org/10.1093/nar/gkq707
Diversity and strength of internal outward-oriented promoters in group IIC-attC introns
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8196–8207, https://doi.org/10.1093/nar/gkq709
Ribonucleotide reductase is not limiting for mitochondrial DNA copy number in mice
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8208–8218, https://doi.org/10.1093/nar/gkq735
Characterization of an interplay between a Mycobacterium tuberculosis MazF homolog, Rv1495 and its sole DNA topoisomerase I
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8219–8230, https://doi.org/10.1093/nar/gkq737
Nucleic Acid Enzymes
The Type II restriction endonuclease MvaI has dual specificity
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8231–8238, https://doi.org/10.1093/nar/gkq676
Critical lysine residues within the overlooked N-terminal domain of human APE1 regulate its biological functions
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8239–8256, https://doi.org/10.1093/nar/gkq691
Sequence-specific cleavage of RNA by Type II restriction enzymes
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8257–8268, https://doi.org/10.1093/nar/gkq702
Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8269–8276, https://doi.org/10.1093/nar/gkq720
RNA
Stimulation of ribosomal frameshifting by antisense LNA
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8277–8283, https://doi.org/10.1093/nar/gkq650
Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8284–8294, https://doi.org/10.1093/nar/gkq662
Dissecting the role of conserved box C/D sRNA sequences in di-sRNP assembly and function
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8295–8305, https://doi.org/10.1093/nar/gkq690
Selection of RNA aptamers that bind HIV-1 LTR DNA duplexes: strand invaders
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8306–8315, https://doi.org/10.1093/nar/gkq696
Dissecting functional cooperation among protein subunits in archaeal RNase P, a catalytic ribonucleoprotein complex
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8316–8327, https://doi.org/10.1093/nar/gkq668
Functional microRNA generated from a cytoplasmic RNA virus
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8328–8337, https://doi.org/10.1093/nar/gkq681
MicroRNA-target pairs in human renal epithelial cells treated with transforming growth factor β1: a novel role of miR-382
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8338–8347, https://doi.org/10.1093/nar/gkq718
Anti-tumor activity of splice-switching oligonucleotides
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8348–8356, https://doi.org/10.1093/nar/gkq731
Structural Biology
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8357–8369, https://doi.org/10.1093/nar/gkq692
Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8370–8376, https://doi.org/10.1093/nar/gkq700
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8377–8389, https://doi.org/10.1093/nar/gkq711
Methods Online
Pronuclear injection-based mouse targeted transgenesis for reproducible and highly efficient transgene expression
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page e198, https://doi.org/10.1093/nar/gkq860
MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page e199, https://doi.org/10.1093/nar/gkq862
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page e200, https://doi.org/10.1093/nar/gkq873
Isothermal DNA amplification using the T4 replisome: circular nicking endonuclease-dependent amplification and primase-based whole-genome amplification
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page e201, https://doi.org/10.1093/nar/gkq795
Analysis of DNA double-strand break response and chromatin structure in mitosis using laser microirradiation
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page e202, https://doi.org/10.1093/nar/gkq836
Identification of species by multiplex analysis of variable-length sequences
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page e203, https://doi.org/10.1093/nar/gkq865
Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page e204, https://doi.org/10.1093/nar/gkq871
Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page e205, https://doi.org/10.1093/nar/gkq872
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 38 ISSUE 22 2010
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page i, https://doi.org/10.1093/nar/gkq1310
Nucleic Acids Research
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page ii, https://doi.org/10.1093/nar/gkq1309
Subscriptions
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Page iii, https://doi.org/10.1093/nar/gkq1311
