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Volume 41, Issue 10, 1 May 2013
Computational Biology
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5149–5163, https://doi.org/10.1093/nar/gkt216
Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5164–5174, https://doi.org/10.1093/nar/gkt227
Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5175–5188, https://doi.org/10.1093/nar/gkt241
Accurate detection of differential RNA processing
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5189–5198, https://doi.org/10.1093/nar/gkt211
Gene Regulation, Chromatin and Epigenetics
Dissecting the roles of the histone chaperones reveals the evolutionary conserved mechanism of transcription-coupled deposition of H3.3
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5199–5209, https://doi.org/10.1093/nar/gkt220
Ribosomal protein S7 regulates arsenite-induced GADD45α expression by attenuating MDM2-mediated GADD45α ubiquitination and degradation
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5210–5222, https://doi.org/10.1093/nar/gkt223
Nrf2 activation is associated with Z-DNA formation in the human HO-1 promoter
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5223–5234, https://doi.org/10.1093/nar/gkt243
Quantitative in vivo analysis of chromatin binding of Polycomb and Trithorax group proteins reveals retention of ASH1 on mitotic chromatin
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5235–5250, https://doi.org/10.1093/nar/gkt217
Large-scale organization of ribosomal DNA chromatin is regulated by Tip5
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5251–5262, https://doi.org/10.1093/nar/gkt218
Mechanism of DNA organization by Mycobacterium tuberculosis protein Lsr2
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5263–5272, https://doi.org/10.1093/nar/gkt249
Heat shock factor 1 counteracts epigenetic silencing of nuclear transgenes in Chlamydomonas reinhardtii
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5273–5289, https://doi.org/10.1093/nar/gkt224
Induced DNA demethylation can reshape chromatin topology at the IGF2-H19 locus
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5290–5302, https://doi.org/10.1093/nar/gkt240
Genome Integrity, Repair and Replication
Functional interplay of DnaE polymerase, DnaG primase and DnaC helicase within a ternary complex, and primase to polymerase hand-off during lagging strand DNA replication in Bacillus subtilis
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5303–5320, https://doi.org/10.1093/nar/gkt207
Non-erythroid alpha spectrin prevents telomere dysfunction after DNA interstrand cross-link damage
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5321–5340, https://doi.org/10.1093/nar/gkt235
Lif1 SUMOylation and its role in non-homologous end-joining
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5341–5353, https://doi.org/10.1093/nar/gkt236
Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, ε, θ and β reveals a highly flexible arrangement of the proofreading domain
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5354–5367, https://doi.org/10.1093/nar/gkt162
Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5368–5381, https://doi.org/10.1093/nar/gkt225
Genomics
Characterization of genome-reduced fission yeast strains
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5382–5399, https://doi.org/10.1093/nar/gkt233
Molecular Biology
miR-23b regulates cytoskeletal remodeling, motility and metastasis by directly targeting multiple transcripts
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5400–5412, https://doi.org/10.1093/nar/gkt245
Nucleic Acid Enzymes
The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5413–5427, https://doi.org/10.1093/nar/gkt186
Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5428–5443, https://doi.org/10.1093/nar/gkt195
The role of DNA bending in type IIA topoisomerase function
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5444–5456, https://doi.org/10.1093/nar/gkt238
Zebrafish AID is capable of deaminating methylated deoxycytidines
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5457–5468, https://doi.org/10.1093/nar/gkt212
RNA
The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5469–5482, https://doi.org/10.1093/nar/gkt208
Reprogramming of microRNAs by adenosine-to-inosine editing and the selective elimination of edited microRNA precursors in mouse oocytes and preimplantation embryos
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5483–5493, https://doi.org/10.1093/nar/gkt247
A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5494–5502, https://doi.org/10.1093/nar/gkt219
Loop-miRs: active microRNAs generated from single-stranded loop regions
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5503–5512, https://doi.org/10.1093/nar/gkt251
The Yin and Yang of tRNA: proper binding of acceptor end determines the catalytic balance of editing and aminoacylation
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5513–5523, https://doi.org/10.1093/nar/gkt252
Structural Biology
Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing pyrimidine transition mutations
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5524–5532, https://doi.org/10.1093/nar/gkt198
Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5533–5541, https://doi.org/10.1093/nar/gkt264
Synthetic Biology and Chemistry
An engineered small RNA-mediated genetic switch based on a ribozyme expression platform
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Pages 5542–5552, https://doi.org/10.1093/nar/gkt253
Corrigendum
Widespread inference of weighted microRNA-mediated gene regulation in cancer transcriptome analysis
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page 5553, https://doi.org/10.1093/nar/gkt248
Methods Online
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page e105, https://doi.org/10.1093/nar/gkt183
Fluorescence monitoring of riboswitch transcription regulation using a dual molecular beacon assay
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page e106, https://doi.org/10.1093/nar/gkt190
Re-engineering an alphoidtetO-HAC-based vector to enable high-throughput analyses of gene function
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page e107, https://doi.org/10.1093/nar/gkt205
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page e108, https://doi.org/10.1093/nar/gkt214
Probabilistic error correction for RNA sequencing
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page e109, https://doi.org/10.1093/nar/gkt215
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page e110, https://doi.org/10.1093/nar/gkt229
A capture approach for supercoiled plasmid DNA using a triplex-forming oligonucleotide
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page e111, https://doi.org/10.1093/nar/gkt239
Reflex: intramolecular barcoding of long-range PCR products for sequencing multiple pooled DNAs
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page e112, https://doi.org/10.1093/nar/gkt228
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 41 ISSUE 10 2013
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page i, https://doi.org/10.1093/nar/gks1367
Nucleic Acids Research - Editorial Board
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page ii, https://doi.org/10.1093/nar/gks1391
Subscriptions
Nucleic Acids Research, Volume 41, Issue 10, 1 May 2013, Page iii, https://doi.org/10.1093/nar/gks1415
