Nucleic Acids Research

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. 2022

DNAcycP: a deep learning tool for DNA cyclizability prediction..  50:3142-3154. 2022

MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage.  49:11787-11799. 2021

Bach1 recruits nanog and histone h3 lysine 4 methyltransferase mll/set1 complexes to regulate enhancer-promoter activity and maintains pluripotency.  49:1972-1986. 2021

BastionHub: A universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria.  49:D651-D659. 2021

PAGER-CoV: A comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.  49:D589-D599. 2021

RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data..  48:12016-12029. 2020

Structural basis of DNA replication origin recognition by human Orc6 protein binding with DNA.  48:11146-11161. 2020

Hedgehog signaling enables repair of ribosomal DNA double-strand breaks.  48:10342-10352. 2020

Enhancer RNAs predict enhancer–gene regulatory links and are critical for enhancer function in neuronal systems.  48:9550-9570. 2020

Binding of a viral IRES to the 40S subunit occurs in two successive steps mediated by eS25.  48:8063-8073. 2020

Quantification of splice variants using real-time PCR.  29. 2020

CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries.  47:E84. 2019

BEERE: a web server for biomedical entity expansion, ranking and explorations.  47:W578-W586. 2019

Splice-Break: Exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders.  47. 2019

Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters.  47:4586-4596. 2019

Erratum: Non-canonical translation initiation of the spliced mRNA encoding the human T-cell leukemia virus type 1 basic leucine zipper protein (Nucleic Acids Research (2018) 46:20 (11030-11047) DOI: 10.1093/nar/gky802).  47:1599. 2019

A dual-functional priming-capping loop of rhabdoviral RNA polymerases directs terminal de novo initiation and capping intermediate formation.  47:299-309. 2019

Non-canonical translation initiation of the spliced mRNA encoding the human T-cell leukemia virus type 1 basic leucine zipper protein.  46:11030-11047. 2018

PAGER 2.0: An update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.  46:D668-D676. 2018

Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV).  46:D708-D717. 2018

PARP1 changes from three-dimensional DNA damage searching to one-dimensional diffusion after auto-PARylation or in the presence of APE1.  45:12834-12847. 2017

Molecular mechanisms by which oxidative DNA damage promotes telomerase activity.  45:11752-11765. 2017

Activities of gyrase and topoisomerase IV on positively supercoiled DNA.  45:9611-9624. 2017

Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate.  45:2829-2837. 2017

DNA polymerase β contains a functional nuclear localization signal at its N-terminus.  45:1958-1970. 2017

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV) 2017

Entropic stabilization of folded RNA in crowded solutions measured by SAXS.  44:9452-9461. 2016

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering.  44:W272-W276. 2016

Do nucleic acids moonlight as molecular chaperones?.  44:4835-4845. 2016

Signature motifs of GDP polyribonucleotidyltransferase, a non-segmented negative strand RNA viral mRNA capping enzyme, domain in the L protein are required for covalent enzyme-pRNA intermediate formation.  44:330-341. 2016

LKB1 preserves genome integrity by stimulating BRCA1 expression.  43:259-271. 2015

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme.  43:1170-1176. 2015

The Rat Genome Database 2015: Genomic, phenotypic and environmental variations and disease.  43:D743-D750. 2015

tRFdb: A database for transfer RNA fragments.  43:D141-D145. 2015

Blocking of targeted microRNAs from next-generation sequencing libraries.  43. 2015

Massively parallel determination and modeling of endonuclease substrate specificity.  42:13839-13852. 2014

Retinoid acid-related orphan receptor γ, RORγ, participates in diurnal transcriptional regulation of lipid metabolic genes.  42:10448-10459. 2014

Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus.  42:6463-6475. 2014

Suicidal cross-linking of PARP-1 to AP site intermediates in cells undergoing base excision repair.  42:6337-6351. 2014

Characterization of the imprinting signature of mouse embryo fibroblasts by RNA deep sequencing.  42:1772-1783. 2014

Redox-Active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism.  42:1593-1605. 2014

Reprogramming homing endonuclease specificity through computational design and directed evolution.  42:2564-2576. 2014

Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes.  41. 2013

Prospero-related homeobox 1 (Prox1) functions as a novel modulator of retinoic acid-related orphan receptors α- and γ-mediated transactivation.  41:6992-7008. 2013

Nucleocapsid protein structures from orthobunyaviruses reveal insight into ribonucleoprotein architecture and RNA polymerization.  41:5912-5926. 2013

Topoisomerase IV-quinolone interactions are mediated through a water-metal ion bridge: Mechanistic basis of quinolone resistance.  41:4628-4639. 2013

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.  41:2779-2796. 2013

Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism.  gkt1090-gkt1090. 2013

Phosphorylation of PNKP by ATM prevents its proteasomal degradation and enhances resistance to oxidative stress.  40:11404-11415. 2012

Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution.  40:10832-10850. 2012

RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo.  40:8519-8535. 2012

In vivo functional analysis of the Dicistroviridae intergenic region internal ribosome entry sites.  39:7276-7288. 2011

Retinoic acid-related orphan receptor γ directly regulates neuronal PAS domain protein 2 transcription in vivo.  39:4769-4782. 2011

Coordinated allele-specific histone acetylation at the differentially methylated regions of imprinted genes.  38:7974-7990. 2010

Beyond Affymetrix arrays: Expanding the set of known hybridization isotherms and observing pre-wash signal intensities.  38. 2009

Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion.  37:6454-6465. 2009

The Rat Genome Database 2009: Variation, ontologies and pathways.  37. 2009

Functional analysis of the zinc finger and activation domains of Glis3 and mutant Glis3(NDH1).  36:1690-1702. 2008

Allosteric control of the RNA polymerase by the elongation factor RfaH.  35:5694-5705. 2007

Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays.  35. 2007

Ubiquitin-interaction motifs of RAP80 are critical in its regulation of estrogen receptor α.  35:1673-1686. 2007

DisProt: The database of disordered proteins.  35. 2007

DAXX interacts with phage ΦC31 integrase and inhibits recombination.  34:6298-6304. 2006

Selection and cloning of poly(rC)-binding protein 2 and Raf kinase inhibitor protein RNA activators of 2′,5′-oligoadenylate synthetase from prostate cancer cells.  34:6684-6695. 2006

Elongation complexes of thermus thermophilus RNA polymerase that possess distinct translocation conformations.  34:4036-4045. 2006

Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted.  34. 2006

Krüppel-like zinc finger protein Gli-similar 2 (Glis2) represses transcription through interaction with C-terminal binding protein 1 (CtBP1).  33:6805-6815. 2005

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.  33. 2005

The ELAV RNA-stability factor HuR binds the 5′-untranslated region of the human IGF-IR transcript and differentially represses cap-dependent and IRES-mediated translation.  33:2962-2979. 2005

Expression and regulation of the Msx1 natural antisense transcript during development.  33:5208-5218. 2005

Novel DNA-binding properties of the RNA-binding protein TIAR.  33:4507-4518. 2005

Poxvirus Bioinformatics Resource Center: A comprehensive Poxviridae informational and analytical resource.  33. 2005

Erratum: Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene (Nucleic Acids Research (2003) vol. 31 (4201-4210)).  32:6716. 2004

TIP27: A novel repressor of the nuclear orphan receptor TAK1/TR4.  32:4194-4204. 2004

Mathematical algorithm for discovering states of expression from direct genetic comparison by microarrays.  32:3807-3814. 2004

A Fugu-human genome synteny viewer: Web software for graphical display and annotation reports of synteny between Fugu genomic sequence and human genes.  32:2618-2622. 2004

ORFDB: An information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection.  32. 2004

ORFDB: an information resource linking scientific content to a high‐quality Open Reading Frame (ORF) collection.  32:d595-d599. 2004

Rapid tagging of endogenous mouse genes by recombineering and ES cell complementation of tetraploid blastocysts..  32. 2004

Comparative analysis of editosome proteins in trypanosomatids.  31:6392-6408. 2003

GLIS3, a novel member of the GLIS subfamily of Krüppel-like zinc finger proteins with repressor and activation functions.  31:5513-5525. 2003

Structure-function relationships of the initiation complex of HIV-1 reverse transcription: The case of mutant viruses using tRNA^His as primer.  31:5764-5775. 2003

Stability of the Sp3-DNA complex is promoter-specific: Sp3 efficiently competes with Sp1 for binding to promoters containing multiple Sp-sites.  31:5368-5376. 2003

Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene.  31:4201-4210. 2003

Mitochondria-mediated nuclear mutator phenotype in Saccharomyces cerevisiae.  31:3909-3917. 2003

Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence.  31:3510-3517. 2003

A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.  31:1805-1812. 2003

Self-association and conformational properties of RAG1: Implications for formation of the V(D)J recombinase.  31:2014-2023. 2003

Uracil-DNA glycosylase-deficient yeast exhibit a mitochondrial mutator phenotype.  29:4935-4940. 2001

Overexpression of human RAD51 and RAD52 reduces double-strand break-induced homologous recombination in mammalian cells.  29:4352-4360. 2001

Mi2, an auto-antigen for dermatomyositis, is an ATP-dependent nucleosome remodeling factor.  29:2517-2521. 2001

A reliable assessment of 8-oxo-2-deoxyguanosine levels in nuclear and mitochondrial DNA using the sodium iodide method to isolate DNA.  29:2117-2126. 2001

The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis.  29:2145-2153. 2001

Transcription of the Schizosaccharomyces pombe U2 gene in vivo and in vitro is directed by two essential promoter elements.  29:2003-2011. 2001

Ku80 is required for addition of N nucleotides to V(D)J recombination junctions by terminal deoxynucleotidyl transferase.  29:1638-1646. 2001

Inactivation of Saccharomyces cerevisiae OGG1 DNA repair gene leads to an increased frequency of mitochondrial mutants.  29:1381-1388. 2001

Polymorphism in the 3′-untranslated region of TNFα mRNA impairs binding of the post-transcriptional regulatory protein HuR to TNFα mRNA.  29:863-871. 2001

Essential regions of the tRNA primer required for HIV-1 infectivity.  28:4783-4789. 2000

Human β-globin gene promoter element regulates human β-globin gene developmental specificity.  28:2736-2740. 2000

A method for quantification of absolute amounts of nucleic acids by (RT)-PCR and a new mathematical model for data analysis..  28. 2000

RNA-binding analyses of HuC and HuD with the VEGF and c-myc 3'-untranslated regions using a novel ELISA-based assay..  28. 2000

Binding of the glucose-dependent Mig1p repressor to the GAL1 and GAL4 promoters in vivo: Regulation by glucose and chromatin structure.  27:1350-1358. 1999

Stochastic, stage-specific mechanisms account for the variegation of a human globin transgene.  26:2849-2858. 1998

Characterization of the RNA binding proteins forming complexes with a novel putative regulatory region in the 3'-UTR of TNF-α mRNA.  26:2803-2812. 1998

Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein.  25:814-821. 1997

A 39 amino acid fragment of the cell cycle regulator p21 is sufficient to bind PCNA and partially inhibit DNA replication in vivo.  24:1727-1733. 1996

Phosphorylation of human replication protein A by the DNA-dependent protein kinase is involved in the modulation of DNA replication.  24:3107-3112. 1996

Photoaffinity approaches to determining the sequence selectivities of DNA-small molecule interactions: Actinomycin D and ethidium.  23:1252-1259. 1995

Rapid confirmation of single copy lambda prophage integration by PCR.  23:1278. 1995

Construction of a genomic DNA 'feature map' by sequencing from nested deletions: Application to the HLA class I region.  23:117-122. 1995

Mouse silver. Mutation is caused by a single base insertion in the putative cytoplasmic domain of Pmel 17.  23:154-158. 1995

Daunomycin modifies the sequence-selective recognition of DNA by actinomycin.  22:5241-5246. 1994

Rapid confirmation of single copy lambda prophage integration by PCR.  22:5765-5766. 1994

Retroviral vector sequences inhibit human β-globin gene expression in transgenic mice.  22:4477-4481. 1994

Mutagenesis of the cyclic AMP receptor protein of Escherichia coli: Targeting positions 83, 127 and 128 the cyclic nucleotide binding pocket.  22:2894-2901. 1994

Cloning and functional characterization of LCR-F1: A bZIP transcription factor that activates erythroid-specific, human globin gene expression.  22:2383-2391. 1994

Oligo[d(C) · (G)] runs exhibit a helical repeat of 11.1 bp in solution and cause slight DNA curvature when properly phased.  22:1562-1566. 1994

Multiple elements in human β-globin locus control region 5′ HS 2 are involved in enhancer activity and position independent, transgene expression.  22:1006-1011. 1994

Sensitivity of HincW to CpG methylation.  21:2021. 1993

Improved sequencing of cosmids using new primers and linearized DNA.  20:6421-6422. 1992

Nucleotide sequence of the intron of the germline human x immunoglobulin gene connecting the J and C regions reveals a matrix association region (MAR) next to the enhancer.  20:4929-4930. 1992

Upstream regions of the c-jun promoter regulate phorbol ester-induced transcription in U937 leukemic cells.  20:897-902. 1992

Dinucleotide repeat polymorphism located at D4S169.  19:6347. 1991

Taql RFLP at D21S137.  19:4020. 1991

Identification of polymorphisms by genomic denaturing gradient gel electrophoresis: Application to the proximal region of human chromosome 21.  19:1475-1481. 1991

Immunoglobulin variable heavy chain cDNA sequence from a patient with X-linked agammaglobulinemia.  19:673. 1991

Dinucleotide repeat polymorphism located at D21S120.  18:6754. 1990

Sequence of the TCR β chain gene used by a t cell clone specific for the synthetic polymer, GAT.  18:5881. 1990

cis-acting elements required for RNA polymerase II and III transcription in the human U2 and U6 snRNA promoters..  18:2891-2899. 1990

Thermodynamics of the interactions of m-AMSA and o-AMSA with nucleic acids: Influence of ionic strength and DNA base composition.  17:9933-9946. 1989

Rom transcript of plasmid ColE1.  17:4309-4326. 1989

Isolation and mapping of a polymorphic DNA sequence pH30 on chromosome 4 [HGM provisional no. IMS 139].  17:4002. 1989

Cooperative binding of m-AMSA to nucleic acids.  16:9707-9719. 1988

¹H NMR study of the solution structure of the self-complementary dodecanucleotide d(TGCA)3.  16:7133-7143. 1988

Cosmid mapping of the human chorionic gonadotropin β subunit genes by field-inversion gel elect rophoresis.  15:4437-4448. 1987

A mouse Ulb-2 gene with extensive sequence similarity to a rat Ula gene for 670 nucleotides 5' to the gene..  15:3622. 1987

Purification of the gam gene-product of bacteriophage mu and determination of the nucleotide sequence of the gam gene.  14:6901-6914. 1986

Nucleotide sequence of the human γ cytoskeletal actin mRNA: Anomalous evolution of vertebrate non-muscle actin genes.  14:5275-5294. 1986

Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli.  13:3891-3902. 1985

Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis.  13:3111-3129. 1985

Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis.  13:3131-3145. 1985

A chicken repetitive DNA sequence that is highly sensitive to single-strand specific endonucleases.  11:8495-8508. 1983

Isolation and characterization of two linked mouse U1b small nuclear RNA genes..  11:6255-6270. 1983

The early promoter of bacteriophage mu: Definition of the site of transcript initiation.  11:5483-5495. 1983

The spc rtbosomal protein operon of Eschenchia coli: Sequence and cotranscriptlon of the rlbosomal protein genes and a protein export gene.  11:2599-2616. 1983

The binding of gyrase to DNA: Analysis by retention by nitrocellulose filters.  10:6833-6847. 1982

Characterization of a cloned histone gene cluster of the newt notophthalmus viridescens.  9:2281-2295. 1981

DNA gyrase subunit stoichiometry and the covalent attachment of subunit a to DNA during DNA cleavage.  8:3865-3874. 1980

Addition of oligonucleotides to the 5′-terminus of DNA by T4 RNA ligase.  6:1013-1024. 1979

Bacteriophage T4 RNA ligase: Preparation of a physically homogeneous, nuclease-free enzyme from hyperproducing infected cells.  4:3175-3186. 1977