Nucleic Acids Res

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  Publication Venue For

  • SMAD3 promotes expression and activity of the androgen receptor in prostate cancer..  51:2655-2670. 2023
  • MiMeDB: the Human Microbial Metabolome Database..  51:D611-D620. 2023
  • Resistance of mitochondrial DNA to cadmium and Aflatoxin B1 damage-induced germline mutation accumulation in C. elegans..  50:8626-8642. 2022
  • Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease..  50:8290-8301. 2022
  • Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides..  50:6890-6902. 2022
  • Phosphorylated MED1 links transcription recycling and cancer growth..  50:4450-4463. 2022
  • m6A and YTHDF proteins contribute to the localization of select neuronal mRNAs..  50:4464-4483. 2022
  • Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA..  49:12540-12555. 2021
  • Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U..  49:10136-10149. 2021
  • RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data..  49:8505-8519. 2021
  • RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data..  49:7925-7938. 2021
  • The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ..  49:5623-5636. 2021
  • Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer..  49:4971-4988. 2021
  • Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations..  49:4155-4170. 2021
  • 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states..  48:12365-12379. 2020
  • A role of the CTCF binding site at enhancer Eα in the dynamic chromatin organization of the Tcra-Tcrd locus..  48:9621-9636. 2020
  • Crystal structure of an Escherichia coli Hfq Core (residues 2-69)-DNA complex reveals multifunctional nucleic acid binding sites..  48:3987-3997. 2020
  • Molecular determinants for enzalutamide-induced transcription in prostate cancer..  47:10104-10114. 2019
  • Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site..  47:7105-7117. 2019
  • QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants..  47:W127-W135. 2019
  • Structures of maintenance of carboxysome distribution Walker-box McdA and McdB adaptor homologs..  47:5950-5962. 2019
  • Mismatch recognition and subsequent processing have distinct effects on mitotic recombination intermediates and outcomes in yeast..  47:4554-4568. 2019
  • Genome-wide analysis of genomic alterations induced by oxidative DNA damage in yeast..  47:3521-3535. 2019
  • Creation of versatile cloning platforms for transgene expression and dCas9-based epigenome editing..  47:e23. 2019
  • The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA..  47:2130-2142. 2019
  • Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?.  46:11099-11114. 2018
  • Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis..  46:8832-8847. 2018
  • A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease..  46:7772-7792. 2018
  • The crystal structure of the RsbN-σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor..  46:7405-7417. 2018
  • The crystal structure of the RsbN-σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor..  46:7467-7468. 2018
  • Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies..  45:11684-11699. 2017
  • Prediction of genome-wide DNA methylation in repetitive elements..  45:8697-8711. 2017
  • Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics..  45:e134. 2017
  • Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence..  45:6993. 2017
  • Statistical analysis of genetic interactions in Tn-Seq data..  45:e93. 2017
  • The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex..  45:6923-6933. 2017
  • N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein..  45:6051-6063. 2017
  • Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A..  45:5586-5601. 2017
  • A three-dimensional ParF meshwork assembles through the nucleoid to mediate plasmid segregation..  45:3158-3171. 2017
  • Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis..  45:2629-2643. 2017
  • Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization..  45:2490-2502. 2017
  • Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1..  44:7540-7554. 2016
  • Parallel analysis of ribonucleotide-dependent deletions produced by yeast Top1 in vitro and in vivo..  44:7714-7721. 2016
  • Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila..  44:7204-7218. 2016
  • Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein..  44:5438-5449. 2016
  • Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence..  44:4105-4122. 2016
  • Rad18 confers hematopoietic progenitor cell DNA damage tolerance independently of the Fanconi Anemia pathway in vivo..  44:4174-4188. 2016
  • Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus..  44:3082-3094. 2016
  • Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation..  44:426-436. 2016
  • Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme..  44:402-412. 2016
  • Topoisomerase 1-dependent deletions initiated by incision at ribonucleotides are biased to the non-transcribed strand of a highly activated reporter..  43:9306-9313. 2015
  • Structures of the T. brucei kRNA editing factor MRB1590 reveal unique RNA-binding pore motif contained within an ABC-ATPase fold..  43:7096-7109. 2015
  • New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey..  43:3420-3433. 2015
  • Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data..  43:D1071-D1078. 2015
  • Ubiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain..  42:13997-14005. 2014
  • New tools provide a second look at HDV ribozyme structure, dynamics and cleavage..  42:12833-12846. 2014
  • cnvCapSeq: detecting copy number variation in long-range targeted resequencing data..  42:e158. 2014
  • Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection..  42:11865-11878. 2014
  • Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity..  42:11792-11804. 2014
  • COUGER--co-factors associated with uniquely-bound genomic regions..  42:W461-W467. 2014
  • Molecular evolutionary and structural analysis of the cytosolic DNA sensor cGAS and STING..  42:8243-8257. 2014
  • Hydrolytic function of Exo1 in mammalian mismatch repair..  42:7104-7112. 2014
  • Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer..  42:3607-3622. 2014
  • Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors..  42:2856-2869. 2014
  • Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching..  42:2736-2749. 2014
  • Protein-DNA binding: complexities and multi-protein codes..  42:2099-2111. 2014
  • Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR..  42:2774-2788. 2014
  • TFBSshape: a motif database for DNA shape features of transcription factor binding sites..  42:D148-D155. 2014
  • Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure..  41:10462-10475. 2013
  • Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain..  41:1998-2008. 2013
  • DictyBase 2013: integrating multiple Dictyostelid species..  41:D676-D683. 2013
  • Gene Ontology annotations and resources..  41:D530-D535. 2013
  • The Disease and Gene Annotations (DGA): an annotation resource for human disease..  41:D553-D560. 2013
  • Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract..  40:11023-11035. 2012
  • Primer3--new capabilities and interfaces..  40:e115. 2012
  • Delivery of chemo-sensitizing siRNAs to HER2+-breast cancer cells using RNA aptamers..  40:6319-6337. 2012
  • VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era..  40:W76-W81. 2012
  • Integrated analysis identifies a class of androgen-responsive genes regulated by short combinatorial long-range mechanism facilitated by CTCF..  40:4754-4764. 2012
  • Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation..  40:2734-2746. 2012
  • Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch..  40:1345-1355. 2012
  • Yin Yang 1 contains G-quadruplex structures in its promoter and 5'-UTR and its expression is modulated by G4 resolvase 1..  40:1033-1049. 2012
  • Disease Ontology: a backbone for disease semantic integration..  40:D940-D946. 2012
  • FlyRNAi.org--the database of the Drosophila RNAi screening center: 2012 update..  40:D715-D719. 2012
  • New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation..  40:892-904. 2012
  • The Gene Ontology: enhancements for 2011..  40:D559-D564. 2012
  • The DEAH-box RNA helicase RHAU binds an intramolecular RNA G-quadruplex in TERC and associates with telomerase holoenzyme..  39:9390-9404. 2011
  • The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding..  39:9433-9447. 2011
  • G4 resolvase 1 tightly binds and unwinds unimolecular G4-DNA..  39:7161-7178. 2011
  • Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant..  39:6201-6212. 2011
  • Novel retrotransposed imprinted locus identified at human 6p25..  39:5388-5400. 2011
  • Identification of a novel epigenetic regulatory region within the pluripotency associated microRNA cluster, EEmiRC..  39:3574-3581. 2011
  • Efficient detection of RNA-protein interactions using tethered RNAs..  39:e53. 2011
  • Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators..  39:2931-2942. 2011
  • dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa..  39:D620-D624. 2011
  • RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription..  38:8131-8140. 2010
  • Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU..  38:6219-6233. 2010
  • Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes..  38:4514-4526. 2010
  • Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays..  38:e105. 2010
  • Finding regulatory DNA motifs using alignment-free evolutionary conservation information..  38:e90. 2010
  • EuroPhenome: a repository for high-throughput mouse phenotyping data..  38:D577-D585. 2010
  • The Gene Ontology in 2010: extensions and refinements..  38:D331-D335. 2010
  • DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2..  37:7381-7393. 2009
  • The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes..  37:6970-6983. 2009
  • Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships..  37:e92. 2009
  • Mismatch repair and nucleotide excision repair proteins cooperate in the recognition of DNA interstrand crosslinks..  37:4420-4429. 2009
  • Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition..  37:3670-3679. 2009
  • Structural and biochemical characterization of MepR, a multidrug binding transcription regulator of the Staphylococcus aureus multidrug efflux pump MepA..  37:1211-1224. 2009
  • dictyBase--a Dictyostelium bioinformatics resource update..  37:D515-D519. 2009
  • GenoWatch: a disease gene mining browser for association study..  36:W336-W340. 2008
  • The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme..  36:2990-3000. 2008
  • The effect of sequence context on spontaneous Polzeta-dependent mutagenesis in Saccharomyces cerevisiae..  36:2082-2093. 2008
  • Chromatin-associated HMG-17 is a major regulator of homeodomain transcription factor activity modulated by Wnt/beta-catenin signaling..  36:462-476. 2008
  • Model-based variance-stabilizing transformation for Illumina microarray data..  36:e11. 2008
  • Modulation of utrophin A mRNA stability in fast versus slow muscles via an AU-rich element and calcineurin signaling..  36:826-838. 2008
  • PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice..  36:D729-D734. 2008
  • The Gene Ontology project in 2008..  36:D440-D444. 2008
  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids..  35:W375-W383. 2007
  • OligoCalc: an online oligonucleotide properties calculator..  35:W43-W46. 2007
  • PrimerZ: streamlined primer design for promoters, exons and human SNPs..  35:W63-W65. 2007
  • Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers..  35:4535-4541. 2007
  • Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase..  35:4275-4288. 2007
  • Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos..  35:152-164. 2007
  • PLP/DM20 ratio is regulated by hnRNPH and F and a novel G-rich enhancer in oligodendrocytes..  35:4164-4178. 2007
  • Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes..  35:e20. 2007
  • Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition..  35:1698-1713. 2007
  • TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)..  35:D445-D451. 2007
  • Xanthusbase: adapting wikipedia principles to a model organism database..  35:D422-D426. 2007
  • FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization..  34:W635-W641. 2006
  • A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments..  34:e106. 2006
  • FlyRNAi: the Drosophila RNAi screening center database..  34:D489-D494. 2006
  • GOBASE--a database of organelle and bacterial genome information..  34:D697-D699. 2006
  • H1 RNA polymerase III promoter-driven expression of an RNA aptamer leads to high-level inhibition of intracellular protein activity..  34:3577-3584. 2006
  • High potency silencing by single-stranded boranophosphate siRNA..  34:2773-2781. 2006
  • High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer..  34:555-563. 2006
  • Histone deacetylase 3 binds to and regulates the GCMa transcription factor..  34:1459-1469. 2006
  • Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction..  34:5943-5950. 2006
  • Probing the DNA sequence specificity of Escherichia coli RECA protein..  34:2463-2471. 2006
  • The Gene Ontology (GO) project in 2006..  34:D322-D326. 2006
  • The hepatitis C virus 3'-untranslated region or a poly(A) tract promote efficient translation subsequent to the initiation phase..  34:1293-1303. 2006
  • dictyBase, the model organism database for Dictyostelium discoideum..  34. 2006
  • dictyBase, the model organism database for Dictyostelium discoideum..  34:D423-D427. 2006
  • Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays..  33:409-421. 2005
  • Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE..  33:2838-2851. 2005
  • Mutagenic effects of abasic and oxidized abasic lesions in Saccharomyces cerevisiae..  33:6196-6202. 2005
  • MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes..  32:W615-W619. 2004
  • Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping..  32:e27. 2004
  • RNA interference using boranophosphate siRNAs: structure-activity relationships..  32:5991-6000. 2004
  • The Gene Ontology (GO) database and informatics resource..  32:D258-D261. 2004
  • dictyBase: a new Dictyostelium discoideum genome database..  32:D332-D333. 2004
  • CRP: Cleavage of Radiolabeled Phosphoproteins..  31:3859-3861. 2003
  • GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders.  31:3601-3604. 2003
  • A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes..  31:1805-1812. 2003
  • DNA-XPA interactions: a (31)P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA..  29:2635-2643. 2001
  • Identification of the yeast cytidine deaminase CDD1 as an orphan C-->U RNA editase..  29:1772-1780. 2001
  • Juglone, an inhibitor of the peptidyl-prolyl isomerase Pin1, also directly blocks transcription..  29:767-773. 2001
  • Precise arrangement of factor-binding sites is required for murine CD4 promoter function..  28:2664-2671. 2000