Nucleic Acids Research

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  Publication Venue For

  • RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data..  49:7925-7938. 2021
  • Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor..  49:6474-6488. 2021
  • A role of the CTCF binding site at enhancer Eα in the dynamic chromatin organization of the Tcra-Tcrd locus..  48:9621-9636. 2020
  • Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems..  48:9550-9570. 2020
  • Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins..  48:9872-9885. 2020
  • Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans..  48:7653-7664. 2020
  • Free energy landscape of salt-actuated reconfigurable DNA nanodevices..  48:548-560. 2020
  • G-quadruplex structures trigger RNA phase separation..  47:11746-11754. 2019
  • LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data.  47:e111-e111. 2019
  • Prophage Hunter: an integrative hunting tool for active prophages..  47:W74-W80. 2019
  • Creation of versatile cloning platforms for transgene expression and dCas9-based epigenome editing..  47:e23. 2019
  • Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor..  47:1404-1415. 2019
  • The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA..  47:2130-2142. 2019
  • Insights into the development of chemical probes for RNA..  46:8025-8037. 2018
  • Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2..  45:e167. 2017
  • A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea..  45:9990-10001. 2017
  • Differential expression analysis for RNAseq using Poisson mixed models..  45:e106. 2017
  • A 'Semi-Protected Oligonucleotide Recombination' Assay for DNA Mismatch Repair in vivo Suggests Different Modes of Repair for Lagging Strand Mismatches..  45:e63. 2017
  • A three-dimensional ParF meshwork assembles through the nucleoid to mediate plasmid segregation..  45:3158-3171. 2017
  • TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.  44:e117-e117. 2016
  • Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage..  44:2474. 2016
  • Quantification of DNA cleavage specificity in Hi-C experiments..  44:e4. 2016
  • Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage..  43:8924-8941. 2015
  • Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector..  42:e147. 2014
  • Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes..  42:9691-9699. 2014
  • Molecular evolutionary and structural analysis of the cytosolic DNA sensor cGAS and STING..  42:8243-8257. 2014
  • Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea..  41:8546-8558. 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
  • Recovering ensembles of chromatin conformations from contact probabilities..  41:63-75. 2013
  • Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract..  40:11023-11035. 2012
  • Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.  40:7690-7704. 2012
  • Gene targeting to the ROSA26 locus directed by engineered zinc finger nucleases..  40:3741-3752. 2012
  • Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation..  40:2734-2746. 2012
  • Mitochondrial dynamics and autophagy aid in removal of persistent mitochondrial DNA damage in Caenorhabditis elegans.  40:7916-7931. 2012
  • Unraveling the structural complexity in a single-stranded RNA tail: Implications for efficient ligand binding in the prequeuosine riboswitch.  40:1345-1355. 2012
  • Towards resolving the transcription factor network controlling myelin gene expression..  39:7974-7991. 2011
  • Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase..  39:7868-7878. 2011
  • Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon..  39:2519-2533. 2011
  • Directed evolution of recombinase specificity by split gene reassembly..  38:4198-4206. 2010
  • Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.  38. 2010
  • Finding regulatory DNA motifs using alignment-free evolutionary conservation information.  38. 2010
  • The Gene Oncology (GO) database and informatics resource.  32. 2004
  • dictyBase: A new Dictyostelium discoideum genome database.  32. 2004
  • Boron-containing aptamers to ATP..  30:1401-1407. 2002
  • Mutational fingerprints of aging..  30:545-549. 2002
  • Quantitative analysis of mRNA amplification by in vitro transcription..  29:E29. 2001
  • Synthesis of 5-substituted 2'-deoxycytidine 5'-(alpha-P-borano)triphosphates, their incorporationinto DNA and effects on exonuclease..  27:1788-1794. 1999
  • A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduceskinetic trapping of inactive conformations..  27:795-802. 1999
  • Sp1, but not Sp3, functions to mediate promoter activation by TGF-beta through canonical Sp1 binding sites..  26:2449-2456. 1998
  • Sp1 activation of a TATA-less promoter requires a species-specific interaction involving transcription factor IID..  26:839-846. 1998
  • TAR RNA decoys inhibit tat-activated HIV-1 transcription after preinitiation complex formation..  25:4481-4486. 1997
  • Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus..  25:4085-4092. 1997
  • Direct PCR sequencing with boronated nucleotides..  25:1611-1617. 1997
  • Inhibition of the erbB-2 tyrosine kinase receptor in breast cancer cells by phosphoromonothioate and phosphorodithioate antisense oligonucleotides..  24:4558-4564. 1996
  • Efficient random subcloning of DNA sheared in a recirculating point-sink flow system..  24:3879-3886. 1996
  • A small circular TAR RNA decoy specifically inhibits Tat-activated HIV-1 transcription..  24:3733-3738. 1996
  • Base-boronated dinucleotides: synthesis and effect of N7-cyanoborane substitution on the base protons..  24:2150-2157. 1996
  • Two-dimensional gel analysis of rolling circle replication in the presence and absence of bacteriophage T4 primase..  24:2166-2175. 1996
  • The 5' and 3' splice sites come together via a three dimensional diffusion mechanism..  24:1638-1645. 1996
  • Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage..  24:1314-1321. 1996
  • The DNA-binding protein Hdf1p (a putative Ku homologue) is required for maintaining normal telomere length in Saccharomyces cerevisiae..  24:582-585. 1996
  • Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies..  23:4495-4501. 1995
  • U1 snRNP-ASF/SF2 interaction and 5' splice site recognition: characterization of required elements..  23:3260-3267. 1995
  • Mimosine, a novel inhibitor of DNA replication, binds to a 50 kDa protein in Chinese hamster cells..  23:261-268. 1995
  • Structure and regulation of the chicken erythroid delta-aminolevulinate synthase gene..  22:1226-1233. 1994
  • The Oct-2 transcription factor represses tyrosine hydroxylase expression via a heptamer TAATGARAT-like motif in the gene promoter..  22:1023-1028. 1994
  • A circular trans-acting hepatitis delta virus ribozyme..  21:4253-4258. 1993
  • Assessment of disparate structural features in three models of the hepatitis delta virus ribozyme..  21:3959-3965. 1993
  • Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons..  20:5357-5364. 1992
  • RNA binding specificity of a Drosophila snRNP protein that shares sequence homology with mammalian U1-A and U2-B" proteins..  20:3645-3650. 1992
  • Rapid shotgun cloning utilizing the two base recognition endonuclease CviJI..  20:3753-3762. 1992
  • A StuI polymorphism on chromosome 3p14.1-14.2 (D3S622) defined by two polymorphic StuI sites 2.4 kb apart..  19:6349. 1991
  • The isolation and characterization of a novel cDNA demonstrating an altered mRNA level in nontumorigenic Wilms' microcell hybrid cells..  19:5763-5769. 1991
  • Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures..  19:5409-5416. 1991
  • U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts..  19:4931-4936. 1991
  • Replication control of autonomously replicating human sequences..  19:5053-5058. 1991
  • RsaI RFLP for electron transport flavoprotein-beta(ETFB)..  19:4021. 1991
  • A highly polymorphic cDNA probe in the NF1 gene..  19:3754. 1991
  • The human TTP protein: sequence, alignment with related proteins, and chromosomal localization of the mouse and human genes..  19:3454. 1991
  • A rapid micropreparation technique for extraction of DNA-binding proteins from limiting numbers of mammalian cells..  19:2499. 1991
  • The self-cleaving domain from the genomic RNA of hepatitis delta virus: Sequence requirements and the effects of denaturant.  19:1979. 1991
  • Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products..  19:1154. 1991
  • MspI RFLP for microtubule associated protein-2 (MAP2)..  19:960. 1991
  • Nucleotide sequence of mouse SCIP cDNA, a POU-domain transcription factor..  19:956. 1991
  • A polymorphic cDNA probe on chromosome 17q11.2 located within the NF1 gene [D17S376]..  19:197. 1991
  • Molecular cloning of a cDNA of a camptothecin-resistant human DNA topoisomerase I and identification of mutation sites..  19:69-75. 1991
  • The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant..  18:6821-6827. 1990
  • A three allele TaqI polymorphism at TOP1 gene..  18:5919. 1990
  • Location of the host attachment site for phage HPl within a cluster of Haemophilus influenzae tRNA genes..  18:5305. 1990
  • D21S194, a jump clone from D21S16..  18:1931. 1990
  • Mutations at arginine residues in two Asian hemophilia B patients..  18:1924. 1990
  • A highly conserved RNA folding region coincident with the Rev response element of primate immunodeficiency viruses..  18:1613-1623. 1990
  • A frequent human CD20 (B1) differentiation antigen DNA polymorphism detected with MspI is located near 11q12-13..  18:207. 1990
  • Cassettes of the f1 intergenic region..  17:4413. 1989
  • Sequence of the cDNA for the alpha subunit of calmodulin kinase II from mouse brain..  17:3992. 1989
  • A Bgl II polymorphism detected by LDR152 [D19S19]..  16:9063. 1988
  • Mismatch-containing oligonucleotide duplexes bound by the E. coli mutS-encoded protein..  16:7843-7853. 1988
  • pYAC-RC, a yeast artificial chromosome vector for cloning DNA cut with infrequently cutting restriction endonucleases..  16:7743. 1988
  • In vivo functional analysis of in vitro protein binding sites in the immunoglobulin heavy chain enhancer..  16:3239-3253. 1988
  • Identification of an X-ray induced deletion mutant flanked by direct repeats..  15:7641. 1987
  • Identification and cell type specificity of the tyrosine hydroxylase gene promoter..  15:2363-2384. 1987
  • RFLPs at the D19S19 locus of human chromosome 19 linked to myotonic dystrophy (DM)..  14:5569. 1986
  • Isolation and characterization of a Ty element inserted into the ribosomal DNA of the yeast Saccharomyces cerevisiae..  14:2939-2949. 1986
  • Sites of circularization of the Tetrahymena rRNA IVS are determined by sequence and influenced by position and secondary structure..  13:8389-8408. 1985
  • Analysis of repetitive sequence elements containing tRNA-like sequences..  13:4239-4252. 1985
  • Beta-thalassemia resulting from a single nucleotide substitution in an acceptor splice site..  13:777-790. 1985
  • Tandemly arranged variant 5S ribosomal RNA genes in the yeast Saccharomyces cerevisiae..  12:8001-8016. 1984
  • 'Interactive' recognition in EcoRI restriction enzyme-DNA complex..  12:7285-7292. 1984
  • X-ray structure of cytidine-5'-O-dimethylphosphate. Novel stacking between the ribosyl O(2') hydroxyl oxygen atom and the base..  12:6813-6825. 1984
  • Nucleotide sequence preference at rat liver and wheat germ type 1 DNA topoisomerase breakage sites in duplex SV40 DNA..  12:3097-3114. 1984
  • Genomic organization of rat rDNA..  11:6437-6452. 1983
  • Isolation of cDNA clones for basal lamina components: type IV procollagen..  11:6199-6209. 1983
  • Identification and sequence of the initiation site for rat 45S ribosomal RNA synthesis..  11:3317-3332. 1983
  • Effect of intron size on splicing efficiency in retroviral transcripts..  10:6177-6190. 1982
  • Structural differences in the chromatin from compartmentalized cells of the sea urchin embryo: differential nuclease accessibility of micromere chromatin..  9:5609-5621. 1981
  • Abundant androgen regulated mRNAs in mouse submandibular gland: cell-free translation of renin precursor mRNA..  9:3433-3449. 1981
  • The isolation of ecdysterone inducible genes by hybridization subtraction chromatography..  9:1191-1202. 1981
  • Breakage of single-stranded DNA by rat liver nicking-closing enzyme with the formation of a DNA-enzyme complex..  8:6129-6142. 1980
  • Substrate dependence of the mechanism of EcoRI endonuclease..  5:2991-2997. 1978
  • Novikoff hepatoma deoxyribonucleic acid polymerase. Sensitivity of the beta-polymerase to sulfhydryl blocking agents..  3:2341-2352. 1976
  • Duplication of single stranded DNA catalyzed by calf thymus DNA polymerase alpha..  3:129-147. 1976
  • Thermal denaturation of DNA from bromodeoxyuridine substituted cells..  3:49-62. 1976