Nucleic acids research

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GenoPipe: identifying the genotype of origin within (epi)genomic datasets. 2023
The RNA export factor TbMex67 connects transcription and RNA export in Trypanosoma brucei and sets boundaries for RNA polymerase I. 2023
Cellular responses to long-term phosphate starvation of fission yeast: Maf1 determines fate choice between quiescence and death associated with aberrant tRNA biogenesis. 2023
SMAD3 promotes expression and activity of the androgen receptor in prostate cancer. 2023
Molecular architecture and oligomerization of Candida glabrata Cdc13 underpin its telomeric DNA-binding and unfolding activity. 2023
Mycobacterial helicase Lhr abets resistance to DNA crosslinking agents mitomycin C and cisplatin.. 51. 2023
Efficient detection and assembly of non-reference DNA sequences with synthetic long reads. 2022
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?. 50. 2022
RBFOX2 is required for establishing RNA regulatory networks essential for heart development.. 50. 2022
Genetic screen for suppression of transcriptional interference reveals fission yeast 14-3-3 protein Rad24 as an antagonist of precocious Pol2 transcription termination. 2021
Division of labor between SOS and PafBC in mycobacterial DNA repair and mutagenesis.. 49. 2021
Dynamic queuosine changes in tRNA couple nutrient levels to codon choice in Trypanosoma brucei.. 49. 2021
Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14.. 49. 2021
Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing.. 49. 2021
Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin.. 49. 2021
CNCDatabase: a database of non-coding cancer drivers.. 49. 2021
Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes.. 48. 2020
A genetic screen for suppressors of hyper-repression of the fission yeast PHO regulon by Pol2 CTD mutation T4A implicates inositol 1-pyrophosphates as agonists of precocious lncRNA transcription termination.. 48. 2020
Genetic interactions and transcriptomics implicate fission yeast CTD prolyl isomerase Pin1 as an agent of RNA 3' processing and transcription termination that functions via its effects on CTD phosphatase Ssu72.. 48. 2020
Synthetic CRISPR/Cas9 reagents facilitate genome editing and homology directed repair.. 48. 2020
GO: a functional reporter system to identify and enrich base editing activity.. 48. 2020
Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.. 47. 2019
Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA.. 47. 2019
Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3' processing and transcription termination.. 47. 2019
The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112.. 47. 2019
Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence.. 47. 2019
Translation initiation factor IF2 contributes to ribosome assembly and maturation during cold adaptation.. 47. 2019
Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders.. 47. 2019
Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome.. 47. 2019
Unexpected diversity in eukaryotic transcription revealed by the retrotransposon hotspot family of Trypanosoma brucei.. 47. 2019
ERASE: a novel surface reconditioning strategy for single-molecule experiments.. 47. 2019
ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci.. 47. 2019
Distinctive structural basis for DNA recognition by the fission yeast Zn2Cys6 transcription factor Pho7 and its role in phosphate homeostasis.. 46. 2018
In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets.. 46. 2018
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.. 46. 2018
A novel transcript isoform of STING that sequesters cGAMP and dominantly inhibits innate nucleic acid sensing.. 46. 2018
Direct observation of nucleic acid binding dynamics by the telomerase essential N-terminal domain.. 46. 2018
Proteomic identification of histone post-translational modifications and proteins enriched at a DNA double-strand break.. 45. 2017
Crosstalk between histone modifications indicates that inhibition of arginine methyltransferase CARM1 activity reverses HIV latency.. 45. 2017
De novo pathway-based biomarker identification.. 45. 2017
STN1-POLA2 interaction provides a basis for primase-pol α stimulation by human STN1.. 45. 2017
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud.. 45. 2017
Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell.. 45. 2017
Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex.. 45. 2017
Homologous recombination mediated by the mycobacterial AdnAB helicase without end resection by the AdnAB nucleases.. 45. 2016
Division of labor among Mycobacterium smegmatis RNase H enzymes: RNase H1 activity of RnhA or RnhC is essential for growth whereas RnhB and RnhA guard against killing by hydrogen peroxide in stationary phase.. 45. 2016
Regulation of oxidized base damage repair by chromatin assembly factor 1 subunit A.. 45. 2016
Identification of distinct biological functions for four 3'-5' RNA polymerases.. 44. 2016
Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast.. 44. 2016
The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome.. 44. 2016
deepTools2: a next generation web server for deep-sequencing data analysis.. 44. 2016
Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA.. 44. 2015
The ubiquitin ligase HERC3 attenuates NF-κB-dependent transcription independently of its enzymatic activity by delivering the RelA subunit for degradation.. 43. 2015
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.. 43. 2015
Functional interaction of Rpb1 and Spt5 C-terminal domains in co-transcriptional histone modification.. 43. 2015
How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets.. 43. 2015
CTNNBL1 facilitates the association of CWC15 with CDC5L and is required to maintain the abundance of the Prp19 spliceosomal complex.. 43. 2015
Combinatorial recognition of a complex telomere repeat sequence by the Candida parapsilosis Cdc13AB heterodimer.. 43. 2015
Fungal Ku prevents permanent cell cycle arrest by suppressing DNA damage signaling at telomeres.. 43. 2015
Adhesin competence repressor (AdcR) from Streptococcus pyogenes controls adaptive responses to zinc limitation and contributes to virulence.. 43. 2014
BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers.. 43. 2014
Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).. 43. 2014
Ensembl 2015.. 43. 2014
Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28.. 42. 2014
Requirement of CRTC1 coactivator for hepatitis B virus transcription.. 42. 2014
The ubiquitin-selective chaperone Cdc48/p97 associates with Ubx3 to modulate monoubiquitylation of histone H2B.. 42. 2014
Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing.. 42. 2014
deepTools: a flexible platform for exploring deep-sequencing data.. 42. 2014
Structure-function analysis of the Yhc1 subunit of yeast U1 snRNP and genetic interactions of Yhc1 with Mud2, Nam8, Mud1, Tgs1, U1 snRNA, SmD3 and Prp28.. 42. 2014
Ensembl 2014.. 42. 2013
DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families.. 42. 2013
InvFEST, a database integrating information of polymorphic inversions in the human genome.. 42. 2013
Malaria parasites utilize both homologous recombination and alternative end joining pathways to maintain genome integrity.. 42. 2013
A signature motif mediating selective interactions of BCL11A with the NR2E/F subfamily of orphan nuclear receptors.. 41. 2013
Structure-function analysis of the 5' end of yeast U1 snRNA highlights genetic interactions with the Msl5*Mud2 branchpoint-binding complex and other spliceosome assembly factors.. 41. 2013
Polycomb recruitment attenuates retinoic acid-induced transcription of the bivalent NR2F1 gene.. 41. 2013
Impaired in vivo binding of MeCP2 to chromatin in the absence of its DNA methyl-binding domain.. 41. 2013
A dual role for mycobacterial RecO in RecA-dependent homologous recombination and RecA-independent single-strand annealing.. 41. 2013
One size does not fit all: on how Markov model order dictates performance of genomic sequence analyses.. 41. 2012
Ensembl 2013.. 41. 2012
The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics.. 41. 2012
Structure-function analysis and genetic interactions of the yeast branchpoint binding protein Msl5.. 40. 2012
Crucial elements that maintain the interactions between the regulatory TnaC peptide and the ribosome exit tunnel responsible for Trp inhibition of ribosome function.. 40. 2011
Ensembl 2012.. 40. 2011
Epigenetic regulation by RARα maintains ligand-independent transcriptional activity.. 40. 2011
A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling.. 39. 2011
Composition of yeast snRNPs and snoRNPs in the absence of trimethylguanosine caps reveals nuclear cap binding protein as a gained U1 component implicated in the cold-sensitivity of tgs1Δ cells.. 39. 2011
A method to sequence and quantify DNA integration for monitoring outcome in gene therapy.. 39. 2011
An essential role for trimethylguanosine RNA caps in Saccharomyces cerevisiae meiosis and their requirement for splicing of SAE3 and PCH2 meiotic pre-mRNAs.. 39. 2011
Determinants of Nam8-dependent splicing of meiotic pre-mRNAs.. 39. 2011
MIPS: curated databases and comprehensive secondary data resources in 2010.. 39. 2010
Protein inactivation in mycobacteria by controlled proteolysis and its application to deplete the beta subunit of RNA polymerase.. 39. 2010
Ensembl 2011.. 39. 2010
A multivalent DNA aptamer specific for the B-cell receptor on human lymphoma and leukemia.. 39. 2010
Determinants of eukaryal cell killing by the bacterial ribotoxin PrrC.. 39. 2010
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences.. 38. 2010
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.. 38. 2010
Segmental duplications in the human genome reveal details of pseudogene formation.. 38. 2010
Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays.. 38. 2010
Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.. 38. 2010
Ensembl's 10th year.. 38. 2009
High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers.. 37. 2009
Improved tetracycline repressors for gene silencing in mycobacteria.. 37. 2009
Ensembl 2009.. 37. 2008
Pseudofam: the pseudogene families database.. 37. 2008
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens.. 37. 2008
The G-quartet containing FMRP binding site in FMR1 mRNA is a potent exonic splicing enhancer.. 36. 2008
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches.. 36. 2008
MassTRIX: mass translator into pathways.. 36. 2008
The microRNA.org resource: targets and expression.. 36. 2007
SIMAP--structuring the network of protein similarities.. 36. 2007
Ensembl 2008.. 36. 2007
In vivo construction of recombinant molecules within the Caenorhabditis elegans germ line using short regions of terminal homology.. 35. 2007
Sinefungin resistance of Saccharomyces cerevisiae arising from Sam3 mutations that inactivate the AdoMet transporter or from increased expression of AdoMet synthase plus mRNA cap guanine-N7 methyltransferase.. 35. 2007
CG dinucleotide clustering is a species-specific property of the genome.. 35. 2007
Modeling and structure function analysis of the putative anchor site of yeast telomerase.. 35. 2007
Topology of Type II REases revisited; structural classes and the common conserved core.. 35. 2007
Biochemical and genetic analysis of RNA cap guanine-N2 methyltransferases from Giardia lamblia and Schizosaccharomyces pombe.. 35. 2007
Ensembl 2007.. 35. 2006
Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.. 35. 2006
Structure-based prediction of insertion-site preferences of transposons into chromosomes.. 34. 2006
Modulation of telomere terminal structure by telomerase components in Candida albicans.. 34. 2006
Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog.. 34. 2006
Structure-function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase.. 33. 2005
An Oct-1 binding site mediates activation of the gata2 promoter by BMP signaling.. 33. 2005
Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor.. 33. 2005
Site-specific labeling of the ribosome for single-molecule spectroscopy.. 33. 2005
The Biomolecular Interaction Network Database and related tools 2005 update.. 33. 2005
High sensitivity EndoV mutation scanning through real-time ligase proofreading.. 32. 2004
Determination and augmentation of RNA sequence specificity of the Nova K-homology domains.. 32. 2004
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.. 32. 2004
CaspR: a web server for automated molecular replacement using homology modelling.. 32. 2004
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.. 32. 2004
Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis.. 32. 2004
Sensing complex regulatory networks by conformationally controlled hairpin ribozymes.. 32. 2004
Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples.. 32. 2004
Real-time measurement of in vitro transcription.. 32. 2004
Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica.. 32. 2004
Yeast telomerase is capable of limited repeat addition processivity.. 32. 2004
FusionDB: a database for in-depth analysis of prokaryotic gene fusion events.. 32. 2004
Optimizing spotting solutions for increased reproducibility of cDNA microarrays.. 31. 2003
A chemical enucleation method for the transfer of mitochondrial DNA to rho(o) cells.. 31. 2003
Building protein diagrams on the web with the residue-based diagram editor RbDe.. 31. 2003
Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes.. 31. 2003
Single-chain Tet transregulators.. 31. 2003
TissueInfo: high-throughput identification of tissue expression profiles and specificity.. 29. 2001
Transformation of malaria parasites by the spontaneous uptake and expression of DNA from human erythrocytes.. 29. 2001
Characterization of Schizosaccharomyces pombe RNA triphosphatase.. 29. 2001
Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs.. 29. 2001
MethyLight: a high-throughput assay to measure DNA methylation.. 28. 2000
Interaction of the yeast DExH-box RNA helicase prp22p with the 3' splice site during the second step of nuclear pre-mRNA splicing.. 28. 2000
Ligation reaction specificities of an NAD(+)-dependent DNA ligase from the hyperthermophile Aquifex aeolicus.. 28. 2000
The catalytic subunit DNA-dependent protein kinase (DNA-PKcs) facilitates recovery from radiation-induced inhibition of DNA replication.. 28. 2000
Improved fidelity of thermostable ligases for detection of microsatellite repeat sequences using nucleoside analogs.. 27. 1999
Ligase-based detection of mononucleotide repeat sequences.. 27. 1999
Mutational analysis of Escherichia coli DNA ligase identifies amino acids required for nick-ligation in vitro and for in vivo complementation of the growth of yeast cells deleted for CDC9 and LIG4.. 27. 1999
The promyelocytic leukemia zinc finger (PLZF) protein binds DNA in a high molecular weight complex associated with cdc2 kinase.. 27. 1999
Sequence-specific and conformation-dependent binding of yeast telomerase RNA to single-stranded telomeric DNA.. 27. 1999
Nucleotide analogs and new buffers improve a generalized method to enrich for low abundance mutations.. 27. 1999
Nucleotide analogs facilitate base conversion with 3' mismatch primers.. 27. 1999
Targeted gene repair directed by the chimeric RNA/DNA oligonucleotide in a mammalian cell-free extract.. 27. 1999
Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D.. 27. 1999
The LAZ3(BCL-6) oncoprotein recruits a SMRT/mSIN3A/histone deacetylase containing complex to mediate transcriptional repression.. 26. 1998
Accelerated mRNA decay in conditional mutants of yeast mRNA capping enzyme.. 26. 1998
Negative regulation of yeast telomerase activity through an interaction with an upstream region of the DNA primer.. 26. 1998
Species-specific and sequence-specific recognition of the dG-rich strand of telomeres by yeast telomerase.. 26. 1998
Effects of deletion mutations in the yeast Ces1 protein on cell growth and morphology and on high copy suppression of mutations in mRNA capping enzyme and translation initiation factor 4A.. 26. 1998
Identification and characterization of a telomerase activity from Schizosaccharomyces pombe.. 25. 1997
Identification of rapid turnover transcripts overexpressed in thyroid tumors and thyroid cancer cell lines: use of a targeted differential RNA display method to select for mRNA subsets.. 25. 1997
The Elav-like proteins bind to AU-rich elements and to the poly(A) tail of mRNA.. 25. 1997
Functional and physical interaction between the yeast splicing factors Slu7 and Prp18.. 25. 1997
The p53 status of Chinese hamster V79 cells frequently used for studies on DNA damage and DNA repair.. 25. 1997
Identification of essential residues in Thermus thermophilus DNA ligase.. 24. 1996
Improving the fidelity of Thermus thermophilus DNA ligase.. 24. 1996
Identification of a 27 bp 5'-flanking region element responsible for the low level constitutive expression of the human cytosolic phospholipase A2 gene.. 23. 1995
Transfer of a constitutive viral promoter-cystic fibrosis transmembrane conductance regulator cDNA to human epithelial cells conveys resistance to down-regulation of cAMP-regulated Cl- secretion in the presence of inflammatory stimuli.. 22. 1994
The DNA binding domains of the varicella-zoster virus gene 62 and herpes simplex virus type 1 ICP4 transactivator proteins heterodimerize and bind to DNA.. 22. 1994
Mutation of a single lysine residue severely impairs the DNA recognition and regulatory functions of the VZV gene 62 transactivator protein.. 22. 1994
The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure.. 21. 1993
Protection of human endothelial cells from oxidant injury by adenovirus-mediated transfer of the human catalase cDNA.. 21. 1993
The DNA binding domain of the varicella-zoster virus gene 62 protein interacts with multiple sequences which are similar to the binding site of the related protein of herpes simplex virus type 1.. 21. 1993
Adenovirus DNA replication facilitates binding of the MLTF/USF transcription factor to the viral major late promoter within infected cells.. 20. 1992
Interaction of the erythroid transcription factor cGATA-1 with a critical auto-regulatory element.. 20. 1992
Cationic lipid-mediated transfection of liver cells in primary culture.. 20. 1992
Expression of the human cystic fibrosis transmembrane conductance regulator gene in the mouse lung after in vivo intratracheal plasmid-mediated gene transfer.. 20. 1992
Expression of the cystic fibrosis transmembrane conductance regulator gene in cells of non-epithelial origin.. 19. 1991
Location of the fpg gene on the Escherichia coli chromosome.. 19. 1991
Sequence analysis of a DNA fragment with yeast autonomously replicating sequence activity from the extrachromosomal ribosomal DNA circle of Entamoeba histolytica.. 19. 1991
A Taq 1 polymorphism for the human platelet glycoprotein IIIa gene (GP3A).. 16. 1988
Sequence analysis and in vivo expression show that alternative splicing of ED-B and ED-A regions of the human fibronectin gene are independent events.. 16. 1988
Adenovirus 2 VA RNAI synthesized in SP6 system.. 16. 1988
Alternative use of chromosome fragmentation sites in the ciliated protozoan Oxytricha nova.. 16. 1988
A complex Hind III polymorphism in the human apolipoprotein-B gene (APOB).. 15. 1987
Discrimination among multiple AATAAA sequences correlates with interspecies conservation of select 3' untranslated nucleotides.. 14. 1986
Analysis of the promoter region and the N-propeptide domain of the human pro alpha 2(I) collagen gene.. 13. 1985
Transcription termination occurs within a 1000 base pair region downstream from the poly(A) site of the mouse beta-globin (major) gene.. 12. 1984
ATA box transcription mutation in beta-thalassemia.. 11. 1983
Infectivity and structure of molecular clones obtained from two genetically transmitted Moloney leukemia proviral genomes.. 10. 1982
Secondary structures for splice junctions in eukaryotic and viral messenger RNA precursors.. 8. 1980
The nucleotide sequence of an untranslated but conserved domain at the 3' end of the avian sarcoma virus genome.. 8. 1980
Structural organization of a 17 KB segment of the alpha 2 collagen gene: evaluation by R loop mapping.. 8. 1980
Construction and characterization of a cDNA clone containing a portion of the bovine prolactin sequence.. 8. 1980
Molecular models for the tissue specificity of DNA mismatch repair-deficient carcinogenesis. 2006

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