An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs.

abstract：:We have isolated a human cDNA (kup), encoding a new protein with two distantly spaced zinc fingers of the C2H2 type. This gene is highly conserved in mammals and is expressed mainly in hematopoietic cells and testis. Its expression was not higher in the various transformed cells tested than in the normal corresponding...

journal_title：Nucleic acids research

authors： Chardin P,Courtois G,Mattei MG,Gisselbrecht S

更新日期：1991-04-11 00:00:00

abstract：:The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...

journal_title：Nucleic acids research

authors： Markowitz VM,Chen IM,Palaniappan K,Chu K,Szeto E,Grechkin Y,Ratner A,Jacob B,Huang J,Williams P,Huntemann M,Anderson I,Mavromatis K,Ivanova NN,Kyrpides NC

更新日期：2012-01-01 00:00:00

abstract：:BRCA1 expression is repressed by aberrant cytosine methylation in sporadic breast cancer. We hypothesized that aberrant cytosine methylation of the BRCA1 promoter was associated with the transcriptionally repressive effects of histone hypoacetylation and chromatin condensation. To address this question, we developed a...

journal_title：Nucleic acids research

authors： Rice JC,Futscher BW

更新日期：2000-09-01 00:00:00

abstract：:Ribosome biogenesis in Saccharomyces cerevisiae involves a regulon of >200 genes (Ribi genes) coordinately regulated in response to nutrient availability and cellular growth rate. Two cis-acting elements called PAC and RRPE are known to mediate Ribi gene repression in response to nutritional downshift. Here, we show t...

journal_title：Nucleic acids research

authors： Bosio MC,Fermi B,Spagnoli G,Levati E,Rubbi L,Ferrari R,Pellegrini M,Dieci G

更新日期：2017-05-05 00:00:00

abstract：:After ionising radiation double-strand breaks (dsb) are lethal if not repaired or misrepaired. Cell killing is greatly enhanced by hyperthermia and it is questioned here whether heat not only affects dsb repair capacity but also fidelity in a chromosomal context. dsb repair experiments were designed so as to mainly sc...

journal_title：Nucleic acids research

authors： El-Awady RA,Dikomey E,Dahm-Daphi J

更新日期：2001-05-01 00:00:00

abstract：:Conventional chemotherapy remains the primary treatment option for triple-negative breast cancer (TNBC). However, the current chemotherapeutic drugs have limited effects on TNBC, and often lead to serious side effects as well as drug resistance. Thus, more effective therapeutic options are sorely needed. As c-MYC onco...

journal_title：Nucleic acids research

authors： Hu MH,Wu TY,Huang Q,Jin G

更新日期：2019-11-18 00:00:00

abstract：:We have determined the nucleotide sequence at the 3' end of the vesicular stomatitis virus (VSV) polymerase or L gene and compared it to that obtained from a defective interfering particle (DI) RNA generated by this virus. The latter (DI 0.50) contains a large internal deletion within this gene. The deletion begins ex...

journal_title：Nucleic acids research

authors： De BK,Perrault J

更新日期：1982-11-11 00:00:00

abstract：:Unmethylated CpG rich islands are a feature of vertebrate DNA: they are associated with housekeeping and many tissue specific genes. CpG islands on the active X chromosome of mammals are also unmethylated. However, islands on the inactive X chromosome are heavily methylated. We have identified a CpG island in the 5' r...

journal_title：Nucleic acids research

authors： Alcalay M,Toniolo D

更新日期：1988-10-25 00:00:00

abstract：:The products of the RAG-1 and RAG-2 genes are essential for the recombination of the DNA encoding the antigen receptors of the developing immune system. Little is known of the specific role these genes play. We have explored the sequences encoding mouse RAG-1 by deleting large parts of the gene and by introducing loca...

journal_title：Nucleic acids research

authors： Sadofsky MJ,Hesse JE,McBlane JF,Gellert M

更新日期：1993-12-11 00:00:00

abstract：:Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intron. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this ...

journal_title：Nucleic acids research

authors： Ogg SC,Anderson P,Wickens MP

更新日期：1990-01-11 00:00:00

abstract：:The two genes encoding the class IIS restriction-modification system MboII from Moraxella bovis were cloned separately in two compatible plasmids and expressed in E. coli RR1 delta M15. The nucleotide sequences of the MboII endonuclease (R.MboII) and methylase (M.MboII) genes were determined and the putative start cod...

journal_title：Nucleic acids research

authors： Bocklage H,Heeger K,Müller-Hill B

更新日期：1991-03-11 00:00:00

abstract：:Rad2/XPG belongs to the flap nuclease family and is responsible for a key step of the eukaryotic nucleotide excision DNA repair (NER) pathway. To elucidate the mechanism of DNA binding by Rad2/XPG, we solved crystal structures of the catalytic core of Rad2 in complex with a substrate. Rad2 utilizes three structural mo...

journal_title：Nucleic acids research

authors： Miętus M,Nowak E,Jaciuk M,Kustosz P,Studnicka J,Nowotny M

更新日期：2014-01-01 00:00:00

abstract：:Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom availa...

journal_title：Nucleic acids research

authors： Azad RN,Zafiropoulos D,Ober D,Jiang Y,Chiu TP,Sagendorf JM,Rohs R,Tullius TD

更新日期：2018-03-16 00:00:00

abstract：:In continuation with work regarding the evaluation of the energy of association of various RNA bases with various base pairs, the results of the computations of the electrostatic interaction energy of A-U base pair with four RNA bases viz. Adenine, Uracil, Guanine and Cytosine have been reported. Non bonded induced po...

journal_title：Nucleic acids research

authors： Sanyal NK,Kumar U,Roychoudhury M

更新日期：1980-09-11 00:00:00

abstract：:For sophisticated gene targeting procedures requiring two sequential selective steps to operate efficiently it is essential that the marker genes used are not prone to position effects. The double replacement gene targeting procedure, to produce mice with subtle gene alterations, is based on the use of hypoxanthine ph...

journal_title：Nucleic acids research

authors： Melton DW,Ketchen AM,Selfridge J

更新日期：1997-10-01 00:00:00

abstract：:The interaction of several synthetic analogues of d-ApA with Poly U and Poly dT was examined to explore the effects of substituents at phosphorus on binding properties of oligonucleotides. These analogues contained a bulky, lipophilic group (2,2,2-trichloroethoxy or 2,2,2-trichloro-1,1-dimethylethoxy) a small, uncharg...

journal_title：Nucleic acids research

authors： Letsinger RL,Bach SA,Eadie JS

更新日期：1986-04-25 00:00:00

abstract：:Differential scanning microcalorimetry (DSC), UV absorption and circular dichroism (CD) have been used to study structure and stability of linear (lin), open circular (oc), supercoiled (cd) and relaxed circular duplex (rd) DNA and calf thymus (CT) DNA. Investigations were made in low salt buffer and in the presence of...

journal_title：Nucleic acids research

authors： Thumm W,Seidl A,Hinz HJ

更新日期：1988-12-23 00:00:00

abstract：:By means of titration viscometry a number of distinct modes could be resolved for the interaction between the antibiotic netropsin and DNA species of 50, 58, and 69 mole + (A+T) below r = 0.04 netropsin molecules bound per DNA phosphate group. The number of corresponding binding sites increases with a high power of th...

journal_title：Nucleic acids research

authors： Reinert KE,Stutter E,Schweiss H

更新日期：1979-11-10 00:00:00

abstract：:U1-snRNA is an integral part of the U1 ribonucleoprotein pivotal for pre-mRNA splicing. Toll-like receptor (TLR) signaling has recently been associated with immunoregulatory capacities of U1-snRNA. Using lung A549 epithelial/carcinoma cells, we report for the first time on interferon regulatory factor (IRF)-3 activati...

journal_title：Nucleic acids research

authors： Sadik CD,Bachmann M,Pfeilschifter J,Mühl H

更新日期：2009-08-01 00:00:00

abstract：:Fluorescence-based sequencing is playing an increasingly important role in efforts to identify DNA polymorphisms and mutations of biological and medical interest. The application of this technology in generating the reference sequence of simple and complex genomes is also driving the development of new computer progra...

journal_title：Nucleic acids research

authors： Nickerson DA,Tobe VO,Taylor SL

更新日期：1997-07-15 00:00:00

abstract：:Several plasmids which direct the expression of human interferon-gamma (IFN-gamma) cDNA in the yeast Saccharomyces cerevisiae under the transcriptional control of the 3-phosphoglycerate kinase (PGK) promoter have been constructed. Up to 25 x 10(6) units per liter culture of biologically active IFN-gamma are synthesize...

journal_title：Nucleic acids research

authors： Derynck R,Singh A,Goeddel DV

更新日期：1983-03-25 00:00:00

abstract：UNLABELLED:Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation frequency and patterns, and GC compositions. Quantification of codon usage ...

journal_title：Nucleic acids research

authors： Angellotti MC,Bhuiyan SB,Chen G,Wan XF

更新日期：2007-07-01 00:00:00

abstract：:Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest...

journal_title：Nucleic acids research

authors： Mishra GR,Suresh M,Kumaran K,Kannabiran N,Suresh S,Bala P,Shivakumar K,Anuradha N,Reddy R,Raghavan TM,Menon S,Hanumanthu G,Gupta M,Upendran S,Gupta S,Mahesh M,Jacob B,Mathew P,Chatterjee P,Arun KS,Sharma S,Chand

更新日期：2006-01-01 00:00:00

abstract：:A peculiar phenomenon is observed in several adenovirus type 2 or 5 (Ad2 or Ad5) transformed cell lines: the right hand and left hand terminal regions of the viral genome present in the viral DNA insertions of these cell lines are found to be linked together. A large part of the viral DNA insertion present in the Ad5 ...

journal_title：Nucleic acids research

authors： Visser L,Reemst AC,van Mansfeld AD,Rozijn TH

更新日期：1982-04-10 00:00:00

abstract：:A repeated sequence element which is located about 200 nucleotides upstream from the protein-coding portion of the muscle actin gene (probably within a large 5' intron) in the genome of the sea urchin, Strongylocentrotus purpuratus has been characterized, and shown to contain the sequence features which indicate that ...

journal_title：Nucleic acids research

authors： Nisson PE,Hickey RJ,Boshar MF,Crain WR Jr

更新日期：1988-02-25 00:00:00

abstract：:The Yeast Protein Localization database (YPL.db) contains information about the localization patterns of yeast proteins resulting from microscopic analyses. The data and parameters of the experiments to obtain the localization information, together with images from confocal or video microscopy, are stored in a relatio...

journal_title：Nucleic acids research

authors： Habeler G,Natter K,Thallinger GG,Crawford ME,Kohlwein SD,Trajanoski Z

更新日期：2002-01-01 00:00:00

abstract：:The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences...

journal_title：Nucleic acids research

authors： Casper J,Zweig AS,Villarreal C,Tyner C,Speir ML,Rosenbloom KR,Raney BJ,Lee CM,Lee BT,Karolchik D,Hinrichs AS,Haeussler M,Guruvadoo L,Navarro Gonzalez J,Gibson D,Fiddes IT,Eisenhart C,Diekhans M,Clawson H,Barber GP,

更新日期：2018-01-04 00:00:00

abstract：:We have identified cDNAs encoding Mel-N1, the mouse homologue of a human nervous system-specific RNA-binding protein, Hel-N1. Two major mRNA transcripts of Mel-N1 were detected predominantly in the adult mouse brain by Northern blot analysis. To gain insight into the RNA binding specificity of Mel-N1, we performed ite...

journal_title：Nucleic acids research

authors： Abe R,Yamamoto K,Sakamoto H

更新日期：1996-06-01 00:00:00

abstract：:MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post...

journal_title：Nucleic acids research

authors： Bisognin A,Sales G,Coppe A,Bortoluzzi S,Romualdi C

更新日期：2012-07-01 00:00:00

abstract：:Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arra...

journal_title：Nucleic acids research

authors： Richter C,Dy RL,McKenzie RE,Watson BN,Taylor C,Chang JT,McNeil MB,Staals RH,Fineran PC

更新日期：2014-07-01 00:00:00