PathPred: an enzyme-catalyzed metabolic pathway prediction server.

abstract：:PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecula...

journal_title：Nucleic acids research

authors： McDowall MD,Harris MA,Lock A,Rutherford K,Staines DM,Bähler J,Kersey PJ,Oliver SG,Wood V

更新日期：2015-01-01 00:00:00

abstract：:The SRPDB (signal recognition particle database) provides annotated SRP RNA sequences from Eucaryotes and Archaea, phylogenetically ordered and aligned with their bacterial equivalents. We also make available representative RNA secondary structure diagrams, where each base pair is proven by comparative sequence analys...

journal_title：Nucleic acids research

authors： Larsen N,Zwieb C

更新日期：1993-07-01 00:00:00

abstract：:DNA double stranded breaks (DSBs) are one of the most deleterious types of DNA lesions. The main pathways responsible for repairing these breaks in eukaryotic cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). However, a third group of still poorly characterized DSB repair pathways, collect...

journal_title：Nucleic acids research

authors： Kostyrko K,Mermod N

更新日期：2016-04-07 00:00:00

abstract：:DNA methylation, the most intensively studied epigenetic modification, plays an important role in understanding the molecular basis of diseases. Furthermore, epigenome-wide association study (EWAS) provides a systematic approach to identify epigenetic variants underlying common diseases/phenotypes. However, there is n...

journal_title：Nucleic acids research

authors： Liu D,Zhao L,Wang Z,Zhou X,Fan X,Li Y,Xu J,Hu S,Niu M,Song X,Li Y,Zuo L,Lei C,Zhang M,Tang G,Huang M,Zhang N,Duan L,Lv H,Zhang M,Li J,Xu L,Kong F,Feng R,Jiang Y

更新日期：2019-01-08 00:00:00

abstract：:In this paper we focus on the detection of differentially expressed genes according to changes in hybridization signals using statistical tests. These tests were applied to 14 208 zebrafish cDNA clones that were immobilized on a nylon support and hybridized with radioactively labeled target mRNA from wild-type and lit...

journal_title：Nucleic acids research

authors： Herwig R,Aanstad P,Clark M,Lehrach H

更新日期：2001-12-01 00:00:00

abstract：:Chlorella virus PBCV-1 DNA ligase seals nicked DNA substrates consisting of a 5'-phosphate-terminated strand and a 3'-hydroxyl-terminated strand annealed to a bridging DNA template strand. The enzyme discriminates at the DNA binding step between substrates containing a 5'-phosphate versus a 5'-hydroxyl at the nick. Mu...

journal_title：Nucleic acids research

authors： Sriskanda V,Shuman S

更新日期：1998-01-15 00:00:00

abstract：:We determined the structure around the gap region between 28S alpha and 28S beta rRNA of Bombyx mori, a lepidopteran insect, to know the introduction mechanism of the hidden break, an interruption of the phosphodiester bond specific to the 28S rRNA of protostomes. Sequence analysis and S1 nuclease mapping suggested th...

journal_title：Nucleic acids research

authors： Fujiwara H,Ishikawa H

更新日期：1986-08-26 00:00:00

abstract：:The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered...

journal_title：Nucleic acids research

authors： Flores S,Echols N,Milburn D,Hespenheide B,Keating K,Lu J,Wells S,Yu EZ,Thorpe M,Gerstein M

更新日期：2006-01-01 00:00:00

abstract：:Cell specific expression of the insulin gene is achieved through transcriptional mechanisms operating on 5' flanking DNA elements. In the enhancer of rat I insulin gene, two elements, the Nir and Far boxes, located at positions -104 and -233 respectively and containing the same octameric motif are essential for B cell...

journal_title：Nucleic acids research

authors： Reibel L,Besnard C,Lores P,Jami J,Gacon G

更新日期：1993-04-11 00:00:00

abstract：:Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PR...

journal_title：Nucleic acids research

authors： Eckweiler D,Dudek CA,Hartlich J,Brötje D,Jahn D

更新日期：2018-01-04 00:00:00

abstract：:In a bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP)/transcription factor binding screen, we identified Mycobacterium smegmatis Ms6479 as the first c-di-GMP-responsive transcriptional factor in mycobacteria. Ms6479 could specifically bind with c-di-GMP and recognize the promoters of 37 lipid transport an...

journal_title：Nucleic acids research

authors： Li W,He ZG

更新日期：2012-12-01 00:00:00

abstract：:A number of cysteine-rich proteins have recently been isolated by homology screening, differential library screens, and association with other proteins. In this report, we describe the isolation of the rat cysteine-rich protein from a rat brain library during a search for clones with homology to the delta-opioid recep...

journal_title：Nucleic acids research

authors： McLaughlin CR,Tao Q,Abood ME

更新日期：1994-12-11 00:00:00

abstract：:Eight base analogs were tested as third strand residues in otherwise homopyrimidine strands opposite each of the 'direct' (A.T and G.C) and 'inverted' (T.A and C.G) Watson-Crick base pairs, using UV melting profiles to assess triplex stability. The target duplexes contained 20 A.T base pairs and a central test base pa...

journal_title：Nucleic acids research

authors： Amosova OA,Fresco JR

更新日期：1999-12-01 00:00:00

abstract：:The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map po...

journal_title：Nucleic acids research

authors： Sprague J,Bayraktaroglu L,Bradford Y,Conlin T,Dunn N,Fashena D,Frazer K,Haendel M,Howe DG,Knight J,Mani P,Moxon SA,Pich C,Ramachandran S,Schaper K,Segerdell E,Shao X,Singer A,Song P,Sprunger B,Van Slyke CE,Weste

更新日期：2008-01-01 00:00:00

abstract：:We investigated how Escherichia coli ClpXP targets the helicase-nuclease (HsdR) subunit of the bacterial Type I restriction-modification enzyme EcoKI during restriction alleviation (RA). RA is a temporary reduction in endonuclease activity that occurs when Type I enzymes bind unmodified recognition sites on the host g...

journal_title：Nucleic acids research

authors： Simons M,Diffin FM,Szczelkun MD

更新日期：2014-10-29 00:00:00

abstract：:We cloned and sequenced a portion of chloroplast DNA from the hornwort Anthoceros formosae. A nucleotide sequence of 7556 bp contained structures similar to those of ndhK, ndhC, trnV, trnM, atpE, atpB, rbcL, trnR and accD. The arrangement of these was the same as that of other chloroplast DNA. However, two nonsense co...

journal_title：Nucleic acids research

authors： Yoshinaga K,Iinuma H,Masuzawa T,Uedal K

更新日期：1996-03-15 00:00:00

abstract：:One of the obstacles hindering a better understanding of cancer is its heterogeneity. However, computational approaches to model cancer heterogeneity have lagged behind. To bridge this gap, we have developed a new probabilistic approach that models individual cancer cases as mixtures of subtypes. Our approach can be s...

journal_title：Nucleic acids research

authors： Cho DY,Przytycka TM

更新日期：2013-09-01 00:00:00

abstract：:Increasingly large-scale expression compendia for different species are becoming available. By exploiting the modularity of the coexpression network, these compendia can be used to identify biological processes for which the expression behavior is conserved over different species. However, comparing module networks ac...

journal_title：Nucleic acids research

authors： Zarrineh P,Fierro AC,Sánchez-Rodríguez A,De Moor B,Engelen K,Marchal K

更新日期：2011-04-01 00:00:00

abstract：:Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells w...

journal_title：Nucleic acids research

authors： Melançon P,Lemieux C,Brakier-Gingras L

更新日期：1988-10-25 00:00:00

abstract：:Sequence-specific binding of proteins to their DNA targets involves a complex spectrum of processes that often induce DNA conformational variation in the bound complex. The forces imposed by protein binding that cause the helical deformations are intimately interrelated and difficult to parse or rank in importance. To...

journal_title：Nucleic acids research

authors： Grant BN,Dourlain EM,Araneda JN,Throneberry ML,McFail-Isom LA

更新日期：2013-08-01 00:00:00

abstract：:Expression of a proof-reading deficient form of mitochondrial DNA (mtDNA) polymerase gamma, POLG, causes early death accompanied by features of premature ageing in mouse. However, the mechanism of cellular senescence remains unresolved. In addition to high levels of point mutations of mtDNA, the POLG mutator mouse har...

journal_title：Nucleic acids research

authors： Bailey LJ,Cluett TJ,Reyes A,Prolla TA,Poulton J,Leeuwenburgh C,Holt IJ

更新日期：2009-04-01 00:00:00

abstract：:Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence o...

journal_title：Nucleic acids research

authors： Sano T,Uyeda I,Shikata E,Ohno T,Okada Y

更新日期：1984-04-25 00:00:00

abstract：:Cloned DNA from the EcoRI J fragment of EBV has been used as template for in vitro transcription experiments using cell-free extracts prepared from HeLa or KB cells. Two EBV specific RNAs each about 175 bases in length were synthesised and nuclease 51 mapping experiments determined that these in vitro products corresp...

journal_title：Nucleic acids research

authors： Jat P,Arrand JR

更新日期：1982-06-11 00:00:00

abstract：:The stability of chromosome ends, the telomeres, is dependent on the ribonucleoprotein telomerase. In vitro, telomerase requires at least one RNA molecule and a reverse transcriptase-like protein. However, for telomere homeostasis in vivo, additional proteins are required. Telomerase RNAs of different species vary in ...

journal_title：Nucleic acids research

authors： Laterreur N,Eschbach SH,Lafontaine DA,Wellinger RJ

更新日期：2013-09-01 00:00:00

abstract：:The ARF tumour suppressor stabilizes p53 by negatively regulating the E3 ubiquitin ligase MDM2 to promote cell cycle arrest and cell death. However, ARF is also able to arrest cell proliferation by inhibiting ribosome biogenesis. In greater part this is achieved by targeting the transcription termination factor I (TTF...

journal_title：Nucleic acids research

authors： Lessard F,Stefanovsky V,Tremblay MG,Moss T

更新日期：2012-07-01 00:00:00

abstract：:We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI (Gene and miRNA Network-based Integration) method statistically ranks computationally predicted ...

journal_title：Nucleic acids research

authors： Yan Z,Shah PK,Amin SB,Samur MK,Huang N,Wang X,Misra V,Ji H,Gabuzda D,Li C

更新日期：2012-09-01 00:00:00

abstract：:Escherichia coli cells lacking the ribosomal RNA processing enzyme RNase III do no excise the normal RNA precursors p16a (17S) and p23a from nascent rRNA transcripts. These cells produce, instead, slightly larger p16b and p23b precursors. Digestion of p16b or p23b rRNA with RNases A plus T1 yields double-stranded frag...

journal_title：Nucleic acids research

authors： Gegenheimer P,Apirion D

更新日期：1980-04-25 00:00:00

abstract：:BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along ...

journal_title：Nucleic acids research

authors： Dai HJ,Huang CH,Lin RT,Tsai RT,Hsu WL

更新日期：2008-07-01 00:00:00

abstract：:With the recent increase in the number of mammalian genomes being sequenced, large-scale genome scans for human-specific positive selection are now possible. Selection can be inferred through phylogenetic analysis by comparing the rates of silent and replacement substitution between related species. Maximum-likelihood...

journal_title：Nucleic acids research

authors： Nickel GC,Tefft D,Adams MD

更新日期：2008-01-01 00:00:00

abstract：:A fiber optic biosensor was used for the fluorimetric detection of T/AT triple-helical DNA formation. The surfaces of two sets of fused silica optical fibers were functionalized with hexaethylene oxide linkers from which decaadenylic acid oligonucleotides were grown in the 3'to 5'and 5'to 3'direction, respectively, us...

journal_title：Nucleic acids research

authors： Uddin AH,Piunno PA,Hudson RH,Damha MJ,Krull UJ

更新日期：1997-10-15 00:00:00