The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update.

abstract：:The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subuni...

journal_title：Nucleic acids research

authors： Iacovella MG,Bremang M,Basha O,Giacò L,Carotenuto W,Golfieri C,Szakal B,Dal Maschio M,Infantino V,Beznoussenko GV,Joseph CR,Visintin C,Mironov AA,Visintin R,Branzei D,Ferreira-Cerca S,Yeger-Lotem E,De Wulf P

更新日期：2018-09-06 00:00:00

abstract：:RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikin...

journal_title：Nucleic acids research

authors： Sharma D,Mohanty D,Surolia A

更新日期：2009-07-01 00:00:00

abstract：:The nucleotide sequence of Neurospora crassa 5.8 S rDNA and adjacent regions has been determined. The deduced 5.8 S rRNA sequence of Neurospora differs from the 5.8 S rRNA sequence of Saccharomyces cerevisiae at 13 of 158 residues. Nine of these differences are clustered in a segment capable of forming a short hairpin...

journal_title：Nucleic acids research

authors： Selker E,Yanofsky C

更新日期：1979-06-11 00:00:00

abstract：:The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (c...

journal_title：Nucleic acids research

authors： Cullen D,Wilson LJ,Grey GL,Henner DJ,Turner G,Ballance DJ

更新日期：1987-11-25 00:00:00

abstract：:To address how eukaryotic replication forks respond to fork stalling caused by strong non-covalent protein-DNA barriers, we engineered the controllable Fob-block system in Saccharomyces cerevisiae. This system allows us to strongly induce and control replication fork barriers (RFB) at their natural location within the...

journal_title：Nucleic acids research

authors： Bentsen IB,Nielsen I,Lisby M,Nielsen HB,Gupta SS,Mundbjerg K,Andersen AH,Bjergbaek L

更新日期：2013-03-01 00:00:00

abstract：:In Arabidopsis thaliana, endogenous trans-acting and exogenous siRNA pathways are initiated by the interaction of DRB4 with trigger dsRNA. Further, DCL4:DRB4 complex cleaves the dsRNA into 21 bp siRNA. Understanding molecular determinants and mechanistic details of dsRNA recognition by DRB4 is vital for inducing long-...

journal_title：Nucleic acids research

authors： Chiliveri SC,Aute R,Rai U,Deshmukh MV

更新日期：2017-08-21 00:00:00

abstract：:The rabbit homolog to the locus control region (LCR) of the human beta-like globin gene cluster was isolated, and long segments containing the DNase I hypersensitive sites (HS) were sequenced. The order and spacing of HS4, HS3, HS2 and HS1 are conserved between rabbit and human. Alignment of these sequences with their...

journal_title：Nucleic acids research

authors： Hardison R,Xu J,Jackson J,Mansberger J,Selifonova O,Grotch B,Biesecker J,Petrykowska H,Miller W

更新日期：1993-03-11 00:00:00

abstract：:Strategies to regulate gene function frequently use small interfering RNAs (siRNAs) that can be made from their shRNA precursors via Dicer. However, when the duplex components of these siRNA effectors are expressed from their respective coding genes, the RNA interference (RNAi) activity is much reduced. Here, we explo...

journal_title：Nucleic acids research

authors： Jin X,Sun T,Zhao C,Zheng Y,Zhang Y,Cai W,He Q,Taira K,Zhang L,Zhou D

更新日期：2012-02-01 00:00:00

abstract：:Increasing numbers of proteins, nucleic acids and other molecular entities have been explored as therapeutic targets, hundreds of which are targets of approved and clinical trial drugs. Knowledge of these targets and corresponding drugs, particularly those in clinical uses and trials, is highly useful for facilitating...

journal_title：Nucleic acids research

authors： Zhu F,Han B,Kumar P,Liu X,Ma X,Wei X,Huang L,Guo Y,Han L,Zheng C,Chen Y

更新日期：2010-01-01 00:00:00

abstract：:Cells deficient in the Werner syndrome protein (WRN) or BRCA1 are hypersensitive to DNA interstrand cross-links (ICLs), whose repair requires nucleotide excision repair (NER) and homologous recombination (HR). However, the roles of WRN and BRCA1 in the repair of DNA ICLs are not understood and the molecular mechanisms...

journal_title：Nucleic acids research

authors： Cheng WH,Kusumoto R,Opresko PL,Sui X,Huang S,Nicolette ML,Paull TT,Campisi J,Seidman M,Bohr VA

更新日期：2006-05-19 00:00:00

abstract：:Polyadenylation of nascent transcripts is one of the key mRNA processing events in eukaryotic cells. A large number of human and mouse genes have alternative polyadenylation sites, or poly(A) sites, leading to mRNA variants with different protein products and/or 3'-untranslated regions (3'-UTRs). PolyA_DB 2 contains p...

journal_title：Nucleic acids research

authors： Lee JY,Yeh I,Park JY,Tian B

更新日期：2007-01-01 00:00:00

abstract：:Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the impact of mutations on protein structure and function relying upon sta...

journal_title：Nucleic acids research

authors： Rodrigues CH,Pires DE,Ascher DB

更新日期：2018-07-02 00:00:00

abstract：:The reported binding preference of human hnRNP protein A1 for the 3'-splice site of some introns (Swanson and Dreyfuss (1988) EMBO J. 7, 3519-3529; Mayrand and Pederson (1990) Nucleic Acids Res. 18, 3307-3318) was tested by assaying in vitro the binding of purified recombinant A1 protein (expressed in bacteria) to syn...

journal_title：Nucleic acids research

authors： Buvoli M,Cobianchi F,Biamonti G,Riva S

更新日期：1990-11-25 00:00:00

abstract：:Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerne...

journal_title：Nucleic acids research

authors： Attimonelli M,Cooper JM,D'Elia D,de Montalvo A,De Robertis M,Lehväslaiho H,Malladi SB,Memeo F,Stevens K,Schapira AH,Saccone C

更新日期：1999-01-01 00:00:00

abstract：:Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast...

journal_title：Nucleic acids research

authors： Ståhlberg A,Krzyzanowski PM,Jackson JB,Egyud M,Stein L,Godfrey TE

更新日期：2016-06-20 00:00:00

abstract：:Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for diva...

journal_title：Nucleic acids research

authors： Leonarski F,D'Ascenzo L,Auffinger P

更新日期：2017-01-25 00:00:00

abstract：:The Escherichia coli cyclic AMP receptor protein (CRP) is a global regulator that controls transcription initiation from more than 100 promoters by binding to a specific DNA sequence within cognate promoters. Many genes in the CRP regulon have been predicted simply based on the presence of DNA-binding sites within gen...

journal_title：Nucleic acids research

authors： Zheng D,Constantinidou C,Hobman JL,Minchin SD

更新日期：2004-11-01 00:00:00

abstract：:The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) land...

journal_title：Nucleic acids research

authors： Xie Q,Li C,Song X,Wu L,Jiang Q,Qiu Z,Cao H,Yu K,Wan C,Li J,Yang F,Huang Z,Niu B,Jiang Z,Zhang T

更新日期：2017-03-17 00:00:00

abstract：:According to the recruitment model of transcriptional activation, an activator helps initiate transcription by bringing the RNA polymerase to a specific location on the DNA through interaction with components of the transcriptional machinery. However, it is difficult to isolate and define the activities of specific ac...

journal_title：Nucleic acids research

authors： Wang S,Shepard JR,Shi H

更新日期：2010-04-01 00:00:00

abstract：:FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence analysis results, curated functional annotation information and additional descriptions, including Gene Ontology terms. RIK...

journal_title：Nucleic acids research

authors： Bono H,Kasukawa T,Furuno M,Hayashizaki Y,Okazaki Y

更新日期：2002-01-01 00:00:00

abstract：:The catalytic function of the hairpin ribozyme has been investigated by modification-interference analysis of both ribozyme and substrate, using ribonucleoside phosphorothioates. Thiophosphate substitutions in two ribozyme domains were examined by using a novel and highly efficient two-piece ribozyme assembled from tw...

journal_title：Nucleic acids research

authors： Chowrira BM,Burke JM

更新日期：1992-06-11 00:00:00

abstract：:While antibiotic selection has been routinely used for the selection of genetically modified cells, administration of cytotoxic drugs often leads to deleterious effects not only to inert cells but also to transfected or transduced ones. In this study, we propose an Antigen-MEdiated Genetically modified cell Amplificat...

journal_title：Nucleic acids research

authors： Kawahara M,Ueda H,Morita S,Tsumoto K,Kumagai I,Nagamune T

更新日期：2003-04-01 00:00:00

abstract：:Hepatitis C virus (HCV) translation initiation is directed by an internal ribosome entry site (IRES) and regulated by distant regions at the 3'-end of the viral genome. Through a combination of improved RNA chemical probing methods, SHAPE structural analysis and screening of RNA accessibility using antisense oligonucl...

journal_title：Nucleic acids research

authors： Romero-López C,Barroso-Deljesus A,García-Sacristán A,Briones C,Berzal-Herranz A

更新日期：2012-12-01 00:00:00

abstract：:Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor expressed in metazoan cells that is responsible for eliciting the production of type I interferons and pro-inflammatory cytokines upon detection of intracellular, non-self RNA. Structural studies of RIG-I have identified a novel Pincer domain com...

journal_title：Nucleic acids research

authors： Rawling DC,Kohlway AS,Luo D,Ding SC,Pyle AM

更新日期：2014-10-01 00:00:00

abstract：:5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancer...

journal_title：Nucleic acids research

authors： Liu RJ,Long T,Li J,Li H,Wang ED

更新日期：2017-06-20 00:00:00

abstract：:We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28,199 'UniTraps', i.e. distinct collections of unambiguous insertions at the same subgenic regi...

journal_title：Nucleic acids research

authors： Roma G,Sardiello M,Cobellis G,Cruz P,Lago G,Sanges R,Stupka E

更新日期：2008-01-01 00:00:00

abstract：:Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected...

journal_title：Nucleic acids research

authors： Sharp PM,Tuohy TM,Mosurski KR

更新日期：1986-07-11 00:00:00

abstract：:The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype-phenotype relationships. Here, we describe a computational method, dubbed C...

journal_title：Nucleic acids research

authors： Li S,Alvarez RV,Sharan R,Landsman D,Ovcharenko I

更新日期：2017-03-17 00:00:00

abstract：:The replication origin (oriC) of the Escherichia coli chromosome has been cloned and the region essential for chromosomal replication has been delimited to 245 base pairs. In previous studies the ability of recombinants between oriC and ColE1-type vectors, to transform E. coli polA- strains was used to determine which...

journal_title：Nucleic acids research

authors： Stuitje AR,Meijer M

更新日期：1983-11-25 00:00:00

abstract：:X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 368 entries from 318 unrelated families showing 228 unique molecular events. In addi...

journal_title：Nucleic acids research

authors： Vihinen M,Belohradsky BH,Haire RN,Holinski-Feder E,Kwan SP,Lappalainen I,Lehväslaiho H,Lester T,Meindl A,Ochs HD,Ollila J,Vorechovsky I,Weiss M,Smith CI

更新日期：1997-01-01 00:00:00