JN "nucleic acids research" on 2009-05-07 03:56 PM

Sequence-non-specific effects of RNA interference triggers and microRNA regulators.

Olejniczak, Marta; Krzyzosiak, Wlodzimierz J.; Galka, Paulina

Nucleic acids research; 01/01/2010
(AN IND44306976)
Agricola

Modeling tissue-specific structural patterns in human and mouse promoters.

Vandenbon, Alexis; Nakai, Kenta

Nucleic acids research; 01/01/2010
(AN IND44306981)
Agricola

Martini: using literature keywords to compare gene sets.

Nucleic acids research; 01/01/2010
(AN IND44306990)
Agricola

Drosophila mini-white model system: new insights into positive position effects and the role of transcriptional terminators and gypsy insulator in transgene shielding.

Nucleic acids research; 01/01/2010
(AN IND44306997)
Agricola

Expression of stress-response ATF3 is mediated by Nrf2 in astrocytes.

Kim, Kyu-Han; Kim, Kyu-Won; Surh, Young-Joon; Jeong, Jae-Yeon

Nucleic acids research; 01/01/2010
(AN IND44306998)
Agricola

Comparing effects of mTR and mTERT deletion on gene expression and DNA damage response: a critical examination of telomere length maintenance-independent roles of telomerase.

Vidal-Cardenas, Sofia L.; Greider, Carol W.

Nucleic acids research; 01/01/2010
(AN IND44306999)
Agricola

FtsK translocation on DNA stops at XerCD-dif.

Graham, James E.; Arciszewska, Lidia K.; Sherratt, David J.; Sivanathan, Viknesh

Nucleic acids research; 01/01/2010
(AN IND44307000)
Agricola

Two modules in the BRC repeats of BRCA2 mediate structural and functional interactions with the RAD51 recombinase.

Rajendra, Eeson; Venkitaraman, Ashok R.

Nucleic acids research; 01/01/2010
(AN IND44307001)
Agricola

Energetic signatures of single base bulges: thermodynamic consequences and biological implications.

Nucleic acids research; 01/01/2010
(AN IND44307002)
Agricola

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources.

Cochrane, Guy R.; Galperin, Michael Y.

Nucleic acids research; 01/01/2010
(AN IND44303487)
Agricola

Database resources of the National Center for Biotechnology Information.

Nucleic acids research; 01/01/2010
(AN IND44303555)
Agricola

Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways.

Zeng, Tao; Li, Jinyan

Nucleic acids research; 01/01/2010
(AN IND44307003)
Agricola

Profiling the selectivity of DNA ligases in an array format with mass spectrometry.

Kim, Joohoon; Mrksich, Milan

Nucleic acids research; 01/01/2010
(AN IND44307004)
Agricola

Efficient gene silencing by delivery of locked nucleic acid antisense oligonucleotides, unassisted by transfection reagents.

Nucleic acids research; 01/01/2010
(AN IND44307005)
Agricola

MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays.

Turro, Ernest; Dallman, Margaret J.; Richardson, Sylvia; Lewin, Alex; Rose, Anna

Nucleic acids research; 01/01/2010
(AN IND44307006)
Agricola

'RNA walk' a novel approach to study RNA-RNA interactions between a small RNA and its target.

Lustig, Yaniv; Liu, Li; Michaeli, Shulamit; Wachtel, Chaim; Safro, Mark

Nucleic acids research; 01/01/2010
(AN IND44307007)
Agricola

CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

Nucleic acids research; 01/01/2010
(AN IND44307008)
Agricola

Novel recognition motifs and biological functions of the RNA-binding protein HuD revealed by genome-wide identification of its targets.

Bolognani, Federico; Perrone-Bizzozero, Nora I.; Contente-Cuomo, Tania

Nucleic acids research; 01/01/2010
(AN IND44306977)
Agricola

Single-cell transcriptional analysis of taste sensory neuron pair in Caenorhabditis elegans.

Nucleic acids research; 01/01/2010
(AN IND44306978)
Agricola

Comparative analyses of time-course gene expression profiles of the long-lived sch9Δ mutant.

Nucleic acids research; 01/01/2010
(AN IND44306979)
Agricola

DNA topoisomerase I inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the human HIF-1Îł gene locus.

Nucleic acids research; 01/01/2010
(AN IND44306980)
Agricola

Understanding how the crowded interior of cells stabilizes DNA/DNA and DNA/RNA hybrids-in silico predictions and in vitro evidence.

Harve, Karthik S.; Raghunath, Michael; Rajagopalan, Raj; Lareu, Ricky

Nucleic acids research; 01/01/2010
(AN IND44306982)
Agricola

Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination.

Nucleic acids research; 01/01/2010
(AN IND44306983)
Agricola

Transposition of the human Hsmar1 transposon: rate-limiting steps and the importance of the flanking TA dinucleotide in second strand cleavage.

Claeys Bouuaert, Corentin; Chalmers, Ronald

Nucleic acids research; 01/01/2010
(AN IND44306984)
Agricola

The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent.

Nucleic acids research; 01/01/2010
(AN IND44306985)
Agricola

Mesenchymal stem cell secretes microparticles enriched in pre-microRNAs.

Nucleic acids research; 01/01/2010
(AN IND44306986)
Agricola

NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif.

Nucleic acids research; 01/01/2010
(AN IND44306987)
Agricola

Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3'UTR.

Sun, Guihua; Rossi, John J.; Li, Haitang

Nucleic acids research; 01/01/2010
(AN IND44306988)
Agricola

The neurofibromatosis type I pre-mRNA is a novel target of CELF protein-mediated splicing regulation.

Barron, Victoria A.; Ladd, Andrea N.; Lou, Hua; Zhu, Hui; Hinman, Melissa N.

Nucleic acids research; 01/01/2010
(AN IND44306989)
Agricola

Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana.

Nucleic acids research; 01/01/2010
(AN IND44306991)
Agricola

Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance.

Nucleic acids research; 01/01/2010
(AN IND44306992)
Agricola

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

Nucleic acids research; 01/01/2010
(AN IND44306993)
Agricola

Fine tuning of the E. coli NusB:NusE complex affinity to BoxA RNA is required for processive antitermination.

Burmann, Bj©œrn M.; Wahl, Markus C.; Gottesman, Max E.; Luo, Xiao; R©œsch, Paul

Nucleic acids research; 01/01/2010
(AN IND44306994)
Agricola

Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA.

Zheng, Ke-wei; Tan, Zheng; Hao, Yu-hua; Chen, Zhao

Nucleic acids research; 01/01/2010
(AN IND44306995)
Agricola

DNA adducts of aristolochic acid II: total synthesis and site-specific mutagenesis studies in mammalian cells.

Nucleic acids research; 01/01/2010
(AN IND44306996)
Agricola

The European Bioinformatics Institute's data resources.

Brooksbank, Catherine; Thornton, Janet; Cameron, Graham

Nucleic acids research; 01/01/2010
(AN IND44303498)
Agricola

NBRP databases: databases of biological resources in Japan.

Nucleic acids research; 01/01/2010
(AN IND44303511)
Agricola

DDBJ launches a new archive database with analytical tools for next-generation sequence data.

Nucleic acids research; 01/01/2010
(AN IND44303523)
Agricola

Improvements to services at the European Nucleotide Archive.

Nucleic acids research; 01/01/2010
(AN IND44303533)
Agricola

GenBank.

Nucleic acids research; 01/01/2010
(AN IND44303547)
Agricola

Non-redundant patent sequence databases with value-added annotations at two levels.

Nucleic acids research; 01/01/2010
(AN IND44303560)
Agricola

ACLAME: A CLAssification of Mobile genetic Elements, update 2010.

Leplae, Rapha©±l; Toussaint, Ariane; Lima-Mendez, Gipsi

Nucleic acids research; 01/01/2010
(AN IND44303568)
Agricola

ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes.

Nucleic acids research; 01/01/2010
(AN IND44303576)
Agricola

Recode-2: new design, new search tools, and many more genes.

Nucleic acids research; 01/01/2010
(AN IND44303587)
Agricola

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.

Nucleic acids research; 01/01/2010
(AN IND44303597)
Agricola

ChimerDB 2.0--a knowledgebase for fusion genes updated.

Nucleic acids research; 01/01/2010
(AN IND44303607)
Agricola

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Nucleic acids research; 01/01/2010
(AN IND44303615)
Agricola

3D-footprint: a database for the structural analysis of protein-DNA complexes.

Contreras-Moreira, Bruno

Nucleic acids research; 01/01/2010
(AN IND44303618)
Agricola

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

Yamashita, Riu; Suzuki, Yutaka; Nakai, Kenta; Wakaguri, Hiroyuki; Sugano, Sumio

Nucleic acids research; 01/01/2010
(AN IND44303619)
Agricola

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.

Nucleic acids research; 01/01/2010
(AN IND44303488)
Agricola

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.

Nucleic acids research; 01/01/2010
(AN IND44303489)
Agricola

TransmiR: a transcription factor-microRNA regulation database.

Wang, Juan; Cui, Qinghua; Qiu, Chengxiang; Lu, Ming

Nucleic acids research; 01/01/2010
(AN IND44303490)
Agricola

deepBase: a database for deeply annotating and mining deep sequencing data.

Yang, Jian-Hua; Chen, Yue-Qin; Qu, Liang-Hu; Shao, Peng; Zhou, Hui

Nucleic acids research; 01/01/2010
(AN IND44303491)
Agricola

IRESite--a tool for the examination of viral and cellular internal ribosome entry sites.

Nucleic acids research; 01/01/2010
(AN IND44303492)
Agricola

miRGen 2.0: a database of microRNA genomic information and regulation.

Nucleic acids research; 01/01/2010
(AN IND44303493)
Agricola

HHMD: the human histone modification database.

Nucleic acids research; 01/01/2010
(AN IND44303494)
Agricola

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.

Nucleic acids research; 01/01/2010
(AN IND44303495)
Agricola

PROSITE, a protein domain database for functional characterization and annotation.

Nucleic acids research; 01/01/2010
(AN IND44303496)
Agricola

ELM: the status of the 2010 eukaryotic linear motif resource.

Nucleic acids research; 01/01/2010
(AN IND44303497)
Agricola

MeMotif: a database of linear motifs in Îł-helical transmembrane proteins.

Nucleic acids research; 01/01/2010
(AN IND44303499)
Agricola

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.

Nucleic acids research; 01/01/2010
(AN IND44303500)
Agricola

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Nucleic acids research; 01/01/2010
(AN IND44303501)
Agricola

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Nucleic acids research; 01/01/2010
(AN IND44303502)
Agricola

The Pfam protein families database.

Nucleic acids research; 01/01/2010
(AN IND44303503)
Agricola

SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.

Nucleic acids research; 01/01/2010
(AN IND44303504)
Agricola

MEROPS: the peptidase database.

Rawlings, Neil D.; Bateman, Alex; Barrett, Alan J.

Nucleic acids research; 01/01/2010
(AN IND44303505)
Agricola

REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.

Roberts, Richard J.; Macelis, Dana; Posfai, Janos; Vincze, Tamas

Nucleic acids research; 01/01/2010
(AN IND44303506)
Agricola

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

Nucleic acids research; 01/01/2010
(AN IND44303507)
Agricola

FunSimMat update: new features for exploring functional similarity.

Schlicker, Andreas; Albrecht, Mario

Nucleic acids research; 01/01/2010
(AN IND44303508)
Agricola

Chemical Entities of Biological Interest: an update.

Nucleic acids research; 01/01/2010
(AN IND44303509)
Agricola

An overview of the PubChem BioAssay resource.

Nucleic acids research; 01/01/2010
(AN IND44303510)
Agricola

3DNALandscapes: a database for exploring the conformational features of DNA.

Zheng, Guohui; Olson, Wilma K.; Lu, Xiang-Jun; Colasanti, Andrew V.

Nucleic acids research; 01/01/2010
(AN IND44303512)
Agricola

The ITS2 Database III--sequences and structures for phylogeny.

Nucleic acids research; 01/01/2010
(AN IND44303513)
Agricola

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.

Turner, Douglas H.; Mathews, David H.

Nucleic acids research; 01/01/2010
(AN IND44303514)
Agricola

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder.

Nucleic acids research; 01/01/2010
(AN IND44303515)
Agricola

fPOP: footprinting functional pockets of proteins by comparative spatial patterns.

Tseng, Yan Yuan; Li, Wen-Hsiung; Chen, Z. Jeffrey

Nucleic acids research; 01/01/2010
(AN IND44303516)
Agricola

Gene3D: merging structure and function for a Thousand genomes.

Lees, Jonathan; Clegg, Andrew; Orengo, Christine; Yeats, Corin; Redfern, Oliver

Nucleic acids research; 01/01/2010
(AN IND44303517)
Agricola

IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF.

Nucleic acids research; 01/01/2010
(AN IND44303518)
Agricola

PDBe: Protein Data Bank in Europe.

Nucleic acids research; 01/01/2010
(AN IND44303519)
Agricola

PDBselect 1992-2009 and PDBfilter-select.

Griep, Sven; Hobohm, Uwe

Nucleic acids research; 01/01/2010
(AN IND44303520)
Agricola

Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry.

Berkholz, Donald S.; Karplus, P. Andrew; Davidson, John R.; Krenesky, Peter B.

Nucleic acids research; 01/01/2010
(AN IND44303521)
Agricola

PTGL: a database for secondary structure-based protein topologies.

May, Patrick; Koch, Ina; Steinke, Thomas; Kreuchwig, Annika

Nucleic acids research; 01/01/2010
(AN IND44303522)
Agricola

The Protein Naming Utility: a rules database for protein nomenclature.

Nucleic acids research; 01/01/2010
(AN IND44303524)
Agricola

The comprehensive microbial resource.

Nucleic acids research; 01/01/2010
(AN IND44303525)
Agricola

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.

Nucleic acids research; 01/01/2010
(AN IND44303526)
Agricola

KEGG for representation and analysis of molecular networks involving diseases and drugs.

Kanehisa, Minoru; Tanabe, Mao; Hirakawa, Mika; Goto, Susumu; Furumichi, Miho

Nucleic acids research; 01/01/2010
(AN IND44303527)
Agricola

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

Uchiyama, Ikuo; Kawai, Mikihiko; Higuchi, Toshio

Nucleic acids research; 01/01/2010
(AN IND44303528)
Agricola

phiSITE: database of gene regulation in bacteriophages.

Klucar, Lubos; Hajduk, Matus; Stano, Matej

Nucleic acids research; 01/01/2010
(AN IND44303529)
Agricola

ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.

Nucleic acids research; 01/01/2010
(AN IND44303530)
Agricola

CyanoBase: the cyanobacteria genome database update 2010.

Nucleic acids research; 01/01/2010
(AN IND44303531)
Agricola

The integrated microbial genomes system: an expanding comparative analysis resource.

Nucleic acids research; 01/01/2010
(AN IND44303532)
Agricola

Megx.net: integrated database resource for marine ecological genomics.

Nucleic acids research; 01/01/2010
(AN IND44303534)
Agricola

MicrobesOnline: an integrated portal for comparative and functional genomics.

Nucleic acids research; 01/01/2010
(AN IND44303535)
Agricola

The MiST2 database: a comprehensive genomics resource on microbial signal transduction.

Ulrich, Luke E.; Zhulin, Igor B.

Nucleic acids research; 01/01/2010
(AN IND44303536)
Agricola

Pathema: a clade-specific bioinformatics resource center for pathogen research.

Nucleic acids research; 01/01/2010
(AN IND44303537)
Agricola

EuPathDB: a portal to eukaryotic pathogen databases.

Nucleic acids research; 01/01/2010
(AN IND44303538)
Agricola

The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.

Nucleic acids research; 01/01/2010
(AN IND44303539)
Agricola

New tools at the Candida Genome Database: biochemical pathways and full-text literature search.

Nucleic acids research; 01/01/2010
(AN IND44303540)
Agricola

Saccharomyces Genome Database provides mutant phenotype data.

Nucleic acids research; 01/01/2010
(AN IND44303541)
Agricola

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum.

Nucleic acids research; 01/01/2010
(AN IND44303542)
Agricola

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