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

A single rare σ70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82

Tue, 01 Oct 2024 00:00:00 -0400

Nucleic Acids Research; 10/01/2024
(AN IND609209623); ISSN: 0305-1048
Agricola

CuGenDBv2: an updated database for cucurbit genomics

Sat, 01 Oct 2022 00:00:00 -0400

Nucleic Acids Research; 10/01/2022
(AN IND608786434); ISSN: 0305-1048
Agricola

De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing

Faulk, Christopher — Wed, 01 Jun 2022 00:00:00 -0400

Nucleic Acids Research; 06/01/2022
(AN IND607887702); ISSN: 0305-1048
Agricola

Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services

Hu, Zhi-Liang; Park, Carissa A.; Reecy, James M. — Sat, 01 Jan 2022 00:00:00 -0500

Nucleic Acids Research; 01/01/2022
(AN IND607887697); ISSN: 0305-1048
Agricola

MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species

Sat, 01 Jan 2022 00:00:00 -0500

Nucleic Acids Research; 01/01/2022
(AN IND607887701); ISSN: 0305-1048
Agricola

CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer

Sat, 01 Jan 2022 00:00:00 -0500

Nucleic Acids Research; 01/01/2022
(AN IND607887700); ISSN: 0305-1048
Agricola

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Sat, 01 Jan 2022 00:00:00 -0500

Nucleic Acids Research; 01/01/2022
(AN IND607887696); ISSN: 0305-1048
Agricola

Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation

Sat, 01 May 2021 00:00:00 -0400

Nucleic Acids Research; 05/01/2021
(AN IND607887699); ISSN: 0305-1048
Agricola

A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database

Fri, 01 Jan 2021 00:00:00 -0500

Nucleic Acids Research; 01/01/2021
(AN IND607373110); ISSN: 0305-1048
Agricola

dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates

Fri, 01 Jan 2021 00:00:00 -0500

Nucleic Acids Research; 01/01/2021
(AN IND607373115); ISSN: 0305-1048
Agricola

AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses

Fri, 01 Jan 2021 00:00:00 -0500

Nucleic Acids Research; 01/01/2021
(AN IND607373116); ISSN: 0305-1048
Agricola

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Fri, 01 Jan 2021 00:00:00 -0500

Nucleic Acids Research; 01/01/2021
(AN IND607373117); ISSN: 1362-4962
Agricola

Building a tRNA thermometer to estimate microbial adaptation to temperature

Cimen, Emre; Jensen, Sarah E; Buckler, Edward S — Tue, 01 Dec 2020 00:00:00 -0500

Nucleic Acids Research; 12/01/2020
(AN IND607373109); ISSN: 1362-4962
Agricola

Activation of DNA-PK by hairpinned DNA ends reveals a stepwise mechanism of kinase activation

Meek, Katheryn — Tue, 01 Sep 2020 00:00:00 -0400

Nucleic Acids Research; 09/01/2020
(AN IND607373114); ISSN: 1362-4962
Agricola

RNA aptamer capture of macromolecular complexes for mass spectrometry analysis

Tue, 01 Sep 2020 00:00:00 -0400

Nucleic Acids Research; 09/01/2020
(AN IND607373113); ISSN: 0305-1048
Agricola

AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses

Yi, Haidong; Huang, Le; Yang, Bowen; Gomez, Javi; Zhang, Han; Yin, Yanbin — Wed, 01 Jul 2020 00:00:00 -0400

Nucleic Acids Research; 07/01/2020
(AN IND607373112); ISSN: 1362-4962
Agricola

Prediction of condition-specific regulatory genes using machine learning

Song, Qi; Lee, JiYoung,; Akter, Shamima; Rogers, Matthew; Grene, Ruth; Li, Song — Mon, 01 Jun 2020 00:00:00 -0400

Nucleic Acids Research; 06/01/2020
(AN IND607373111); ISSN: 0305-1048
Agricola

Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA

Wed, 01 Apr 2020 00:00:00 -0400

Nucleic Acids Research; 04/01/2020
(AN IND607373108); ISSN: 1362-4962
Agricola

Effector gene silencing mediated by histone methylation underpins host adaptation in an oomycete plant pathogen

Sat, 01 Feb 2020 00:00:00 -0500

Nucleic Acids Research; 02/01/2020
(AN IND607373122); ISSN: 1362-4962
Agricola

Ensembl Genomes 2020-enabling non-vertebrate genomic research

Wed, 01 Jan 2020 00:00:00 -0500

Nucleic Acids Research; 01/01/2020
(AN IND607373123); ISSN: 1362-4962
Agricola

15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Tue, 01 Jan 2019 00:00:00 -0500

Nucleic Acids Research; 01/01/2019
(AN IND607373118); ISSN: 1362-4962
Agricola

MaizeGDB 2018: the maize multi-genome genetics and genomics database

Tue, 01 Jan 2019 00:00:00 -0500

Nucleic Acids Research; 01/01/2019
(AN IND607373119); ISSN: 1362-4962
Agricola

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

Tue, 01 Jan 2019 00:00:00 -0500

Nucleic Acids Research; 01/01/2019
(AN IND607373121); ISSN: 1362-4962
Agricola

In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets

Sat, 01 Sep 2018 00:00:00 -0400

Nucleic Acids Research; 09/01/2018
(AN IND607373120); ISSN: 1362-4962
Agricola

The i5k Workspace@ NAL-enabling genomic data access, visualization and curation of arthropod genomes

Thu, 01 Jan 2015 00:00:00 -0500

Nucleic Acids Research; 01/01/2015
(AN IND600060559); ISSN: 0305-1048
Agricola

Taxonomic classification of metagenomic shotgun sequences with CARMA3

Gerlach, Wolfgang; Stoye, Jens — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613740); ISSN: 0305-1048
Agricola

Re-engineering multicloning sites for function and convenience

Crook, Nathan C.; Freeman, Elizabeth S.; Alper, Hal S. — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613741); ISSN: 0305-1048
Agricola

TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots

Bon, Michaël; Orland, Henri — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613742); ISSN: 0305-1048
Agricola

Biological insights from topology independent comparison of protein 3D structures

Nguyen, Minh N.; Madhusudhan, M.S. — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613743); ISSN: 0305-1048
Agricola

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

Cai, Yunpeng; Sun, Yijun — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613744); ISSN: 0305-1048
Agricola

A protein shuttle system to target RNA into mitochondria

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613745); ISSN: 0305-1048
Agricola

A rapid, inexpensive yeast-based dual-fluorescence assay of programmed--1 ribosomal frameshifting for high-throughput screening

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613746); ISSN: 0305-1048
Agricola

How does DNA break during chromosomal translocations?

Nambiar, Mridula; Raghavan, Sathees C. — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613697); ISSN: 0305-1048
Agricola

In silico characterization and prediction of global protein-mRNA interactions in yeast

Pancaldi, Vera; Bähler, Jürg — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613698); ISSN: 0305-1048
Agricola

Cryptic splice sites and split genes

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613699); ISSN: 0305-1048
Agricola

RNIE: genome-wide prediction of bacterial intrinsic terminators

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613700); ISSN: 0305-1048
Agricola

A hyper-mutant of the unusual σ⁷⁰-Pr promoter bypasses synergistic ppGpp/DksA co-stimulation

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613701); ISSN: 0305-1048
Agricola

RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613702); ISSN: 0305-1048
Agricola

Cellular heat shock factor 1 positively regulates human immunodeficiency virus-1 gene expression and replication by two distinct pathways

Rawat, Pratima; Mitra, Debashis — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613703); ISSN: 0305-1048
Agricola

Long-range chromatin interactions at the mouse Igf2/H19 locus reveal a novel paternally expressed long non-coding RNA

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613704); ISSN: 0305-1048
Agricola

Extracellular signal-regulated kinase 1/2-mediated phosphorylation of p300 enhances myosin heavy chain I/β gene expression via acetylation of nuclear factor of activated T cells c1

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613705); ISSN: 0305-1048
Agricola

8-Oxo-7,8-dihydroguanine in DNA does not constitute a barrier to transcription, but is converted into transcription-blocking damage by OGG1

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613706); ISSN: 0305-1048
Agricola

The relative efficiency of homology-directed repair has distinct effects on proper anaphase chromosome separation

Laulier, Corentin; Cheng, Anita; Stark, Jeremy M. — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613707); ISSN: 0305-1048
Agricola

High-throughput analysis of the mutagenic and cytotoxic properties of DNA lesions by next-generation sequencing

Yuan, Bifeng; Wang, Jianshuang; Cao, Huachuan; Sun, Ruobai; Wang, Yinsheng — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613708); ISSN: 0305-1048
Agricola

Efficient mutagenesis of the rhodopsin gene in rod photoreceptor neurons in mice

Chan, Fung; Hauswirth, William W.; Wensel, Theodore G.; Wilson, John H. — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613709); ISSN: 0305-1048
Agricola

Mechanistic analysis of Xenopus EXO1's function in 5'-strand resection at DNA double-strand breaks

Liao, Shuren; Toczylowski, Thomas; Yan, Hong — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613710); ISSN: 0305-1048
Agricola

Cdt1 proteolysis is promoted by dual PIP degrons and is modulated by PCNA ubiquitylation

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613711); ISSN: 0305-1048
Agricola

Evidence for an evolutionary antagonism between Mrr and Type III modification systems

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613712); ISSN: 0305-1048
Agricola

Zim17/Tim15 links mitochondrial iron-sulfur cluster biosynthesis to nuclear genome stability

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613713); ISSN: 0305-1048
Agricola

Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613714); ISSN: 0305-1048
Agricola

Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes

Reineke, Anna R.; Bornberg-Bauer, E.; Gu, Jenny — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613715); ISSN: 0305-1048
Agricola

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA

Bundschuh, R.; Altmüller, J.; Becker, C.; Nürnberg, P.; Gott, J.M. — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613716); ISSN: 0305-1048
Agricola

Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613717); ISSN: 0305-1048
Agricola

Crosstalk between c-Jun and TAp73α/β contributes to the apoptosis-survival balance

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613718); ISSN: 0305-1048
Agricola

MicroRNA 130 family regulates the hypoxia response signal through the P-body protein DDX6

Saitō, Ken.; Kondo, Eisaku; Matsushita, Masayuki — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613719); ISSN: 0305-1048
Agricola

Point mutations in the Rpb9-homologous domain of Rpc11 that impair transcription termination by RNA polymerase III

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613720); ISSN: 0305-1048
Agricola

A novel DNA nuclease is stimulated by association with the GINS complex

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613721); ISSN: 0305-1048
Agricola

Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613722); ISSN: 0305-1048
Agricola

Zinc is essential for high-affinity DNA binding and recombinase activity of φC31 integrase

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613723); ISSN: 0305-1048
Agricola

Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t⁶A modification of tRNAs

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613724); ISSN: 0305-1048
Agricola

Regulation of the alternative splicing of tau exon 10 by SC35 and Dyrk1A

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613725); ISSN: 0305-1048
Agricola

Differential usage of transcriptional start sites and polyadenylation sites in FMR1 premutation alleles

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613726); ISSN: 0305-1048
Agricola

Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613727); ISSN: 0305-1048
Agricola

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613728); ISSN: 0305-1048
Agricola

Messenger RNA degradation is initiated at the 5' end and follows sequence- and condition-dependent modes in chloroplasts

Salvador, Maria L.; Suay, Loreto; Klein, Uwe — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613729); ISSN: 0305-1048
Agricola

Additional roles of a peripheral loop-loop interaction in the Neurospora VS ribozyme

DeAbreu, Diane M.; Olive, Joan E.; Collins, Richard A. — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613730); ISSN: 0305-1048
Agricola

G-quadruplex formation at the 3' end of telomere DNA inhibits its extension by telomerase, polymerase and unwinding by helicase

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613731); ISSN: 0305-1048
Agricola

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 Å

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613732); ISSN: 0305-1048
Agricola

Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613733); ISSN: 0305-1048
Agricola

The origin of genetic instability in CCTG repeats

Lam, Sik Lok; Wu, Feng; Yang, Hao; Chi, Lai Man — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613734); ISSN: 0305-1048
Agricola

A DNA minor groove electronegative potential genome map based on photo-chemical probing

Lindemose, Søren; Nielsen, Peter Eigil; Hansen, Morten; Møllegaard, Niels Erik — Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613735); ISSN: 0305-1048
Agricola

5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613736); ISSN: 0305-1048
Agricola

Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613737); ISSN: 0305-1048
Agricola

Mechanism of RecO recruitment to DNA by single-stranded DNA binding protein

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613738); ISSN: 0305-1048
Agricola

Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes

Mon, 01 Aug 2011 00:00:00 -0400

Nucleic acids research; 08/01/2011
(AN IND44613739); ISSN: 0305-1048
Agricola

The 2011 bioinformatics links directory update: more resources, tools and databases and features to empower the bioinformatics community

Brazas, Michelle D.; Yim, David S.; Yamada, Joseph T.; Ouellette, B.F. Francis — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595725); ISSN: 0305-1048
Agricola

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences

Sahraeian, Sayed Mohammad Ebrahim; Yoon, Byung-Jun — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595779); ISSN: 0305-1048
Agricola

Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis

Everett, Logan J.; Jensen, Shane T.; Hannenhalli, Sridhar — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597757); ISSN: 0305-1048
Agricola

cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597758); ISSN: 0305-1048
Agricola

Analysis of microRNA signatures using size-coded ligation-mediated PCR

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597759); ISSN: 0305-1048
Agricola

A method for counting PCR template molecules with application to next-generation sequencing

Casbon, James A.; Osborne, Robert J.; Brenner, Sydney; Lichtenstein, Conrad P. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597760); ISSN: 0305-1048
Agricola

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597761); ISSN: 0305-1048
Agricola

A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597762); ISSN: 0305-1048
Agricola

Measurement of telomere DNA content by dot blot analysis

Kimura, M.; Aviv, Abraham — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597763); ISSN: 0305-1048
Agricola

Single-molecule analysis of genome rearrangements in cancer

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603009); ISSN: 0305-1048
Agricola

Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays

Lu, Jun; Kerns, Robnet T.; Peddada, Shyamal D.; Bushel, Pierre R. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603010); ISSN: 0305-1048
Agricola

NOA: a novel Network Ontology Analysis method

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603011); ISSN: 0305-1048
Agricola

QuartetS: a fast and accurate algorithm for large-scale orthology detection

Yu, Chenggang; Zavaljevski, Nela; Desai, Valmik; Reifman, Jaques — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603012); ISSN: 0305-1048
Agricola

An all-statistics, high-speed algorithm for the analysis of copy number variation in genomes

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603013); ISSN: 0305-1048
Agricola

Sequence-specific error profile of Illumina sequencers

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603014); ISSN: 0305-1048
Agricola

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595694); ISSN: 0305-1048
Agricola

iPBA: a tool for protein structure comparison using sequence alignment strategies

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595704); ISSN: 0305-1048
Agricola

CLICK--topology-independent comparison of biomolecular 3D structures

Nguyen, M.N.; Tan, K.P.; Madhusudhan, M.S. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595714); ISSN: 0305-1048
Agricola

HMMER web server: interactive sequence similarity searching

Finn, Robert D.; Clements, Jody; Eddy, Sean R. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595723); ISSN: 0305-1048
Agricola

FFAS server: novel features and applications

Jaroszewski, Lukasz; Li, Zhanwen; Cai, Xiao-hui; Weber, Christoph; Godzik, Adam — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595739); ISSN: 0305-1048
Agricola

R3D-BLAST: a search tool for similar RNA 3D substructures

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595751); ISSN: 0305-1048
Agricola

WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs

Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595761); ISSN: 0305-1048
Agricola

SLiMSearch 2.0: biological context for short linear motifs in proteins

Davey, Norman E.; Haslam, Niall J.; Shields, Denis C.; Edwards, Richard J. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595772); ISSN: 0305-1048
Agricola

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595775); ISSN: 0305-1048
Agricola

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Blanchet, Christophe; Pasi, Marco; Zakrzewska, Krystyna; Lavery, Richard — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595776); ISSN: 0305-1048
Agricola

ConTra v2: a tool to identify transcription factor binding sites across species, update 2011

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595777); ISSN: 0305-1048
Agricola

Genome surveyor 2.0: cis-regulatory analysis in Drosophila

Kazemian, Majid; Brodsky, Michael H.; Sinha, Saurabh — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595778); ISSN: 0305-1048
Agricola

RSAT 2011: regulatory sequence analysis tools

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595780); ISSN: 0305-1048
Agricola

The RNAmute web server for the mutational analysis of RNA secondary structures

Churkin, Alexander; Gabdank, Idan; Barash, Danny — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595781); ISSN: 0305-1048
Agricola

Mapping the sequences of potential guanine quadruplex motifs

Todd, Alan K.; Neidle, Stephen — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597723); ISSN: 0305-1048
Agricola

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597724); ISSN: 0305-1048
Agricola

Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597725); ISSN: 0305-1048
Agricola

Integrative genomic analysis of human ribosomal DNA

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597726); ISSN: 0305-1048
Agricola

Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597727); ISSN: 0305-1048
Agricola

G4 motifs correlate with promoter-proximal transcriptional pausing in human genes

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597728); ISSN: 0305-1048
Agricola

Modulation of Dnmt3b function in vitro by interactions with Dnmt3L, Dnmt3a and Dnmt3b splice variants

Van Emburgh, Beth O.; Robertson, Keith D. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597729); ISSN: 0305-1048
Agricola

Massive production of small RNAs from a non-coding region of Cauliflower mosaic virus in plant defense and viral counter-defense

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597730); ISSN: 0305-1048
Agricola

Genomic mapping of 5-hydroxymethylcytosine in the human brain

Jin, Seung-Gi; Wu, Xiwei; Li, Arthur X.; Pfeifer, Gerd P. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597731); ISSN: 0305-1048
Agricola

Requirement of TFIIH kinase subunit Mat1 for RNA Pol II C-terminal domain Ser5 phosphorylation, transcription and mRNA turnover

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597732); ISSN: 0305-1048
Agricola

Identification of altered function alleles that affect Bacillus subtilis PerR metal ion selectivity

Ma, Zhen; Lee, Jin-Won; Helmann, John D. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597733); ISSN: 0305-1048
Agricola

PARG is recruited to DNA damage sites through poly(ADP-ribose)- and PCNA-dependent mechanisms

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597734); ISSN: 0305-1048
Agricola

Crosslinking of DNA repair and replication proteins to DNA in cells treated with 6-thioguanine and UVA

Gueranger, Quentin; Kia, Azadeh; Frith, David; Karran, Peter — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597735); ISSN: 0305-1048
Agricola

Nuclear protein LEDGF/p75 recognizes supercoiled DNA by a novel DNA-binding domain

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597736); ISSN: 0305-1048
Agricola

Segrosome assembly at the pliable parH centromere

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597737); ISSN: 0305-1048
Agricola

Actin and myosin contribute to mammalian mitochondrial DNA maintenance

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597738); ISSN: 0305-1048
Agricola

Escherichia coli σ⁷⁰ senses sequence and conformation of the promoter spacer region

Singh, Shivani S.; Typas, Athanasios; Hengge, Regine; Grainger, David C. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597739); ISSN: 0305-1048
Agricola

Identification and characterization of the mitochondrial RNA polymerase and transcription factor in the fission yeast Schizosaccharomyces pombe

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597740); ISSN: 0305-1048
Agricola

Dynamic competition of DsrA and rpoS fragments for the proximal binding site of Hfq as a means for efficient annealing

Hwang, Wonseok; Arluison, Véronique.; Hohng, Sungchul — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597741); ISSN: 0305-1048
Agricola

Activation of XerCD-dif recombination by the FtsK DNA translocase

Grainge, Ian; Lesterlin, Christian; Sherratt, David J. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597742); ISSN: 0305-1048
Agricola

Characterization of PvuRts1I endonuclease as a tool to investigate genomic 5-hydroxymethylcytosine

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597743); ISSN: 0305-1048
Agricola

Human microRNA hsa-miR-125a-5p interferes with expression of hepatitis B virus surface antigen

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597744); ISSN: 0305-1048
Agricola

The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing

Dutca, Laura M.; Gallagher, Jennifer E.G.; Baserga, Susan J. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597745); ISSN: 0305-1048
Agricola

Elimination of a group II intron from a plastid gene causes a mutant phenotype

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597746); ISSN: 0305-1048
Agricola

Rapid binding and release of Hfq from ternary complexes during RNA annealing

Hopkins, Julia F.; Panja, Subrata; Woodson, Sarah A. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597747); ISSN: 0305-1048
Agricola

The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597748); ISSN: 0305-1048
Agricola

Activation of a microRNA response in trans reveals a new role for poly(A) in translational repression

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597749); ISSN: 0305-1048
Agricola

Ribosomal scanning on the 5'-untranslated region of the human immunodeficiency virus RNA genome

Berkhout, Ben; Arts, Kelly; Abbink, Truus E.M. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597750); ISSN: 0305-1048
Agricola

Reconstitution and characterization of the unconventional splicing of XBP1u mRNA in vitro

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597751); ISSN: 0305-1048
Agricola

On the structure and dynamics of the complex of the nucleosome and the linker histone

Pachov, Georgi V.; Gabdoulline, Razif R.; Wade, Rebecca C. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597752); ISSN: 0305-1048
Agricola

Structural basis for the binding of IRES RNAs to the head of the ribosomal 40S subunit

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597753); ISSN: 0305-1048
Agricola

Guanine radical chemistry reveals the effect of thermal fluctuations in gene promoter regions

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597754); ISSN: 0305-1048
Agricola

PepFect 14, a novel cell-penetrating peptide for oligonucleotide delivery in solution and as solid formulation

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597755); ISSN: 0305-1048
Agricola

Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules

Babiskin, Andrew H.; Smolke, Christina D. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44597756); ISSN: 0305-1048
Agricola

LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602968); ISSN: 0305-1048
Agricola

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants

Parra, G.; Bradnam, K.; Rose, Alan B.; Korf, Ian — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602969); ISSN: 0305-1048
Agricola

In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602970); ISSN: 0305-1048
Agricola

Specific inhibition of NF-Y subunits triggers different cell proliferation defects

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602971); ISSN: 0305-1048
Agricola

Discovery of SMAD4 promoters, transcription factor binding sites and deletions in juvenile polyposis patients

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602972); ISSN: 0305-1048
Agricola

Characterization of plastid psbT sense and antisense RNAs

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602973); ISSN: 0305-1048
Agricola

Novel retrotransposed imprinted locus identified at human 6p25

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602974); ISSN: 0305-1048
Agricola

The alternative protein isoform NK2B, encoded by the vnd/NK-2 proneural gene, directly activates transcription and is expressed following the start of cells differentiation

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602975); ISSN: 0305-1048
Agricola

Translational and transcriptional control of Sp1 against ischaemia through a hydrogen peroxide-activated internal ribosomal entry site pathway

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602976); ISSN: 0305-1048
Agricola

Bromodomain protein 7 interacts with PRMT5 and PRC2, and is involved in transcriptional repression of their target genes

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602977); ISSN: 0305-1048
Agricola

Monitoring the reversible B to A-like transition of DNA in eukaryotic cells using Fourier transform infrared spectroscopy

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602978); ISSN: 0305-1048
Agricola

The activity of the histone chaperone yeast Asf1 in the assembly and disassembly of histone H3/H4-DNA complexes

Donham, Douglas C. II.; Scorgie, Jean K.; Churchill, Mair E.A. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602979); ISSN: 0305-1048
Agricola

The FANC pathway is activated by adenovirus infection and promotes viral replication-dependent recombination

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602980); ISSN: 0305-1048
Agricola

Irreparable complex DNA double-strand breaks induce chromosome breakage in organotypic three-dimensional human lung epithelial cell culture

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602981); ISSN: 0305-1048
Agricola

Cleavage of a model DNA replication fork by a methyl-specific endonuclease

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602982); ISSN: 0305-1048
Agricola

Widespread occurrence of non-canonical transcription termination by human RNA polymerase III

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602983); ISSN: 0305-1048
Agricola

Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602984); ISSN: 0305-1048
Agricola

Evolutionary expansion of the Ras switch regulatory module in eukaryotes

Díez, Diego; Sánchez-Jiménez, Francisca; Ranea, Juan A.G. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602985); ISSN: 0305-1048
Agricola

Intrinsic restriction activity by apolipoprotein B mRNA editing enzyme APOBEC1 against the mobility of autonomous retrotransposons

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602986); ISSN: 0305-1048
Agricola

Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602987); ISSN: 0305-1048
Agricola

Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation

Xiao, Botao; Zhang, Houyin; Johnson, Reid C.; Marko, John F. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602988); ISSN: 0305-1048
Agricola

Inhibition of mutant huntingtin expression by RNA duplex targeting expanded CAG repeats

Fiszer, Agnieszka; Mykowska, Agnieszka; Krzyzosiak, Wlodzimierz J. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602989); ISSN: 0305-1048
Agricola

Identification of a methylated oligoribonucleotide as a potent inhibitor of HIV-1 reverse transcription complex

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602990); ISSN: 0305-1048
Agricola

A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300

Xu, Shuang-yong; Corvaglia, Anna R.; Chan, Siu-Hong; Zheng, Yu; Linder, Patrick — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602991); ISSN: 0305-1048
Agricola

Paired mutations abolish and restore the balanced annealing and melting activities of ORF1p that are required for LINE-1 retrotransposition

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602992); ISSN: 0305-1048
Agricola

Antisense RNA associated with biological regulation of a restriction-modification system

Mruk, Iwona; Liu, Yaoping; Ge, Liying; Kobayashi, Ichizo — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602993); ISSN: 0305-1048
Agricola

An essential role for trimethylguanosine RNA caps in Saccharomyces cerevisiae meiosis and their requirement for splicing of SAE3 and PCH2 meiotic pre-mRNAs

Qiu, Zhicheng R.; Shuman, Stewart; Schwer, Beate — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602994); ISSN: 0305-1048
Agricola

The type II poly(A)-binding protein PABP-2 genetically interacts with the let-7 miRNA and elicits heterochronic phenotypes in Caenorhabditis elegans

Hurschler, Benjamin A.; Harris, David T.; Grosshans, Helge — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602995); ISSN: 0305-1048
Agricola

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602996); ISSN: 0305-1048
Agricola

A structural determinant required for RNA editing

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602997); ISSN: 0305-1048
Agricola

Transcriptional gene silencing in mammalian cells by miRNA mimics that target gene promoters

Younger, Scott T.; Corey, David R. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602998); ISSN: 0305-1048
Agricola

Analysis of microRNA turnover in mammalian cells following Dicer1 ablation

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44602999); ISSN: 0305-1048
Agricola

RNA binding properties of conserved protein subunits of human RNase P

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603000); ISSN: 0305-1048
Agricola

The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603001); ISSN: 0305-1048
Agricola

Direct measurement of DNA bending by type IIA topoisomerases: implications for non-equilibrium topology simplification

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603002); ISSN: 0305-1048
Agricola

Crystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603003); ISSN: 0305-1048
Agricola

Evidence for a remodelling of DNA-PK upon autophosphorylation from electron microscopy studies

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603004); ISSN: 0305-1048
Agricola

The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603005); ISSN: 0305-1048
Agricola

Novel post-synthetic generation, isomeric resolution, and characterization of Fapy-dG within oligodeoxynucleotides: differential anomeric impacts on DNA duplex properties

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603006); ISSN: 0305-1048
Agricola

Assembly of custom TALE-type DNA binding domains by modular cloning

Morbitzer, Robert; Elsaesser, Janett; Hausner, Jens; Lahaye, Thomas — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603007); ISSN: 0305-1048
Agricola

Effect of base sequence on the DNA cross-linking properties of pyrrolobenzodiazepine (PBD) dimers

Rahman, Khondaker M.; James, Colin H.; Thurston, David E. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44603008); ISSN: 0305-1048
Agricola

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595689); ISSN: 0305-1048
Agricola

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

Seemann, Stefan E.; Menzel, Peter; Backofen, Rolf; Gorodkin, Jan — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595690); ISSN: 0305-1048
Agricola

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595691); ISSN: 0305-1048
Agricola

ncFANs: a web server for functional annotation of long non-coding RNAs

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595692); ISSN: 0305-1048
Agricola

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling

Plaisier, Christopher L.; Bare, J. Christopher; Baliga, Nitin S. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595693); ISSN: 0305-1048
Agricola

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

Hackenberg, Michael; Rodríguez-Ezpeleta, Naiara.; Aransay, Ana M. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595695); ISSN: 0305-1048
Agricola

mirAct: a web tool for evaluating microRNA activity based on gene expression data

Liang, Zhi; Zhou, Hong; He, Zongxiao; Zheng, Haoran; Wu, Jiarui — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595696); ISSN: 0305-1048
Agricola

DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595697); ISSN: 0305-1048
Agricola

RNApredator: fast accessibility-based prediction of sRNA targets

Eggenhofer, Florian; Tafer, Hakim; Stadler, Peter F.; Hofacker, Ivo L. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595698); ISSN: 0305-1048
Agricola

psRNATarget: a plant small RNA target analysis server

Dai, Xinbin; Zhao, Patrick Xuechun — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595699); ISSN: 0305-1048
Agricola

corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs

Lam, Edmund; Kam, Alfred; Waldispühl, Jérôme — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595700); ISSN: 0305-1048
Agricola

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map

Tjioe, Elina; Lasker, Keren; Webb, Ben; Wolfson, Haim J.; Sali, Andrej — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595701); ISSN: 0305-1048
Agricola

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction

Roche, Daniel B.; Buenavista, Maria T.; Tetchner, Stuart J.; McGuffin, Liam J. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595702); ISSN: 0305-1048
Agricola

KINARI-Web: a server for protein rigidity analysis

Fox, Naomi; Jagodzinski, Filip; Li, Yang; Streinu, Ileana — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595703); ISSN: 0305-1048
Agricola

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

Poitevin, Frédéric.; Orland, Henri; Doniach, S.; Koehl, Patrice; Delarue, Marc — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595705); ISSN: 0305-1048
Agricola

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595706); ISSN: 0305-1048
Agricola

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595707); ISSN: 0305-1048
Agricola

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595708); ISSN: 0305-1048
Agricola

The FALC-Loop web server for protein loop modeling

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595709); ISSN: 0305-1048
Agricola

SDM--a server for predicting effects of mutations on protein stability and malfunction

Worth, Catherine L.; Preissner, Robert; Blundell, Tom L. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595710); ISSN: 0305-1048
Agricola

GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing

Kantardjiev, Alexander A. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595711); ISSN: 0305-1048
Agricola

PRUNE and PROBE--two modular web services for protein-protein docking

Mitra, Pralay; Pal, Debnath — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595712); ISSN: 0305-1048
Agricola

firestar--advances in the prediction of functionally important residues

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595713); ISSN: 0305-1048
Agricola

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Tan, Kuan Pern; Varadarajan, Raghavan; Madhusudhan, M.S. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595715); ISSN: 0305-1048
Agricola

Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions

London, Nir; Raveh, Barak; Cohen, Eyal; Fathi, Guy; Schueler-Furman, Ora — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595716); ISSN: 0305-1048
Agricola

PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes

Liu, Yixin.; Lo, Yu-Shu; Yang, Jinn-Moon — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595717); ISSN: 0305-1048
Agricola

Swimming into peptidomimetic chemical space using pepMMsMIMIC

Floris, Matteo; Masciocchi, Joel; Fanton, Marco; Moro, Stefano — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595718); ISSN: 0305-1048
Agricola

SwissDock, a protein-small molecule docking web service based on EADock DSS

Grosdidier, Aurélien; Zoete, Vincent; Michielin, Olivier — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595719); ISSN: 0305-1048
Agricola

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595720); ISSN: 0305-1048
Agricola

PredUs: a web server for predicting protein interfaces using structural neighbors

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595721); ISSN: 0305-1048
Agricola

MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence

Passerini, Andrea; Lippi, Marco; Frasconi, Paolo — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595722); ISSN: 0305-1048
Agricola

RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology

Gruca, Aleksandra; Sikora, Marek; Polanski, Andrzej — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595724); ISSN: 0305-1048
Agricola

ADGO 2.0: interpreting microarray data and list of genes using composite annotations

Chi, Sang-Mun; Kim, Jin; Kim, Seon-Young; Nam, Dougu — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595726); ISSN: 0305-1048
Agricola

g:Profiler--a web server for functional interpretation of gene lists (2011 update)

Reimand, Jüri; Arak, Tambet; Vilo, Jaak — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595727); ISSN: 0305-1048
Agricola

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595728); ISSN: 0305-1048
Agricola

BioProfiling.de: analytical web portal for high-throughput cell biology

Antonov, Alexey V. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595729); ISSN: 0305-1048
Agricola

AnnotQTL: a new tool to gather functional and comparative information on a genomic region

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595730); ISSN: 0305-1048
Agricola

PINTA: a web server for network-based gene prioritization from expression data

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595731); ISSN: 0305-1048
Agricola

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595732); ISSN: 0305-1048
Agricola

PHAST: A Fast Phage Search Tool

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595733); ISSN: 0305-1048
Agricola

GCView: the genomic context viewer for protein homology searches

Grin, Iwan; Linke, Dirk — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595734); ISSN: 0305-1048
Agricola

MarkUs: a server to navigate sequence-structure-function space

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595735); ISSN: 0305-1048
Agricola

NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595736); ISSN: 0305-1048
Agricola

PILGRM: an interactive data-driven discovery platform for expert biologists

Greene, Casey S.; Troyanskaya, Olga G. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595737); ISSN: 0305-1048
Agricola

MemPype: a pipeline for the annotation of eukaryotic membrane proteins

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595738); ISSN: 0305-1048
Agricola

PepServe: a web server for peptide analysis, clustering and visualization

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595740); ISSN: 0305-1048
Agricola

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

Rao, H.B.; Zhu, F.; Yang, G.B.; Li, Z.R.; Chen, Y.Z. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595741); ISSN: 0305-1048
Agricola

CENTDIST: discovery of co-associated factors by motif distribution

Zhang, Zhizhuo; Zhang, Chengwei.; Goh, Wan Ling; Sung, Wing-Kin; Cheung, Edwin — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595742); ISSN: 0305-1048
Agricola

GLAMM: Genome-Linked Application for Metabolic Maps

Bates, John T.; Chivian, Dylan; Arkin, Adam P. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595743); ISSN: 0305-1048
Agricola

The University of Minnesota Pathway Prediction System: multi-level prediction and visualization

Gao, Junfeng; Ellis, Lynda B.M.; Wackett, Lawrence P. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595744); ISSN: 0305-1048
Agricola

iPath2.0: interactive pathway explorer

Yamada, Takuji; Letunic, Ivica; Okuda, Shujiro; Kanehisa, Minoru; Bork, Peer — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595745); ISSN: 0305-1048
Agricola

mirConnX: condition-specific mRNA-microRNA network integrator

Huang, Grace T.; Athanassiou, Charalambos; Benos, Panayiotis V. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595746); ISSN: 0305-1048
Agricola

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595747); ISSN: 0305-1048
Agricola

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

Qin, Jing; Li, Mulin Jun; Wang, Panwen; Zhang, Michael Q.; Wang, Junwen — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595748); ISSN: 0305-1048
Agricola

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework

Zhang, Kunlin; Chang, Suhua; Cui, Sijia; Guo, Liyuan; Zhang, Liuyan; Wang, Jing — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595749); ISSN: 0305-1048
Agricola

SNPsyn: detection and exploration of SNP-SNP interactions

Curk, Tomaz; Rot, Gregor; Zupan, Blaz — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595750); ISSN: 0305-1048
Agricola

CoPub update: CoPub 5.0 a text mining system to answer biological questions

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595752); ISSN: 0305-1048
Agricola

Génie: literature-based gene prioritization at multi genomic scale

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595753); ISSN: 0305-1048
Agricola

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595754); ISSN: 0305-1048
Agricola

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595755); ISSN: 0305-1048
Agricola

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Letunic, Ivica; Bork, Peer — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595756); ISSN: 0305-1048
Agricola

PhyleasProg: a user-oriented web server for wide evolutionary analyses

Busset, Joël; Cabau, Cédric; Meslin, Camille; Pascal, Géraldine — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595757); ISSN: 0305-1048
Agricola

ChemMine tools: an online service for analyzing and clustering small molecules

Backman, Tyler W.H.; Cao, Yiqun; Girke, Thomas — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595758); ISSN: 0305-1048
Agricola

DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595759); ISSN: 0305-1048
Agricola

Detecting selection in immunoglobulin sequences

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595760); ISSN: 0305-1048
Agricola

ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry

Askenazi, Manor; Linial, Michal — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595762); ISSN: 0305-1048
Agricola

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595763); ISSN: 0305-1048
Agricola

CoMet--a web server for comparative functional profiling of metagenomes

Lingner, Thomas; Asshauer, Kathrin Petra; Schreiber, Fabian; Meinicke, Peter — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595764); ISSN: 0305-1048
Agricola

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595765); ISSN: 0305-1048
Agricola

The BioExtract Server: a web-based bioinformatic workflow platform

Lushbough, Carol M.; Jennewein, Douglas M.; Brendel, Volker P. — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595766); ISSN: 0305-1048
Agricola

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595767); ISSN: 0305-1048
Agricola

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595768); ISSN: 0305-1048
Agricola

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences

Yeats, Corin; Lees, Jonathan; Carter, Phil; Sillitoe, Ian; Orengo, Christine — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595769); ISSN: 0305-1048
Agricola

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595770); ISSN: 0305-1048
Agricola

HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

Kim, J. H.; Kim, Woo-Cheol; Li, Lei M.; Park, Sanghyun — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595771); ISSN: 0305-1048
Agricola

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies

Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595773); ISSN: 0305-1048
Agricola

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

Qi, Ji; Zhao, Fangqing — Fri, 01 Jul 2011 00:00:00 -0400

Nucleic acids research; 07/01/2011
(AN IND44595774); ISSN: 0305-1048
Agricola

A method to sequence and quantify DNA integration for monitoring outcome in gene therapy

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591481); ISSN: 0305-1048
Agricola

A random mutation capture assay to detect genomic point mutations in mouse tissue

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591482); ISSN: 0305-1048
Agricola

ROS-DET: robust detector of switching mechanisms in gene expression

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591483); ISSN: 0305-1048
Agricola

Predicting promoter activities of primary human DNA sequences

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591484); ISSN: 0305-1048
Agricola

Finding subtypes of transcription factor motif pairs with distinct regulatory roles

Bais, Abha Singh; Kaminski, Naftali; Benos, Panayiotis V. — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591485); ISSN: 0305-1048
Agricola

Correction of PCR-bias in quantitative DNA methylation studies by means of cubic polynomial regression

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591486); ISSN: 0305-1048
Agricola

DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements

Dryden, David T.F.; Edwardson, J.M.; Henderson, Robert M. — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591450); ISSN: 0305-1048
Agricola

A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

Zhang, Dapeng; Iyer, Lakshminarayan M.; Aravind, L. — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591451); ISSN: 0305-1048
Agricola

Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591452); ISSN: 0305-1048
Agricola

Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C₂H₂ zinc fingers

Yanover, Chen; Bradley, Philip — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591453); ISSN: 0305-1048
Agricola

Human imprinted retrogenes exhibit non-canonical imprint chromatin signatures and reside in non-imprinted host genes

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591454); ISSN: 0305-1048
Agricola

Translational recoding as a feedback controller: systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591455); ISSN: 0305-1048
Agricola

Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591456); ISSN: 0305-1048
Agricola

Distant positioning of proteasomal proteolysis relative to actively transcribed genes

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591457); ISSN: 0305-1048
Agricola

Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591458); ISSN: 0305-1048
Agricola

The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3'-UTR

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591459); ISSN: 0305-1048
Agricola

Regulation of gene expression in restriction-modification system Eco29kI

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591460); ISSN: 0305-1048
Agricola

Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591461); ISSN: 0305-1048
Agricola

Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591462); ISSN: 0305-1048
Agricola

A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq

Pandey, Shree P.; Minesinger, Brenda K.; Kumar, Janesh; Walker, Graham C. — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591463); ISSN: 0305-1048
Agricola

A cytoplasm-specific activity encoded by the Trithorax-like ATX1 gene

Ndamukong, Ivan; Lapko, Hanna; Cerny, Ronald L.; Avramova, Zoya — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591464); ISSN: 0305-1048
Agricola

A role for the arginine methylation of Rad9 in checkpoint control and cellular sensitivity to DNA damage

He, Wei.; Ma, Xiaoyan; Yang, Xiao; Zhao, Yun; Qiu, Junkang; Hang, Haiying — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591465); ISSN: 0305-1048
Agricola

Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591466); ISSN: 0305-1048
Agricola

Association between translation efficiency and horizontal gene transfer within microbial communities

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591467); ISSN: 0305-1048
Agricola

2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591468); ISSN: 0305-1048
Agricola

Retinoic acid-related orphan receptor γ directly regulates neuronal PAS domain protein 2 transcription in vivo

Takeda, Yukimasa; Kang, Hong Soon; Angers, Martin; Jetten, Anton M. — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591469); ISSN: 0305-1048
Agricola

Strand bias influences the mechanism of gene editing directed by single-stranded DNA oligonucleotides

Falgowski, Kerry; Falgowski, Carly; York-Vickers, Cassie; Kmiec, Eric B. — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591470); ISSN: 0305-1048
Agricola

Mechanisms of single-stranded phosphorothioate modified antisense oligonucleotide accumulation in hepatocytes

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591471); ISSN: 0305-1048
Agricola

Use of divalent metal ions in the DNA cleavage reaction of topoisomerase IV

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591472); ISSN: 0305-1048
Agricola

Assay of both activities of the bifunctional tRNA-modifying enzyme MnmC reveals a kinetic basis for selective full modification of cmnm⁵s²U to mnm⁵s²U

Pearson, David; Carell, Thomas — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591473); ISSN: 0305-1048
Agricola

The conformation of microRNA seed regions in native microRNPs is prearranged for presentation to mRNA targets

Lambert, Nicole J.; Gu, Sam G.; Zahler, Alan M. — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591474); ISSN: 0305-1048
Agricola

Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591475); ISSN: 0305-1048
Agricola

Common conformational changes induced in type 2 picornavirus IRESs by cognate trans-acting factors

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591476); ISSN: 0305-1048
Agricola

An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591477); ISSN: 0305-1048
Agricola

Depletion of key protein components of the RISC pathway impairs pre-ribosomal RNA processing

Liang, Xue-hai; Crooke, Stanley T. — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591478); ISSN: 0305-1048
Agricola

Antisense RNA protects mRNA from RNase E degradation by RNA-RNA duplex formation during phage infection

Stazic, Damir; Lindell, Debbie; Steglich, Claudia — Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591479); ISSN: 0305-1048
Agricola

Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq

Wed, 01 Jun 2011 00:00:00 -0400

Nucleic acids research; 06/01/2011
(AN IND44591480); ISSN: 0305-1048
Agricola

Towards more robust methods of alien gene detection

Azad, Rajeev K.; Lawrence, Jeffrey G. — Sun, 01 May 2011 00:00:00 -0400

Nucleic acids research; 05/01/2011
(AN IND44577493); ISSN: 0305-1048
Agricola

RATT: Rapid Annotation Transfer Tool

Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.; Berriman, Matthew — Sun, 01 May 2011 00:00:00 -0400

Nucleic acids research; 05/01/2011
(AN IND44577494); ISSN: 0305-1048
Agricola

QDMR: a quantitative method for identification of differentially methylated regions by entropy

Sun, 01 May 2011 00:00:00 -0400

Nucleic acids research; 05/01/2011
(AN IND44577495); ISSN: 0305-1048
Agricola

Optimization of turn-back primers in isothermal amplification

Sun, 01 May 2011 00:00:00 -0400

Nucleic acids research; 05/01/2011
(AN IND44577496); ISSN: 0305-1048
Agricola

Monitoring DNA replication in fission yeast by incorporation of 5-ethynyl-2'-deoxyuridine

Hua, Hui; Kearsey, Stephen E. — Sun, 01 May 2011 00:00:00 -0400

Nucleic acids research; 05/01/2011
(AN IND44577497); ISSN: 0305-1048
Agricola

Isoform-level microRNA-155 target prediction using RNA-seq

Sun, 01 May 2011 00:00:00 -0400

Nucleic acids research; 05/01/2011
(AN IND44577498); ISSN: 0305-1048
Agricola

Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest

Roshan, Usman; Chikkagoudar, Satish; Wei, Zhi; Wang, Kai; Hakonarson, Hakon — Sun, 01 May 2011 00:00:00 -0400

Nucleic acids research; 05/01/2011
(AN IND44577499); ISSN: 0305-1048
Agricola

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