Abstract:
:The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publication, Galaxy HiCExplorer has been expanded considerably with new tools to facilitate the analysis of cHi-C and to provide an in-depth analysis of Hi-C data. Moreover, it supports the analysis of scHi-C data by offering a broad range of tools. With the help of the standard graphical user interface of Galaxy, presented workflows, extensive documentation and tutorials, novices as well as Hi-C experts are supported in their Hi-C data analysis with Galaxy HiCExplorer.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wolff J,Rabbani L,Gilsbach R,Richard G,Manke T,Backofen R,Grüning BAdoi
10.1093/nar/gkaa220subject
Has Abstractpub_date
2020-07-02 00:00:00pages
W177-W184issue
W1eissn
0305-1048issn
1362-4962pii
5821269journal_volume
48pub_type
杂志文章abstract::Nucleic acids possess the unique property of being enzymatically amplifiable, and have therefore been a popular choice for the combinatorial selection of functional sequences, such as aptamers or ribozymes. However, amplification typically requires known sequence segments that serve as primer binding sites, which can ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks004
更新日期:2012-05-01 00:00:00
abstract::Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg457
更新日期:2003-07-15 00:00:00
abstract::Upstream open reading frame (uORF)-mediated translational inhibition is important in controlling key regulatory genes expression. However, understanding the underlying molecular mechanism of such uORF-mediated control system in vivo is challenging in the absence of an animal model. Therefore, we generated a zebrafish ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr645
更新日期:2011-11-01 00:00:00
abstract::DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv251
更新日期:2015-04-30 00:00:00
abstract::Population-scale sequencing is increasingly uncovering large numbers of rare single-nucleotide variants (SNVs) in coding regions of the genome. The rarity of these variants makes it challenging to evaluate their deleteriousness with conventional phenotype-genotype associations. Protein structures provide a way of addr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw927
更新日期:2016-12-01 00:00:00
abstract::Melting of DNA in a segment bounded at both ends by regions of greater stability during electrophoresis in denaturing gradient gels show complex properties, not accommodated with standard melting theory. Compact bands of some DNA molecules become anomalously broadened at the retardation level in a denaturing gradient,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.14.2775
更新日期:1995-07-25 00:00:00
abstract::Multiplexed tandem PCR (MT-PCR) is a process for highly multiplexed gene expression profiling. In the first step, multiple primer pairs are added to the RNA to be analysed together with reverse transcriptase and Taq DNA polymerase. Following reverse transcription, the multiplexed amplicons are simultaneously amplified...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni182
更新日期:2005-11-24 00:00:00
abstract::Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (N...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.10.2457
更新日期:1998-05-15 00:00:00
abstract::DNA double stranded breaks (DSBs) are one of the most deleterious types of DNA lesions. The main pathways responsible for repairing these breaks in eukaryotic cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). However, a third group of still poorly characterized DSB repair pathways, collect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1349
更新日期:2016-04-07 00:00:00
abstract::Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1270
更新日期:2021-01-12 00:00:00
abstract::Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction-modification (R-M) systems in this bacterium creates a barrier against natural transformatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt024
更新日期:2013-03-01 00:00:00
abstract::Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep)...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw689
更新日期:2016-10-14 00:00:00
abstract::A RNA interference (RNAi) like mechanism is involved in elimination of thousands of DNA segments from the developing somatic macronucleus of Tetrahymena, yet how specific internal eliminated sequences (IESs) are recognized remains to be fully elucidated. To define requirements for DNA rearrangement, we performed mutag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl699
更新日期:2006-01-01 00:00:00
abstract::The repeating nucleotide sequence of 68 base pairs in the mtDNA from an ethidium-induced cytoplasmic petite mutant of yeast has been determined. For sequence analysis specifically primed and terminated RNA copies, obtained by in vitro transcription of the separated strands, were use. The sequence consists of 66 consec...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.7.2369
更新日期:1977-07-01 00:00:00
abstract::The generalized mismatch repair system of Streptococcus pneumoniae (the Hex system) can eliminate base pair mismatches arising in heteroduplex DNA during transformation or by DNA polymerase errors during replication. Mismatch repair is most likely initiated at nicks or gaps. The present work was started to examine the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.20.5525
更新日期:1991-10-25 00:00:00
abstract::The nucleotide sequence of Drosophila melanogaster tRNA 5 Lys is pGCCCGGAUAm2GCUCAGDCGGDAGAGCA psi psi GGACUsU*UUt6A*A psi CCAAGGm7GDm5CCAGGGTm psi CAm1AGUCCCUGUUCGGGCGCCA. The sU* is probably 5-methylcarboxymethyl-2-thiouridine and t6A* is a mixture of modified derivatives of t6A including t6A itself and a component ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.20.6393
更新日期:1982-10-25 00:00:00
abstract::We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl471
更新日期:2006-07-19 00:00:00
abstract::Gene trap mutagenesis of mouse embryonic stem cells generates random loss-of-function mutations, which can be identified by a sequence tag and can often report the endogenous expression of the mutated gene. The Centre for Modeling Human Disease is performing expression- and sequence-based screens of gene trap insertio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh106
更新日期:2004-01-01 00:00:00
abstract::Synonymous codon usage significantly impacts translational and transcriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has been implicated in various diseases. However, population-specific differences in codon usage biases remain largely unexplored. Here, we present a web se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa863
更新日期:2020-11-04 00:00:00
abstract::Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq110
更新日期:2010-06-01 00:00:00
abstract::Structural Maintenance of Chromosomes (SMC) proteins are vital for a wide range of processes including chromosome structure and dynamics, gene regulation and DNA repair. Eukaryotes have three SMC complexes, consisting of heterodimeric pairs of six different SMC proteins along with several specific regulatory subunits....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq038
更新日期:2010-06-01 00:00:00
abstract::YdiV is a negative regulator of cell motility. It interacts with FlhD(4)C(2) complex, a product of flagellar master operon, which works as the transcription activator of all other flagellar operons. Here, we report the crystal structures of YdiV and YdiV(2)-FlhD(2) complex at 1.9 Å and 2.9 Å resolutions, respectively....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks869
更新日期:2012-11-01 00:00:00
abstract::We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemente...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1111
更新日期:2016-02-29 00:00:00
abstract::The pyrrole-imidazole (Py-Im) triamide-cyclopropa pyrroloindole (CPI) conjugates ImPyImLDu86 (7) and ImImPyLDu86 (14) were synthesized and their alkylating activities and inhibitory effects on DNA hydrolysis by restriction endonucleases were examined. Sequencing gel analysis demonstrated that conjugates 7 and 14 speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf486
更新日期:2002-09-01 00:00:00
abstract::TP63, a member of the p53 gene family gene, encodes the ΔNp63 protein and is one of the most frequently amplified genes in squamous cell carcinomas (SCC) of the head and neck (HNSCC) and lungs (LUSC). Using an epiallelic series of siRNAs with intrinsically different knockdown abilities, we show that the complete loss ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw036
更新日期:2016-04-20 00:00:00
abstract::YB-1 is a universal major protein of cytoplasmic mRNPs, a member of the family of multifunctional cold shock domain proteins (CSD proteins). Depending on its amount on mRNA, YB-1 stimulates or inhibits mRNA translation. In this study, we have analyzed complexes formed in vitro at various YB-1 to mRNA ratios, including...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh889
更新日期:2004-10-19 00:00:00
abstract::The discovery of hydroxymethyl-, formyl- and carboxylcytosine, generated through oxidation of methylcytosine by TET dioxygenases, raised the question how these modifications contribute to epigenetic regulation. As they are subjected to complex regulation in vivo, we dissected links to gene expression with in vitro mod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku552
更新日期:2014-07-01 00:00:00
abstract::SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg535
更新日期:2003-07-01 00:00:00
abstract::The cDNA encoding Chinese hamster O6-alkylguanine-DNA-alkyltransferase (ATase) has been isolated from a library prepared from RNA isolated from V79 lung fibroblasts which had an upregulated level of this repair activity following stepwise selection with a chloroethylating agent (1, 2). Expression of the cDNA in E. col...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.8.1891
更新日期:1992-04-25 00:00:00
abstract::In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt617
更新日期:2013-09-01 00:00:00