解剖学和形态学
麻醉学
听力与言语-语言病理学
行为科学
心脏和心血管系统
细胞和组织工程学
临床神经病学
危重症监护医学
牙科,口腔外科和医学
皮肤病学
急诊医学
内分泌学和新陈代谢
肠胃学和肝脏学
老人病学和老年医学
卫生保健科学和服务
血液学
免疫学
传染病
综合和补充性医学
医学伦理学
医学信息学
医学实验室技术
医学,全科和内科
医学,法律
医学,研究和试验
神经系统科学
护理
营养学和饮食学
产科医学和妇科医学
肿瘤学
眼科学
整形外科学
耳鼻喉科学
病理学
儿科学
周围血管疾病
药理学和药剂学
生理学
基本医疗保健
精神病学
公共、环境和职业卫生
放射学,核医学和医学成像
康复学
生殖生物学
呼吸系统
风湿病学
运动科学
外科学
毒理学
热带医学
泌尿学和肾脏学
病毒学
老年医学
健康政策和服务
心理学,临床
abstract::Non-coding genetic variants/mutations can play functional roles in the cell by disrupting regulatory interactions between transcription factors (TFs) and their genomic target sites. For most human TFs, a myriad of DNA-binding models are available and could be used to predict the effects of DNA mutations on TF binding....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz363
更新日期:2019-07-02 00:00:00
abstract::PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz424
更新日期:2019-07-02 00:00:00
abstract::Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein-protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz368
更新日期:2019-07-02 00:00:00
abstract::The Immune Epitope Database Analysis Resource (IEDB-AR, http://tools.iedb.org/) is a companion website to the IEDB that provides computational tools focused on the prediction and analysis of B and T cell epitopes. All of the tools are freely available through the public website and many are also available through a RE...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz452
更新日期:2019-07-02 00:00:00
abstract::The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first released in 2014 to address the key need for interpreting gene expression data within the context of protein-protein interaction (PPI) netwo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz240
更新日期:2019-07-02 00:00:00
abstract::As more and more high-throughput data has been produced by next-generation sequencing, it is still a challenge to classify RNA transcripts into protein-coding or non-coding, especially for poorly annotated species. We upgraded our original coding potential calculator, CNCI (Coding-Non-Coding Index), to CNIT (Coding-No...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz400
更新日期:2019-07-02 00:00:00
abstract::MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz299
更新日期:2019-07-02 00:00:00
abstract::Advances in genomic sequencing have enormous potential to revolutionize personalized medicine, however distinguishing disease-causing from benign variants remains a challenge. The increasing number of human genome and exome sequences available has revealed areas where unfavourable variation is removed through purifyin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz457
更新日期:2019-07-02 00:00:00
abstract::How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz176
更新日期:2019-06-20 00:00:00
abstract::RNA structural complexity and flexibility present a challenge for computational modeling efforts. Experimental information and bioinformatics data can be used as restraints to improve the accuracy of RNA tertiary structure prediction. Regarding utilization of restraints, the fundamental questions are: (i) What is the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz427
更新日期:2019-06-20 00:00:00
abstract::Message-specific translational regulation mechanisms shape the biogenesis of multimeric oxidative phosphorylation (OXPHOS) enzyme in mitochondria from the yeast Saccharomyces cerevisiae. These mechanisms, driven mainly by the action of mRNA-specific translational activators, help to coordinate synthesis of OXPHOS cata...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz266
更新日期:2019-06-20 00:00:00
abstract::Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz296
更新日期:2019-06-20 00:00:00
abstract::The phenotypic adjustments of Mycobacterium tuberculosis are commonly inferred from the analysis of transcript abundance. While mechanisms of transcriptional regulation have been extensively analysed in mycobacteria, little is known about mechanisms that shape the transcriptome by regulating RNA decay rates. The aim o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz251
更新日期:2019-06-20 00:00:00
abstract::Resistance to androgen receptor (AR)-targeted therapies in prostate cancer (PC) is a major clinical problem. A key mechanism of treatment resistance in advanced PC is the generation of alternatively spliced forms of the AR termed AR variants (AR-Vs) that are refractory to targeted agents and drive tumour progression. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz286
更新日期:2019-06-20 00:00:00
abstract::Abasic (AP) sites, the most common DNA lesions are frequently associated with double strand breaks (DSBs) and can pose a block to the final ligation. In many prokaryotes, nonhomologous end joining (NHEJ) repair of DSBs relies on a two-component machinery constituted by the ring-shaped DNA-binding Ku that recruits the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz265
更新日期:2019-06-04 00:00:00
abstract::PRMT5 is an arginine methyltransferase that accounts for the vast majority of the symmetric methylation in cells. PRMT5 exerts its function when complexed with MEP50/WDR77. This activity is often elevated in cancer cells and correlates with poor prognosis, making PRMT5 a therapeutic target. To investigate the PRMT5 si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz200
更新日期:2019-06-04 00:00:00
abstract::Ribosome biogenesis (RiBi) is an extremely energy intensive process that is critical for gene expression. It is thus highly regulated, including through the tightly coordinated expression of over 200 RiBi genes by positive and negative transcriptional regulators. We investigated RiBi regulation as cells initiated meio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz231
更新日期:2019-06-04 00:00:00
abstract::We report a novel system for efficient and specific targeted delivery of large nucleic acids to and into cells. Plasmid DNA and core histones were assembled to chromatin by salt gradient dialysis and subsequently connected to bispecific antibody derivatives (bsAbs) via a nucleic acid binding peptide bridge. The result...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz137
更新日期:2019-06-04 00:00:00
abstract::An elongation cycle of a transcribing RNA polymerase (RNAP) usually consists of multiple kinetics steps, so there exist multiple kinetic checkpoints where non-cognate nucleotides can be selected against. We conducted comprehensive free energy calculations on various nucleotide insertions for viral T7 RNAP employing al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz213
更新日期:2019-05-21 00:00:00
abstract::Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz181
更新日期:2019-05-21 00:00:00
abstract::In most cells, transcriptionally inactive heterochromatin is preferentially localized in the nuclear periphery and transcriptionally active euchromatin is localized in the nuclear interior. Different cell types display characteristic chromatin distribution patterns, which change dramatically during cell differentiatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz123
更新日期:2019-05-21 00:00:00
abstract::Telomeric regions of the genome are inherently difficult-to-replicate due to their propensity to generate DNA secondary structures and form nucleoprotein complexes that can impede DNA replication fork progression. Precisely how cells respond to DNA replication stalling within a telomere remains poorly characterized, l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz158
更新日期:2019-05-21 00:00:00
abstract::Bacterial genomics has revolutionized our understanding of the microbial tree of life; however, mapping and visualizing the distribution of functional traits across bacteria remains a challenge. Here, we introduce AnnoTree-an interactive, functionally annotated bacterial tree of life that integrates taxonomic, phyloge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz246
更新日期:2019-05-21 00:00:00
abstract::Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the repl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz090
更新日期:2019-05-07 00:00:00
abstract::Bacterial small regulatory RNAs (sRNAs) are the most abundant class of post-transcriptional regulators and have been well studied in Gram-negative bacteria. Little is known about the functions and mechanisms of sRNAs in high GC Gram-positive bacteria including Mycobacterium and Streptomyces. Here, we performed an in-d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz149
更新日期:2019-05-07 00:00:00
abstract::IGF2 mRNA-binding protein 1 (IMP1) is a key regulator of messenger RNA (mRNA) metabolism and transport in organismal development and, in cancer, its mis-regulation is an important component of tumour metastasis. IMP1 function relies on the recognition of a diverse set of mRNA targets that is mediated by the combinator...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz136
更新日期:2019-05-07 00:00:00
abstract::Enzymes of intermediary metabolism are often reported to have moonlighting functions as RNA-binding proteins and have regulatory roles beyond their primary activities. Human serine hydroxymethyltransferase (SHMT) is essential for the one-carbon metabolism, which sustains growth and proliferation in normal and tumour c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz129
更新日期:2019-05-07 00:00:00
abstract::Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz054
更新日期:2019-05-07 00:00:00
abstract::A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkz124
更新日期:2019-04-23 00:00:00
abstract::Advances in single-cell RNA-sequencing techniques reveal the existence of distinct cell subpopulations. Identification of transcription factors (TFs) that define the identity of these subpopulations poses a challenge. Here, we postulate that identity depends on background subpopulations, and is determined by a synergi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz147
更新日期:2019-04-23 00:00:00
abstract::Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with miss...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1319
更新日期:2019-04-08 00:00:00
abstract::P53-binding protein 1 (53BP1) mediates DNA repair pathway choice and promotes checkpoint activation. Chromatin marks induced by DNA double-strand breaks and recognized by 53BP1 enable focal accumulation of this multifunctional repair factor at damaged chromatin. Here, we unveil an additional level of regulation of 53B...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz138
更新日期:2019-04-08 00:00:00
abstract::Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz043
更新日期:2019-04-08 00:00:00
abstract::MicroRNAs play important roles in many biological processes. Their aberrant expression can have oncogenic or tumor suppressor function directly participating to carcinogenesis, malignant transformation, invasiveness and metastasis. Indeed, miRNA profiles can distinguish not only between normal and cancerous tissue but...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz016
更新日期:2019-03-18 00:00:00
abstract::PIWI-interacting RNAs (piRNAs) comprise a class of small RNAs best known for suppressing transposable elements in germline tissues. The vector mosquito Aedes aegypti encodes seven PIWI genes, four of which are somatically expressed. This somatic piRNA pathway generates piRNAs from viral RNA during infection with cytop...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1266
更新日期:2019-03-18 00:00:00
abstract::Hippo pathway is involved in tumorigenesis, and its regulation in cytosol has been extensively studied, but its regulatory mechanisms in the nuclear are not clear. In the current study, using a FBS-inducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1317
更新日期:2019-03-18 00:00:00
abstract::RNA can directly bind to purine-rich DNA via Hoogsteen base pairing, forming a DNA:RNA triple helical structure that anchors the RNA to specific sequences and allows guiding of transcription regulators to distinct genomic loci. To unravel the prevalence of DNA:RNA triplexes in living cells, we have established a fast ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1305
更新日期:2019-03-18 00:00:00
abstract::Six 1',5'-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz008
更新日期:2019-03-18 00:00:00
abstract::PIWI-interacting RNAs (piRNAs) engage PIWI proteins to silence transposons and promote germ cell development in animals. In diverse species, piRNA biogenesis occurs near the mitochondrial surface, and involves mitochondrial membrane-anchored factors. In mice, two cytoplasmic PIWI proteins, MIWI and MILI, receive proce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1281
更新日期:2019-03-18 00:00:00
abstract::The tissue specificity of mitochondrial tRNA mutations remains largely elusive. In this study, we demonstrated the deleterious effects of tRNAThr 15927G>A mutation that contributed to pathogenesis of coronary artery disease. The m.15927G>A mutation abolished the highly conserved base-pairing (28C-42G) of anticodon ste...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1241
更新日期:2019-02-28 00:00:00