gRNAde: Geometric Deep Learning for 3D RNA inverse design [PDF]
arXiv, 2023 Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics.
arxiv
Profile Context-Sensitive HMMs for Probabilistic Modeling of Sequences With Complex Correlations [PDF]
, 2006 The profile hidden Markov model is a specific type of HMM that is well suited for describing the common features of a set of related sequences. It has been extensively used in computational biology, where it is still one of the most popular tools.
Vaidyanathan, P. P., Yoon, Byung-Jun
core +2 more sources
Analysis of Small RNA Sequencing Data in Plants [PDF]
, 2022 AbstractOver the past decades, next-generation sequencing (NGS) has been employed extensively for investigating the regulatory mechanisms of small RNAs. Several bioinformatics tools are available for aiding biologists to extract meaningful information from enormous amounts of data generated by NGS platforms.
Garg, V., Varshney, R.K.
openaire +2 more sources
Characteristics of the Kelch domain containing (KLHDC) subfamily and relationships with diseases
FEBS Letters, EarlyView.The Kelch protein superfamily includes 63 members, with the KLHDC subfamily having 10 proteins. While their functions are not fully understood, recent advances in KLHDC2's structure and role in protein degradation have highlighted its potential for drug development, especially in PROTAC therapies.
Courtney Pilcher +6 more
wiley +1 more source
TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data [PDF]
Genomics & Informatics, 2017 High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy.
Jae Hyun Lim, Soo Youn Lee, Ju Han Kim
doaj +1 more source
Specific and non specific hybridization of oligonucleotide probes on microarrays [PDF]
, 2005 Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences than the intended target
Binder, Hans, Preibisch, Stephan
core +3 more sources
FEBS Letters, EarlyView.LHCPs are transported to the thylakoid membrane via the (cp)SRP pathway. This process involves a transit complex of (cp)SRP43, (cp)SRP54 and LHCP, which interacts with (cp)FtsY and Alb3 at the membrane. GTP hydrolysis by (cp)SRP54 and (cp)FtsY triggers complex dissociation.
Victor Zegarra +7 more
wiley +1 more source
ISVASE: identification of sequence variant associated with splicing event using RNA-seq data
BMC Bioinformatics, 2017 Background Exon recognition and splicing precisely and efficiently by spliceosome is the key to generate mature mRNAs. About one third or a half of disease-related mutations affect RNA splicing.
Hasan Awad Aljohi +4 more
doaj +1 more source
Complete Genome Sequence of Mulberry Vein Banding Associated Virus, a New Tospovirus Infecting Mulberry. [PDF]
PLoS ONE, 2015 Mulberry vein banding associated virus (MVBaV) that infects mulberry plants with typical vein banding symptoms had been identified as a tentative species of the genus Tospovirus based on the homology of N gene sequence to those of tospoviruses.
Jiaorong Meng +5 more
doaj +1 more source
Sequence motifs that distinguish ATP(CTP) : tRNA nucleotidyl transferases from eubacterial poly(A) polymerases [PDF]
, 2004 ATP(CTP):tRNA nucleotidyl transferases, tRNA maturing enzymes found in all organisms, and eubacterial poly(A) polymerases, enzymes involved in mRNA degradation, are so similar that until now their biochemical functions could not be distinguished by their
Keller, W., Martin, G.
core +2 more sources