Results 141 to 150 of about 3,346,579 (352)

Evolutionary interplay between viruses and R‐loops

FEBS Letters, EarlyView.
Viruses interact with specialized nucleic acid structures called R‐loops to influence host transcription, epigenetic states, latency, and immune evasion. This Perspective examines the roles of R‐loops in viral replication, integration, and silencing, and how viruses co‐opt or avoid these structures.
Zsolt Karányi, Zita Képes, Zoltán Szabó, Eszter Csoma, Lóránt Székvölgyi   +4 more
wiley   +1 more source

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

BMC Bioinformatics, 2006
Background In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions.
Schultz Jörg, Dandekar Thomas, Müller Tobias, Seibel Philipp N, Wolf Matthias   +4 more
doaj   +1 more source

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection [PDF]

, 2014
The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on comparing the normal and tumor genomes from the same individual. In recent years, it has become routine for projects like The Cancer Genome Atlas (TCGA) to also sequence the tumor ...
arxiv   +1 more source

Intra-species sequence variability in 28s rRNA gene of Oesophagostomum venulosum isolated from goats of West Bengal, India [PDF]

, 2010
ObjectiveTo identify genotypes of Oesophagostmum venulosum (O. venulosum) prevailing in West Bengal, India by comparing variation of nucleotide sequences among 28S rRNA.MethodsPCR amplification of partial segment of 28 S rRNA sequence and analysis of ...
Bandyopadhyay, Samiran, Bandyopadhyay, Subhasish, Bera, Asit Kumar, Bhattacharya, Debasis, Dandapat, Premanshu, De, Sumanta, Ghosh, Subhashree, Rana, Tanmoy, Sikdar, Sourav   +8 more
core   +1 more source

Unlocking the potential of tumor‐derived DNA in urine for cancer detection: methodological challenges and opportunities

Molecular Oncology, EarlyView.
Urine is a rich source of biomarkers for cancer detection. Tumor‐derived material is released into the bloodstream and transported to the urine. Urine can easily be collected from individuals, allowing non‐invasive cancer detection. This review discusses the rationale behind urine‐based cancer detection and its potential for cancer diagnostics ...
Birgit M. M. Wever, Renske D. M. Steenbergen   +1 more
wiley   +1 more source

RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure

Nature Communications, 2017
Adenosine deaminase acting on RNA 1 (ADAR1) edits adenosine to inosine. Here the authors, using parallel analysis of RNA secondary structure sequencing, provide evidence that ADAR1 induces sequence-context-dependent RNA secondary structures changes ...
Oz Solomon, Ayelet Di Segni, Karen Cesarkas, Hagit T. Porath, Victoria Marcu-Malina, Orel Mizrahi, Noam Stern-Ginossar, Nitzan Kol, Sarit Farage-Barhom, Efrat Glick-Saar, Yaniv Lerenthal, Erez Y. Levanon, Ninette Amariglio, Ron Unger, Itamar Goldstein, Eran Eyal, Gidi Rechavi   +16 more
doaj   +1 more source

Phy M: an RNase activity specific for U and A residues useful in RNA sequence analysis.

Nucleic Acids Research, 1980
Physarum polycephalum, an acellular slime mold, produces an endoribonuclease activity (Phy M) useful in direct RNA sequence determination. Under conditions previously described for direct enzymatic RNA sequencing (7M urea, 50 degrees C, pH 5.0)1 Phy M ...
Helen Donis-Keller
semanticscholar   +1 more source

Subpar reporting of pre‐analytical variables in RNA‐focused blood plasma studies

Molecular Oncology, EarlyView.
Pre‐analytical variables strongly influence the analysis of extracellular RNA (cell‐free RNA; exRNA) derived from blood plasma. Their reporting is essential to allow interpretation and replication of results. By evaluating 200 exRNA studies, we pinpoint a lack of reporting pre‐analytical variables associated with blood collection, plasma preparation ...
Céleste Van Der Schueren, Philippe Decruyenaere, Francisco Avila Cobos, Johanna Bult, Jill Deleu, Laudonia Lidia Dipalo, Hetty Hilde Helsmoortel, Eva Hulstaert, Annelien Morlion, Elena Ramos Varas, Kathleen Schoofs, Wim Trypsteen, Eveline Vanden Eynde, Hanne Van Droogenbroeck, Kimberly Verniers, Jo Vandesompele, Anneleen Decock   +16 more
wiley   +1 more source

Integrative in silico and in vitro transcriptomics analysis revealed new lncRNAs related to intrinsic apoptotic genes in colorectal cancer

Cancer Cell International, 2020
Background Pathogenesis of colorectal cancer (CRC) is connected to deregulation of apoptosis while the effect of lncRNAs, as critical regulatory molecules, on this pathway is not clear well.
Fatemeh Akbari, Maryam Peymani, Ali Salehzadeh, Kamran Ghaedi   +3 more
doaj   +1 more source

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

Nucleic Acids Research, 2016
When analyzing single-cell RNA-seq data, constructing a pseudo-temporal path to order cells based on the gradual transition of their transcriptomes is a useful way to study gene expression dynamics in a heterogeneous cell population. Currently, a limited
Zhicheng Ji, Hongkai Ji
semanticscholar   +1 more source