Results 1 to 10 of about 308,842 (252)

Linked-read sequencing for detecting short tandem repeat expansions

Scientific Reports, 2022
Detection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences.
Readman Chiu, Indhu-Shree Rajan-Babu, Inanc Birol, Jan M. Friedman   +3 more
doaj   +1 more source

A multi-platform reference for somatic structural variation detection

Cell Genomics, 2022
Summary: Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality, gold-standard datasets that enable the benchmarking of experimental approaches and ...
Jose Espejo Valle-Inclan, Nicolle J.M. Besselink, Ewart de Bruijn, Daniel L. Cameron, Jana Ebler, Joachim Kutzera, Stef van Lieshout, Tobias Marschall, Marcel Nelen, Peter Priestley, Ivo Renkens, Margaretha G.M. Roemer, Markus J. van Roosmalen, Aaron M. Wenger, Bauke Ylstra, Remond J.A. Fijneman, Wigard P. Kloosterman, Edwin Cuppen   +17 more
doaj   +1 more source

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Pathology and Oncology Research
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points.
Nikolett Szakállas, Barbara K. Barták, Gábor Valcz, Gábor Valcz, Zsófia B. Nagy, István Takács, Béla Molnár   +6 more
doaj   +1 more source

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome

Scientific Data, 2022
Measurement(s) whole genome sequencing Technology Type(s) PacBio long-read and Illumina short-read sequencing ...
Xi-wen Xu, Weiwei Zheng, Zhen Meng, Wenteng Xu, Yingjie Liu, Songlin Chen   +5 more
doaj   +1 more source

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC Genomics, 2021
Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks.
Seth Commichaux, Kiran Javkar, Padmini Ramachandran, Niranjan Nagarajan, Denis Bertrand, Yi Chen, Elizabeth Reed, Narjol Gonzalez-Escalona, Errol Strain, Hugh Rand, Mihai Pop, Andrea Ottesen   +11 more
doaj   +1 more source

Revealing co-infections in pneumonia: A case report on advancing diagnosis with metagenomic sequencing technologies

Journal of Infection and Public Health
Pneumonia, a frequent and serious complication in kidney transplant recipients, is significantly increased by long-term immunosuppressive medication. This case report details a patient with lung cavitation, in which conventional microbiological methods ...
Suzan Alzeer, Reem S. Almaghrabi, Amna Magrashi, Turki Alzahrani, Razan Bakheet, Abdulmohsen Alqasabi, Hamsa Tayeb   +6 more
doaj   +1 more source

Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation

FEBS Letters, EarlyView.
Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe, Tanmay Kumar Mohanty, Rashna Bhandari, Dorothea Fiedler   +3 more
wiley   +1 more source

The (Glg)ABCs of cyanobacteria: modelling of glycogen synthesis and functional divergence of glycogen synthases in Synechocystis sp. PCC 6803

FEBS Letters, EarlyView.
We reconstituted Synechocystis glycogen synthesis in vitro from purified enzymes and showed that two GlgA isoenzymes produce glycogen with different architectures: GlgA1 yields denser, highly branched glycogen, whereas GlgA2 synthesizes longer, less‐branched chains.
Kenric Lee, Dimitrios Bekiari, Sofia Doello, Karl Forchhammer   +3 more
wiley   +1 more source

Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus

Frontiers in Microbiology, 2018
Third-generation sequencing is an emerging technology that is capable of solving several problems that earlier approaches were not able to, including the identification of transcripts isoforms and overlapping transcripts. In this study, we used long-read
Norbert Moldován, Dóra Tombácz, Attila Szűcs, Zsolt Csabai, Michael Snyder, Zsolt Boldogkői   +5 more
doaj   +1 more source

Epigenetic blind spots – the role of DNA methylation dynamics in stem cell‐based models of embryogenesis

FEBS Letters, EarlyView.
Embryo‐like structures (stembryos) are an innovative tool, but they are hindered by experimental variability and limited developmental potential. DNA methylation is crucial for mammalian development, but its status in stembryo models is poorly characterized.
Sara Canil, Anna Corrà, Annalisa Scapolatiello, Chengxiang Qiu, Gianluca Amadei   +4 more
wiley   +1 more source