Results 31 to 40 of about 339,780 (261)

Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. [version 1; peer review: 2 approved, 1 approved with reservations]

F1000Research, 2023
Background: Advancements in DNA sequencing technology have transformed the field of bacterial genomics, allowing for faster and more cost effective chromosome level assemblies compared to a decade ago.
Tatiana Amabile de Campos, Georgios Joannis Pappas Jr, Felipe Marques de Almeida   +2 more
doaj   +1 more source

Reciprocal control of viral infection and phosphoinositide dynamics

FEBS Letters, EarlyView.
Phosphoinositides, although scarce, regulate key cellular processes, including membrane dynamics and signaling. Viruses exploit these lipids to support their entry, replication, assembly, and egress. The central role of phosphoinositides in infection highlights phosphoinositide metabolism as a promising antiviral target.
Marie Déborah Bancilhon, Bruno Mesmin
wiley   +1 more source

The genome sequence of the common toad, Bufo bufo (Linnaeus, 1758) [version 1; peer review: 2 approved]

Wellcome Open Research, 2021
We present a genome assembly from an individual male Bufo bufo (the common toad; Chordata; Amphibia; Anura; Bufonidae). The genome sequence is 5.04 gigabases in span. The majority of the assembly (99.1%) is scaffolded into 11 chromosomal pseudomolecules.
Jeffrey W. Streicher
doaj   +1 more source

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes [PDF]

Nucleic Acids Research, 2005
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to ...
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, Crécy-Lagard, Valérie de, Diaz, Naryttza N., Disz, Terry, Edwards, Robert, Fonstein, Michael, Frank, Ed D., Gerdes, Svetlana, Glass, Elizabeth M., Goesmann, Alexander, Hanson, Andrew, Iwata-Reuyl, Dirk, Jensen, Roy, Jamshidi, Neema, Krause, Lutz, Kubal, Michael, Larsen, Niels, Linke, Burkhard, McHardy, Alice C., Meyer, Folker, Neuweger, Heiko, Olsen, Gary, Olson, Robert, Osterman, Andrei, Portnoy, Vasiliy, Pusch, Gordon D., Rodionov, Dmitry A., Rückert, Christian, Steiner, Jason, Stevens, Rick, Thiele, Ines, Vassieva, Olga, Ye, Yuzhen, Zagnitko, Olga, Vonstein, Veronika   +39 more
openaire   +8 more sources

An upstream open reading frame regulates expression of the mitochondrial protein Slm35 and mitophagy flux

FEBS Letters, EarlyView.
This study reveals how the mitochondrial protein Slm35 is regulated in Saccharomyces cerevisiae. The authors identify stress‐responsive DNA elements and two upstream open reading frames (uORFs) in the 5′ untranslated region of SLM35. One uORF restricts translation, and its mutation increases Slm35 protein levels and mitophagy.
Hernán Romo‐Casanueva, Ariann E. Mendoza‐Martínez, P. Abril Medina‐Flores, Carlos Campero‐Basaldua, Alexander DeLuna, Soledad Funes   +5 more
wiley   +1 more source

AnnoTrack - a tracking system for genome annotation

BMC Genomics, 2010
Background As genome sequences are determined for increasing numbers of model organisms, demand has grown for better tools to facilitate unified genome annotation efforts by communities of biologists. Typically this process involves numerous experts from
Hubbard Tim, Harrow Jennifer, Kokocinski Felix   +2 more
doaj   +1 more source

Tau acetylation at K331 has limited impact on tau pathology in vivo

FEBS Letters, EarlyView.
We mapped tau post‐translational modifications in humanized MAPT knock‐in mice and in amyloid‐bearing double knock‐in mice. Acetylation within the repeat domain, particularly around K331, showed modest increases under amyloid pathology. To test functional relevance, we generated MAPTK331Q knock‐in mice.
Shoko Hashimoto, Yukio Matsuba, Mika Takahashi, Takaomi C. Saido   +3 more
wiley   +1 more source

Improving eukaryotic genome annotation using single molecule mRNA sequencing

BMC Genomics, 2018
Background The advantages of Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology include long reads, low systematic bias, and high consensus read accuracy.
Vincent Magrini, Xin Gao, Bruce A. Rosa, Sean McGrath, Xu Zhang, Kymberlie Hallsworth-Pepin, John Martin, John Hawdon, Richard K. Wilson, Makedonka Mitreva   +9 more
doaj   +1 more source

Diversity and complexity in neural organoids

FEBS Letters, EarlyView.
Neural organoid research aims to expand genetic diversity on one side and increase tissue complexity on the other. Chimeroids integrate multiple donor genomes within single organoids. Self‐organising multi‐identity organoids, exogenous cell seeding, or enforced assembly of region‐specific organoids contribute to tissue complexity.
Ilaria Chiaradia, Madeline A. Lancaster
wiley   +1 more source

The automatic annotation of bacterial genomes [PDF]

Briefings in Bioinformatics, 2012
With the development of ultra-high-throughput technologies, the cost of sequencing bacterial genomes has been vastly reduced. As more genomes are sequenced, less time can be spent manually annotating those genomes, resulting in an increased reliance on automatic annotation pipelines. However, automatic pipelines can produce inaccurate genome annotation
Emily J. Richardson, Mick Watson
openaire   +3 more sources