Results 91 to 100 of about 2,481,819 (312)

Building and Improving Reference Genome Assemblies [PDF]

Proceedings of the IEEE, 2017
A genome sequence assembly provides the foundation for studies of genotypic and phenotypic variation, genome structure, and evolution of the target organism. In the past four decades, there has been a surge of new sequencing technologies, and with these developments, computational scientists have developed new algorithms to improve genome assembly ...
Karyn Meltz Steinberg, Valerie A. Schneider, Can Alkan, Michael J. Montague, Wesley C. Warren, Deanna M. Church, Richard K. Wilson   +6 more
openaire   +3 more sources

Kermit: linkage map guided long read assembly

Algorithms for Molecular Biology, 2019
Background  With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost.
Riku Walve, Pasi Rastas, Leena Salmela
doaj   +1 more source

Membrane composition and thermodynamic identity as boundaries of life for synthetic cell research

FEBS Letters, EarlyView.
What makes a cell a cell? The boundary of a living cell is not just a wall. Read as a Markov blanket, the membrane separates internal from external states, generating identity and non‐equilibrium order. Can this identity be rebuilt from scratch in a synthetic cell?
Caterina Presutti, Bert Poolman
wiley   +1 more source

Modernizing Reference Genome Assemblies

PLoS Biology, 2011
I have read the journal's policy and have the following conflicts: Paul Flicek is married to the deputy editor of PLoS Medicine, Melissa Norton. Evan Eichler is on the board of Pacific Biosciences. Support for this work came from the Intramural Research Program of the NIH, The National Library of Medicine, the European Molecular Biology ...
Church, Deanna M, Schneider, Valerie A, Graves, Tina, Auger, Katherine, Cunningham, Fiona, Bouk, Nathan, Chen, Hsiu-Chuan, Agarwala, Richa, McLaren, William M, Ritchie, Graham R S, Albracht, Derek, Kremitzki, Milinn, Rock, Susan, Kotkiewicz, Holland, Kremitzki, Colin, Wollam, Aye, Trani, Lee, Fulton, Lucinda, Fulton, Robert, Matthews, Lucy, Whitehead, Siobhan, Chow, Will, Torrance, James, Dunn, Matthew, Harden, Glenn, Threadgold, Glen, Wood, Jonathan, Collins, Joanna, Heath, Paul, Griffiths, Guy, Pelan, Sarah, Grafham, Darren, Eichler, Evan E, Weinstock, George, Mardis, Elaine R, Wilson, Richard K, Howe, Kerstin, Flicek, Paul, Hubbard, Tim   +38 more
openaire   +5 more sources

Finding novel vulnerabilities of hypomorphic BRCA1 alleles

Molecular Oncology, EarlyView.
Synthetic lethality screens performed to identify novel vulnerabilities often model complete gene loss, thereby overlooking patient‐derived hypomorphic mutations. In this study, we have performed genome‐wide CRISPR screens on BRCA1 hypomorphic mutations, showing BRCA1I26A behaves like wild‐type, while BRCA1R1699Q mimics deficiency. Furthermore, we have
Anne Schreuder, Klaas de Lint, Hồ Mỹ Phúc Võ, Mariana M. Góis, Rosalie A. Kampen, Marta San Martin Alonso, Ilse Nootenboom, Veronica Garzero, Tiemen J. Wendel, Rob M. F. Wolthuis, Sylvie M. Noordermeer   +10 more
wiley   +1 more source

GAM: Genomic Assemblies Merger

EMBnet.journal, 2012
Motivations. In the last 3 years more than 20 assemblers have been proposed to tackle the hard task of assembling. Recent evaluation efforts (Assemblathon 1 and GAGE) demonstrated that none of these tools clearly outperforms the others. However, results clearly show that some assemblers performs better than others on specific regions and statistics ...
A Policriti, S Scalabrin, F Vezzi, R Vicedomini   +3 more
openaire   +3 more sources

Oncogenic DMTF1β promotes cancer cell motility by regulating autophagy through ULK1 stabilization

Molecular Oncology, EarlyView.
In the current study, we demonstrate that the oncogene DMTF1β regulates ULK1 stability by reducing its proteasomal degradation in cancer cells. This stabilization enables ULK1 to induce autophagy, which in turn facilitates cancer cell migration. Consequently, reduced DMTF1β levels lead to decreased autophagy and impaired cancer cell migration.
Jun Xu, Nicolas J. Niklaus, Anna M. Schläfli, Igor Tokarchuk, Magali Humbert, Federico La Manna, Bich Vu, David Maul, Ramin Radpour, Marianna Kruithof‐de Julio, Inti Zlobec, Jörn Dengjel, Bruce E. Torbett, Mario P. Tschan   +13 more
wiley   +1 more source

Metagenomic assembly and draft genome sequence of an Uncharacterized prevotella sp. from Nelore rumen

, 2015
Prevotella is one of the most abundant genera in bovine rumen, although no genome has yet been assembled by a metagenomics approach applied to Brazilian Nelore.
Lemos, Eliana G M [UNESP], Lemos, Eliana G.M., Kishi, Luciano T. [UNESP], Souza, Jackson A. M. de [UNESP], Jesus, Raphael B. de, Kishi, Luciano T., de Jesus, Raphael B., Jesus, Raphael B. de [UNESP], Pavani, Claudio D., Souza, Jackson A. M. de, Pavani, Claudio D. [UNESP], Lemos, Eliana G M, Lemos, Eliana G. M. [UNESP], de Souza, Jackson A.M., Lemos, Eliana G.M. [UNESP], Lemos, Eliana G. M.   +15 more
core   +1 more source

Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies

Scientific Data
Black carp (Mylopharyngodon piceus) is one of the “four famous domestic fishes” in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this ...
Yuxuan Zhang, Yanwen Shao, Xudong Liu, Liang Zhong, Zhaoyan Zhong, Weiwei Zeng, Jiping Zhang, Wenlong Cai, Runsheng Li   +8 more
doaj   +1 more source

Translating whole‐genome doubling into precision medicine in cancer

Molecular Oncology, EarlyView.
Whole‐genome doubling creates a WGD‐positive tumor state characterized by persistent chromosomal instability, karyotypic diversification, and cellular stress. These same biological pressures drive aggressive tumor evolution while exposing therapeutic vulnerabilities, providing a rationale for WGD‐informed precision medicine. Whole‐genome doubling (WGD)
Sejung Lee, Junghyeok Lim, Jinhyuk Bhin
wiley   +1 more source