Searching journal content for articles similar to Baudement et al. 28 (11): 1733.

Displaying results 1-10 of 6191

For checked items

view abstracts
download to citation manager

Select this article
Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...phenomenon of a specific intron being retained in a stable nuclear RNPs.Almost all known regulatory RNAs function via forming RNA-protein complexes (RNPs). RNPs are formed through highly stable intermolecular interactions between RNA and protein(s). It is also known that RNPs form biomolecular...
Select this article
Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...explore the impact of dikaryotism on the biology of a long-term asexual clone of the wheat pathogenic fungus Puccinia striiformis f. sp. tritici. We use Oxford Nanopore Technologies (ONT) duplex sequencing combined with Hi-C to generate a T2T nuclear-phased assembly with >99.999% consensus accuracy. We...
OPEN ACCESS ARTICLE
Select this article
Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...nonmammalian vertebrates, for example, Xenopus tropicalis (tropical frog) and Danio rerio (zebrafish), as well as two invertebrates, for example, Drosophila melanogaster and Caenorhabditis elegans, was limited to the prenatal stages. mtDNA and nuclear DNA–encoded subunits of OXPHOS complexes I, III, IV, and V...
Select this article
Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...dataWe then tested all methods on reconstructing repeat units for satellite DNA in human Chromosome 5 (Paar et al. 2007). This known satellite DNA consists of 13 units (i.e., 13 monomers), each of which is ∼171 bp in size. To construct the input sequence for methods to predict, we concatenated the 13...
OPEN ACCESS ARTICLE
Select this article
Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...in insertion of a 1.6 Mb foreign DNA sequence containing several newly formed NUPTs, NUMTs, and sequences from the nuclear (Yue et al. 2022). DSBR could also result in complex insertions originating from various regions on different chromosomes via multiple sequential invasion and annealing events (Min et al...
Select this article
Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
..., Universitat Pompeu Fabra, 08003 Barcelona, Spain; 8Institució Catalana de Recerca i Estudis Avançats, ICREA, 08003 Barcelona, Spain Corresponding author: lu.cheng.ac@gmail.comAbstractIdentifying and illustrating patterns in DNA sequences are crucial tasks in various biological data analyses. In this task...
OPEN ACCESS ARTICLE
Select this article
Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...- sequencing (WGS) read libraries. We aimed to identify if aneuploidy is an ancestral or derived feature in these organisms, as well as what is the long-term impact of chromosomal duplication during the evolution of these parasites.ResultsAneuploidy is an ancestral characteristic in trypanosomatids...
OPEN ACCESS ARTICLE
Select this article
Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...often contain gaps in which sequences are unknown owing to technical limitations. Initial assemblies might have ambiguous or poorly resolved regions because of complex genetic structures or repetitive DNA sequences such as tandem repeats that require longer read sequencing. As sequencing technologies...
OPEN ACCESS ARTICLE
Select this article
Research: A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
- Jesper Eisfeldt,
- Adam Ameur,
- Felix Lenner,
- Esmee Ten Berk de Boer,
- Marlene Ek,
- Josephine Wincent,
- Raquel Vaz,
- Jesper Ottosson,
- Tord Jonson,
- Sofie Ivarsson,
- Sofia Thunström,
- Alexandra Topa,
- Simon Stenberg,
- Anna Rohlin,
- Anna Sandestig,
- Margareta Nordling,
- Pia Palmebäck,
- Magnus Burstedt,
- Frida Nordin,
- Eva-Lena Stattin,
- Maria Sobol,
- Panagiotis Baliakas,
- Marie-Louise Bondeson,
- Ida Höijer,
- Kristine Bilgrav Saether,
- Lovisa Lovmar,
- Hans Ehrencrona,
- Malin Melin,
- Lars Feuk,
- and Anna Lindstrand
Genome Res. November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124
...or duplications. Understanding the complexity of these events and their clinical consequences requires pinpointing breakpoint junctions and resolving the derivative chromosome structure. This task often surpasses the capabilities of short-read sequencing technologies. In contrast, long-read sequencing techniques...
OPEN ACCESS ARTICLE
Select this article
Method: A simple method for finding related sequences by adding probabilities of alternative alignments
- Martin C. Frith
Genome Res. August 2024 34: 1165-1173; Published in Advance August 16, 2024, doi:10.1101/gr.279464.124
...dependence and directly using probabilities of matches, mismatches, and gaps. Allison et al. (1992) estimated such probabilities from a pair of related sequences, allowing complex gap-length distributions. They also used a log likelihood ratio to compare hypotheses that two whole sequences are related or not...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Baudement et al. 28 (11): 1733.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: