Searching journal content for articles similar to Zhang et al. 33 (11): 1994.

Displaying results 1-10 of 62

For checked items

view abstracts
download to citation manager

Select this article
Method: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...novo assembler is identifying paths in assembly graphs that correspond to the reconstructed genomic sequences. The existing algorithmic methods struggle with this, primarily due to repetitive regions causing complex graph tangles, leading to fragmented assemblies. Here, we introduce GNNome, a framework...
Select this article
Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...(SINEs), and dictyostelium intermediate repeats (DIRs), increased in proportion to the size of the assemblies, whereas terminal inverted repeats (TIRs) and miniature inverted-repeat transposable elements (MITEs) varied independently. Satellite DNA and simple repeats represented <1% of the repetitive DNA...
OPEN ACCESS ARTICLE
Select this article
Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...) comparing the exons to the repeats. Next, for each repName, we compared observed distributions of JIs to distributions obtained by 100 rounds of randomization of the de novo transcriptome. To detect deviations of observed distributions of JIs from random, we plotted reverse empirical cumulative...
OPEN ACCESS ARTICLE
Select this article
Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...of the crowSat1 satellite in nearby primary sequence. Hence, the sequence is likely not composed of short tandem repeats as, for example, human centromeric alpha satellites with repeat units of ∼170 bp (Willard 1991). Few examples of centromeric, heterochromatic repeats exhibit motif sizes >1 kb. Miga et al...
Select this article
Resource: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- Valerie A. Schneider,
- Tina Graves-Lindsay,
- Kerstin Howe,
- Nathan Bouk,
- Hsiu-Chuan Chen,
- Paul A. Kitts,
- Terence D. Murphy,
- Kim D. Pruitt,
- Françoise Thibaud-Nissen,
- Derek Albracht,
- Robert S. Fulton,
- Milinn Kremitzki,
- Vincent Magrini,
- Chris Markovic,
- Sean McGrath,
- Karyn Meltz Steinberg,
- Kate Auger,
- William Chow,
- Joanna Collins,
- Glenn Harden,
- Timothy Hubbard,
- Sarah Pelan,
- Jared T. Simpson,
- Glen Threadgold,
- James Torrance,
- Jonathan M. Wood,
- Laura Clarke,
- Sergey Koren,
- Matthew Boitano,
- Paul Peluso,
- Heng Li,
- Chen-Shan Chin,
- Adam M. Phillippy,
- Richard Durbin,
- Richard K. Wilson,
- Paul Flicek,
- Evan E. Eichler,
- and Deanna M. Church
Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
...), was identified by RepeatMasker as alpha-satellite centromeric repeat (ftp://ftp.1000s.ebi.ac.uk/vol1/ftp/ technical/reference/phase2_reference_assembly_sequence/) (The 1000Genomes Project Consortium2015). Each centromeremodel represents the variants and monomer ordering of the chromosome-specific alpha-satellite...
OPEN ACCESS ARTICLE
Select this article
Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative...
OPEN ACCESS ARTICLE
Select this article
PERSPECTIVE: Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed
- Mariano Rocchi,
- Nicoletta Archidiacono,
- and Roscoe Stanyon
Genome Res. December 2006 16: 1441-1444; Published in Advance October 19, 2006, doi:10.1101/gr.5687906
...the inactivation of the old centromere. The evolutionary new centromere rapidly acquires the “normal” complexity characterized by centromeric satellite heterochromatin repeats. Several examples of CR events have been reported in primates ( Montefalcone et al. 1999 ; Eder et al. 2003 ; Ventura et al. 2003 , 2004...
Select this article
Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
.... Taken together, these findings show that in D. melanogaster the close proximity of coding exons to large, simple satellite blocks (and the ensuing sequencing bias) is not restricted to the Y Chromosome.All cases of sequencing bias we detected so far involve simple satellites, with repeat units of up...
Select this article
Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...are differentially distributed among chromosomes. These caps are composed of hundreds of kilobase pairs of long satellite arrays in which the basic repeat unit, known as pCht satellite (also called as StSat or subterminal satellite), is 32 bp in length (Royle et al. 1994; Koga et al. 2011; Ventura et al. 2012...
OPEN ACCESS ARTICLE
Select this article
Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Zhang et al. 33 (11): 1994.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: