Searching journal content for articles similar to Makova et al. 14 (4): 567.

Displaying results 1-10 of 5206

For checked items

view abstracts
download to citation manager

Select this article
Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...and was mostly pre-WGD (Fig. 4B,E). Yet, the distributions of Kimura distances for TE-CRE insertions (except those from families enriched in both tissues) suggests that TE-CREs are biased toward insertions happening around the time of, or more recent than the WGD (median Kimura distance <10) (Fig. 4A). One...
Select this article
Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
..., 10, 12, 15, 17, 20, 25, and 30× assuming a 3.1 Gbp haploid size. We applied standard practice algorithms and procedures and evaluated precision and recall of each algorithm for single-nucleotide variants (SNVs), small (<50 bp) indels (insertions and deletions), and SVs with respect to the human...
OPEN ACCESS ARTICLE
Select this article
Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...variants in his or her parents at sites where the parent is heterozygous (for more details, see Methods). Even after filtering out crossover events that are supported by at least 100 heterozygous sites, this method produces far too many spurious crossover calls, as shown in Figure 5.View larger version...
Select this article
Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...homozygous calls with too low sequence support for the nonrepresented allele. Indeed, on average, heterozygous sites had significantly higher coverage than homozygous sites (Supplemental Figs. S5, S6).More narrow depth filters (Supplemental Figs. S7–S17) made patterns of heterozygosity more block...
Select this article
Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...runs over the different numbers of cores except for core = 1 (for which the computing resource is too limited) for the other methods (Fig. 4B). Both MuSE 2 and Strelka2 achieve much faster SNV calling compared with all the other methods. For the WES data, MuSE 2 accelerates 28–58 times (mean = 44...
OPEN ACCESS ARTICLE
Select this article
Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human s Chong Li1,2, Marc Jan Bonder3,4, Sabriya Syed5, Matthew Jensen6,7, Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Mark B...
Select this article
Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
...; Supplemental Fig. S4F). Furthermore, we observed a few cells, from different individuals, that carried similar CNAs. Some other cells carried multiple CNAs across the whole (Fig. 1D). As in previous reports (Knouse et al. 2016), copy number deletions occurred much more often than did copy number amplifications...
OPEN ACCESS ARTICLE
Select this article
Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
.... A standard Gaussian prior is the most common choice; however, it is often too simple, and a lot of effort has been made to make the approximate posterior richer with normalizing flows and additional stochastic layers (Rezende and Mohamed 2015; Kingma et al. 2016; Sønderby et al. 2016).In our proposed method...
Select this article
Method: Whole-genome bisulfite sequencing with improved accuracy and cost
- Masako Suzuki,
- Will Liao,
- Frank Wos,
- Andrew D. Johnston,
- Justin DeGrazia,
- Jennifer Ishii,
- Toby Bloom,
- Michael C. Zody,
- Soren Germer,
- and John M. Greally
Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
...enough coverage to represent cytosines at CG dinucleotides and elsewhere in the , the amount of sequencing required has been too costly for most research budgets. The decision has therefore been made to sacrifice comprehensiveness and to survey the instead, attempting to focus on the loci believed...
Select this article
Research: Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
- Eric R. Lucas,
- Alistair Miles,
- Nicholas J. Harding,
- Chris S. Clarkson,
- Mara K.N. Lawniczak,
- Dominic P. Kwiatkowski,
- David Weetman,
- Martin J. Donnelly,
- and The Anopheles gambiae 1000 Genomes Consortium
Genome Res. August 2019 29: 1250-1261; Published in Advance July 25, 2019, doi:10.1101/gr.245795.118
...sequence is deleted or duplicated, potentially affecting both the structure and expression levels of coding sequences and playing a crucial role in evolution and adaptation (Redon et al. 2006; Chen et al. 2008; Emerson et al. 2008). Part of the importance of CNVs lies in the wide range of effects...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Makova et al. 14 (4): 567.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: