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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
...prior to the WGD. Analysis of individual TE insertions, however, revealed enrichment of TE-CREs originating from WGD-associated TE activity, particularly for the DTT (Tc1-Mariner) DNA elements. Furthermore, coexpression analyses supported the presence of TE-driven gene regulatory network evolution...
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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
...as a major contributing caller to reach final consensus calls by The Cancer Genome Atlas (TCGA) PanCanAtlas project (Ellrott et al. 2018), across approximately 13,000 tumor samples, and the International Cancer Genome Consortium Pan-Cancer Analysis of Whole Genomes (ICGC-PCAWG) initiative (The ICGC/TCGA Pan...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...An atlas of fish evolution reveals delayed rediploidization following the teleost whole- duplication Elise Parey1,2, Alexandra Louis1, Jérôme Montfort2, Yann Guiguen2, Hugues Roest Crollius1 and Camille Berthelot1,3 1Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de...
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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
...with read-based methods. To evaluate this, the ratio of log10(1-Precision) was compared in read- and assembly-based methods (Supplemental Fig. S7) revealing a mean ratio of 1.78 (TR/NOTR) in read-based methods. Assembly-based methods were less affected by these regions with a precision ratio near 1 (0...
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Method: Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease
- Alexander Xi Fu,
- Kathy Nga-Chu Lui,
- Clara Sze-Man Tang,
- Ray Kit Ng,
- Frank Pui-Ling Lai,
- Sin-Ting Lau,
- Zhixin Li,
- Maria-Mercè Garcia-Barcelo,
- Pak-Chung Sham,
- Paul Kwong-Hang Tam,
- Elly Sau-Wai Ngan,
- and Kevin Y. Yip
Genome Res. November 2020 30: 1618-1632; Published in Advance September 18, 2020, doi:10.1101/gr.264473.120
..., our results reveal an unprecedentedly broad linkage between noncoding genetic variants associated with S-HSCR and NC genes and clearly demonstrate that these genetic variants distribute across many different regulatory elements and genes that converge to key functional pathways.As an additional way...
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Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
...RNAs show enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.In eukaryotes, gene transcription by RNA polymerase (Pol...
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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
...reproducing ovophilic mouthbrooder from Western Africa. Our laboratory observations revealed that a wild-caught individual produced repeatedly viable offspring in absence of a mating partner. By analyzing -wide single-nucleotide polymorphism (SNP) data, we compare that individual and two of its offspring...
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Research: Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
- Akihiro Fujimoto,
- Masashi Fujita,
- Takanori Hasegawa,
- Jing Hao Wong,
- Kazuhiro Maejima,
- Aya Oku-Sasaki,
- Kaoru Nakano,
- Yuichi Shiraishi,
- Satoru Miyano,
- Go Yamamoto,
- Kiwamu Akagi,
- Seiya Imoto,
- and Hidewaki Nakagawa
Genome Res. March 2020 30: 334-346; Published in Advance March 24, 2020, doi:10.1101/gr.255026.119
...in microsatellites for 2913 International Cancer Genome Consortium (ICGC) pan-cancer samples from 21 tissues (The International Cancer Genome Consortium 2010; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020) to reveal the whole- mutational landscape of microsatellite regions. We developed a method...
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Method: Accurate assembly of circular RNAs with TERRACE
- Tasfia Zahin,
- Qian Shi,
- Xiaofei Carl Zang,
- and Mingfu Shao
Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
...to incorporate additional types of data. Leveraging long reads and/or circRNA-enriched libraries for detection may reveal less obvious circRNAs, enhancing the assembly accuracy.MethodsTERRACE takes the alignment of paired-end total RNA-seq reads and, optionally, a reference annotation as input. TERRACE first...
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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
...Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole- profiling Lu Liu1,10, He Chen1,10, Cheng Sun2,10, Jianyun Zhang3,10, Juncheng Wang2, Meijie Du4, Jie Li4, Lin Di1, Jie Shen5, Shuang Geng1, Yuhong Pang1, Yingying Luo6, Chen Wu6...
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