Searching journal content for articles similar to Boot et al..

Displaying results 1-10 of 5746

For checked items

view abstracts
download to citation manager

Select this article
Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...(CAFs), on the other hand.Indeed, when we explored the behavior of previously published EMT signatures using the ANS scoring method on single cells from the ESCC (Zhang et al. 2021a), lung adenocarcinoma by Xing et al. (2021) (LUAD_Xing), and CRC (Pelka et al. 2021) and BRCA (Wu et al. 2021) tumors, we...
OPEN ACCESS ARTICLE
Select this article
Research: Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types
- Arnoud Boot,
- Alvin W.T. Ng,
- Fui Teen Chong,
- Szu-Chi Ho,
- Willie Yu,
- Daniel S.W. Tan,
- N. Gopalakrishna Iyer,
- and Steven G. Rozen
Genome Res. June 2020 30: 803-813; Published in Advance July 6, 2020, doi:10.1101/gr.255620.119
...also observed strong enrichment for AAAA immediately 5′ of thymine SBSs (Fig. 2C). No enrichment of adenines 5′ of mutated cytosines was observed (Supplemental Fig. S4).View larger version: In this window In a new window Figure 2. In-depth characterization of SBS_AnT in the whole- data from tumor...
Select this article
Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
- Siwei Chen,
- Yuan Liu,
- Yingying Zhang,
- Shayne D. Wierbowski,
- Steven M. Lipkin,
- Xiaomu Wei,
- and Haiyuan Yu
Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
...that characterizes the functional relevance of all 1107 published mutational hotspots identified in approximately 25,000 tumor samples across 41 cancer types in the context of a human 3D interactome network, in which the interface of each interaction is mapped at residue resolution. Hotspots reside in network hub...
Select this article
Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...offers a powerful route to untangle this complexity, comprehensive data sets in ducks remain scarce. Meanwhile, the contributions of peripheral systems beyond neuroendocrine regulation on poultry egg production are still largely unexplored. Here, we generate 979 RNA-seq samples from the liver, ovary...
Select this article
Research: Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer
- Myrthe Jager,
- Francis Blokzijl,
- Ewart Kuijk,
- Johanna Bertl,
- Maria Vougioukalaki,
- Roel Janssen,
- Nicolle Besselink,
- Sander Boymans,
- Joep de Ligt,
- Jakob Skou Pedersen,
- Jan Hoeijmakers,
- Joris Pothof,
- Ruben van Boxtel,
- and Edwin Cuppen
Genome Res. July 2019 29: 1067-1077; Published in Advance June 20, 2019, doi:10.1101/gr.246223.118
...or cisplatin treatment (Waddell et al. 2015; Davies et al. 2017). However, linking DNA repair deficiencies to specific mutational signatures remains complicated, as tumors are genomically highly unstable and multiple processes have contributed to mutation accumulation, typically in a tissue-specific manner...
OPEN ACCESS ARTICLE
Select this article
Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...to emphasize the relevance of kidney and liver functions to evolutionary changes in mammalian carnivory score.By including more species in our analyses, we provide a clearer picture of which diet-specific selection signatures are clade-specific and which are apparent across Mammalia. For example, Kim et al...
Select this article
Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date preferentially bind to the methylated probes, along with a range of new mC-binding protein candidates. Functional characterization of these mC readers, focused...
Select this article
Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...gene-specific transcriptional dosage compensation does occur for ∼12% of amplified genes. Furthermore, we find that CNV strains do not show previously described transcriptional signatures of aneuploidy. Our study reveals the extent to which local and global mutational tolerance is modified by CNVs...
OPEN ACCESS ARTICLE
Select this article
Research: Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors
- Mi Ni Huang,
- Willie Yu,
- Wei Wei Teoh,
- Maude Ardin,
- Apinya Jusakul,
- Alvin Wei Tian Ng,
- Arnoud Boot,
- Behnoush Abedi-Ardekani,
- Stephanie Villar,
- Swe Swe Myint,
- Rashidah Othman,
- Song Ling Poon,
- Adriana Heguy,
- Magali Olivier,
- Monica Hollstein,
- Patrick Tan,
- Bin Tean Teh,
- Kanaga Sabapathy,
- Jiri Zavadil,
- and Steven G. Rozen
Genome Res. September 2017 27: 1475-1486; Published in Advance July 24, 2017, doi:10.1101/gr.220038.116
...(International Agency for Research on Cancer) Group 1 carcinogen that causes hepatocellular carcinoma (HCC). Here, we present the first whole- data on the mutational signatures of AFB1 exposure from a total of >40,000mutations in four experimental systems: two different human cell lines, in liver tumors...
OPEN ACCESS ARTICLE
Select this article
Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...in two to 14 patients, and merely 4.3% found in more than half of all male tumors analyzed (Supplemental Fig. S1A).View larger version: In this window In a new window Figure 2. Characterization of enhancers ranked from commonly to less frequently bound by ESR1 shows distinct biological features. (A...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Boot et al..

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: