Searching journal content for articles similar to Khatib et al. 4 (1): 13.

Displaying results 1-10 of 183

For checked items

view abstracts
download to citation manager

Select this article
Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
..., Ye J, Ou H, Jiang T, Guo B, Yang Q, Liang W, et al. 2021. Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function. Mol Psychiatry 26: 6630–6642. doi:10.1038/s41380...
Select this article
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
..., and approximately 10 million microsatellites have been identified across the human . Microsatellites are vulnerable to DNA mismatch errors and have thus been used to detect cancers with mismatch repair deficiency. To reveal the mutational landscape of microsatellite repeat regions at the level, we analyzed...
OPEN ACCESS ARTICLE
Select this article
Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...deviations. (B) Monte Carlo simulations are used to search for the TF that best explains the observations in cfDNA given the known tumor variants and their variant allele frequency (VAF) in the tumor. Created with BioRender (for detailed methods, please see Methods: “Tumor fraction estimation from somatic...
OPEN ACCESS ARTICLE
Select this article
Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...was knocked out, there was an increase in the proportions of di- and trinucleosomal plasma DNA molecules (Serpas et al. 2019). Additionally, the relative frequencies of specific four-base motifs at the 5′ ends of plasma DNA fragments were significantly perturbed in Dnase1l3 knockout mice, in which the six...
OPEN ACCESS ARTICLE
Select this article
Method: Accurate sequencing of DNA motifs able to form alternative (non-B) structures
- Matthias H. Weissensteiner,
- Marzia A. Cremona,
- Wilfried M. Guiblet,
- Nicholas Stoler,
- Robert S. Harris,
- Monika Cechova,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 11, 2023 ; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
...that elevated sequencing errors at non-B DNA motifs should be considered in lowread-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA. [Supplemental material...
OPEN ACCESS ARTICLE
Select this article
Method: MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq
- Jonathon T. Hill,
- Bradley L. Demarest,
- Brent W. Bisgrove,
- Bushra Gorsi,
- Yi-Chu Su,
- and H. Joseph Yost
Genome Res. April 2013 23: 687-697; Published in Advance January 8, 2013, doi:10.1101/gr.146936.112
.... 2011). However, mapping mutants in many species traditionally has been labor intensive and often inconclusive, especially in organisms with relatively complex s. Several methods exist to expedite genetic mapping. For example, genotyping DNA pooled from phenotype-sorted individuals (bulk segregant...
OPEN ACCESS ARTICLE
Select this article
METHODS: Pooled Genotyping of Microsatellite Markers in Parent–Offspring Trios
- George Kirov,
- Nigel Williams,
- Pak Sham,
- Nick Craddock,
- and Michael J. Owen
Genome Res. January 1, 2000 10: 105-115; doi:10.1101/gr.10.1.105
...) Determination of allele frequencies at loci with length polymorphism by quantitative analysis of DNA amplified from pooled samples. PCR Methods Applic. 2 : 313 – 317 . ↵ Perlin M.W. , Lancia G. , Ng S.-K. ( 1995 ) Toward fully automated genotyping: Genotyping microsatellite...
Select this article
METHODS: High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR
- Søren Germer,
- Michael J. Holland,
- and Russell Higuchi
Genome Res. February 1, 2000 10: 258-266; doi:10.1101/gr.10.2.258
...High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR Søren Germer 1 , Michael J. Holland 2 , and Russell Higuchi 1 1Roche Molecular Systems, Alameda, California 94501 USA;2Department of Biological Chemistry...
Select this article
Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
- Wilfried M. Guiblet,
- Marzia A. Cremona,
- Monika Cechova,
- Robert S. Harris,
- Iva Kejnovská,
- Eduard Kejnovsky,
- Kristin Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
...(i.e., polymerization kinetics) and polymerase errors are affected by non-B DNA, we utilized data from Single-Molecule Real-Time (SMRT) sequencing. In addition to determining the primary nucleotide sequence, this technology, which uses an engineered bacteriophage phi29 polymerase (Eid et al. 2009...
OPEN ACCESS ARTICLE
Select this article
Research: Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
- Marco L. Leung,
- Alexander Davis,
- Ruli Gao,
- Anna Casasent,
- Yong Wang,
- Emi Sei,
- Eduardo Vilar,
- Dipen Maru,
- Scott Kopetz,
- and Nicholas E. Navin
Genome Res. August 2017 27: 1287-1299; Published in Advance May 25, 2017, doi:10.1101/gr.209973.116
...of these mutations exist at frequencies below our detection sensitivity (1 × 10−3) in the primary tumor.Mutational substructure of primary and metastatic tumorsTo resolve the clonal substructure of the primary and metastatic tumors, we applied highly multiplexed single-cell DNA sequencing (Leung et al. 2016...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Khatib et al. 4 (1): 13.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: