Results 11 to 20 of about 40,175 (267)

cuteHap: Haplotype‐Aware Structural Variant Detection in Phased Long‐Read Sequencing Data [PDF]

Advanced Science
Long‐read sequencing has enabled comprehensive exploration of human genome at an unprecedented scale, particularly enhancing our understanding of structural variants (SVs).
Shuqi Cao, Yadong Liu, Miao Cui, Runtian Gao, Weimin Guo, Guohua Wang, Yadong Wang, Tao Jiang   +7 more
doaj   +2 more sources

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

Methods in Ecology and Evolution, 2023
Organisms such as allopolyploids and F1 hybrids contain multiple distinct subgenomes, each potentially with its own evolutionary history. These organisms present a challenge for multilocus phylogenetic inference and other analyses since it is not ...
William A. Freyman, Matthew G. Johnson, Carl J. Rothfels   +2 more
doaj   +1 more source

The predictive power of data-processing statistics

IUCrJ, 2020
This study describes a method to estimate the likelihood of success in determining a macromolecular structure by X-ray crystallography and experimental single-wavelength anomalous dispersion (SAD) or multiple-wavelength anomalous dispersion (MAD) phasing
Melanie Vollmar, James M. Parkhurst, Dominic Jaques, Arnaud Baslé, Garib N. Murshudov, David G. Waterman, Gwyndaf Evans   +6 more
doaj   +1 more source

High-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification

HGG Advances, 2023
Summary: Phasing of heterozygous alleles is critical for interpretation of cis-effects of disease-relevant variation. We sequenced 477 individuals with cystic fibrosis (CF) using linked-read sequencing, which display an average phase block N50 of 4.39 Mb.
Scott Mastromatteo, Angela Chen, Jiafen Gong, Fan Lin, Bhooma Thiruvahindrapuram, Wilson W.L. Sung, Joe Whitney, Zhuozhi Wang, Rohan V. Patel, Katherine Keenan, Anat Halevy, Naim Panjwani, Julie Avolio, Cheng Wang, Guillaume Côté-Maurais, Stéphanie Bégin, Damien Adam, Emmanuelle Brochiero, Candice Bjornson, Mark Chilvers, April Price, Michael Parkins, Richard van Wylick, Dimas Mateos-Corral, Daniel Hughes, Mary Jane Smith, Nancy Morrison, Elizabeth Tullis, Anne L. Stephenson, Pearce Wilcox, Bradley S. Quon, Winnie M. Leung, Melinda Solomon, Lei Sun, Felix Ratjen, Lisa J. Strug   +35 more
doaj   +1 more source

Phase retrieval with random phase illumination [PDF]

Journal of the Optical Society of America A, 2012
This paper presents a detailed, numerical study on the performance of the standard phasing algorithms with random phase illumination (RPI). Phasing with high resolution RPI and the oversampling ratio $σ=4$ determines a unique phasing solution up to a global phase factor. Under this condition, the standard phasing algorithms converge rapidly to the true
Fannjiang, Albert, Liao, Wenjing
openaire   +3 more sources

Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells

IUCrJ, 2014
X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the `diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by
Haiguang Liu, Nadia A. Zatsepin, John C. H. Spence   +2 more
doaj   +1 more source

A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm

eLife, 2022
Recently published single-cell sequencing data from individual human sperm (n=41,189; 969–3377 cells from each of 25 donors) offer an opportunity to investigate questions of inheritance with improved statistical power, but require new methods tailored to
Sara A Carioscia, Kathryn J Weaver, Andrew N Bortvin, Hao Pan, Daniel Ariad, Avery Davis Bell, Rajiv C McCoy   +6 more
doaj   +1 more source

Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq

Cell Genomics, 2023
Summary: Hundreds of loci in human genomes have alleles that are methylated differentially according to their parent of origin. These imprinted loci generally show little variation across tissues, individuals, and populations.
Vahid Akbari, Vincent C.T. Hanlon, Kieran O’Neill, Louis Lefebvre, Kasmintan A. Schrader, Peter M. Lansdorp, Steven J.M. Jones   +6 more
doaj   +1 more source

Phases, phase equilibria, and phase rules in low-dimensional systems [PDF]

The Journal of Chemical Physics, 2015
We present a unified approach to thermodynamic description of one, two, and three dimensional phases and phase transformations among them. The approach is based on a rigorous definition of a phase applicable to thermodynamic systems of any dimensionality. Within this approach, the same thermodynamic formalism can be applied for the description of phase
Frolov, Timofey, Mishin, Yuri
openaire   +3 more sources

Long-Read Sequencing Emerging in Medical Genetics

Frontiers in Genetics, 2019
The wide implementation of next-generation sequencing (NGS) technologies has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing approaches pose a limitation for the identification of structural ...
Tuomo Mantere, Tuomo Mantere, Simone Kersten, Simone Kersten, Simone Kersten, Alexander Hoischen, Alexander Hoischen, Alexander Hoischen   +7 more
doaj   +1 more source