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Journal articles on the topic 'Genome architecture mapping'

Author: Grafiati

Published: 24 June 2021

Last updated: 29 July 2025

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1

Tavallaee, Ghazaleh, and Elias Orouji. "Mapping the 3D genome architecture." Computational and Structural Biotechnology Journal 27 (2025): 89–101. https://doi.org/10.1016/j.csbj.2024.12.018.

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McKay, Daniel J., Alexis V. Stutzman, and Jill M. Dowen. "Advancements in mapping 3D genome architecture." Methods 170 (January 2020): 75–81. http://dx.doi.org/10.1016/j.ymeth.2019.06.002.

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Feng, Yi, Leslie Y. Beh, Wei-Jen Chang, and Laura F. Landweber. "SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping." Genome Biology and Evolution 12, no. 10 (2020): 1711–18. http://dx.doi.org/10.1093/gbe/evaa147.

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Abstract Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to it

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Chowdhary, Surabhi, Amoldeep S. Kainth, and David S. Gross. "Methods for mapping three-dimensional genome architecture." Methods 170 (January 2020): 1–3. http://dx.doi.org/10.1016/j.ymeth.2019.10.011.

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Danchin, Antoine, Pascale Guerdoux-Jamet, Ivan Moszer, and Patrick Nitschké. "Mapping the bacterial cell architecture into the chromosome." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 355, no. 1394 (2000): 179–90. http://dx.doi.org/10.1098/rstb.2000.0557.

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A genome is not a simple collection of genes. We propose here that it can be viewed as being organized as a ;‘celluloculus’ similar to the homunculus of preformists, but pertaining to the category of programmes (or algorithms) rather than to that of architectures or structures: a significant correlation exists between the distribution of genes along the chromosome and the physical architecture of the cell. W e review here data supporting this observation, stressing physical constraints operating on the cell's architecture and dynamics, and their consequences in terms of gene and genome structu

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Schmitt, Anthony D., Ming Hu, and Bing Ren. "Genome-wide mapping and analysis of chromosome architecture." Nature Reviews Molecular Cell Biology 17, no. 12 (2016): 743–55. http://dx.doi.org/10.1038/nrm.2016.104.

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Beagrie, Robert A., Antonio Scialdone, Markus Schueler, et al. "Complex multi-enhancer contacts captured by genome architecture mapping." Nature 543, no. 7646 (2017): 519–24. http://dx.doi.org/10.1038/nature21411.

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Maluszynska, J., and J. S. Heslop-Harrison. "Physical mapping of rDNA loci in Brassica species." Genome 36, no. 4 (1993): 774–81. http://dx.doi.org/10.1139/g93-102.

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The number of major rDNA loci (the genes coding for 18S–5.8S–26S rRNA) was investigated in the economically important Brassica species and their wild relatives by in situ hybridization of an rDNA probe to metaphase chromosomes and interphase nuclei. The diploid species B. nigra (B genome) has two major pairs of rDNA loci, B. oleracea (C genome) has two major pairs and one minor pair of loci, while B. campestris (A genome) has five pairs of loci. Among the three tetraploid species arising from these three diploid ancestors, B. carinata (BBCC genomes) has four loci, B. juncea (AABB genomes) has

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Ramani, Vijay, Darren A. Cusanovich, Ronald J. Hause, et al. "Mapping 3D genome architecture through in situ DNase Hi-C." Nature Protocols 11, no. 11 (2016): 2104–21. http://dx.doi.org/10.1038/nprot.2016.126.

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Burridge, James D., Hannah M. Schneider, Bao-Lam Huynh, Philip A. Roberts, Alexander Bucksch, and Jonathan P. Lynch. "Genome-wide association mapping and agronomic impact of cowpea root architecture." Theoretical and Applied Genetics 130, no. 2 (2016): 419–31. http://dx.doi.org/10.1007/s00122-016-2823-y.

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Jaroszewicz, Artur, and Jason Ernst. "An integrative approach for fine-mapping chromatin interactions." Bioinformatics 36, no. 6 (2019): 1704–11. http://dx.doi.org/10.1093/bioinformatics/btz843.

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Abstract Motivation Chromatin interactions play an important role in genome architecture and gene regulation. The Hi-C assay generates such interactions maps genome-wide, but at relatively low resolutions (e.g. 5-25 kb), which is substantially coarser than the resolution of transcription factor binding sites or open chromatin sites that are potential sources of such interactions. Results To predict the sources of Hi-C-identified interactions at a high resolution (e.g. 100 bp), we developed a computational method that integrates data from DNase-seq and ChIP-seq of TFs and histone marks. Our met

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Lee, Ling Sze, Beatriz M. Navarro-Domínguez, Zhiqiang Wu, et al. "Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes." Genes 11, no. 8 (2020): 928. http://dx.doi.org/10.3390/genes11080928.

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Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use optical mapping to improve the contiguity of the painted turtle (Chrysemys picta) genome assembly and use de novo fluorescent in situ hybridization (FISH) of bacterial artificial chromosome (BAC) clones, BAC-FISH, to physically map the genomes of the painted and slider tur

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Wang, Jiachi, Andy Pang, Karl Hong, Jill Lai, Dipa Roychoudhury, and Joyce L. Murata-Colllins. "Integrative structural variant and breakpoint detection using optical genome mapping in a patient with a transformed diffuse large B-cell lymphoma from chronic lymphocytic leukemia." Journal of Clinical Oncology 39, no. 15_suppl (2021): e19511-e19511. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e19511.

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e19511 Background: The finding of complex karyotypes has been a clinically significant finding in cancers of advanced stage or during cancer progression. Conventional cytogenetic and FISH analyses have been limited by the low-resolution of chromosomes and the number of FISH probes which can be implemented in one assay. Recent study revealed the potential of using optical genome mapping to decipher the architecture of cancer genome at nucleotide level. Methods: Karyotyping, FISH and optical genome mapping of bone marrow specimen. Results: We reported on a 63-year-old female with chronic lymphoc

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Yost, Kathryn E., Yanding Zhao, King L. Hung, et al. "Three-dimensional genome landscape of primary human cancers." Nature Genetics 57, no. 5 (2025): 1189–200. https://doi.org/10.1038/s41588-025-02188-0.

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Abstract Genome conformation underlies transcriptional regulation by distal enhancers, and genomic rearrangements in cancer can alter critical regulatory interactions. Here we profiled the three-dimensional genome architecture and enhancer connectome of 69 tumor samples spanning 15 primary human cancer types from The Cancer Genome Atlas. We discovered the following three archetypes of enhancer usage for over 100 oncogenes across human cancers: static, selective gain or dynamic rewiring. Integrative analyses revealed the enhancer landscape of noncancer cells in the tumor microenvironment for ge

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ZENG, ZHAO-BANG, CHEN-HUNG KAO, and CHRISTOPHER J. BASTEN. "Estimating the genetic architecture of quantitative traits." Genetical Research 74, no. 3 (1999): 279–89. http://dx.doi.org/10.1017/s0016672399004255.

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Understanding and estimating the structure and parameters associated with the genetic architecture of quantitative traits is a major research focus in quantitative genetics. With the availability of a well-saturated genetic map of molecular markers, it is possible to identify a major part of the structure of the genetic architecture of quantitative traits and to estimate the associated parameters. Multiple interval mapping, which was recently proposed for simultaneously mapping multiple quantitative trait loci (QTL), is well suited to the identification and estimation of the genetic architectu

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Dutta, Anik, Bruce A. McDonald, and Daniel Croll. "Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen." PLOS Pathogens 19, no. 11 (2023): e1011801. http://dx.doi.org/10.1371/journal.ppat.1011801.

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Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures

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Thoen, Manus P. M., Nelson H. Davila Olivas, Karen J. Kloth, et al. "Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping." New Phytologist 213, no. 3 (2016): 1346–62. http://dx.doi.org/10.1111/nph.14220.

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18

Younessi-Hamzekhanlu, Mehdi, and Oliver Gailing. "Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection." International Journal of Molecular Sciences 23, no. 20 (2022): 12315. http://dx.doi.org/10.3390/ijms232012315.

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The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback. Genomics and transcriptomics studies using next-generation sequencing (NGS) methods can help reve

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19

Kumar, Anand, Laxmidas Verma, Anup Pratap Singh, Shubham Singh, Keshav Babu, and Soyal Kumar. "Quantitative Traits Loci Associated with Biotic and Abiotic Resistance in Maize (Zea mays L.)." International Journal of Plant & Soil Science 35, no. 18 (2023): 1061–69. http://dx.doi.org/10.9734/ijpss/2023/v35i183371.

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Maize is an essential crop rank first, cultivated all over the world. Maize is being consumed by both humans and animals inspite that it is utilized as an industrial product viz., starch, pharmaceuticals, alcoholic beverages, oil, cosmetics, textiles, etc. In ancient times, landraces were more popular due to presence of more genetic variability, resistant to biotic and abiotic factors and have heterogeneous nature. But due to continuous use of uniform cultivars, landraces were replaced by higher yielder. Modern maize has more homogeneity which is vulnerable to any dangerous pathogen strain. In

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20

Whiting, James R., Josephine R. Paris, Paul J. Parsons, et al. "On the genetic architecture of rapidly adapting and convergent life history traits in guppies." Heredity 128, no. 4 (2022): 250–60. http://dx.doi.org/10.1038/s41437-022-00512-6.

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AbstractThe genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- and low-predation environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use four independent F2 QTL cros

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21

Tetteh, Michael, Allan de de Lima, Jack McEllin, Aidan Murphy, Douglas Mota Dias, and Conor Ryan. "Evolving Multi-Output Digital Circuits Using Multi-Genome Grammatical Evolution." Algorithms 16, no. 8 (2023): 365. http://dx.doi.org/10.3390/a16080365.

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Grammatical Evolution is a Genetic Programming variant which evolves problems in any arbitrary language that is BNF compliant. Since its inception, Grammatical Evolution has been used to solve real-world problems in different domains such as bio-informatics, architecture design, financial modelling, music, software testing, game artificial intelligence and parallel programming. Multi-output problems deal with predicting numerous output variables simultaneously, a notoriously difficult problem. We present a Multi-Genome Grammatical Evolution better suited for tackling multi-output problems, spe

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22

Yu, Kang, Dongcheng Liu, Yong Chen, et al. "Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling." Journal of Experimental Botany 70, no. 18 (2019): 4671–88. http://dx.doi.org/10.1093/jxb/erz247.

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Genome-wide linkage and homology mapping revealed 17 genomic regions harboring 42 QTLs affecting grain size in einkorn wheat. Transcriptomic analysis identified 20 genes involved in grain development and starch biosynthesis with differential expression between two parental lines.

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23

Ungerer, Mark C., Solveig S. Halldorsdottir, Jennifer L. Modliszewski, Trudy F. C. Mackay, and Michael D. Purugganan. "Quantitative Trait Loci for Inflorescence Development in Arabidopsis thaliana." Genetics 160, no. 3 (2002): 1133–51. http://dx.doi.org/10.1093/genetics/160.3.1133.

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Abstract Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting eith

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24

Seda, Ondrej, Frantisek Liska, Drahomira Krenova, et al. "Dynamic genetic architecture of metabolic syndrome attributes in the rat." Physiological Genomics 21, no. 2 (2005): 243–52. http://dx.doi.org/10.1152/physiolgenomics.00230.2004.

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The polydactylous rat strain (PD/Cub) is a highly inbred (F > 90) genetic model of metabolic syndrome. The aim of this study was to analyze the genetic architecture of the metabolic derangements found in the PD/Cub strain and to assess its dynamics in time and in response to diet and medication. We derived a PD/Cub × BN/Cub (Brown Norway) F2 intercross population of 149 male rats and performed metabolic profiling and genotyping and multiple levels of genetic linkage and statistical analyses at five different stages of ontogenesis and after high-sucrose diet feeding and dexamethasone adminis

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Heckel, D. G., L. J. Gahan, J. C. Daly, and S. Trowell. "A genomic approach to understanding Heliothis and Helicoverpa resistance to chemical and biological insecticides." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 353, no. 1376 (1998): 1713–22. http://dx.doi.org/10.1098/rstb.1998.0323.

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Genomics is the comparative study of the structure and function of entire genomes. Although the complete sequencing of the genome of any insect pest is far in the future, a genomic approach can be useful in the study of mechanisms of insecticide resistance. We describe this strategy for Heliothis and Helicoverpa , two of the most destructive genera of pest moths (Lepidoptera) worldwide. Genome–wide linkage mapping provides the location of major and minor resistance genes. Positional cloning identifies novel resistance genes, even when the mechanisms are poorly understood, as with resistance to

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Zurek, Paul R., Christopher N. Topp, and Philip N. Benfey. "Quantitative Trait Locus Mapping Reveals Regions of the Maize Genome Controlling Root System Architecture." Plant Physiology 167, no. 4 (2015): 1487–96. http://dx.doi.org/10.1104/pp.114.251751.

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27

Tian, Feng, Peter J. Bradbury, Patrick J. Brown, et al. "Genome-wide association study of leaf architecture in the maize nested association mapping population." Nature Genetics 43, no. 2 (2011): 159–62. http://dx.doi.org/10.1038/ng.746.

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28

Yang, Fangping, Jindong Liu, Ying Guo, et al. "Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat (Triticum aestivum)." Plant Disease 104, no. 8 (2020): 2174–80. http://dx.doi.org/10.1094/pdis-10-19-2116-re.

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Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated

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Ma, Yu, Afef Marzougui, Clarice J. Coyne, et al. "Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study." International Journal of Molecular Sciences 21, no. 6 (2020): 2129. http://dx.doi.org/10.3390/ijms21062129.

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Lentil (Lens culinaris Medikus) is an important source of protein for people in developing countries. Aphanomyces root rot (ARR) has emerged as one of the most devastating diseases affecting lentil production. In this study, we applied two complementary quantitative trait loci (QTL) analysis approaches to unravel the genetic architecture underlying this complex trait. A recombinant inbred line (RIL) population and an association mapping population were genotyped using genotyping by sequencing (GBS) to discover novel single nucleotide polymorphisms (SNPs). QTL mapping identified 19 QTL associat

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Lee, Tong Geon, Samuel F. Hutton, and Reza Shekasteband. "Fine Mapping of the brachytic Locus on the Tomato Genome." Journal of the American Society for Horticultural Science 143, no. 4 (2018): 239–47. http://dx.doi.org/10.21273/jashs04423-18.

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Mechanization of farm work is increasingly demanded for the current system of fresh-market tomato (Solanum lycopersicum) production. One essential element for the adoption of mechanical harvest of fresh-market tomatoes is modification of plant architecture so that the crop can be grown without staking. To address this in the current production system, the stem length should be reduced. The tomato brachytic (br) locus has been shown to be a primary source of reducing stem length. To improve the effectiveness of marker-assisted selection (MAS) for the br-mediated trait and to provide resources f

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Mukuze, Clever, Ulemu M. Msiska, Afang Badji, et al. "Genome-wide association mapping of bruchid resistance loci in soybean." PLOS ONE 20, no. 1 (2025): e0292481. https://doi.org/10.1371/journal.pone.0292481.

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Soybean is a globally important industrial, food, and cash crop. Despite its importance in present and future economies, its production is severely hampered by bruchids (Callosobruchus chinensis), a destructive storage insect pest, causing considerable yield losses. Therefore, the identification of genomic regions and candidate genes associated with bruchid resistance in soybean is crucial as it helps breeders to develop new soybean varieties with improved resistance and quality. In this study, 6 multi-locus methods of the mrMLM model for genome-wide association study were used to dissect the

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Jowhar, Ziad, Sigal Shachar, Prabhakar R. Gudla, et al. "Effects of human sex chromosome dosage on spatial chromosome organization." Molecular Biology of the Cell 29, no. 20 (2018): 2458–69. http://dx.doi.org/10.1091/mbc.e18-06-0359.

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Sex chromosome aneuploidies (SCAs) are common genetic syndromes characterized by the presence of an aberrant number of X and Y chromosomes due to meiotic defects. These conditions impact the structure and function of diverse tissues, but the proximal effects of SCAs on genome organization are unknown. Here, to determine the consequences of SCAs on global genome organization, we have analyzed multiple architectural features of chromosome organization in a comprehensive set of primary cells from SCA patients with various ratios of X and Y chromosomes by use of imaging-based high-throughput chrom

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Zhang, Ning, and Xueqing Huang. "Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize." PLOS ONE 16, no. 1 (2021): e0245129. http://dx.doi.org/10.1371/journal.pone.0245129.

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Leaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed a F3:4 recombinant inbred lines (RIL) population to map QTL for leaf angle. The RIL was derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture. A sum of eight QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf ang

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Kitony, Justine K., Hidehiko Sunohara, Mikako Tasaki, et al. "Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice." Plants 10, no. 6 (2021): 1255. http://dx.doi.org/10.3390/plants10061255.

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A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study

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Zhang, Wenmin, Hamed Najafabadi, and Yue Li. "SparsePro: An efficient fine-mapping method integrating summary statistics and functional annotations." PLOS Genetics 19, no. 12 (2023): e1011104. http://dx.doi.org/10.1371/journal.pgen.1011104.

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Identifying causal variants from genome-wide association studies (GWAS) is challenging due to widespread linkage disequilibrium (LD) and the possible existence of multiple causal variants in the same genomic locus. Functional annotations of the genome may help to prioritize variants that are biologically relevant and thus improve fine-mapping of GWAS results. Classical fine-mapping methods conducting an exhaustive search of variant-level causal configurations have a high computational cost, especially when the underlying genetic architecture and LD patterns are complex. SuSiE provided an itera

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Demetci, Pinar, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, and Lorin Crawford. "Multi-scale inference of genetic trait architecture using biologically annotated neural networks." PLOS Genetics 17, no. 8 (2021): e1009754. http://dx.doi.org/10.1371/journal.pgen.1009754.

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In this article, we present Biologically Annotated Neural Networks (BANNs), a nonlinear probabilistic framework for association mapping in genome-wide association (GWA) studies. BANNs are feedforward models with partially connected architectures that are based on biological annotations. This setup yields a fully interpretable neural network where the input layer encodes SNP-level effects, and the hidden layer models the aggregated effects among SNP-sets. We treat the weights and connections of the network as random variables with prior distributions that reflect how genetic effects manifest at

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Wu, Zhiqiang, Jocelyn M. Cuthbert, Douglas R. Taylor, and Daniel B. Sloan. "The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes." Proceedings of the National Academy of Sciences 112, no. 33 (2015): 10185–91. http://dx.doi.org/10.1073/pnas.1421397112.

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Across eukaryotes, mitochondria exhibit staggering diversity in genomic architecture, including the repeated evolution of multichromosomal structures. Unlike in the nucleus, where mitosis and meiosis ensure faithful transmission of chromosomes, the mechanisms of inheritance in fragmented mitochondrial genomes remain mysterious. Multichromosomal mitochondrial genomes have recently been found in multiple species of flowering plants, including Silene noctiflora, which harbors an unusually large and complex mitochondrial genome with more than 50 circular-mapping chromosomes totaling ∼7 Mb in size.

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Martin, Anke, Paula Moolhuijzen, Yongfu Tao, et al. "Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping." Phytopathology® 110, no. 4 (2020): 881–91. http://dx.doi.org/10.1094/phyto-10-19-0372-r.

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Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australia

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Luo, Z. W., Chung-I. Wu, and M. J. Kearsey. "Precision and High-Resolution Mapping of Quantitative Trait Loci by Use of Recurrent Selection, Backcross or Intercross Schemes." Genetics 161, no. 2 (2002): 915–29. http://dx.doi.org/10.1093/genetics/161.2.915.

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Abstract Dissecting quantitative genetic variation into genes at the molecular level has been recognized as the greatest challenge facing geneticists in the twenty-first century. Tremendous efforts in the last two decades were invested to map a wide spectrum of quantitative genetic variation in nearly all important organisms onto their genome regions that may contain genes underlying the variation, but the candidate regions predicted so far are too coarse for accurate gene targeting. In this article, the recurrent selection and backcross (RSB) schemes were investigated theoretically and by sim

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Markowski, Julia, Rieke Kempfer, Alexander Kukalev, et al. "GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data." Bioinformatics, April 8, 2021. http://dx.doi.org/10.1093/bioinformatics/btab238.

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Abstract Motivation Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of

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Belokopytova, Polina, and Veniamin Fishman. "Predicting Genome Architecture: Challenges and Solutions." Frontiers in Genetics 11 (January 22, 2021). http://dx.doi.org/10.3389/fgene.2020.617202.

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Genome architecture plays a pivotal role in gene regulation. The use of high-throughput methods for chromatin profiling and 3-D interaction mapping provide rich experimental data sets describing genome organization and dynamics. These data challenge development of new models and algorithms connecting genome architecture with epigenetic marks. In this review, we describe how chromatin architecture could be reconstructed from epigenetic data using biophysical or statistical approaches. We discuss the applicability and limitations of these methods for understanding the mechanisms of chromatin org

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Liu, Lei, Xinmeng Cao, Bokai Zhang, and Changbong Hyeon. "Dissecting the co-segregation probability from genome architecture mapping." Biophysical Journal, September 2022. http://dx.doi.org/10.1016/j.bpj.2022.09.018.

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Gao, Xin D., Xin D. Gao, Li-Chun Tu, et al. "Mapping subnuclear proteomes onto genome architecture via C-BERST." Protocol Exchange, May 8, 2018. http://dx.doi.org/10.1038/protex.2018.036.

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"Genome architecture mapping detects transcriptionally active, multiway chromatin contacts." Nature Methods, June 19, 2023. http://dx.doi.org/10.1038/s41592-023-01905-z.

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Zhu, Kaiyuan, Matthew Gregory Jones, Jens Luebeck, et al. "CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing." Genome Research, July 9, 2024, gr.279131.124. http://dx.doi.org/10.1101/gr.279131.124.

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Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early-stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpo

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Pombo, Ana, Robert A. Beagrie, Antonio Scialdone, et al. "Complex Multi‐Enhancer Contacts Captured By Genome Architecture Mapping, A Novel Ligation‐Free Approach." FASEB Journal 30, S1 (2016). http://dx.doi.org/10.1096/fasebj.30.1_supplement.99.3.

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The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key elements of transcriptional control and their disruption causes disease. Technologies based on chromosome conformation capture (3C) have profoundly expanded our understanding of the role of genome architecture in gene regulation. However, 3C‐based techniques have important limitations, many of which arise from their reliance on digestion and ligation of the interacting DNA segments. We present a new genome‐wide method, Genome Architecture Mapping (GAM) for measuring three‐dimensio

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Low, Eng-Ti Leslie, Kuang-Lim Chan, Noorhariza Mohd Zaki, et al. "Chromosome-scale Elaeis guineensis and E. oleifera assemblies: Comparative genomics of oil palm and other Arecaceae." G3: Genes, Genomes, Genetics, June 26, 2024. http://dx.doi.org/10.1093/g3journal/jkae135.

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Abstract Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping and genetic mapping. High interspecific genome conservation is observed between the two species. The s

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Beagrie, Robert A., Christoph J. Thieme, Carlo Annunziatella, et al. "Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C." Nature Methods, June 19, 2023. http://dx.doi.org/10.1038/s41592-023-01903-1.

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AbstractTechnology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that

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Pinglay, Sudarshan, Jean-Benoît Lalanne, Riza M. Daza, et al. "Multiplex generation and single-cell analysis of structural variants in mammalian genomes." Science 387, no. 6733 (2025). https://doi.org/10.1126/science.ado5978.

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Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) methods to generate, map, and characterize SVs in model systems are underdeveloped. To address these challenges, we developed Genome-Shuffle-seq, a method that enables the multiplex generation and mapping of thousands of SVs (deletions, inversions, translocations, and extrachromosomal circles) throughout mammalian genomes. We also demonstrate the co-capture of SV identity with single-cell transcri

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Murphy, William J., and Andrew J. Harris. "Toward telomere-to-telomere cat genomes for precision medicine and conservation biology." Genome Research, June 7, 2024. http://dx.doi.org/10.1101/gr.278546.123.

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Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natu

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