Results 21 to 30 of about 98,363 (283)

Optical mapping in plant comparative genomics [PDF]

GigaScience, 2015
Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline. Optical mapping provides long-range information of the genome and can more easily identify large structural variations.
Tang, Haibao, Lyons, Eric, Town, Christopher D   +2 more
openaire   +2 more sources

OM2Seq: Learning retrieval embeddings for optical genome mapping

Bioinformatics Advances, 2023
AbstractMotivationGenomics-based diagnostic methods that are quick, precise, and economical are essential for the advancement of precision medicine, with applications spanning the diagnosis of infectious diseases, cancer, and rare diseases. One technology that holds potential in this field is optical genome mapping (OGM), which is capable of detecting ...
Yevgeni Nogin, Danielle Sapir, Tahir Detinis Zur, Nir Weinberger, Yonatan Belinkov, Yuval Ebenstein, Yoav Shechtman   +6 more
openaire   +2 more sources

Multiplex structural variant detection by whole-genome mapping and nanopore sequencing

Scientific Reports, 2022
Identification of structural variants (SVs) breakpoints is important in studying mutations, mutagenic causes, and functional impacts. Next-generation sequencing and whole-genome optical mapping are extensively used in SV discovery and characterization ...
Lahari Uppuluri, Yilin Wang, Eleanor Young, Jessica S. Wong, Heba Z. Abid, Ming Xiao   +5 more
doaj   +1 more source

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding [PDF]

, 2016
We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish ...
A Bairoch, A Christoffels, A Gurevich, A Kozomara, A McKenna, A Mitchell, A Morgulis, A Morgulis, A Pradhan, A Reiner, A Rodriguez-Mari, A Stamatakis, A Yates, AI Makunin, AJ Enright, AL Price, AL Price, Alan Christoffels, Aleksey Komissarov, Alexey Tupikin, Amy Hin Yan Tong, Andrey A. Yurchenko, AR Quinlan, B Langmead, B Star, C Berthelot, C Camacho, C Holt, C Wang, Chen-Shan Chin, CS Chin, D Brawand, D Ellinghaus, DA Benson, Darrell Green, DC Hardie, Dean R. Jerry, DH Alexander, Doreen Lau, DR Kelley, DRS-K, C. Jerry, E Casacuberta, E. TG Staristina, EW Myers, F Abascal, F Chen, F Yang, FC Jones, FJ Krsticevic, Fritz J. Sedlazeck, G Abrusan, G Benson, G Lin, G Marcais, G Parra, G Parra, G Tamazian, GH Yue, GH Yue, Gopikrishna Gopalapillai, Gregory W. Vurture, GS Slater, GT Valente, H Li, H Saiga, Heiner Kuhl, HH Kazazian Jr., I Braasch, Inna S. Kuznetsova, IS Kuznetsova, J Castresana, J Eid, J Huerta-Cepas, J Jurka, J Lin, James P. Drake, JG Ruby, JN Volff, JN Volff, Jolly M. Saju, Jonas Korlach, JS Chew, Junhui Jiang, K Howe, K Katoh, K Prufer, Kathiresan Purushothaman, KD Pruitt, KJ Hoff, KP Koepfli, KW Tzung, Lawrence S. Hon, László Orbán, M Blanchette, M Kanehisa, M Kasahara, M Kolmogorov, M Krzywinski, M Martin, M Schartl, M Tarailoâ-Graovac, M Tine, MA Larkin, Mario Jonas, Marsel Kabilov, Matthew Boitano, MB Stocks, MG Grabherr, Michael C. Schatz, MJ Chaisson, MR Friedlander, N Siegel, Natascha M. Thevasagayam, NM Thevasagayam, O Jaillon, O Otero, P Cingolani, P Ravi, P Schattner, P Shannon, P Xu, Paul M. Richardson, PE Warburton, Peter Van Heusden, R Kajitani, R Lorenz, R Luo, R Moore, R Pethiyagoda, R Poulter, R She, R Sreenivasan, Ramkumar Lachumanan, RD Ward, RD Ward, Richard Hall, RJ Roberts, S Chen, S Guindon, S Hoegg, S Hoegg, S Koren, S Vij, S Zhou, Sai Rama Sridatta Prakki, Sarah Mwangi, SF Altschul, Shubha Vij, Si Lok, Si Yan Ngoh, Siddharth Singh, Simon Moxon, SM Kielbasa, Sridhar Sivasubbu, Stanley Kimbung Mbandi, Stephen J. O'Brien, Stephen W. Turner, T Anantharaman, Tamás Dalmay, Tansyn H. Noble, TD Wu, TF DeLuca, TH O'Hare, TLO Davis, TS Anantharaman, Tyler Garvin, U Consortium, U Grimholt, V Douard, V Ravi, Vinaya Kumar Katneni, Vinod Scaria, Vladimir Trifonov, W Xue, WC Liew, Woei Chang Liew, WS Davidson, X Huang, X Zheng, XG Wang, XG Wang, Xueyan Shen, Y Guiguen, Y Han, Y Hashiguchi, Y Moriya, Y Sato, Y Sato, Y Sato, Z Lai, Ø Hammer   +190 more
core   +9 more sources

A Gene-Based Method for Cytogenetic Mapping of Repeat-Rich Mosquito Genomes

Insects, 2021
Long-read sequencing technologies have opened up new avenues of research on the mosquito genome biology, enabling scientists to better understand the remarkable abilities of vectors for transmitting pathogens.
Reem A. Masri, Dmitriy A. Karagodin, Atashi Sharma, Maria V. Sharakhova   +3 more
doaj   +1 more source

Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis. [PDF]

, 2020
We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following ...
Alverdy, John C, Christley, Scott, Gilbert, Jack, Guyton, Kristina, Koo, Hyun, Levine, Zoe, Owens, Sarah, Shogan, Benjamin, Zaborina, Olga   +8 more
core   +1 more source

Long-read technologies identify a hidden inverted duplication in a family with choroideremia

HGG Advances, 2021
Summary: The lack of molecular diagnoses in rare genetic diseases can be explained by limitations of current standard genomic technologies. Upcoming long-read techniques have complementary strengths to overcome these limitations, with a particular ...
Zeinab Fadaie, Kornelia Neveling, Tuomo Mantere, Ronny Derks, Lonneke Haer-Wigman, Amber den Ouden, Michael Kwint, Luke O’Gorman, Dyon Valkenburg, Carel B. Hoyng, Christian Gilissen, Lisenka E.L.M. Vissers, Marcel Nelen, Frans P.M. Cremers, Alexander Hoischen, Susanne Roosing   +15 more
doaj   +1 more source

Optical genome mapping in an atypical Pelizaeus-Merzbacher prenatal challenge

Frontiers in Genetics, 2023
Pathogenic genetic variants represent a challenge in prenatal counseling, especially when clinical presentation in familial carriers is atypical. We describe a prenatal case involving a microarray-detected duplication of PLP1 which causes X-linked ...
Mihael Rogac, Mihael Rogac, Anja Kovanda, Anja Kovanda, Luca Lovrečić, Luca Lovrečić, Borut Peterlin, Borut Peterlin   +7 more
doaj   +1 more source

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin. [PDF]

, 2020
Membraneless pericentromeric heterochromatin (PCH) domains play vital roles in chromosome dynamics and genome stability. However, our current understanding of 3D genome organization does not include PCH domains because of technical challenges associated ...
Acevedo, David, Beliveau, Brian, Cavalli, Giacomo, KARPEN, Gary H., Lee, Yuh, Martins, Nuno, Ogiyama, Yuki, Wu, C-Ting   +7 more
core   +3 more sources

Genome maps across 26 human populations reveal population-specific patterns of structural variation. [PDF]

, 2019
Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in ...
Cao, Han, Chan, Ting-Fung, Chow, Eugene YC, Chu, Catherine, Chung, Claire YL, Hastie, Alex R, Jin, Nana, Kwok, Pui-Yan, Lam, Ernest T, Leung, Alden KY, Levy-Sakin, Michal, Li, Le, Lin, Chin, Ma, Walfred, McCaffrey, Jennifer, Mostovoy, Yulia, Naguib, Ahmed, Pastor, Steven, Poon, Annie, Rajagopalan, Ramakrishnan, Sibert, Justin, Wang, Wei-Ping, Wong, Karen HY, Xiao, Ming, Yip, Kevin Y, Young, Eleanor   +25 more
core   +2 more sources