Results 21 to 30 of about 99,235 (279)

OMGS: Optical Map-based Genome Scaffolding [PDF]

Journal of Computational Biology, 2019
Abstract Due to the current limitations of sequencing technologies, de novo genome assembly is typically carried out in two stages, namely contig (sequence) assembly and scaffolding.
Weihua Pan, Tao Jiang 0001, Stefano Lonardi   +2 more
openaire   +4 more sources

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

Identification of an NF1 Microdeletion with Optical Genome Mapping

International Journal of Molecular Sciences, 2023
Neurofibromatosis type 1 (NF1) is a clinically heterogeneous neurocutaneous disorder inherited in autosomal dominant manner. Approximately 5–10% of the cases are caused by NF1 microdeletions involving the NF1 gene and its flanking regions. Microdeletions, which lead to more severe clinical manifestations, can be subclassified into four different types (
Gergely Büki, Anna Bekő, Csaba Bödör, Péter Urbán, Krisztina Németh, Kinga Hadzsiev, György Fekete, Hildegard Kehrer-Sawatzki, Judit Bene   +8 more
openaire   +2 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

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

Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. [PDF]

, 2020
Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits.
Andrés, Aida M, Dennis, Megan Y, Kaya, Gulhan, Mastoras, Mira, Sahasrabudhe, Ruta, Schmidt, Joshua M, Shew, Colin, Soto, Daniela C   +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

OM2Seq: Learning retrieval embeddings for optical genome mapping

Bioinformatics Advances, 2023
Abstract Motivation Genomics-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.
Yevgeni Nogin, Danielle Sapir, Tahir Detinis Zur, Nir Weinberger, Yonatan Belinkov, Yuval Ebenstein, Yoav Shechtman   +6 more
openaire   +2 more sources

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   +5 more sources