The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms [version 1; peer review: 1 approved, 2 approved with reservations]

Autor: Fawaz Dabbaghie, Divya Kalra, Elbay Aliyev, Wouter De Coster, Kimberley Billingsley, Nicolae Sapoval, Shangzhe Zhang, Gaojianyong Wang, Kimberly Walker, Deepak Choubey, Li Chuin Chong, Alejandro R. Gener, Yilei Fu, Pavel Avdeyev, Ben Busby, Daniel Paiva Agustinho, Sairam Behera, Enrico R. Barrozo, Luis F Paulin, Ahmad Al Khleifat, Susanne P. Pfeifer, Muhammad Sohail Raza, Guangyi Chen, Rebecca Lowdon, Daniela C. Soto, David Molik, Anneri Lötter, Chunhsuan Lo, Suresh Kumar Mendem, Sina Majidian, Damaris Lattimer, Priya Lakra, Bai-Wei Lo, Chia-Sin Liew, Rupesh K. Kesharwani, Maria Jose, Jędrzej Kubica, Sree Rohit Raj Kolora, Wolfram Höps, David Morgan Henke, Michael D. Jochum, Anastasia Illarionova, Fritz J Sedlazeck, Weiyu Zhou, Todd Treangen, Philippe Sanio, Jianzhi Yang, Tiancheng Xu, Ramanandan Prabhakaran, Chi-Lam Poon, Aditi Sammi, Marie Saitou, Hiroko Ohmiya, Rajarshi Mondal, Najeeb Syed, Carolina Peralta, Nasrin Parvin, Timothy Hefferon, Medhat Mahmoud

Publikováno v: F1000Research, Vol 11 (2022)

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural varia

Externí odkaz: https://doaj.org/article/d8c7d88e226245f696a211630add1947

Implicit Transpositions in DCJ Scenarios

Autor: Pavel Avdeyev, Shuai Jiang, Max A. Alekseyev

Publikováno v: Frontiers in Genetics, Vol 8 (2017)

Genome rearrangements are large-scale evolutionary events that shuffle genomic architectures. The minimal number of such events between two genomes is often used in phylogenomic studies to measure the evolutionary distance between the genomes. Double

Externí odkaz: https://doaj.org/article/225ff57c6f4e42eb94cd0c32ed3518ee

A complete reference genome improves analysis of human genetic variation

Autor: Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D. Olson, Michael E. G. Sauria, Mitchell R. Vollger, Arang Rhie, Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey A. Rosenfeld, Benedict Paten, Ryan Layer, Chen-Shan Chin, Fritz J. Sedlazeck, Nancy F. Hansen, Danny E. Miller, Adam M. Phillippy, Karen H. Miga, Rajiv C. McCoy, Megan Y. Dennis, Justin M. Zook, Michael C. Schatz

Publikováno v: Science
Science (New York, N.Y.), vol 376, iss 6588

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. W

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e5beca7b37f397ee4479667b1452da27
https://europepmc.org/articles/PMC9336181/

Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes

Autor: James P Bernot, Pavel Avdeyev, Anton Zamyatin, Niklas Dreyer, Nikita Alexeev, Marcos Pérez-Losada, Keith A Crandall

Publikováno v: Bernot, J P, Avdeyev, P, Zamyatin, A, Dreyer, N, Alexeev, N, Prez-Losada, M & Crandall, K A 2022, ' Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes ', GigaScience, vol. 11, giac021 . https://doi.org/10.1093/gigascience/giac021

Background The barnacles are a group of >2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8a3ce7e1c5f416c4be13fd4138476ef8
https://pubmed.ncbi.nlm.nih.gov/35277961

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

Autor: Chujia Chen, Varvara Lukyanchikova, Zhijian Tu, Igor V. Sharakhov, Max A. Alekseyev, Nikita Alexeev, Pavel Avdeyev, Atashi Sharma, Jiangtao Liang, Anton Zamyatin

Publikováno v: GigaScience

BackgroundAnopheles coluzzii and An. arabiensis belong to the An. gambiae complex and are among the major malaria vectors in Sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mos

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::817e077f04190602178c62726cf59860
https://doi.org/10.1093/gigascience/giab017