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  1. Article ; Online: Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis.

    Wang, Gaojianyong / Anastassiou, Dimitris

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 17199

    Abstract: Analysis of large gene expression datasets from biopsies of cancer patients can identify co-expression signatures representing particular biomolecular events in cancer. Some of these signatures involve genomically co-localized genes resulting from the ... ...

    Abstract Analysis of large gene expression datasets from biopsies of cancer patients can identify co-expression signatures representing particular biomolecular events in cancer. Some of these signatures involve genomically co-localized genes resulting from the presence of copy number alterations (CNAs), for which analysis of the expression of the underlying genes provides valuable information about their combined role as oncogenes or tumor suppressor genes. Here we focus on the discovery and interpretation of such signatures that are present in multiple cancer types due to driver amplifications and deletions in particular regions of the genome after doing a comprehensive analysis combining both gene expression and CNA data from The Cancer Genome Atlas.
    MeSH term(s) DNA Copy Number Variations/genetics ; Data Analysis ; Gene Dosage/genetics ; Gene Expression/genetics ; Genomics/methods ; Humans ; Neoplasms/genetics ; Oncogenes/genetics
    Language English
    Publishing date 2020-10-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-74276-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population.

    Wilder, Aryn P / Dudchenko, Olga / Curry, Caitlin / Korody, Marisa / Turbek, Sheela P / Daly, Mark / Misuraca, Ann / Wang, Gaojianyong / Khan, Ruqayya / Weisz, David / Fronczek, Julie / Aiden, Erez Lieberman / Houck, Marlys L / Shier, Debra M / Ryder, Oliver A / Steiner, Cynthia C

    Genome biology and evolution

    2022  Volume 14, Issue 8

    Abstract: High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), ... ...

    Abstract High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.
    MeSH term(s) Animals ; Chromosomes ; Genome ; Homozygote ; Inbreeding ; Mice ; Sequence Analysis, DNA
    Language English
    Publishing date 2022-07-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2495328-3
    ISSN 1759-6653 ; 1759-6653
    ISSN (online) 1759-6653
    ISSN 1759-6653
    DOI 10.1093/gbe/evac122
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

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

    F1000Research

    2022  Volume 11, Page(s) 530

    Abstract: 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 variants ( ...

    Abstract 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 variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19 ; Genomics ; Software
    Language English
    Publishing date 2022-05-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.110194.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates.

    Mc Cartney, Ann M / Mahmoud, Medhat / Jochum, Michael / Agustinho, Daniel Paiva / Zorman, Barry / Al Khleifat, Ahmad / Dabbaghie, Fawaz / K Kesharwani, Rupesh / Smolka, Moritz / Dawood, Moez / Albin, Dreycey / Aliyev, Elbay / Almabrazi, Hakeem / Arslan, Ahmed / Balaji, Advait / Behera, Sairam / Billingsley, Kimberley / L Cameron, Daniel / Daw, Joyjit /
    T Dawson, Eric / De Coster, Wouter / Du, Haowei / Dunn, Christopher / Esteban, Rocio / Jolly, Angad / Kalra, Divya / Liao, Chunxiao / Liu, Yunxi / Lu, Tsung-Yu / M Havrilla, James / M Khayat, Michael / Marin, Maximillian / Monlong, Jean / Price, Stephen / Rafael Gener, Alejandro / Ren, Jingwen / Sagayaradj, Sagayamary / Sapoval, Nicolae / Sinner, Claude / C Soto, Daniela / Soylev, Arda / Subramaniyan, Arun / Syed, Najeeb / Tadimeti, Neha / Tater, Pamella / Vats, Pankaj / Vaughn, Justin / Walker, Kimberly / Wang, Gaojianyong / Zeng, Qiandong / Zhang, Shangzhe / Zhao, Tingting / Kille, Bryce / Biederstedt, Evan / Chaisson, Mark / English, Adam / Kronenberg, Zev / J Treangen, Todd / Hefferon, Timothy / Chin, Chen-Shan / Busby, Ben / J Sedlazeck, Fritz

    F1000Research

    2021  Volume 10, Page(s) 246

    Abstract: In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research.   The ... ...

    Abstract In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research.   The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at  https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
    MeSH term(s) Animals ; COVID-19 ; Genome, Viral ; Humans ; SARS-CoV-2 ; Vertebrates
    Language English
    Publishing date 2021-03-26
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.51477.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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