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  1. AU=Layer Ryan M.
  2. AU="Rotaru, Luciana Teodora"
  3. AU="Nash, Kevin M"
  4. AU="Kubo, Sousuke"
  5. AU="Ingo Eitel"
  6. AU="van der Horst, A."
  7. AU="Di Mattia, A" AU="Di Mattia, A"
  8. AU="Di Pumpo, Marcello"
  9. AU="Doung, Yee-Cheen"
  10. AU="Saha, Moumita"
  11. AU="Wertz, Ashlee E"
  12. AU="Cowan, Michael J"
  13. AU=Togliatto Gabriele
  14. AU="Bassett, Dani S."
  15. AU="James Lemon"
  16. AU="Gros, Stephanie J"
  17. AU="Saeed Khademi"
  18. AU="Lallet-Daher, Helene"
  19. AU="Greenblatt, M"
  20. AU="Patwa, Ajay K"
  21. AU=Mastaglia F L
  22. AU="De Croock, Femke"
  23. AU=Robinson Michael J
  24. AU=Singh Romil
  25. AU="Martin, S J"
  26. AU="Szendrői, Miklós"
  27. AU="Moncel, Marie-Hélène"
  28. AU=Otu Akaninyene AU=Otu Akaninyene
  29. AU="Chiba, Kentaro"
  30. AU="Zhou, Jihua"
  31. AU="Ronald Bartels"
  32. AU="Liñares, J"
  33. AU="Valle, Valentina"
  34. AU="Tóth, András"
  35. AU="Pawar, Atul Darasing"
  36. AU="Semper, Chelsea"
  37. AU="Kraus, Joanne F"

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  1. Artikel ; Online: Embracing firefly flash pattern variability with data-driven species classification.

    Martin, Owen / Nguyen, Chantal / Sarfati, Raphael / Chowdhury, Murad / Iuzzolino, Michael L / Nguyen, Dieu My T / Layer, Ryan M / Peleg, Orit

    Scientific reports

    2024  Band 14, Heft 1, Seite(n) 3432

    Abstract: Many nocturnally active fireflies use precisely timed bioluminescent patterns to identify mates, making them especially vulnerable to light pollution. As urbanization continues to brighten the night sky, firefly populations are under constant stress, and ...

    Abstract Many nocturnally active fireflies use precisely timed bioluminescent patterns to identify mates, making them especially vulnerable to light pollution. As urbanization continues to brighten the night sky, firefly populations are under constant stress, and close to half of the species are now threatened. Ensuring the survival of firefly biodiversity depends on a large-scale conservation effort to monitor and protect thousands of populations. While species can be identified by their flash patterns, current methods require expert measurement and manual classification and are infeasible given the number and geographic distribution of fireflies. Here we present the application of a recurrent neural network (RNN) for accurate automated firefly flash pattern classification. Using recordings from commodity cameras, we can extract flash trajectories of individuals within a swarm and classify their species with an accuracy of approximately seventy percent. In addition to its potential in population monitoring, automated classification provides the means to study firefly behavior at the population level. We employ the classifier to measure and characterize the variability within and between swarms, unlocking a new dimension of their behavior. Our method is open source, and deployment in community science applications could revolutionize our ability to monitor and understand firefly populations.
    Mesh-Begriff(e) Humans ; Animals ; Fireflies ; Sexual Behavior, Animal
    Sprache Englisch
    Erscheinungsdatum 2024-02-10
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-024-53671-3
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX.

    Chowdhury, Murad / Pedersen, Brent S / Sedlazeck, Fritz J / Quinlan, Aaron R / Layer, Ryan M

    Nature methods

    2022  Band 19, Heft 6, Seite(n) 770

    Sprache Englisch
    Erscheinungsdatum 2022-05-26
    Erscheinungsland United States
    Dokumenttyp Published Erratum
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01538-8
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Searching thousands of genomes to classify somatic and novel structural variants using STIX.

    Chowdhury, Murad / Pedersen, Brent S / Sedlazeck, Fritz J / Quinlan, Aaron R / Layer, Ryan M

    Nature methods

    2022  Band 19, Heft 4, Seite(n) 445–448

    Abstract: Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics ... ...

    Abstract Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics and filtering limits the use of current structural variant catalogs. We present STIX, a method that, instead of relying on variant calls, indexes and searches the raw alignments from thousands of samples to enable more comprehensive allele frequency estimation.
    Mesh-Begriff(e) Algorithms ; Genome ; Genomic Structural Variation/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Neoplasms/genetics ; Software
    Sprache Englisch
    Erscheinungsdatum 2022-04-08
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01423-4
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel: A parallel algorithm for

    Layer, Ryan M / Quinlan, Aaron R

    Proceedings of the IEEE. Institute of Electrical and Electronics Engineers

    2018  Band 105, Heft 3, Seite(n) 542–551

    Abstract: The comparison of sets of genome intervals (e.g., genes, repeats, ChIP-seq peaks) is essential to genome research, especially as modern sequencing technologies enable ever larger and more complex experiments. Relationships between genomic features are ... ...

    Abstract The comparison of sets of genome intervals (e.g., genes, repeats, ChIP-seq peaks) is essential to genome research, especially as modern sequencing technologies enable ever larger and more complex experiments. Relationships between genomic features are commonly identified by their intersection: that is, if feature sets contain overlapping intervals then it is inferred that they share a common biological function or origin. Using this technique, researchers identify genomic regions that are common among multiple (or unique to individual) datasets. While there have been recent advances in algorithms for pairwise intersections between two sets of genomic intervals, few advances have been made to the intersection of many sets of genomic intervals. Identifying intersections among many interval sets is particularly important when attempting to distill biological insights from the massive, multi-dimensional datasets that are common to modern genome research. For such analyses, speed and efficiency are crucial given the size and sheer number of datasets involved. To solve this problem, we present a novel "slice-then-sweep" algorithm that, given
    Sprache Englisch
    Erscheinungsdatum 2018-10-17
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 0018-9219
    ISSN 0018-9219
    DOI 10.1109/JPROC.2015.2461494
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: RAREsim: A simulation method for very rare genetic variants.

    Null, Megan / Dupuis, Josée / Sheinidashtegol, Pezhman / Layer, Ryan M / Gignoux, Christopher R / Hendricks, Audrey E

    American journal of human genetics

    2022  Band 109, Heft 4, Seite(n) 680–691

    Abstract: Identification of rare-variant associations is crucial to full characterization of the genetic architecture of complex traits and diseases. Essential in this process is the evaluation of novel methods in simulated data that mirror the distribution of ... ...

    Abstract Identification of rare-variant associations is crucial to full characterization of the genetic architecture of complex traits and diseases. Essential in this process is the evaluation of novel methods in simulated data that mirror the distribution of rare variants and haplotype structure in real data. Additionally, importing real-variant annotation enables in silico comparison of methods, such as rare-variant association tests and polygenic scoring methods, that focus on putative causal variants. Existing simulation methods are either unable to employ real-variant annotation or severely under- or overestimate the number of singletons and doubletons, thereby reducing the ability to generalize simulation results to real studies. We present RAREsim, a flexible and accurate rare-variant simulation algorithm. Using parameters and haplotypes derived from real sequencing data, RAREsim efficiently simulates the expected variant distribution and enables real-variant annotations. We highlight RAREsim's utility across various genetic regions, sample sizes, ancestries, and variant classes.
    Mesh-Begriff(e) Computer Simulation ; Genetic Variation/genetics ; Haplotypes/genetics ; Humans ; Models, Genetic ; Multifactorial Inheritance ; Research Design
    Sprache Englisch
    Erscheinungsdatum 2022-03-16
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 219384-x
    ISSN 1537-6605 ; 0002-9297
    ISSN (online) 1537-6605
    ISSN 0002-9297
    DOI 10.1016/j.ajhg.2022.02.009
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel: Editorial: Genomic Colocalization and Enrichment Analyses.

    Kanduri, Chakravarthi / Sandve, Geir Kjetil / Hovig, Eivind / De, Subhajyoti / Layer, Ryan M

    Frontiers in genetics

    2021  Band 11, Seite(n) 617876

    Sprache Englisch
    Erscheinungsdatum 2021-01-26
    Erscheinungsland Switzerland
    Dokumenttyp Editorial
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2020.617876
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Pharmacologic targeting of the p62 ZZ domain enhances both anti-tumor and bone-anabolic effects of bortezomib in multiple myeloma.

    Marino, Silvia / Petrusca, Daniela N / Bishop, Ryan T / Anderson, Judith L / Sabol, Hayley M / Ashby, Cody / Layer, Justin H / Cesarano, Annamaria / Davé, Utpal P / Perna, Fabiana / Delgado-Calle, Jesus / Chirgwin, John M / Roodman, G David

    Haematologica

    2024  Band 109, Heft 5, Seite(n) 1501–1513

    Abstract: Multiple myeloma (MM) is a malignancy of plasma cells whose antibody secretion creates proteotoxic stress relieved by the N-end rule pathway, a proteolytic system that degrades N-arginylated proteins in the proteasome. When the proteasome is inhibited, ... ...

    Abstract Multiple myeloma (MM) is a malignancy of plasma cells whose antibody secretion creates proteotoxic stress relieved by the N-end rule pathway, a proteolytic system that degrades N-arginylated proteins in the proteasome. When the proteasome is inhibited, protein cargo is alternatively targeted for autophagic degradation by binding to the ZZ-domain of p62/ sequestosome-1. Here, we demonstrate that XRK3F2, a selective ligand for the ZZ-domain, dramatically improved two major responses to the proteasome inhibitor bortezomib (Btz) by increasing: i) killing of human MM cells by stimulating both Btz-mediated apoptosis and necroptosis, a process regulated by p62; and ii) preservation of bone mass by stimulating osteoblast differentiation and inhibiting osteoclastic bone destruction. Co-administration of Btz and XRK3F2 inhibited both branches of the bimodal N-end rule pathway exhibited synergistic anti-MM effects on MM cell lines and CD138+ cells from MM patients, and prevented stromal-mediated MM cell survival. In mice with established human MM, co-administration of Btz and XRK3F2 decreased tumor burden and prevented the progression of MM-induced osteolytic disease by inducing new bone formation more effectively than either single agent alone. The results suggest that p62-ZZ ligands enhance the anti- MM efficacy of proteasome inhibitors and can reduce MM morbidity and mortality by improving bone health.
    Mesh-Begriff(e) Bortezomib/pharmacology ; Bortezomib/therapeutic use ; Multiple Myeloma/drug therapy ; Multiple Myeloma/pathology ; Multiple Myeloma/metabolism ; Humans ; Animals ; Mice ; Cell Line, Tumor ; Sequestosome-1 Protein/metabolism ; Apoptosis/drug effects ; Xenograft Model Antitumor Assays ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Protein Domains ; Proteasome Inhibitors/pharmacology ; Proteasome Inhibitors/therapeutic use ; Disease Models, Animal
    Chemische Substanzen Bortezomib (69G8BD63PP) ; Sequestosome-1 Protein ; Antineoplastic Agents ; Proteasome Inhibitors
    Sprache Englisch
    Erscheinungsdatum 2024-05-01
    Erscheinungsland Italy
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2333-4
    ISSN 1592-8721 ; 0017-6567 ; 0390-6078
    ISSN (online) 1592-8721
    ISSN 0017-6567 ; 0390-6078
    DOI 10.3324/haematol.2023.283787
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Editorial

    Chakravarthi Kanduri / Geir Kjetil Sandve / Eivind Hovig / Subhajyoti De / Ryan M. Layer

    Frontiers in Genetics, Vol

    Genomic Colocalization and Enrichment Analyses

    2021  Band 11

    Schlagwörter colocalization analyses ; bioinformatics ; genomics ; genome annotation ; computational biology ; enrichment analyses ; Genetics ; QH426-470
    Sprache Englisch
    Erscheinungsdatum 2021-01-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel: webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering.

    Arumilli, Meharji / Layer, Ryan M / Hytönen, Marjo K / Lohi, Hannes

    Frontiers in genetics

    2020  Band 11, Seite(n) 152

    Abstract: Summary: Genotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a ... ...

    Abstract Summary: Genotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a wide audience as command-line software, the difficulty of constructing queries among non-IT or non-bioinformatics researchers has limited its applicability. To overcome this limitation, we developed webGQT, an easy-to-use tool with a graphical user interface. With pre-built queries across three modules, webGQT allows for pedigree analysis, case-control studies, and population frequency studies. As a package, webGQT allows researchers with less or no applied bioinformatics/IT experience to mine potential disease-causing variants from billions.
    Results: webGQT offers a flexible and easy-to-use interface for model-based candidate variant filtering for Mendelian diseases from thousands to millions of genomes at a reduced computation time. Additionally, webGQT provides adjustable parameters to reduce false positives and rescue missing genotypes across all modules. Using a case study, we demonstrate the applicability of webGQT to query non-human genomes. In addition, we demonstrate the scalability of webGQT on large data sets by implementing complex population-specific queries on the 1000 Genomes Project Phase 3 data set, which includes 8.4 billion variants from 2504 individuals across 26 different populations. Furthermore, webGQT supports filtering single-nucleotide variants, short insertions/deletions, copy number or any other variant genotypes supported by the VCF specification. Our results show that webGQT can be used as an online web service, or deployed on personal computers or local servers within research groups.
    Availability: webGQT is made available to the users in three forms: 1) as a webserver available at https://vm1138.kaj.pouta.csc.fi/webgqt/, 2) as an R package to install on personal computers, and 3) as part of the same R package to configure on the user's own servers. The application is available for installation at https://github.com/arumds/webgqt.
    Sprache Englisch
    Erscheinungsdatum 2020-03-03
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2020.00152
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel: Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing.

    Liu, Sixin / Gao, Guangtu / Layer, Ryan M / Thorgaard, Gary H / Wiens, Gregory D / Leeds, Timothy D / Martin, Kyle E / Palti, Yniv

    Frontiers in genetics

    2021  Band 12, Seite(n) 639355

    Abstract: Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout ( ...

    Abstract Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout (
    Sprache Englisch
    Erscheinungsdatum 2021-02-25
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.639355
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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