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  1. Article ; Online: The emerging role of tandem repeats in complex traits.

    Lamkin, Michael / Gymrek, Melissa

    Nature reviews. Genetics

    2024  

    Language English
    Publishing date 2024-05-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2035157-4
    ISSN 1471-0064 ; 1471-0056
    ISSN (online) 1471-0064
    ISSN 1471-0056
    DOI 10.1038/s41576-024-00736-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5474: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 40: Show issues

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  2. Article ; Online: Haptools: a toolkit for admixture and haplotype analysis.

    Massarat, Arya R / Lamkin, Michael / Reeve, Ciara / Williams, Amy L / D'Antonio, Matteo / Gymrek, Melissa

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 3

    Abstract: Summary: Leveraging local ancestry and haplotype information in genome-wide association studies and downstream analyses can improve the utility of genomics for individuals from diverse and recently admixed ancestries. However, most existing simulation, ... ...

    Abstract Summary: Leveraging local ancestry and haplotype information in genome-wide association studies and downstream analyses can improve the utility of genomics for individuals from diverse and recently admixed ancestries. However, most existing simulation, visualization and variant analysis frameworks are based on variant-level analysis and do not automatically handle these features. We present haptools, an open-source toolkit for performing local ancestry aware and haplotype-based analysis of complex traits. Haptools supports fast simulation of admixed genomes, visualization of admixture tracks, simulation of haplotype- and local ancestry-specific phenotype effects and a variety of file operations and statistics computed in a haplotype-aware manner.
    Availability and implementation: Haptools is freely available at https://github.com/cast-genomics/haptools.
    Documentation: Detailed documentation is available at https://haptools.readthedocs.io.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Haplotypes ; Software ; Genome-Wide Association Study ; Genomics ; Genome
    Language English
    Publishing date 2023-02-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad104
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: A flexible ChIP-sequencing simulation toolkit.

    Zheng, An / Lamkin, Michael / Qiu, Yutong / Ren, Kevin / Goren, Alon / Gymrek, Melissa

    BMC bioinformatics

    2021  Volume 22, Issue 1, Page(s) 201

    Abstract: Background: A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this challenge, but existing frameworks ...

    Abstract Background: A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this challenge, but existing frameworks are either too cumbersome to apply genome-wide or unable to model a number of important experimental conditions in ChIP-seq.
    Results: We present ChIPs, a toolkit for rapidly simulating ChIP-seq data using statistical models of key experimental steps. We demonstrate how ChIPs can be used for a range of applications, including benchmarking analysis tools and evaluating the impact of various experimental parameters. ChIPs is implemented as a standalone command-line program written in C++ and is available from https://github.com/gymreklab/chips .
    Conclusions: ChIPs is an efficient ChIP-seq simulation framework that generates realistic datasets over a flexible range of experimental conditions. It can serve as an important component in various ChIP-seq analyses where ground truth data are needed.
    MeSH term(s) Chromatin Immunoprecipitation Sequencing ; Computer Simulation ; Genome ; High-Throughput Nucleotide Sequencing ; Models, Statistical ; Sequence Analysis, DNA ; Software
    Language English
    Publishing date 2021-04-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-021-04097-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Deep neural networks identify sequence context features predictive of transcription factor binding.

    Zheng, An / Lamkin, Michael / Zhao, Hanqing / Wu, Cynthia / Su, Hao / Gymrek, Melissa

    Nature machine intelligence

    2021  Volume 3, Issue 2, Page(s) 172–180

    Abstract: Transcription factors (TFs) bind DNA by recognizing specific sequence motifs, typically of length 6-12bp. A motif can occur many thousands of times in the human genome, but only a subset of those sites are actually bound. Here we present a machine ... ...

    Abstract Transcription factors (TFs) bind DNA by recognizing specific sequence motifs, typically of length 6-12bp. A motif can occur many thousands of times in the human genome, but only a subset of those sites are actually bound. Here we present a machine learning framework leveraging existing convolutional neural network architectures and model interpretation techniques to identify and interpret sequence context features most important for predicting whether a particular motif instance will be bound. We apply our framework to predict binding at motifs for 38 TFs in a lymphoblastoid cell line, score the importance of context sequences at base-pair resolution, and characterize context features most predictive of binding. We find that the choice of training data heavily influences classification accuracy and the relative importance of features such as open chromatin. Overall, our framework enables novel insights into features predictive of TF binding and is likely to inform future deep learning applications to interpret non-coding genetic variants.
    Language English
    Publishing date 2021-01-18
    Publishing country England
    Document type Journal Article
    ISSN 2522-5839
    ISSN (online) 2522-5839
    DOI 10.1038/s42256-020-00282-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Patterns of de novo tandem repeat mutations and their role in autism.

    Mitra, Ileena / Huang, Bonnie / Mousavi, Nima / Ma, Nichole / Lamkin, Michael / Yanicky, Richard / Shleizer-Burko, Sharona / Lohmueller, Kirk E / Gymrek, Melissa

    Nature

    2021  Volume 589, Issue 7841, Page(s) 246–250

    Abstract: Autism spectrum disorder (ASD) is an early-onset developmental disorder characterized by deficits in communication and social interaction and restrictive or repetitive ... ...

    Abstract Autism spectrum disorder (ASD) is an early-onset developmental disorder characterized by deficits in communication and social interaction and restrictive or repetitive behaviours
    MeSH term(s) Adolescent ; Adult ; Autism Spectrum Disorder/genetics ; Autism Spectrum Disorder/pathology ; Brain/metabolism ; Child ; DNA Copy Number Variations/genetics ; DNA Repeat Expansion/genetics ; Female ; Fetus/metabolism ; Genetic Predisposition to Disease ; Germ-Line Mutation/genetics ; Humans ; Least-Squares Analysis ; Male ; Middle Aged ; Paternal Age ; Young Adult
    Language English
    Publishing date 2021-01-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-020-03078-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

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