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  1. Article ; Online: NIR-red reflectance-based algorithms for chlorophyll-a estimation in mesotrophic inland and coastal waters: Lake Kinneret case study.

    Yacobi, Yosef Z / Moses, Wesley J / Kaganovsky, Semion / Sulimani, Benayahu / Leavitt, Bryan C / Gitelson, Anatoly A

    Water research

    2011  Volume 45, Issue 7, Page(s) 2428–2436

    Abstract: ... and/or time of the year. In this study we tested the performance of NIR-red models in estimating Chl ...

    Abstract A variety of models have been developed for estimating chlorophyll-a (Chl-a) concentration in turbid and productive waters. All are based on optical information in a few spectral bands in the red and near-infra-red regions of the electromagnetic spectrum. The wavelength locations in the models used were meticulously tuned to provide the highest sensitivity to the presence of Chl-a and minimal sensitivity to other constituents in water. But the caveat in these models is the need for recurrent parameterization and calibration due to changes in the biophysical characteristics of water based on the location and/or time of the year. In this study we tested the performance of NIR-red models in estimating Chl-a concentrations in an environment with a range of Chl-a concentrations that is typical for coastal and mesotrophic inland waters. The models with the same spectral bands as MERIS, calibrated for small lakes in the Midwest U.S., were used to estimate Chl-a concentration in the subtropical Lake Kinneret (Israel), where Chl-a concentrations ranged from 4 to 21 mg m(-3) during four field campaigns. A two-band model without re-parameterization was able to estimate Chl-a concentration with a root mean square error less than 1.5 mg m(-3). Our work thus indicates the potential of the model to be reliably applied without further need of parameterization and calibration based on geographical and/or seasonal regimes.
    MeSH term(s) Algorithms ; Chlorophyll/analysis ; Environmental Monitoring/methods ; Fresh Water/chemistry ; Infrared Rays ; Models, Chemical ; Remote Sensing Technology ; Spectrophotometry, Infrared ; Water Pollution/analysis ; Water Pollution/statistics & numerical data
    Chemical Substances Chlorophyll (1406-65-1) ; chlorophyll a (YF5Q9EJC8Y)
    Language English
    Publishing date 2011-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 202613-2
    ISSN 1879-2448 ; 0043-1354
    ISSN (online) 1879-2448
    ISSN 0043-1354
    DOI 10.1016/j.watres.2011.02.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: NIR-red reflectance-based algorithms for chlorophyll-a estimation in mesotrophic inland and coastal waters: Lake Kinneret case study

    Yacobi, Yosef Z / Moses, Wesley J / Kaganovsky, Semion / Sulimani, Benayahu / Leavitt, Bryan C / Gitelson, Anatoly A

    Water research. 2011 Mar., v. 45, no. 7

    2011  

    Abstract: ... and/or time of the year. In this study we tested the performance of NIR-red models in estimating Chl ...

    Abstract A variety of models have been developed for estimating chlorophyll-a (Chl-a) concentration in turbid and productive waters. All are based on optical information in a few spectral bands in the red and near-infra-red regions of the electromagnetic spectrum. The wavelength locations in the models used were meticulously tuned to provide the highest sensitivity to the presence of Chl-a and minimal sensitivity to other constituents in water. But the caveat in these models is the need for recurrent parameterization and calibration due to changes in the biophysical characteristics of water based on the location and/or time of the year. In this study we tested the performance of NIR-red models in estimating Chl-a concentrations in an environment with a range of Chl-a concentrations that is typical for coastal and mesotrophic inland waters. The models with the same spectral bands as MERIS, calibrated for small lakes in the Midwest U.S., were used to estimate Chl-a concentration in the subtropical Lake Kinneret (Israel), where Chl-a concentrations ranged from 4 to 21mgm⁻³ during four field campaigns. A two-band model without re-parameterization was able to estimate Chl-a concentration with a root mean square error less than 1.5mgm⁻³. Our work thus indicates the potential of the model to be reliably applied without further need of parameterization and calibration based on geographical and/or seasonal regimes.
    Keywords algorithms ; case studies ; chlorophyll ; coastal water ; lakes ; models ; wavelengths ; Israel ; Midwestern United States
    Language English
    Dates of publication 2011-03
    Size p. 2428-2436.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 202613-2
    ISSN 1879-2448 ; 0043-1354
    ISSN (online) 1879-2448
    ISSN 0043-1354
    DOI 10.1016/j.watres.2011.02.002
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Theoretical guarantees for phylogeny inference from single-cell lineage tracing.

    Wang, Robert / Zhang, Richard / Khodaverdian, Alex / Yosef, Nir

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 12, Page(s) e2203352120

    Abstract: Lineage-tracing technologies based on Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9 (CRISPR-Cas9) genome editing have emerged as a powerful tool for investigating development in single-cell contexts, but exact ... ...

    Abstract Lineage-tracing technologies based on Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9 (CRISPR-Cas9) genome editing have emerged as a powerful tool for investigating development in single-cell contexts, but exact reconstruction of the underlying clonal relationships in experiment is complicated by features of the data. These complications are functions of the experimental parameters in these systems, such as the Cas9 cutting rate, the diversity of indel outcomes, and the rate of missing data. In this paper, we develop two theoretically grounded algorithms for the reconstruction of the underlying single-cell phylogenetic tree as well as asymptotic bounds for the number of recording sites necessary for exact recapitulation of the ground truth phylogeny at high probability. In doing so, we explore the relationship between the problem difficulty and the experimental parameters, with implications for experimental design. Lastly, we provide simulations showing the empirical performance of these algorithms and showing that the trends in the asymptotic bounds hold empirically. Overall, this work provides a theoretical analysis of phylogenetic reconstruction in single-cell CRISPR-Cas9 lineage-tracing technologies.
    MeSH term(s) CRISPR-Cas Systems/genetics ; Phylogeny ; Cell Lineage/genetics ; Gene Editing ; CRISPR-Associated Protein 9/genetics
    Chemical Substances CRISPR-Associated Protein 9 (EC 3.1.-)
    Language English
    Publishing date 2023-03-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2203352120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data.

    Prillo, Sebastian / Ravoor, Akshay / Yosef, Nir / Song, Yun S

    bioRxiv : the preprint server for biology

    2023  

    Abstract: CRISPR/Cas9 gene editing technology has enabled lineage tracing for thousands of ... ...

    Abstract CRISPR/Cas9 gene editing technology has enabled lineage tracing for thousands of cells
    Language English
    Publishing date 2023-12-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.03.569785
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.

    Liu, Jiayi / Ashuach, Tal / Inoue, Fumitaka / Ahituv, Nadav / Yosef, Nir / Kreimer, Anat

    Nucleic acids research

    2024  Volume 52, Issue 4, Page(s) 1613–1627

    Abstract: The advent of perturbation-based massively parallel reporter assays (MPRAs) technique has facilitated the delineation of the roles of non-coding regulatory elements in orchestrating gene expression. However, computational efforts remain scant to evaluate ...

    Abstract The advent of perturbation-based massively parallel reporter assays (MPRAs) technique has facilitated the delineation of the roles of non-coding regulatory elements in orchestrating gene expression. However, computational efforts remain scant to evaluate and establish guidelines for sequence design strategies for perturbation MPRAs. In this study, we propose a framework for evaluating and comparing various perturbation strategies for MPRA experiments. Within this framework, we benchmark three different perturbation approaches from the perspectives of alteration in motif-based profiles, consistency of MPRA outputs, and robustness of models that predict the activities of putative regulatory motifs. While our analyses show very similar results across multiple benchmarking metrics, the predictive modeling for the approach involving random nucleotide shuffling shows significant robustness compared with the other two approaches. Thus, we recommend designing sequences by randomly shuffling the nucleotides of the perturbed site in perturbation-MPRA, followed by a coherence check to prevent the introduction of other variations of the target motifs. In summary, our evaluation framework and the benchmarking findings create a resource of computational pipelines and highlight the potential of perturbation-MPRA in predicting non-coding regulatory activities.
    MeSH term(s) Nucleotides ; Regulatory Sequences, Nucleic Acid ; Genetic Techniques
    Chemical Substances Nucleotides
    Language English
    Publishing date 2024-01-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkae012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Hotspot identifies informative gene modules across modalities of single-cell genomics.

    DeTomaso, David / Yosef, Nir

    Cell systems

    2021  Volume 12, Issue 5, Page(s) 446–456.e9

    Abstract: Two fundamental aims that emerge when analyzing single-cell RNA-seq data are identifying which genes vary in an informative manner and determining how these genes organize into modules. Here, we propose a general approach to these problems, called " ... ...

    Abstract Two fundamental aims that emerge when analyzing single-cell RNA-seq data are identifying which genes vary in an informative manner and determining how these genes organize into modules. Here, we propose a general approach to these problems, called "Hotspot," that operates directly on a given metric of cell-cell similarity, allowing for its integration with any method (linear or non-linear) for identifying the primary axes of transcriptional variation between cells. In addition, we show that when using multimodal data, Hotspot can be used to identify genes whose expression reflects alternative notions of similarity between cells, such as physical proximity in a tissue or clonal relatedness in a cell lineage tree. In this manner, we demonstrate that while Hotspot is capable of identifying genes that reflect nuanced transcriptional variability between T helper cells, it can also identify spatially dependent patterns of gene expression in the cerebellum as well as developmentally heritable expression programs during embryogenesis. Hotspot is implemented as an open-source Python package and is available for use at http://www.github.com/yoseflab/hotspot. A record of this paper's transparent peer review process is included in the supplemental information.
    MeSH term(s) Gene Regulatory Networks ; Genomics ; Peer Review
    Language English
    Publishing date 2021-05-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2021.04.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Particle physics: let it B.

    Nir, Yosef

    Nature

    2013  Volume 499, Issue 7458, Page(s) 290–291

    Language English
    Publishing date 2013-07-20
    Publishing country England
    Document type Comment ; News
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/499290a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision.

    Jones, Matthew G / Rosen, Yanay / Yosef, Nir

    Cell reports methods

    2022  Volume 2, Issue 4, Page(s) 100200

    Abstract: Recent advances in CRISPR-Cas9 engineering and single-cell assays have enabled the simultaneous measurement of single-cell transcriptomic and phylogenetic profiles. However, there are few computational tools enabling users to integrate and derive insight ...

    Abstract Recent advances in CRISPR-Cas9 engineering and single-cell assays have enabled the simultaneous measurement of single-cell transcriptomic and phylogenetic profiles. However, there are few computational tools enabling users to integrate and derive insight from a joint analysis of these two modalities. Here, we describe "PhyloVision": an open-source software for interactively exploring data from both modalities and for identifying and interpreting heritable gene modules whose concerted expression are associated with phylogenetic relationships. PhyloVision provides a feature-rich, interactive, and shareable web-based report for investigating these modules while also supporting several other data and meta-data exploration capabilities. We demonstrate the utility of PhyloVision using a published dataset of metastatic lung adenocarcinoma cells, whose phylogeny was resolved using a CRISPR-Cas9-based lineage-tracing system. Together, we anticipate that PhyloVision and the methods it implements will be a useful resource for scalable and intuitive data exploration for any assay that simultaneously measures cell state and lineage.
    MeSH term(s) Transcriptome/genetics ; Phylogeny ; Computational Biology/methods ; Software ; Gene Expression Profiling
    Language English
    Publishing date 2022-04-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2667-2375
    ISSN (online) 2667-2375
    DOI 10.1016/j.crmeth.2022.100200
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Evolutionary trade‐off between male colouration and feather moult extent also indirectly determines female moult

    Kiat, Yosef / Sapir, Nir

    Journal of evolutionary biology. 2022 Feb., v. 35, no. 2

    2022  

    Abstract: Males and females are often influenced by different selective forces, frequently resulting in diverging phenotypes, for example in colouration. Since an animal's colouration may strongly influence its fitness, causes and consequences of sexual ... ...

    Abstract Males and females are often influenced by different selective forces, frequently resulting in diverging phenotypes, for example in colouration. Since an animal's colouration may strongly influence its fitness, causes and consequences of sexual dichromatism in birds could aid in understanding important factors affecting sexual and natural selection. Variation in plumage ornamentation may affect mate attraction or intraspecific antagonistic behaviour. In most passerines, body plumage colouration of juveniles is obtained through the process of feather moult. The number of moulted wing and tail feathers, which also influences the bird's appearance, may affect its fitness. Here, we show that body plumage colouration of male, but not female, passerines is correlated with the number of moulted wing and tail feathers in the early stage of the bird's life for both sexes. Thus, the extent of wing and tail moult in females is not modulated by the female's colouration and can prevent females from reaching their sex‐specific optima. This result could be explained by high intersexual genetic correlations, which might make it impossible for the sexes to reach their own trait fitness optima. Our findings may indicate that species‐specific, rather than sex‐specific, internal correlations shaped bird moult strategy, an important avian life‐history trait.
    Keywords Passeriformes ; birds ; color ; females ; life history ; males ; molting ; natural selection
    Language English
    Dates of publication 2022-02
    Size p. 278-287.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 1465318-7
    ISSN 1420-9101 ; 1010-061X
    ISSN (online) 1420-9101
    ISSN 1010-061X
    DOI 10.1111/jeb.13977
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Evaluation of Davis et al.: Exploring Sequence of Determinants of Transcriptional Regulation-The Case of c-AMP Response Element.

    Kreimer, Anat / Yosef, Nir

    Cell systems

    2020  Volume 11, Issue 1, Page(s) 2–4

    Abstract: One snapshot of the peer review process for "Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays" (Davis et al., 2020). ...

    Abstract One snapshot of the peer review process for "Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays" (Davis et al., 2020).
    MeSH term(s) Adenosine Monophosphate ; Gene Expression Regulation ; Genomics ; Plasmids ; Response Elements/genetics
    Chemical Substances Adenosine Monophosphate (415SHH325A)
    Language English
    Publishing date 2020-07-22
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2020.07.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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