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GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data

Rahmani, Elior ; Yedidim, Reut ; Shenhav, Liat ; [et al.]

Oxford University Press (OUP) ; 2017

In: Bioinformatics Vol. 33, No. 12 ( 2017-06-15), p. 1870-1872

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In: Bioinformatics, Oxford University Press (OUP), Vol. 33, No. 12 ( 2017-06-15), p. 1870-1872

Abstract: GLINT is a user-friendly command-line toolset for fast analysis of genome-wide DNA methylation data generated using the Illumina human methylation arrays. GLINT, which does not require any programming proficiency, allows an easy execution of Epigenome-Wide Association Study analysis pipeline under different models while accounting for known confounders in methylation data. Availability and Implementation GLINT is a command-line software, freely available at https://github.com/cozygene/glint/releases. It requires Python 2.7 and several freely available Python packages. Further information and documentation as well as a quick start tutorial are available at http://glint-epigenetics.readthedocs.io.

Type of Medium: Online Resource

ISSN: 1367-4803 , 1367-4811

URL: Article

DOI: 10.1093/bioinformatics/btx059

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2017

detail.hit.zdb_id: 1468345-3

SSG: 12

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Beneficial effect of awake prone position in hypoxaemic patients with COVID ‐19: case reports and literature review

Cohen, Dor ; Wasserstrum, Yishay ; Segev, Amitai ; [et al.]

Wiley ; 2020

In: Internal Medicine Journal Vol. 50, No. 8 ( 2020-08), p. 997-1000

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In: Internal Medicine Journal, Wiley, Vol. 50, No. 8 ( 2020-08), p. 997-1000

Abstract: We hereby present two case reports of moderate coronavirus disease patients, suffering from profound hypoxaemia, further deteriorating later on. A schedule pre‐planned awake prone position manoeuvres were executed during their hospital stay. Following this, the patients' saturation improved, later to be weaned from oxygen support. Paucity of evidence and data regarding this topic led us to review the concept of awake prone position.

Type of Medium: Online Resource

ISSN: 1444-0903 , 1445-5994

URL: Issue

URL: Article

DOI: 10.1111/imj.v50.8

DOI: 10.1111/imj.14926

Language: English

Publisher: Wiley

Publication Date: 2020

detail.hit.zdb_id: 2044081-9

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Efficacy of Corneal Collagen Cross-Linking for the Treatment of Keratoconus : A Systematic Review and Meta-Analysis

Meiri, Zohar ; Keren, Shay ; Rosenblatt, Amir ; [et al.]

Ovid Technologies (Wolters Kluwer Health) ; 2016

In: Cornea Vol. 35, No. 3 ( 2016-03), p. 417-428

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In: Cornea, Ovid Technologies (Wolters Kluwer Health), Vol. 35, No. 3 ( 2016-03), p. 417-428

Type of Medium: Online Resource

ISSN: 0277-3740

URL: Article

DOI: 10.1097/ICO.0000000000000723

RVK:

XA 37258

RVK:

XA 10000

Language: English

Publisher: Ovid Technologies (Wolters Kluwer Health)

Publication Date: 2016

detail.hit.zdb_id: 2045943-9

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Self-control, social support, and aggression among adolescents in divorced and two-parent families

Hamama, Liat ; Ronen-Shenhav, Anat

Elsevier BV ; 2012

In: Children and Youth Services Review Vol. 34, No. 5 ( 2012-5), p. 1042-1049

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In: Children and Youth Services Review, Elsevier BV, Vol. 34, No. 5 ( 2012-5), p. 1042-1049

Type of Medium: Online Resource

ISSN: 0190-7409

URL: Article

DOI: 10.1016/j.childyouth.2012.02.009

Language: English

Publisher: Elsevier BV

Publication Date: 2012

detail.hit.zdb_id: 2019862-0

SSG: 3,4

SSG: 5,3

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Genome-wide methylation data mirror ancestry information

Rahmani, Elior ; Shenhav, Liat ; Schweiger, Regev ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Epigenetics & Chromatin Vol. 10, No. 1 ( 2017-12)

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In: Epigenetics & Chromatin, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2017-12)

Type of Medium: Online Resource

ISSN: 1756-8935

URL: Article

DOI: 10.1186/s13072-016-0108-y

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2462129-8

SSG: 15,3

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Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics

Furman, Ori ; Shenhav, Liat ; Sasson, Goor ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Nature Communications Vol. 11, No. 1 ( 2020-04-20)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2020-04-20)

Abstract: How complex communities assemble through the animal’s life, and how predictable the process is remains unexplored. Here, we investigate the forces that drive the assembly of rumen microbiomes throughout a cow’s life, with emphasis on the balance between stochastic and deterministic processes. We analyse the development of the rumen microbiome from birth to adulthood using 16S-rRNA amplicon sequencing data and find that the animals shared a group of core successional species that invaded early on and persisted until adulthood. Along with deterministic factors, such as age and diet, early arriving species exerted strong priority effects, whereby dynamics of late successional taxa were strongly dependent on microbiome composition at early life stages. Priority effects also manifest as dramatic changes in microbiome development dynamics between animals delivered by C-section vs. natural birth, with the former undergoing much more rapid species invasion and accelerated microbiome development. Overall, our findings show that together with strong deterministic constrains imposed by diet and age, stochastic colonization in early life has long-lasting impacts on the development of animal microbiomes.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-020-15652-8

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2553671-0

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Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability

Schweiger, Regev ; Fisher, Eyal ; Rahmani, Elior ; [et al.]

Mary Ann Liebert Inc ; 2018

In: Journal of Computational Biology Vol. 25, No. 7 ( 2018-07), p. 794-808

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In: Journal of Computational Biology, Mary Ann Liebert Inc, Vol. 25, No. 7 ( 2018-07), p. 794-808

Type of Medium: Online Resource

ISSN: 1557-8666

URL: Article

DOI: 10.1089/cmb.2018.0047

Language: English

Publisher: Mary Ann Liebert Inc

Publication Date: 2018

detail.hit.zdb_id: 2030900-4

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The role of developmental features, environmental crises, and personal resources (self-control and social support) in adolescents' aggressive behavior

Hamama, Liat ; Ronen-Shenhav, Anat

Elsevier BV ; 2013

In: Aggression and Violent Behavior Vol. 18, No. 1 ( 2013-1), p. 26-31

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In: Aggression and Violent Behavior, Elsevier BV, Vol. 18, No. 1 ( 2013-1), p. 26-31

Type of Medium: Online Resource

ISSN: 1359-1789

URL: Article

DOI: 10.1016/j.avb.2012.09.001

Language: English

Publisher: Elsevier BV

Publication Date: 2013

detail.hit.zdb_id: 2019312-9

SSG: 2,1

SSG: 5,2

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Modeling the temporal dynamics of the gut microbial community in adults and infants

Shenhav, Liat ; Furman, Ori ; Briscoe, Leah ; [et al.]

Public Library of Science (PLoS) ; 2019

In: PLOS Computational Biology Vol. 15, No. 6 ( 2019-6-27), p. e1006960-

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In: PLOS Computational Biology, Public Library of Science (PLoS), Vol. 15, No. 6 ( 2019-6-27), p. e1006960-

Type of Medium: Online Resource

ISSN: 1553-7358

URL: Article

DOI: 10.1371/journal.pcbi.1006960

DOI: 10.1371/journal.pcbi.1006960.g001

DOI: 10.1371/journal.pcbi.1006960.g002

DOI: 10.1371/journal.pcbi.1006960.g003

DOI: 10.1371/journal.pcbi.1006960.g004

DOI: 10.1371/journal.pcbi.1006960.g005

DOI: 10.1371/journal.pcbi.1006960.g006

DOI: 10.1371/journal.pcbi.1006960.s001

DOI: 10.1371/journal.pcbi.1006960.s002

DOI: 10.1371/journal.pcbi.1006960.s003

DOI: 10.1371/journal.pcbi.1006960.s004

DOI: 10.1371/journal.pcbi.1006960.s005

DOI: 10.1371/journal.pcbi.1006960.s006

DOI: 10.1371/journal.pcbi.1006960.s007

DOI: 10.1371/journal.pcbi.1006960.s008

DOI: 10.1371/journal.pcbi.1006960.s009

DOI: 10.1371/journal.pcbi.1006960.s010

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2019

detail.hit.zdb_id: 2193340-6

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Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype

Martino, Cameron ; McDonald, Daniel ; Cantrell, Kalen ; [et al.]

American Society for Microbiology ; 2022

In: mSystems Vol. 7, No. 3 ( 2022-06-28)

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In: mSystems, American Society for Microbiology, Vol. 7, No. 3 ( 2022-06-28)

Abstract: Microbiome data have several specific characteristics (sparsity and compositionality) that introduce challenges in data analysis. The integration of prior information regarding the data structure, such as phylogenetic structure and repeated-measure study designs, into analysis, is an effective approach for revealing robust patterns in microbiome data. Past methods have addressed some but not all of these challenges and features: for example, robust principal-component analysis (RPCA) addresses sparsity and compositionality; compositional tensor factorization (CTF) addresses sparsity, compositionality, and repeated measure study designs; and UniFrac incorporates phylogenetic information. Here we introduce a strategy of incorporating phylogenetic information into RPCA and CTF. The resulting methods, phylo-RPCA, and phylo-CTF, provide substantial improvements over state-of-the-art methods in terms of discriminatory power of underlying clustering ranging from the mode of delivery to adult human lifestyle. We demonstrate quantitatively that the addition of phylogenetic information improves effect size and classification accuracy in both data-driven simulated data and real microbiome data. IMPORTANCE Microbiome data analysis can be difficult because of particular data features, some unavoidable and some due to technical limitations of DNA sequencing instruments. The first step in many analyses that ultimately reveals patterns of similarities and differences among sets of samples (e.g., separating samples from sick and healthy people or samples from seawater versus soil) is calculating the difference between each pair of samples. We introduce two new methods to calculate these differences that combine features of past methods, specifically being able to take into account the principles that most types of microbes are not in most samples (sparsity), that abundances are relative rather than absolute (compositionality), and that all microbes have a shared evolutionary history (phylogeny). We show using simulated and real data that our new methods provide improved classification accuracy of ordinal sample clusters and increased effect size between sample groups on beta-diversity distances.

Type of Medium: Online Resource

ISSN: 2379-5077

URL: Article

DOI: 10.1128/msystems.00050-22

Language: English

Publisher: American Society for Microbiology

Publication Date: 2022

detail.hit.zdb_id: 2844333-0

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