scholarly journals Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns

2021 ◽  
Vol 17 (10) ◽  
pp. e1009423
Author(s):  
Maxwell W. Libbrecht ◽  
Rachel C. W. Chan ◽  
Michael M. Hoffman
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Genome Annotation ◽  
Input Data ◽  
Clustering Algorithms ◽  
Methodological Framework ◽  
Chromatin Immunoprecipitation Sequencing ◽  
The Common ◽  
Genome Activity ◽  
Future Work ◽  
Genomic Patterns

Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These algorithms take as input epigenomic datasets, such as chromatin immunoprecipitation-sequencing (ChIP-seq) measurements of histone modifications or transcription factor binding. They partition the genome and assign a label to each segment such that positions with the same label exhibit similar patterns of input data. SAGA algorithms discover categories of activity such as promoters, enhancers, or parts of genes without prior knowledge of known genomic elements. In this sense, they generally act in an unsupervised fashion like clustering algorithms, but with the additional simultaneous function of segmenting the genome. Here, we review the common methodological framework that underlies these methods, review variants of and improvements upon this basic framework, and discuss the outlook for future work. This review is intended for those interested in applying SAGA methods and for computational researchers interested in improving upon them.

scholarly journals CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language

GigaScience ◽  
2019 ◽  
Vol 8 (7) ◽  
Author(s):  
Michael Kotliar ◽  
Andrey V Kartashov ◽  
Artem Barski
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Computational Analysis ◽  
Computational Studies ◽  
Cloud Environment ◽  
Sequencing Data ◽  
Massive Growth ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Version 2.0 ◽  
The Common ◽  
Computational Research

Abstract Background Massive growth in the amount of research data and computational analysis has led to increased use of pipeline managers in biomedical computational research. However, each of the >100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL. Findings Herein, we present CWL-Airflow, a package that adds support for CWL to the Apache Airflow pipeline manager. CWL-Airflow uses CWL version 1.0 specification and can run workflows on stand-alone MacOS/Linux servers, on clusters, or on a variety of cloud platforms. A sample CWL pipeline for processing of chromatin immunoprecipitation sequencing data is provided. Conclusions CWL-Airflow will provide users with the features of a fully fledged pipeline manager and the ability to execute CWL workflows anywhere Airflow can run—from a laptop to a cluster or cloud environment. CWL-Airflow is available under Apache License, version 2.0 (Apache-2.0), and can be downloaded from https://barski-lab.github.io/cwl-airflow, https://scicrunch.org/resolver/RRID:SCR_017196.

scholarly journals Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 729-742 ◽  
Author(s):  
Lena Annika Street ◽  
Ana Karina Morao ◽  
Lara Heermans Winterkorn ◽  
Chen-Yu Jiao ◽  
Sarah Elizabeth Albritton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Protein Complexes ◽  
Regulatory Elements ◽  
Evolutionarily Conserved ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Regulatory Sites

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

scholarly journals Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations

2017 ◽  
Vol 284 (1861) ◽  
pp. 20170706 ◽  
Author(s):  
Valentin Thouzeau ◽  
Philippe Mennecier ◽  
Paul Verdu ◽  
Frédéric Austerlitz
Keyword(s):  
Central Asia ◽  
Linguistic Diversity ◽  
Past History ◽  
Genetic Data ◽  
Human Populations ◽  
Language Diversity ◽  
Methodological Framework ◽  
The Past ◽  
Approximate Bayesian ◽  
Future Work

Linguistic and genetic data have been widely compared, but the histories underlying these descriptions are rarely jointly inferred. We developed a unique methodological framework for analysing jointly language diversity and genetic polymorphism data, to infer the past history of separation, exchange and admixture events among human populations. This method relies on approximate Bayesian computations that enable the identification of the most probable historical scenario underlying each type of data, and to infer the parameters of these scenarios. For this purpose, we developed a new computer program PopLingSim that simulates the evolution of linguistic diversity, which we coupled with an existing coalescent-based genetic simulation program, to simulate both linguistic and genetic data within a set of populations. Applying this new program to a wide linguistic and genetic dataset of Central Asia, we found several differences between linguistic and genetic histories. In particular, we showed how genetic and linguistic exchanges differed in the past in this area: some cultural exchanges were maintained without genetic exchanges. The methodological framework and the linguistic simulation tool developed here can be used in future work for disentangling complex linguistic and genetic evolutions underlying human biological and cultural histories.

scholarly journals Exploration of Factors Affecting Learners' Motivation in E-learning

2019 ◽  
pp. 1269-1275
Author(s):  
Shubham Dubey ◽  
Biro Piroska ◽  
Manjulata Gautam
Keyword(s):  
Dropping Out ◽  
Individual Factor ◽  
Factors Affecting ◽  
E Learning ◽  
Learning Platforms ◽  
The Common ◽  
Khan Academy ◽  
Future Work ◽  
The Impact

The world is changing rapidly, so is academics. E-learning has altered the area of academics and education. ICT enabled learning has given ideal services to students by providing any type of content on demand which is proportional to the performance of students. The concentration of learner has been found instinctive; thus there is a need of engaging mind towards course progress with its entirety till the objectives of the course will be achieved. There are several e-learning platforms available as EdX, Udacity, Khan Academy, Alison those have a number of learners registered for various courses. Studies suggest that these platforms suffer from the common problem of learners’ dropping out. Investigations also claim early leaving rate is increasing due to lack of quality of content, distraction factors, learners’ mind change, outdated and succinct information, and some more detraction factors. These issues have been observed on the basis of early leaving rates in various MOOCs. Thus there is a mammoth scope for minimizing the impact of these reasons on the learners’ mind. It can be achieved by identifying these factors affecting learners’ motivation during the course. This study is aiming on identifying these factors. The approach is to explore some certain keywords on previous literature (total 41) and then calculating their frequencies and co-factors associated with them. Both grouped factors contribution and individual factor contribution have been taken care. The study gives a direction for future work towards overcoming these actor and engaging learners in ICT enabled learning.

The End of Heterosexuality?

2017 ◽  
Author(s):  
Joe Rollins
Keyword(s):  
Queer Theory ◽  
Reproductive Rights ◽  
Methodological Framework ◽  
Women's Bodies ◽  
Cultural Changes ◽  
Thick Description ◽  
Political Conflicts ◽  
Childhood Sexuality ◽  
History Of ◽  
The Common

This chapter outlines the theoretical and methodological framework for the book. The theoretical foundation is developed from a survey of the long history of scholarship on feminism and queer theory in order to examine heterosexuality, reproduction, abortion rights, and childhood in greater detail. Drawing on law and culture scholarship, the chapter proposes a methodology that utilizes thick description to explore the legal and cultural changes in marriage, particularly insofar as the sexuality of the institution has changed in recent decades. The common theme running through the chapter is the elusiveness of heterosexuality as a concept and its resistance to sustained investigation and critique. Working backward across the timeline of life—from adult marriage, to childhood, to fetuses—the chapter foreshadows the end of the book and the ways that the marriage debate is part of the same set of social and political conflicts as childhood sexuality, fetuses, women’s bodies, and reproductive rights.

Local Lotto

2018 ◽  
pp. 387-407
Author(s):  
Vivian Lim ◽  
Erica Deahl ◽  
Laurie Rubel ◽  
Sarah Williams
Keyword(s):  
High School ◽  
High School Students ◽  
Common Core State Standards ◽  
State Standards ◽  
Core State ◽  
School Students ◽  
Web Based ◽  
The Common ◽  
Mathematics Curricula ◽  
Future Work

Local Lotto is a 14-session curriculum designed for high school students to learn mathematics through an examination of the local lottery. The curriculum is organized around investigations of how local lottery games are won, who plays, how many people play, and where lottery revenues and prizes are distributed. A web-based application is integrated into the curriculum to allow students to explore the lottery in their school neighborhood, examine local lottery data, and assemble and justify their own arguments about the lottery. In this chapter, the authors describe technology's role in shaping a rich curriculum that engages students in investigating a local phenomenon while also addressing the content and practices of the Common Core State Standards of Mathematics. The chapter concludes with an outline of the challenges of integrating custom technologies into mathematics curricula and provides recommendations for future work.

scholarly journals Plakinamine P, A Steroidal Alkaloid with Bactericidal Activity against Mycobacterium tuberculosis

Marine Drugs ◽  
2019 ◽  
Vol 17 (12) ◽  
pp. 707 ◽  
Author(s):  
Carolina Rodrigues Felix ◽  
Jill C. Roberts ◽  
Priscilla L. Winder ◽  
Rashmi Gupta ◽  
M. Cristina Diaz ◽  
...  
Keyword(s):  
Axial Position ◽  
Side Chain ◽  
Moderate Activity ◽  
Steroidal Alkaloid ◽  
Magnetic Resonance Data ◽  
Resonance Data ◽  
Low Toxicity ◽  
The Common ◽  
Future Work ◽  
Discovery Pipeline

Tuberculosis is the leading cause of death due to infectious disease worldwide. There is an urgent need for more effective compounds against this pathogen to control the disease. Investigation of the anti-mycobacterial activity of a deep-water sponge of the genus Plakina revealed the presence of a new steroidal alkaloid of the plakinamine class, which we have given the common name plakinamine P. Its structure is most similar to plakinamine L, which also has an acyclic side chain. Careful dissection of the nuclear magnetic resonance data, collected in multiple solvents, suggests that the dimethyl amino group at the 3 position is in an equatorial rather than axial position unlike previously reported plakinamines. Plakinamine P was bactericidal against M. tuberculosis, and exhibited moderate activity against other mycobacterial pathogens, such as M. abscessus and M. avium. Furthermore, it had low toxicity against J774 macrophages, yielding a selectivity index (SI, or IC50/MIC) of 8.4. In conclusion, this work provides a promising scaffold to the tuberculosis drug discovery pipeline. Future work to determine the molecular target of this compound may reveal a pathway essential for M. tuberculosis survival during infection.

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