22 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/19

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

23 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/18

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

18 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/18

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

31 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/17

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

36 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/16

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

36 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/16

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

64 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/15

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

On the post-glacial spread of human commensal Arabidopsis thaliana: journey to the east.

New Phytol. 2019 Jan 13;:

Authors: Hsu CW, Lo CY, Lee CR

Abstract
• With more sequenced genomes, our understanding of the demographic history of Arabidopsis thaliana is rapidly expanding. However, no one has yet compiled previous data to investigate patterns of genetic variation across Eurasia. • While the sub-Saharan accessions were reported to be the most divergent group, in the nuclear genome we found accessions from Yunnan, China to be genetically closest to the sub-Saharan group. In chloroplast, several deeply diverged haplogroups exist only in Eurasia, and the African populations have lower variation in many haplogroups they shared with the Eurasian populations. These patterns cannot be easily explained by a single out-of-Africa event suggested previously. • For more recent demographic history, we dated the non-relict expansion to 10 kya. In the Chinese Yangtze non-relicts, we found clear traces of gene flow with local relicts, and genes under strong selection were enriched for traces of relict introgression, especially those related to biotic and immune responses. The results suggest the ability of non-relicts to obtain locally adaptive alleles through admixture with relicts is important for the expansion across environmental gradients of Eurasia. • Our re-analyses provide another model for the early history as well as elucidating factors contributing to the recent demographic turnover event of this species. This article is protected by copyright. All rights reserved.

PMID: 30636325 [PubMed - as supplied by publisher]

Tools for Understanding miRNA-mRNA Interactions for Reproducible RNA Analysis.

Methods Mol Biol. 2019;1912:199-214

Authors: Bagnacani A, Wolfien M, Wolkenhauer O

Abstract
MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. The use of RNA data in gene expression analysis has become increasingly important to gain insights into the regulatory mechanisms behind miRNA-mRNA interactions. As a result, we are confronted with a growing landscape of tools, while standards for reproducibility and benchmarking lag behind. This work identifies the challenges for reproducible RNA analysis, and highlights best practices on the processing and dissemination of scientific results. We found that the success of a tool does not solely depend on its performances: equally important is how a tool is received, and then supported within a community. This leads us to a detailed presentation of the RNA workbench, a community effort for sharing workflows and processing tools, built on top of the Galaxy framework. Here, we follow the community guidelines to extend its portfolio of RNA tools with the integration of the TriplexRNA ( https://triplexrna.org ). Our findings provide the basis for the development of a recommendation system, to guide users in the choice of tools and workflows.

PMID: 30635895 [PubMed - in process]

Workflow Development for the Functional Characterization of ncRNAs.

Methods Mol Biol. 2019;1912:111-132

Authors: Wolfien M, Brauer DL, Bagnacani A, Wolkenhauer O

Abstract
During the last decade, ncRNAs have been investigated intensively and revealed their regulatory role in various biological processes. Worldwide research efforts have identified numerous ncRNAs and multiple RNA subtypes, which are attributed to diverse functionalities known to interact with different functional layers, from DNA and RNA to proteins. This makes the prediction of functions for newly identified ncRNAs challenging. Current bioinformatics and systems biology approaches show promising results to facilitate an identification of these diverse ncRNA functionalities. Here, we review (a) current experimental protocols, i.e., for Next Generation Sequencing, for a successful identification of ncRNAs; (b) sequencing data analysis workflows as well as available computational environments; and (c) state-of-the-art approaches to functionally characterize ncRNAs, e.g., by means of transcriptome-wide association studies, molecular network analyses, or artificial intelligence guided prediction. In addition, we present a strategy to cover the identification and functional characterization of unknown transcripts by using connective workflows.

PMID: 30635892 [PubMed - in process]

Publisher Correction: Collapse of genetic division of labour and evolution of autonomy in pellicle biofilms.

Nat Microbiol. 2019 Jan 11;:

Authors: Dragoš A, Martin M, Garcia CF, Kricks L, Pausch P, Heimerl T, Bálint B, Maróti G, Bange G, López D, Lieleg O, Kovács ÁT

Abstract
In the version of this Article originally published, author Carolina Falcón Garcia's name was coded wrongly, resulting in it being incorrect when exported to citation databases. This has now been corrected, though no visible changes will be apparent.

PMID: 30635640 [PubMed - as supplied by publisher]

A gene expression map of shoot domains reveals regulatory mechanisms.

Nat Commun. 2019 Jan 11;10(1):141

Authors: Tian C, Wang Y, Yu H, He J, Wang J, Shi B, Du Q, Provart NJ, Meyerowitz EM, Jiao Y

Abstract
Gene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from the SAM peripheral zone. After initiation, leaves develop polarity patterns to form a planar shape. Here we compare translating RNAs among SAM and leaf domains. Using translating ribosome affinity purification and RNA sequencing to quantify gene expression in target domains, we generate a domain-specific translatome map covering representative vegetative stage SAM and leaf domains. We discuss the predicted cellular functions of these domains and provide evidence that dome seemingly unrelated domains, utilize common regulatory modules. Experimental follow up shows that the RABBIT EARS and HANABA TARANU transcription factors have roles in axillary meristem initiation. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals.

PMID: 30635575 [PubMed - in process]

T Cells and Regulated Cell Death: Kill or Be Killed.

Int Rev Cell Mol Biol. 2019;342:27-71

Authors: Spetz J, Presser AG, Sarosiek KA

Abstract
Cell death plays two major complementary roles in T cell biology: mediating the removal of cells that are targeted by T cells and the removal of T cells themselves. T cells serve as major actors in the adaptive immune response and function by selectively killing cells which are infected or dysfunctional. This feature is highly involved during homeostatic maintenance, and is relied upon and modulated in the context of cancer immunotherapy. The vital recognition and elimination of both autoreactive T cells and cells which are unable to recognize threats is a highly selective and regulated process. Moreover, detection of potential threats will result in the activation and expansion of T cells, which on resolution of the immune response will need to be eliminated. The culling of these T cells can be executed via a multitude of cell death pathways which are used in context-specific manners. Failure of these processes may result in an accumulation of misdirected or dysfunctional T cells, leading to complications such as autoimmunity or cancer. This review will focus on the role of cell death regulation in the maintenance of T cell homeostasis, as well as T cell-mediated elimination of infected or dysfunctional cells, and will summarize and discuss the current knowledge of the cellular mechanisms which are implicated in these processes.

PMID: 30635093 [PubMed - in process]

36 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/12

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

30 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/11

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

26 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/11

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

44 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/10

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

38 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/10

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

32 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/09

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

52 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/01/08

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.