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1. Fragile DNA contributes to repeated evolution

Author:
Kratochwil, Claudius F.; Meyer, Axel
Source:
Genome biology 2019 v.20 no.1 pp. 39
ISSN:
1474-760X
Subject:
genomics,   etc   ; DNA; evolution; mutation;     Show all 4 Subjects
Abstract:
... Sequence features that affect DNA fragility might facilitate fast, repeated evolution by elevating mutation rates at genomic hotspots. ...
DOI:
10.1186/s13059-019-1655-x

2. Keen on the tenure track job, are you? Know these things, you should

Author:
Voight, Benjamin F.
Source:
Genome biology 2019 v.20 no.1 pp. 6
ISSN:
1474-760X
Subject:
genomics,   etc   ; geneticists; genome; universities;     Show all 4 Subjects
Abstract:
... Success along the tenure track requires more than hard work and long hours. Here, the experiences of a recently tenured professor are distilled into a collection of tips to assist others along the path. ...
DOI:
10.1186/s13059-018-1617-8

3. A Tumor-Agnostic NTRK (TRK) Inhibitor

Author:
Huang, Franklin W.; Feng, Felix Y.
Source:
Cell 2019 v.177 no.1 pp. 8
ISSN:
0092-8674
Subject:
genomics,   etc   ; enzyme inhibitors; neoplasms;     Show all 3 Subjects
Abstract:
... Larotrectinib is a small-molecule kinase inhibitor that targets NTRK fusions that occur in multiple types of cancer. Its FDA approval represents the first instance of a treatment indication being designated “tumor-agnostic” from the outset, being based on actionable genomic insights. To view this Bench to Bedside, open or download the PDF. ...
DOI:
10.1016/j.cell.2019.02.049

4. Efficiency of PacBio long read correction by 2nd generation Illumina sequencing

Author:
Mahmoud, Medhat; Zywicki, Marek; Twardowski, Tomasz; Karlowski, Wojciech M.
Source:
Genomics 2019 v.111 no.1 pp. 43-49
ISSN:
0888-7543
Subject:
genomics,   etc   ; cost effectiveness; transcriptomics;     Show all 3 Subjects
Abstract:
... Long sequencing reads offer unprecedented opportunities in analysis and reconstruction of complex genomic regions. However, the gain in sequence length is often traded for quality. Therefore, recently several approaches have been proposed (e.g. higher sequencing coverage, hybrid assembly or sequence correction) to enhance the quality of long sequencing reads. A simple and cost-effective approach i ...
DOI:
10.1016/j.ygeno.2017.12.011

5. plyranges: a grammar of genomic data transformation

Author:
Lee, Stuart; Cook, Dianne; Lawrence, Michael
Source:
Genome biology 2019 v.20 no.1 pp. 4
ISSN:
1474-760X
Subject:
genomics,   etc   ; cognition; computer software; infrastructure;     Show all 4 Subjects
Abstract:
... Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class follows “tidy” data principles, we create a grammar of genomic data transformation, defining verbs for p ...
DOI:
10.1186/s13059-018-1597-8

6. Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

Author:
Finn, Elizabeth H.; Pegoraro, Gianluca; Brandão, Hugo B.; Valton, Anne-Laure; Oomen, Marlies E.; Dekker, Job; Mirny, Leonid; Misteli, Tom
Source:
Cell 2019 v.176 no.6 pp. 1502-1515.e10
ISSN:
0092-8674
Subject:
genomics,   etc   ; alleles; chromatin; fibroblasts; humans;     Show all 5 Subjects
Abstract:
... Several general principles of global 3D genome organization have recently been established, including non-random positioning of chromosomes and genes in the cell nucleus, distinct chromatin compartments, and topologically associating domains (TADs). However, the extent and nature of cell-to-cell and cell-intrinsic variability in genome architecture are still poorly characterized. Here, we systemat ...
DOI:
10.1016/j.cell.2019.01.020

7. Efficient clustering in collaborative filtering recommender system: Hybrid method based on genetic algorithm and gravitational emulation local search algorithm

Author:
Mohammadpour, Touraj; Bidgoli, Amir Massoud; Enayatifar, Rasul; Javadi, Hamid Haj Seyyed
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
genomics,   etc   ; algorithms; data collection; genome;     Show all 4 Subjects
Abstract:
... The ultimate goal of the Recommender System (RS) is to offer a proposal that is very close to the user's real opinion. Data clustering can be effective in increasing the accuracy of production proposals by the RS. In this paper, single-objective hybrid evolutionary approach is proposed for clustering items in the offline collaborative filtering RS. This method, after generating a population of ran ...
DOI:
10.1016/j.ygeno.2019.01.001

8. Why polyploid exceptionalism is not accompanied by reduced extinction rates

Author:
Levin, Donald A.
Source:
Plant systematics and evolution 2019 v.305 no.1 pp. 1-11
ISSN:
0378-2697
Subject:
genomics,   etc   ; allopolyploidy; autopolyploidy; diploidy; extinction;     Show all 5 Subjects
Abstract:
... In spite of their success during the past several millions of years, recent analyses indicate that polyploid species may have higher extinction rates than their diploid relatives. The idea that neopolyploid species are relatively short-lived is antithetical to the notion of polyploid exceptionalism. I propose that young, established polyploid species have unusually high extinction rates due to dem ...
DOI:
10.1007/s00606-018-1552-x

9. Improving the usability and archival stability of bioinformatics software

Author:
Mangul, Serghei; Martin, Lana S.; Eskin, Eleazar; Blekhman, Ran
Source:
Genome biology 2019 v.20 no.1 pp. 47
ISSN:
1474-760X
Subject:
genomics,   etc   ; bioinformatics; computer software; product quality;     Show all 4 Subjects
Abstract:
... Implementation of bioinformatics software involves numerous unique challenges; a rigorous standardized approach is needed to examine software tools prior to their publication. ...
DOI:
10.1186/s13059-019-1649-8

10. Author Correction: Identification of a Novel Feruloyl Esterase by Functional Screening of a Soil Metagenomic Library

Author:
Li, Xuanxuan; Guo, Jia; Hu, Yimin; Yang, Yumeng; Jiang, Junwei; Nan, Fang; Wu, Shenglu; Xin, Zhihong
Source:
Applied biochemistry and biotechnology 2019 v.187 no.4 pp. 1582-1583
ISSN:
0273-2289
Subject:
genomic libraries,   etc   ; feruloyl esterase; screening; soil;     Show all 4 Subjects
Abstract:
... The original version of this article unfortunately contained a mistake in the image and caption of Fig. 6. The corrected version of the image and caption is shown here. ...
DOI:
10.1007/s12010-019-02978-3

11. The Genetic Basis of Metabolic Disease

Author:
Barroso, Inês; McCarthy, Mark I.
Source:
Cell 2019 v.177 no.1 pp. 146-161
ISSN:
0092-8674
Subject:
genomics,   etc   ; genome; loci; metabolic diseases; phenotype;     Show all 5 Subjects
Abstract:
... Recent developments in genetics and genomics are providing a detailed and systematic characterization of the genetic underpinnings of common metabolic diseases and traits, highlighting the inherent complexity within systems for homeostatic control and the many ways in which that control can fail. The genetic architecture underlying these common metabolic phenotypes is complex, with each trait infl ...
DOI:
10.1016/j.cell.2019.02.024

12. Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny

Author:
Van Dam, Matthew H.; Trautwein, Michelle; Spicer, Greg S.; Esposito, Lauren
Source:
Molecular ecology resources 2019 v.19 no.2 pp. 465-475
ISSN:
1755-098X
Subject:
genomics,   etc   ; Opiliones; Parasitiformes; genome; loci; mites; paraphyly;     Show all 7 Subjects
Abstract:
... Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resol ...
DOI:
10.1111/1755-0998.12962

13. Refining and expanding nonribosomal peptide synthetase function and mechanism

Author:
McErlean, Matt; Overbay, Jonathan; Van Lanen, Steven
Source:
Journal of industrial microbiology & biotechnology 2019 v.46 no.3-4 pp. 493-513
ISSN:
1367-5435
Subject:
genomics,   etc   ; biosynthesis; biotechnology; genes; ligases; medicine; peptides;     Show all 7 Subjects
Abstract:
... Nonribosomal peptide synthetases (NRPSs) are involved in the biosynthesis of numerous peptide and peptide-like natural products that have been exploited in medicine, agriculture, and biotechnology, among other fields. As a consequence, there have been considerable efforts aimed at understanding how NRPSs orchestrate the assembly of these natural products. This review highlights several recent exam ...
DOI:
10.1007/s10295-018-02130-w

14. RNA Strand Displacement Responsive CRISPR/Cas9 System for mRNA Sensing

Author:
Li, Yue; Teng, Xucong; Zhang, Kaixiang; Deng, Ruijie; Li, Jinghong
Source:
Analytical chemistry 2019 v.91 no.6 pp. 3989-3996
ISSN:
1520-6882
Subject:
genomics,   etc   ; gene editing; messenger RNA; proteins;     Show all 4 Subjects
Abstract:
... CRISPR/Cas9 has already become a powerful tool for genomic manipulation, and further engineering of the system allows it to be precisely regulated in response to external signals, thus, broadening its application possibilities, such as biosensing or bioimaging. However, most stimuli-responsive CRISPR systems are built based on elaborately designed and engineered inducible Cas9 proteins, and extern ...
DOI:
10.1021/acs.analchem.8b05238

15. Correction to: Synthesis of Tinbergen’s four questions and the future of sociogenomics

Author:
Kapheim, Karen M.
Source:
Behavioral ecology and sociobiology 2019 v.73 no.2 pp. 28
ISSN:
0340-5443
Subject:
genomics,   etc   ; evolution; kin selection; social behavior;     Show all 4 Subjects
Abstract:
... This article is a part of the topical collection “Social complexity: patterns, processes, and evolution”. For this reason, though it was originally inadvertently published in 2018, in Vol. 72, Issue 12, citation ID 186, it has now been reassigned and republished in 2019, in Vol. 73, Issue 1, citation ID 186. ...
DOI:
10.1007/s00265-018-2626-z

16. Evolutionary and ecological functional genomics, from lab to the wild

Author:
Zaidem, Maricris L.; Groen, Simon C.; Purugganan, Michael D.
Source:
Theplant journal 2019 v.97 no.1 pp. 40-55
ISSN:
0960-7412
Subject:
genomics,   etc   ; phenotype; phenotypic variation; plant response;     Show all 4 Subjects
Abstract:
... Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutiona ...
DOI:
10.1111/tpj.14167

17. Transcriptomic Resources for Parasitic Nematodes of Veterinary Importance

Author:
Jex, Aaron R.; Gasser, Robin B.; Schwarz, Erich M.
Source:
Trends in parasitology 2019 v.35 no.1 pp. 72-84
ISSN:
1471-4922
Subject:
genomics,   etc   ; Nematoda; animal pathogens; parasitism; transcriptome; transcriptomics;     Show all 6 Subjects
Abstract:
... Parasitic nematodes are important pathogens of animals, causing diseases that impact on agricultural production worldwide. Research on these worms has been constrained by a lack of genetic and genomic tools. Nonetheless, over the past decade this field has made substantial advances, many of which have been led by transcriptomic sequencing. The present review summarises major transcriptomic studies ...
DOI:
10.1016/j.pt.2018.09.010

18. Gene space completeness in complex plant genomes

Author:
Van Bel, Michiel; Bucchini, François; Vandepoele, Klaas
Source:
Current opinion in plant biology 2019
ISSN:
1369-5266
Subject:
genomics,   etc   ; genes; models; quantitative trait loci;     Show all 4 Subjects
Abstract:
... Genome annotations offer ample opportunities to study gene functions, biochemical and regulatory pathways, or quantitative trait loci in plants. Determining the quality and completeness of a genome annotation, and maintaining the balance between them, are major challenges, even for genomes of well-studied model organisms. In this review, we present a historical overview of the complexity in differ ...
DOI:
10.1016/j.pbi.2019.01.001

19. Adding resolution and dimensionality to comparative genomics: moving from reference genomes to clade genomics

Author:
Rogers, Jeffrey
Source:
Genome biology 2018 v.19 no.1 pp. 115
ISSN:
1474-760X
Subject:
genomics,   etc   ; evolution; genome;     Show all 3 Subjects
Abstract:
... The main goal and promise of comparative genomics has been to create a comprehensive catalog of genomic information and function across the phenomenal diversity of living systems. A recent study has demonstrated the evolutionary insights possible by generating high-quality whole-genome assemblies from multiple species of a clade. ...
DOI:
10.1186/s13059-018-1500-7

20. GIVE: portable genome browsers for personal websites

Author:
Cao, Xiaoyi; Yan, Zhangming; Wu, Qiuyang; Zheng, Alvin; Zhong, Sheng
Source:
Genome biology 2018 v.19 no.1 pp. 92
ISSN:
1474-760X
Subject:
genomics,   etc   ; Internet; genome;     Show all 3 Subjects
Abstract:
... Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage interactive visualization of multiple types of genomics data, including genome ...
DOI:
10.1186/s13059-018-1465-6