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1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. Storage, visualization, and navigation of 3D genomics data

Author:
Waldispühl, Jérôme; Zhang, Eric; Butyaev, Alexander; Nazarova, Elena; Cyr, Yan
Source:
Methods 2018 v.142 pp. 74-80
ISSN:
1046-2023
Subject:
genomics,   etc   ; nucleotide sequences; technology;     Show all 3 Subjects
Abstract:
... The field of 3D genomics grew at increasing rates in the last decade. The volume and complexity of 2D and 3D data produced is progressively outpacing the capacities of the technology previously used for distributing genome sequences. The emergence of new technologies provides also novel opportunities for the development of innovative approaches. In this paper, we review the state-of-the-art comput ...
DOI:
10.1016/j.ymeth.2018.05.008

9. Interactions between BTB domain of CP190 and two adjacent regions in Su(Hw) are required for the insulator complex formation

Author:
Melnikova, Larisa; Kostyuchenko, Margarita; Molodina, Varvara; Parshikov, Alexander; Georgiev, Pavel; Golovnin, Anton
Source:
Chromosoma 2018 v.127 no.1 pp. 59-71
ISSN:
0009-5915
Subject:
genomics,   etc   ; Drosophila; chromatin; mutation;     Show all 4 Subjects
Abstract:
... The best-studied Drosophila insulator complex consists of two BTB-containing proteins, the Mod(mdg4)-67.2 isoform and CP190, which are recruited cooperatively to chromatin through interactions with the DNA-binding architectural protein Su(Hw). While Mod(mdg4)-67.2 interacts only with Su(Hw), CP190 interacts with many other architectural proteins. In spite of the fact that CP190 is critical for the ...
DOI:
10.1007/s00412-017-0645-6

10. Solving Mendelian Mysteries: The Non-coding Genome May Hold the Key

Author:
Valente, Enza Maria; Bhatia, Kailash P.
Source:
Cell 2018 v.172 pp. 889-891
ISSN:
0092-8674
Subject:
genomics,   etc   ; genes; mutation; transcriptomics;     Show all 4 Subjects
Abstract:
... Despite revolutionary advances in sequencing approaches, many mendelian disorders have remained unexplained. In this issue of Cell, Aneichyk et al. combine genomic and cell-type-specific transcriptomic data to causally link a non-coding mutation in the ubiquitous TAF1 gene to X-linked dystonia-parkinsonism. ...
DOI:
10.1016/j.cell.2018.02.022

11. Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

Author:
Giladi, Amir; Amit, Ido
Source:
Cell 2018 v.172 no.1-2 pp. 14-21
ISSN:
0092-8674
Subject:
genomics,   etc   ; immunology; immunotherapy;     Show all 3 Subjects
Abstract:
... The immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ability to account for the functional heterogeneity of immune processes. Single-cell genomics hold the potential to revolutionize the way we chara ...
DOI:
10.1016/j.cell.2017.11.011

12. On the contribution of mass spectrometry-based platforms to the field of personalized oncology

Author:
Orlando, Eleonora; Aebersold, Ruedi
Source:
Trends in analytical chemistry 2019 v.110 pp. 129-142
ISSN:
0165-9936
Subject:
genomics,   etc   ; mass spectrometry; neoplasms; patients; phenotype; proteome; proteomics;     Show all 7 Subjects
Abstract:
... Over the last decades, the increasing technical ability to generate extensive molecular profiles of cancer patient cohorts was accompanied by the notion that anticancer strategies could be tailored to the individual patient, thus giving rise to personalized approaches. Implicit in this development is the need to establish informative molecular profiles to guide clinical decisions. Although at pres ...
DOI:
10.1016/j.trac.2018.10.018

13. Strategies for the Enrichment and Selection of Genetically Modified Cells

Author:
Ren, Chonghua; Xu, Kun; Segal, David Jay; Zhang, Zhiying
Source:
Trends in biotechnology 2019 v.37 no.1 pp. 56-71
ISSN:
0167-7799
Subject:
genomics,   etc   ; gene editing; gene therapy; genome; loci; nucleases; screening;     Show all 7 Subjects
Abstract:
... Programmable artificial nucleases have transitioned over the past decade from ZFNs and TALENs to CRISPR/Cas systems, which have been ubiquitously used with great success to modify genomes. The efficiencies of knockout and knockin vary widely among distinct cell types and genomic loci and depend on the nuclease delivery and cleavage efficiencies. Moreover, genetically modified cells are almost phen ...
DOI:
10.1016/j.tibtech.2018.07.017

14. Consumer genomics will change your life, whether you get tested or not

Author:
Khan, Razib; Mittelman, David
Source:
Genome biology 2018 v.19 no.1 pp. 120
ISSN:
1474-760X
Subject:
genomics,   etc   ; consumers (people); genotyping; industry;     Show all 4 Subjects
Abstract:
... With more than 10 million genotyped customers, the consumer genomics industry is maturing and becoming a mainstream phenomenon. At last, innovations and applications, some unforeseen, are being brought to the masses. ...
DOI:
10.1186/s13059-018-1506-1

15. Recent advances in plant and animal genomics are taking agriculture to new heights

Author:
Beiki, Hamid; Eveland, Andrea L.; Tuggle, Christopher K.
Source:
Genome biology 2018 v.19 no.1 pp. 48
ISSN:
1474-760X
Subject:
genomics,   etc   ; animals; genome; United States;     Show all 4 Subjects
Abstract:
... A report on the International Plant and Animal Genomes (PAG) conference held in San Diego, USA, 13–17 January 2018. ...
DOI:
10.1186/s13059-018-1427-z

16. Automated Chemical Oligosaccharide Synthesis: Novel Approach to Traditional Challenges

Author:
Panza, Matteo; Pistorio, Salvatore G.; Stine, Keith J.; Demchenko, Alexei V.
Source:
Chemical reviews 2018 v.118 no.17 pp. 8105-8150
ISSN:
1520-6890
Subject:
genomics,   etc   ; automation; chemistry; oligosaccharides; proteomics;     Show all 5 Subjects
Abstract:
... Advances in carbohydrate chemistry have certainly made common oligosaccharides much more accessible. However, many current methods still rely heavily upon specialized knowledge of carbohydrate chemistry. The application of automated technologies to chemical and life science applications such as genomics and proteomics represents a vibrant field. These automated technologies also present opportunit ...
DOI:
10.1021/acs.chemrev.8b00051

17. Chromaffin cell biology: inferences from The Cancer Genome Atlas

Author:
Fishbein, Lauren; Wilkerson, MatthewD.
Source:
Cell and tissue research 2018 v.372 no.2 pp. 339-346
ISSN:
0302-766X
Subject:
genomics,   etc   ; cell biology; genes; neoplasms;     Show all 4 Subjects
Abstract:
... Pheochromocytomas and paragangliomas (PCC/PGLs) are rare neuroendocrine tumors that are unusually diverse in metabolic profiles, in classes of molecular alterations and across a large number of altered genes. The Cancer Genome Atlas (TCGA) comprehensively profiled the molecular landscape of PCC/PGLs and identified novel genomic alterations and a new molecular classification of PCC/PGLs. In this re ...
DOI:
10.1007/s00441-018-2795-0

18. Hawaiian Drosophila as an Evolutionary Model Clade: Days of Future Past

Author:
O'Grady, Patrick; DeSalle, Rob
Source:
BioEssays 2018 v.40 no.5 pp. e1700246
ISSN:
0265-9247
Subject:
genomics,   etc   ; Drosophila melanogaster; biogeography; models;     Show all 4 Subjects
Abstract:
... The Hawaiian Drosophila have been a model system for evolutionary, ecological, and ethological studies since the inception of the Hawaiian Drosophila Project in the 1960s. Here we review the past and present research on this incredible lineage and provide a prospectus for future directions on genomics and microbial interactions. While the number of publications on this group has waxed and waned ov ...
DOI:
10.1002/bies.201700246

19. Correction to: Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number

Author:
Sukumaran, Sivakumar; Lopes, Marta; Dreisigacker, Susanne; Reynolds, Matthew
Source:
Theoretical and applied genetics 2018 v.131 no.4 pp. 999
ISSN:
0040-5752
Subject:
genomics,   etc   ; genetic analysis; spring wheat;     Show all 3 Subjects
Abstract:
... Unfortunately, the Fig. 1 of this original article was incorrectly published. The corrected Fig. 1 is given below. ...
DOI:
10.1007/s00122-018-3066-x

20. Genomic analysis of three Clostridioidesdifficile isolates from urban water sources

Author:
Numberger, Daniela; Riedel, Thomas; McEwen, Gayle; Nübel, Ulrich; Frentrup, Martinique; Schober, Isabel; Bunk, Boyke; Spröer, Cathrin; Overmann, Jörg; Grossart, Hans-Peter; Greenwood, Alex D.
Source:
Anaerobe 2019 v.56 pp. 22-26
ISSN:
1075-9964
Subject:
genomics,   etc   ; Clostridium difficile; genome; lakes; nontoxigenic strains; polymerase chain reaction; sediments; wastewater; wastewater treatment;     Show all 9 Subjects
Abstract:
... We investigated inflow of a wastewater treatment plant and sediment of an urban lake for the presence of Clostridioides difficile by cultivation and PCR. Among seven colonies we sequenced the complete genomes of three: two non-toxigenic isolates from wastewater and one toxigenic isolate from the urban lake. For all obtained isolates, a close genomic relationship with human-derived isolates was obs ...
DOI:
10.1016/j.anaerobe.2019.01.002