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How to Publish at Pandemic Speed
2021
BioScience
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A s SARS-CoV-2 spread across the world, many researchers sought to contribute to reducing its impacts by rapidly pivoting from their primary research to study COVID-19. Thousands of papers resulted from this wartime-like effort. One estimate suggests that 1 in 20 papers published in 2020 was related to COVID-19 (Else 2020). These articles guided-and continue to guide-policies, interventions, treatments, and our understanding of the pandemic's broader societal impacts at previously unimaginable
doi:10.1093/biosci/biab084
fatcat:dupmt6obbbfsxdz6h3b2xlhioi
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... peeds. But the speed of publication could not keep pace with the speed of research-or of the rapidly spreading pandemic. As the crisis grew, journals did their best to meet this unexpected surge. Many prioritized the review and publication of COVID-19 research and expanded their pool of reviewers while editors and reviewers worked tirelessly to vet submissions (Eisen et al. 2020 , Horbach 2020 , Kwon 2020) . Publication speeds accelerated, often taking a fraction of the time for a process that often takes a year (Björk and Solomon 2013). In one analysis, virology journals halved the time to publish COVID-19-related articles from 117 to 60 days (Horbach 2020). In addition, many journals introduced generous policies that allowed authors to upload preprints to servers and made COVID-19 research open access. Publishers, editors, and reviewers did their best with the standard model of scientific review and publishing during these historic times.
Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology
[article]
2022
bioRxiv
pre-print
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Gene models were filtered with gFACs v1.1.3 (Caballero and Wegrzyn 2019) with the following: unique genes only, mono-exonics missing a start or stop codon or valid protein domain, mult-iexonics missing ...
doi:10.1101/2022.08.02.502577
fatcat:orqnulnjsre6hiktmfo7rpy77m
Open access to tree genomes: the path to a better forest
2013
Genome Biology
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Genome resources are developing rapidly in forest trees in spite of the challenges associated with working with large, long-lived organisms and sometimes very large genomes [2] . Complete genome sequencing, however, has been slow to advance in forest trees owing to funding limitations and the large size of conifer genomes. Black cottonwood (Populus trichocarpa Torr. & Gray) was the fi rst forest tree genome to be sequenced by the US Department of Energy Joint Genome Institute (DOE/JGI) [6] (
doi:10.1186/gb-2013-14-6-120
pmid:23796049
pmcid:PMC3706761
fatcat:qnlety5ajjb3vk4wzfhwormtwu
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... le 1) . Black cottonwood has a relatively small genome (450 Mb) and is a target feedstock species for cellulosic ethanol production, and thus fi ts into the DOE/ JGI priority of sequencing bioenergy feedstock species. Abstract An open-access culture and a well-developed comparative-genomics infrastructure must be developed in forest trees to derive the full potential of genome sequencing in this diverse group of plants that are the dominant species in much of the earth's terrestrial ecosystems.
TreeGenes: A Forest Tree Genome Database
2008
International Journal of Plant Genomics
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The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species,
doi:10.1155/2008/412875
pmid:18725987
pmcid:PMC2517852
fatcat:vhrzlvfakzdcdgxhysz6zkhdfa
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... ons, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange.
Strategies of tolerance reflected in two North American maple genomes
[article]
2021
bioRxiv
pre-print
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Extensive filtering was performed on the predicted gene space using gFACS v1.1 (Caballero & Wegrzyn, 2019) . ...
to hydrolyze the by-product of the activity of S-adenosyl-L-methionine-dependent methyltransferase, and one of these was also absent. ...
L. T., Salzberg, S. L., Feng, L., Jones, M. R., Skelton, R. L., Murray, J. E., Chen, C., Qian, W., Shen, J., Du, P., … Alam, M. (2008) . ...
doi:10.1101/2021.07.19.452996
fatcat:7f4c2372y5b53iqh37e3u3mdom
Algorithms for discovery of cis-eQTL signals in woody species: the vine (Vitis vinifera L.) as a study model
[article]
2021
bioRxiv
pre-print
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This new inventory of cis eQTLs influencing gene expression during the ripening of fruits of Vitis vinifera L. will be an important resource for future research to understand the mechanistic basis for ...
As results from the comparison between stage1 (31 E-L stage 75 BBCH) and stage 3 (36 E-L), which could be the nearest stages to the one used here, showed a large list of downregulated candidates genes ...
Some of these studies have been carried out in grapes (Vitis vinifera L), the target organism of this study. ...
doi:10.1101/2021.07.06.450811
fatcat:dnlopf3brrh3zhj3h6fppflqxm
EnTAP: Bringing Faster and Smarter Functional Annotation to Non-Model Eukaryotic Transcriptomes
[article]
2018
bioRxiv
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EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates. Following filters applied through assessment of true expression and frame selection, open-source tools are leveraged to functionally
doi:10.1101/307868
fatcat:6zcwyval5beedlbwsb3j363tqi
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... nnotate the translated proteins. Downstream features include fast similarity search across three repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology term assignment. The final annotation integrates across multiple databases and selects an optimal assignment from a combination of weighted metrics describing similarity search score, taxonomic relationship, and informativeness. Researchers have the option to include additional filters to identify and remove contaminants, identify associated pathways, and prepare the transcripts for enrichment analysis. This fully featured pipeline is easy to install, configure, and runs significantly faster than comparable annotation packages. It is developed to contend with many of the issues in existing software solutions. EnTAP is optimized to generate extensive functional information for the gene space of organisms with limited or poorly characterized genomic resources.
Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation)
2018
BMC Genomics
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PDA; Merck) washed with 15% (v/v) sterile glycerol and diluted to 5 × 10 4 spores/mL, or mock-inoculated with 15% (v/v) sterile glycerol, at 6 months old by clipping the apical bud and depositing 10 μL ...
Both H. annuus and L. sativa carbohydrate oxidase protein sequences (Genbank accessions AAL77103.1 and AAL77102.1) [26] were used as type sequences for identification of putative PR-18 orthogroups. ...
doi:10.1186/s12864-018-5015-0
pmid:30139335
pmcid:PMC6108113
fatcat:w7kfjghybzfrroq3cnmpdd2oeu
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees
2019
Evolutionary Applications
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L. ...
., 2019; Wegrzyn et al., 2019) . ...
doi:10.1111/eva.12860
pmid:31892954
pmcid:PMC6935593
fatcat:r2zcwfc7irdgdln4faunycp3ui
Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites
2008
BMC Bioinformatics
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Utilization of alternative initiation sites for protein translation directed by non-AUG codons in mammalian mRNAs is observed with increasing frequency. Alternative initiation sites are utilized for the synthesis of important regulatory proteins that control distinct biological functions. It is, therefore, of high significance to define the parameters that allow accurate bioinformatic prediction of alternative translation initiation sites (aTIS). This study has investigated 5'-UTR regions of
doi:10.1186/1471-2105-9-232
pmid:18466625
pmcid:PMC2396638
fatcat:yk5yob5v7bggzizsdn3nnb5eca
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... As to define consensus sequence properties and structural features that allow identification of alternative initiation sites for protein translation. Results: Bioinformatic evaluation of 5'-UTR sequences of mammalian mRNAs was conducted for classification and identification of alternative translation initiation sites for a group of mRNA sequences that have been experimentally demonstrated to utilize alternative non-AUG initiation sites for protein translation. These are represented by the codons CUG, GUG, UUG, AUA, and ACG for aTIS. The first phase of this bioinformatic analysis implements a classification tree that evaluated 5'-UTRs for unique consensus sequence features near the initiation codon, characteristics of 5'-UTR nucleotide sequences, and secondary structural features in a decision tree that categorizes mRNAs into those with potential aTIS, and those without. The second phase addresses identification of the aTIS codon and its location. Critical parameters of 5'-UTRs were assessed by an Artificial Neural Network (ANN) for identification of the aTIS codon and its location. ANNs have previously been used for the purpose of AUG start site prediction and are applicable in complex. ANN analyses demonstrated that multiple properties were required for predicting aTIS codons; these properties included unique consensus nucleotide sequences at positions -7 and -6 combined with positions -3 and +4, 5'-UTR length, ORF length, predicted secondary structures, free energy features, upstream AUGs, and G/C ratio. Importantly, combined results of the classification tree and the ANN analyses provided highly accurate bioinformatic predictions of alternative translation initiation sites. Conclusion: This study has defined the unique properties of 5'-UTR sequences of mRNAs for successful bioinformatic prediction of alternative initiation sites utilized in protein translation. The ability to define aTIS through the described bioinformatic analyses can be of high importance for genomic analyses to provide full predictions of translated mammalian and human gene products required for cellular functions in health and disease.
Comparative mapping in Pinus: sugar pine (Pinus lambertiana Dougl.) and loblolly pine (Pinus taeda L.)
2010
Tree Genetics & Genomes
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Synteny has been reported among the hard pines such as Monterey pine (Pinus radiata L.; Devey et al. 1995) , slash pine (Pinus elliottii Engel.; Brown et al. 2001) , Scots pine (Pinus sylvestris L.; ...
Re-sequencing in sugar pine (CRSP, unpublished) resulted in the discovery of 4,238 SNPs which were identified using PineSap software described in Wegrzyn et al. (2009) . ...
doi:10.1007/s11295-010-0347-1
fatcat:mflbl3wp7vdjradrivfscpxnju
Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)
2010
Molecular Ecology
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Here, we use a genome-wide dataset of single nucleotide polymorphisms (SNPs) typed from 1730 loci in 682 loblolly pine (Pinus taeda L.) trees sampled from 54 local populations covering the full-range of ...
Jill Wegrzyn currently works in the field of bioinformatics with research interests in scientific databases, machine-learning, functional genomics, and proteomics. ...
jX; l ; bÞ $ Nð l þ bY; l ð1 À l ÞXÞ; where b is the linear effect of the environmental variable Y (Coop et al. 2010) . ...
doi:10.1111/j.1365-294x.2010.04698.x
pmid:20723060
fatcat:wlojxwojlne4rphlk6tynlw2vu
Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome
2011
New Phytologist
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NID(0, r 2 rðcÞ )), and e ijkl is the residual variance (l = 1-2, approx. NID(0, r 2 e )). ...
Materials and Methods
Focal species Loblolly pine (Pinus taeda L.) is distributed throughout the southeastern United States, with a range extending from Texas to Delaware (Fig. 1 ). ...
doi:10.1111/j.1469-8137.2011.03976.x
pmid:22129444
fatcat:qizrnr6hd5endmazxcheib4w3q
Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests
2012
Evolutionary Applications
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L. Wegrzyn, B. J. Knaus, J. V. Syring and D. B. ...
No significant DHEW values were found in A. alba and L. decidua in both gene categories. ...
doi:10.1111/j.1752-4571.2012.00256.x
pmid:23144662
pmcid:PMC3492901
fatcat:tqrx5vpzybgstewp7h7tckcrvq
Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource
2013
BMC Genomics
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The sequencing products were resolved on a LI-COR 4200 L sequencing system (LI-COR Biosciences, Lincoln, NE, USA). ...
doi:10.1186/1471-2164-14-702
pmid:24119028
pmcid:PMC4007752
fatcat:xb2l6n4lrnc4rjvxupzbfpzyse
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