Genomics - F1000 Research

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Researching genomics?

Discover rapid, open publication with F1000Research

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F1000Research: An open access publishing platform supporting data deposition and sharing

Rapid, open publication is essential in fast-paced fields of study like genomics. F1000Research offers fully open publication in as few as 14 days, so your genomics research can make an impact sooner.

F1000Research is the ideal publishing platform for all your genomics outputs – from traditional Research Articles, to Software Tool Articles, Data Notes, and Method Articles, which help to tell the full story of your research. We welcome articles covering all areas of genomics, including:

  • Genome biology
  • Genome medicine
  • Plant and animal genomics
  • Genome annotation
  • Epigenomics
  • Genome analysis
  • Structural genomics

The wide range of outputs we publish, combined with our progressive Open Data Policy, makes F1000Research the perfect home for your cutting-edge genomics research.

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Ready to submit?

Whether you're writing a traditional Research Article, or something more unique like a Data Note, there are some simple instructions for authors available to help you. Read our author guidelines now, to ensure you've prepared your genomics article correctly for submission to F1000Research.
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About F1000Research

F1000Research is a fully open access publishing platform, offering rapid publication of articles and other research outputs without editorial bias.

All articles benefit from transparent post-publication peer review, and editorial guidance on making source data openly available.

F1000Research advocates for transparency and reproducibility in research, and our unique publishing model supports this at every stage. Articles can be published in as few as 14 days, with post-publication peer review creating an open dialogue between authors and their research community. This generates feedback which can be used to improve the article and develop the author's skills. 

How it works   Our APCs

Why publish on F1000Research?

Publish without delays

Our rapid publication model offers an innovative alternative to traditional journals publishing, where long delays between submission and publication are expected. On F1000Research, your article could be published online, peer-review ready and in a fully citable format, in as few as 14 days, so your research can make an impact sooner.


Support transparency and reproducibility

The F1000Research publication model puts transparency and reproducibility at the heart of what we do. Our platform facilitates transparent sharing of research by publishing all articles openly, alongside access to any underlying data, software, code, and other resources – even the peer review reports. This focus on transparent, reproducible research supports the credibility and rigor of your published work.


Maximize the impact of your work with Open Access

With fully open publication as standard on F1000Research, anyone can read, cite, and use your work – including policymakers, practitioners, and fellow researchers. This is particularly relevant for fast-paced areas of research like genomics, where results can make real-world impact. Alongside open publication of the article itself, F1000Research also advocates a rigorous Open Data policy so that others can replicate your study, reproduce the original findings, or reuse the data to support their own work.


Publish all your findings

F1000Research publishes articles and other research outputs without editorial bias. All research is suitable regardless of the perceived level of interest of novelty, meaning we welcome confirmatory and negative results, as well as null studies. The peer review process focuses on the academic merit of the paper, rather than the likely impact of the work.


Increase the visibility and reach of your research

Once your genomics article has passed peer review, inclusion in Scopus, PubMed, Google Scholar and other major indexers will help it to reach more readers. Your paper gets an additional discoverability boost on the F1000Research platform, where articles are supported by machine-readable metadata, making it easier for readers to find. Depending on the scope of your article, you could also benefit from inclusion in one of our dedicated Gateways, such as the ISCB Community Journal or Draft Genomes Collection.

Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins

This article presents the complete genome of the Small Cabbage White (also known as the Imported Cabbageworm), a butterfly of particular medical interest as a source of pierisin, a unique protein that shows cytotoxicity to cancer cells. The sequence reveals eight pierisins from Pieris rapae, offering six new candidates as anti-cancer drugs.
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False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors

Sequencing similarity among distinct genomic regions can lead to errors in alignment of short reads from next-gen sequencing. This Method Article by Saha and Battle assesses the potential for incorrect alignment of RNA-sequencing reads to cause false positives in both gene expression quantitative trait locus (eQTL) and co-expression analyses.
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Research outputs come in many forms. So do our article types.

At F1000Research, we really hate research waste. That’s why we welcome traditional Research Articles describing confirmatory or negative results, and why we publish null studies. It’s also why we offer a range of article types, so that all forms of research output can get the credit they deserve.

Here are a few formats which work particularly well for genomics:

Software Tool Article

These articles describe novel software tools created to support or conduct scientific research in any field, but they are particularly popular in genomics.

Software Tool Articles explain:

  • Why the software was developed
  • Details of the code, method, and analysis used
  • Tips on how to maximize the tool’s potential

Software Tool Articles offer research software engineers a great way to get credit for their work with a fully citable, peer-reviewed publication, and increase the visibility of their software so that other researchers can use it too.

 

InferAMP, a python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports [version 3; peer review: 2 approved] 

Paraic A Kenny

This Software Tool Article describes an easy-to-use, Python-based web tool for analyzing clinical genomics reports of amplified genes, supporting healthcare professionals in determining which amplified genes, if any, might be driving tumor growth.  This article is also a great example of the user-friendly versioning system which F1000Research offers, with previous versions (and their associated peer reviews) clearly linked on the right hand panel.

Data Note

Effective data sharing extends beyond finding an appropriate repository: Data Notes offer researchers an easy way to make their data discoverable, useable, reproducible. These articles describe scientific datasets, without including any analysis or conclusions. Instead, they focus on:

  • Dataset rationale, protocol, and validation details
  • Information about any limitations of the dataset
  • Information on where and how to access the dataset

It is worth noting that Data Notes do not undermine the novelty or value of a Research Article which makes use of the published dataset (here’s a handy list of all the journals and publishers which have confirmed this!).

 

Draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae) [version 3; peer review: 2 approved]

J Brate, J Fuss, S Mehrota, K Jakobsen, D Klaveness

This Data Note, included in the Draft Genomes Collection, presents an extensive set of next-generation sequencing data, including genomic short reads and long reads, as well as full length cDNAs and a small RNA dataset, for the golden algae, Hydrurus foetidus (Villars) Trevisan. The new data presented in this article contributes towards a better understanding of the evolution and ecological roles of chrysophyte algae, and helps to resolve the branching patterns at a larger phylogenetic scale.

 

 

Method Article

Method Articles describe new and well-tested experimental, observational, theoretical, or computational methods. This includes novel study methods, substantial modifications to existing methods, and innovative applications of existing methods to new models and scientific questions. Technical articles describing tools that facilitate experimental design or performance, offer data analysis, or assist with medical treatment, are also welcome within this format. These articles support replicability and reproducibility in research, by offering detailed information on the chosen method.

 

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 3 approved]

A Sima, C Dessimoz, K Stockinger, M Zahn-Zabal

This Method Article, included in The OMA Collection, presents four protocols for using SPARQL queries to retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups (HOGs). Identifying orthologs and HOGs supports research in several contexts, including gene function interference and comparative genomics.

How to boost the visibility of your genomics research

Increase the discoverability and reach of your genomics research by publishing in a relevant Gateway or Collection on F1000Research. These pages curate research outputs thematically, and offer dedicated publishing portals for different research communities.

Not sure where to start? Keep reading to learn more about our favorite Gateways and Collections for genomics research.


ISCB Community Journal 

The International Society for Computational Biology Community Journal offers ISCB members an open publication venue for research across all areas of bioinformatics and computational biology, including genomics. First established in 1997, the ISCB has emerged as the leading professional society in these fields, with a diverse membership comprising researchers, practitioners, students and professionals around the world.


Draft Genomes

This Collection on F1000Research showcases articles describing genome data for all organisms (animal, plant, bacterium, archaean, protist or virus). All the underlying data of the draft genomes are accessible through the articles, encouraging and maximizing data-sharing, collaboration and reuse in the community.


EMBL-EBI 

Do you work at the European Bioinformatics Institute (EMBL-EBI)? This Collection offers EMBL-EBI staff a rapid, open publication venue for their research papers, technical documents, white papers, posters, and training materials. The EMBL-EBI Collection covers a range of bioinformatics and computational biology topics, including genomics.


Nanopore Analysis

Nanopore sequencing is an exciting new technology with direct applications in DNA sequencing. Research in this fast-paced field of study needs to be published rapidly in order to keep up with the pace of change. This innovative Gateway on F1000Research supports nanopore analysis research by providing an open publication venue for related data and results, with publication available in as few as 14 days.

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