Preprints (not yet peer-reviewed)

19 downloads
164 views

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3266v3
11 downloads
66 views

The mutational processes responsible for the somatic mutations observed in tumor samples can significantly vary not only between tumor types but also among the individual cancers within a tumor class. Mutational processes can be represented by so called “mutational...

["Bioinformatics","Computational Biology","Genomics","Oncology"]
doi:10.7287/peerj.preprints.3257v1
14 downloads
130 views

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low...

["Evolutionary Studies","Genomics","Virology"]
doi:10.7287/peerj.preprints.3153v2
11 downloads
105 views

Computational biology is rapidly advancing thanks to the many new tools developed and published each month. A systematic benchmarking practice would help biomedical researchers leverage this technological expansion to optimize their projects. Several aspects of...

["Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3236v1
30 downloads
113 views

Standard procedures for NGS data analysis involve a pre-processing step of reads quality assessment, followed by the alignment of the filtered reads to a reference genome. Typically the amount of reads that correctly maps to the specific reference genome ranges...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3230v1
14 downloads
144 views

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports...

["Bioinformatics","Genomics","Mathematical Biology"]
doi:10.7287/peerj.preprints.3223v1
42 downloads
181 views

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However,...

["Biotechnology","Genomics","Microbiology","Mycology","Plant Science"]
doi:10.7287/peerj.preprints.3219v1
10 downloads
61 views

Propensities for different amino acids within a protein site change in the course of evolution, so that an amino acid deleterious in a particular species may be acceptable at the same site in a different species. Here, we study the amino acid-changing variants...

["Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3211v1
221 downloads
598 views

RNA sequencing (RNA-Seq) is a powerful technique for thegene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies.Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis,...

["Bioinformatics","Genomics","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2761v2
275 downloads
171 views

Emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring...

["Conservation Biology","Ecology","Genetics","Genomics","Zoology"]
doi:10.7287/peerj.preprints.3209v1
839 downloads
1,982 views

Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated....

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.3090v2
55 downloads
162 views

The USA National Center for Biotechnology Information (NCBI) is one of the world’s most important sources of biological information. NCBI databases like PubMed and GenBank contain millions of records describing bibliographic, genetic, genomic, and medical data....

["Bioinformatics","Genetics","Genomics","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3179v2
11 downloads
119 views

Integrating genomic information into cattle breeding is an important approach to exploring the molecular mechanism for complex traits related to diary and meat production. To assist with genomic-based selection, a reference map of interactome is needed to fully...

["Agricultural Science","Genetics","Genomics"]
doi:10.7287/peerj.preprints.3178v1
28 downloads
158 views

A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases,...

["Evolutionary Studies","Genetics","Genomics","Molecular Biology","Plant Science"]
doi:10.7287/peerj.preprints.3171v1
225 downloads
1,470 views

Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide...

["Bioinformatics","Genomics","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.2278v4
What is a PeerJ Preprint?

A PeerJ Preprint is a draft of an article, abstract, or poster that has not yet been peer-reviewed for formal publication. Submit a draft, incomplete, or final version of your work for free.

Submissions today can be approved by Editorial Staff and online in 24 hours.

Establish precedent. Solicit feedback. Publish updates.

Top subject areas - Preprints

Top subject areas - People

View all subject areas