Preprints (not yet peer-reviewed)

8 downloads
91 views

While the benefits of undergraduate research experiences (UREs) are recognized for undergraduates, the advantages of UREs for graduate students, post-doctoral scholars, and faculty are not clearly outlined. The analysis of genomic data is particularly well-suited...

["Bioinformatics","Genomics","Science and Medical Education"]
doi:10.7287/peerj.preprints.3149v1
3 downloads
44 views

We present in this article a lightweight ontology named PGxO and a set of rules for its instantiation, which we developed as a frame for reconciling and tracing pharmacogenomics (PGx) knowledge. PGx studies how genomic variations impact variations in drug response...

["Bioinformatics","Artificial Intelligence","Data Mining and Machine Learning","Databases","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.3140v1
95 downloads
462 views

Species diversity of metazoan bulk samples can be rapidly assessed using cytochrome c oxidase I (COI) metabarcoding. However, in some applications often only degraded DNA is available, e.g. from poorly conserved museum specimens, environmental DNA (eDNA) filtered...

["Biodiversity","Bioinformatics","Molecular Biology"]
doi:10.7287/peerj.preprints.3037v2
76 downloads
211 views

Metabarcoding and metagenomic approaches are becoming routine techniques in biodiversity assessment and ecological studies. The assignment of taxonomic information to sequences is challenging, as many reference libraries are lacking information on certain taxonomic...

["Biodiversity","Bioinformatics","Ecology","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3133v1
12 downloads
93 views

Bacterial surfaces are complex, built of from membranes, peptide-glycans and, importantly, proteins. The proteins play crucial roles as the key regulator of how the bacterium interacts with its environment. A full catalog of the motifs in coiled-coil proteins and...

["Bioinformatics","Infectious Diseases","Data Science"]
doi:10.7287/peerj.preprints.3118v1
21 downloads
143 views

Analysis of DNA microarray data has been very useful for experimental molecular biology, as it provides unprecedented opportunities to study a wide variety of biological processes. As a part of this analysis, biclustering has been consolidated as one of the first...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3110v2
15 downloads
109 views

LuxS is commonly found in various bacterial species, like A. hydrophila which causes infection in fish, shrimps, and prawns and is a great threat to aquaculture industry as well as public health. It is an essential enzyme and highly conserved in various bacterial...

["Bioinformatics","Microbiology"]
doi:10.7287/peerj.preprints.3109v1
33 downloads
157 views

Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmodial data. The package categorizes data into one of three categories,...

["Bioinformatics","Computational Biology","Mathematical Biology","Statistics","Data Science"]
doi:10.7287/peerj.preprints.3116v1
23 downloads
192 views

We present PIsCO, a server-side JavaScript framework for the collection, registration and sharing of metrics that can be used to evaluate the impact of bioinformatics-related resources such as software, repositories, training or databases. The metrics framework...

["Bioinformatics","Computer Architecture","Software Engineering"]
doi:10.7287/peerj.preprints.3112v1
1,898 downloads
19,238 views

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent...

["Bioinformatics","Legal Issues","Science and Medical Education","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.3100v1
21 downloads
143 views

We have developed a machine learning approach to predict context specific enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3093v1
559 downloads
1,425 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.3090v1
153 downloads
765 views

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2452v4
12 downloads
190 views

Human papillomavirus type 16 (HPV16) is the most carcinogenic HPV, causing >50% of cervical cancers. Its unique oncogenicity is unsolved, e.g., the second most carcinogenic type (HPV18, causing ~16% of cancers) is relatively distantly related to HPV16. Mirabello...

["Bioinformatics","Evolutionary Studies","Infectious Diseases","Oncology","Women's Health"]
doi:10.7287/peerj.preprints.3070v1
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