Preprints (not yet peer-reviewed)

4 downloads
30 views

Predicting disease status for a complex human disease using genomic data is an important, yet challenging, step in personalized medicine. Among many challenges, the so-called curse of dimensionality problem results in unsatisfied performances of many state-of-art...

["Bioinformatics","Computational Biology","Genomics","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.27123v1
34 downloads
65 views

The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it recognized that early-life microbiota acquisition is a pivotal event for later life health. Recent studies show that gut microbiota diversity and functional activity...

["Agricultural Science","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.27120v1
22 downloads
61 views

The WD40 gene family in Prunusmume was identified by bioinformatics analysis., The evolution and function of WD40 gene family were predicted by phylogenetic analysis, chromosome localization analysis, protein sequence analysis, exon-intron structure analysis. The...

["Biotechnology","Genetics","Genomics"]
doi:10.7287/peerj.preprints.27106v1
130 downloads
214 views

Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular...

["Biodiversity","Entomology","Genomics","Microbiology","Virology"]
doi:10.7287/peerj.preprints.27093v1
68 downloads
94 views

With the popularization of the CRISPR-Cas gene editing system there has been an explosion of new techniques made possible by this versatile technology. However, the computational field has lagged behind with a current lack of computational tools for developing...

["Bioinformatics","Genomics","Synthetic Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.27094v1
103 downloads
397 views

The success of personalized medicine does not only rely on methodological advances but also on the availability of data to learn from. While the generation and sharing of large data sets is becoming increasingly easier, there is a remarkable lack of diversity within...

["Genomics","Neuroscience","Ethical Issues","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.27079v1
19 downloads
89 views

Background. DNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative regulation in the promoter region. However, its correlation with gene expression at population level has not been well studied....

["Bioinformatics","Computational Biology","Genomics","Epidemiology","Statistics"]
doi:10.7287/peerj.preprints.27055v1
56 downloads
99 views

Symbiotic relationships between host and microbiome can play a major role in local adaptation. Previous studies with freshwater organisms have shown that microbiome performs numerous important biochemical functions for the host, playing a key role in metabolism,...

["Evolutionary Studies","Genomics","Microbiology","Freshwater Biology"]
doi:10.7287/peerj.preprints.27058v1
105 downloads
251 views

The rhizobium-legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating...

["Computational Biology","Genetics","Genomics","Microbiology","Synthetic Biology"]
doi:10.7287/peerj.preprints.27033v2
227 downloads
609 views

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome,...

["Biodiversity","Evolutionary Studies","Genomics","Taxonomy"]
doi:10.7287/peerj.preprints.27035v1
66 downloads
200 views

Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous...

["Animal Behavior","Ecology","Ecosystem Science","Genomics","Freshwater Biology"]
doi:10.7287/peerj.preprints.27032v1
68 downloads
154 views

There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this...

["Bioinformatics","Genomics","Population Biology"]
doi:10.7287/peerj.preprints.27017v1
622 downloads
1,251 views

Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to...

["Bioengineering","Biotechnology","Cell Biology","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.26821v2
270 downloads
766 views

Horizontal gene transfer has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that horizontal gene transfer (HGT) between non-animals...

["Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3462v3
199 downloads
399 views

Bacteria and other microbes play a crucial role in human health and disease. Medicine and clinical microbiology have traditionally attempted to identify the etiological agents that causes disease, and how to eliminate them. Yet this traditional paradigm is becoming...

["Ecology","Evolutionary Studies","Genomics","Infectious Diseases","Translational Medicine"]
doi:10.7287/peerj.preprints.26969v2
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