Preprints (not yet peer-reviewed)

178 downloads
390 views

Background. The availability of large databases containing high resolution three-dimensional (3D) models of proteins in conjunction with functional annotation allows the exploitation of advanced supervised machine learning techniques for automatic protein function...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.2778v1
34 downloads
271 views

Background. The phytohormone jasmonates (JAs) regulate fundamental plant processes; such as the anthocyanin accumulation during ripening of strawberry, a non-climacteric fruit model. Jasmonoyl-isoleucine (JA-Ile), one of the bioactive JA molecules, mediates binding...

["Biochemistry","Bioinformatics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2772v1
104 downloads
428 views

Introduction 2nd generation sequencing or better known as next-generation sequencing (NGS) represents a cutting-edge technology in life sciences and current foundation for unravelling nucleotide sequences. Since advent of first platforms in 2005 the number of different...

["Bioinformatics","Biotechnology","Genomics","Molecular Biology"]
doi:10.7287/peerj.preprints.2771v1
30 downloads
199 views

Knowledge about the three dimensional structure of proteins is crucial in order to learn about their behavior, stability, or role as a target in drug design. Unfortunately, traditional experimental methods used in structure determination such as X-ray crystallography...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2768v1
20 downloads
167 views

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data...

["Bioinformatics","Microbiology"]
doi:10.7287/peerj.preprints.2766v1
185 downloads
431 views

Background RNA sequencing (RNA-Seq) is a powerful technique for transcriptome profiling of the organisms that uses the capabilities of next-generation sequencing (NGS) technologies. Recent advances in NGS let to measure the expression levels of tens to thousands...

["Bioinformatics","Genomics","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2761v1
43 downloads
377 views

Research collaborations are hampered by copyright law. While these laws are aimed at solving sustainability of writing and later other creative processes, and nowadays knowledge too, the make it harder in a time where research is funded with on temporary projects....

["Bioinformatics","Ethical Issues","Legal Issues"]
doi:10.7287/peerj.preprints.2753v1
121 downloads
336 views

Introduction Next Generation Sequencing (NGS) platforms have radically changed the field of genomics and are routinely applied to a variety of functional genomics problems. Although NGS has markedly accelerated multiple areas of genomics research it is a massively...

["Bioinformatics","Genomics","Molecular Biology","Computational Science"]
doi:10.7287/peerj.preprints.2752v1
50 downloads
480 views

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Mycology"]
doi:10.7287/peerj.preprints.2397v2
69 downloads
239 views

The scientific literature contains an historic record of the changing ways in which we describe the world. Shifts in understanding of scientific concepts are reflected in the introduction of new terms and the changing usage and context of existing ones. We conducted...

["Biodiversity","Bioinformatics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2747v1
43 downloads
253 views

The filamentous fungus Rhizopus delemar naturally accumulates relatively high amounts of fumarate. Although the culture conditions that increase fumarate yields are well established, the network underlying the accumulation of fumarate is not yet fully understood....

["Biochemistry","Bioinformatics","Biotechnology","Microbiology"]
doi:10.7287/peerj.preprints.2742v1
108 downloads
271 views

Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN/dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it...

["Bioinformatics","Computational Biology","Evolutionary Studies","Statistics"]
doi:10.7287/peerj.preprints.2739v1
100 downloads
105 views

Drug discovery process plays an important role in identifying new investigational drug-likes and developing new potential inhibitors related to a determinate target, in biopharmaceutical field [1]. An alternative promising and efficient used to identify new active...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2721v1
51 downloads
199 views

The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral...

["Bioinformatics","Computational Biology","Developmental Biology","Plant Science"]
doi:10.7287/peerj.preprints.2724v1
27 downloads
116 views

Structure informs function, and this may be the evolutionary reason why alternative splicing, which is capable of generating different variants of the same protein, arise. But, given the energetic cost of generating different splice variants for testing their capability...

["Biochemistry","Bioinformatics","Genomics","Molecular Biology","Anatomy and Physiology"]
doi:10.7287/peerj.preprints.2717v1
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