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Examples of data from previous years

  • I plan to reconstruct the phylogeny of neotropical Ficus sect. Pharmacosycea by using nuclear regions publicly available in GenBank (e.g., ITS, ETS, G3pdh), and previously used by Pederneiras et al. (2015) and Machado et al. (2018). The phylogenetic tree will aid in clarifying species concepts in this widely cryptic clade through phylogenetic comparative methods.

  • I plan to work on the phylogeny of genus Frasera from Gentianaceae using the sequences available on GenBank. There are 15 species in this genus and there are 54 sequences available.

  • I am interested in reconstructing the phylogeny of a group of Hawaiian Lobeliads, Clermontia (Fig.1), by using whole plastomes and a few single copy nuclear genes. The data were not published and were provided by my lab group. Data have been assembled (Karimi et al. 2020) but for the purpose of learning I have raw data to conduct quality control. This project might reveal how this fast radiating plant group evolved and potentially estimate drivers for diversification of this lineage.

  • I am interested in analysing homologous proteins across transposon insertion sequencing studies. Data will be collected from genome data from NCBI. Bacterias: Vibrio fischeri, Acinetobacter baumanii, Vibrio cholerae, Bacteroides thetaiotaomicron, Porphyromonas gingivalis, Pseudomonas aeruginosa, Staphylococcus aureus and many others.

  • I am looking at the methyltransferase gene family in the copepod E. affinis and related arthropods such as D. melanogaster. This data is coming from online databases like GenBank and i5k. Homologs have been identified through the use of BLAST against known genes on the E. affinis genome.

  • The Min System is a mechanism composed of three proteins MinC, MinD, and MinE used by E. coli as a means of properly localizing the septum prior to cell division. Each component participates in generating a dynamic oscillation of FtsZ protein inhibition between the two bacterial poles to precisely specify the mid-zone of the cell, allowing the cell to accurately divide in two. This system is known to function in conjunction with a second negative regulatory system, the nucleoid occlusion system (NO), to ensure proper spatial and temporal regulation of chromosomal segregation and division. I just downloaded first 500 sequences of this gene from NCBI.