Final Report Summary - INTRON42 (Evolution of eukaryotic intron splicing)
** Summary of progress: research project
*** Evolution of intron boundaries in eukaryotic genes
The project's research component aimed at examining the evolution of eukaryotic gene structure, especially by scrutinizing point mutations near intron splice sites. In an exploratory study during the first half of the Fellowship, we examined intron evolution in oomycetes. Our analysis highlighted severe shortcomings in existing genome annotations for the purposes of evaluating splice site homologies between orthologous genes. The insight from the analysis also suggested a more robust algorithmic approach towards a joint modeling of splice site homology and intron gain by different means. The findings are published as an open-access journal article, and the developed software package is available for download.
*** Scientific collaboration with local research group
During the tenure of the Fellowship, I developed a collaboration on a method for diagnosing aneuploidy from next-generation sequencing of cell-free fetal DNA. In particular, I helped designing and evaluating multiple rounds of pilot experiments while mentoring a Masters student and closely collaborating with a post-doctoral researcher in Lajos Haracska's research group at the Institute of Genetics. Based on the results, we plan to carry on the project to refine the methodology.
** Summary of progress: transfer of knowledge
*** Graduate class on computational genomics
In Spring 2015, I held a graduate course at the Szeged University, entitled "Informatikai módszerek a genomikában" (Computational methods in genomics), with the participation of 3 doctoral students in Computer Science. The course material was developed in Hungarian, and covered a basic introduction to genomics, as well as contemporary methods for assembly, annotation, comparison and variation analysis. The material was posted regularly on the class website at http://szegedinfogenom2015.wordpress.com.
*** Hands-on genome annotation course
In Spring 2016, I taught a university course on computer-aided genome annotation for biology majors at the University of Szeged. The class was quite popular (attracted 36 students in 2 sessions, including undergraduates at the university and graduate students in the Biological Research Centre's programs). My main objective was to provide hands-on training mixing biology (genomics, molecular genetics, and cellular biology) with bioinformatics skills (including basic Linux literacy, programming, use of Web services and appropriate software).
For this class, we sequenced two strains of Agrobacteria, assembled their genomes and annotated their genes and other features. Each week, we discussed a particular bioinformatics problem or biological aspect, coupled with the adequate computer tools and mathematical techniques. The class was held in a computer laboratory, so that the students - working in pairs - can have hands-on experience with the techniques, while performing actual research activities (i.e. annotating and interpreting the genomes). The class notes (in Hungarian) are available at the site https://szagenann2016.wordpress.com. As a didactic experiment, I mounted the course with a dedicated "genome wiki" (custom bilingual Mediawiki backed by MySQL, where students added their observations to articles on annotated genes) and genome browser (JBrowse): these are available from the course web server at running on Amazon Web Services. I found that the students' work was remarkably good. The students felt that the course helped them acquire the basic bioinformatics competences (based on surveys at the beginning and the end of the course, asking their self-assessment in different skills).
I am in the process of finalizing the genome assemblies and annotations for public release.
*** Evolution of intron boundaries in eukaryotic genes
The project's research component aimed at examining the evolution of eukaryotic gene structure, especially by scrutinizing point mutations near intron splice sites. In an exploratory study during the first half of the Fellowship, we examined intron evolution in oomycetes. Our analysis highlighted severe shortcomings in existing genome annotations for the purposes of evaluating splice site homologies between orthologous genes. The insight from the analysis also suggested a more robust algorithmic approach towards a joint modeling of splice site homology and intron gain by different means. The findings are published as an open-access journal article, and the developed software package is available for download.
*** Scientific collaboration with local research group
During the tenure of the Fellowship, I developed a collaboration on a method for diagnosing aneuploidy from next-generation sequencing of cell-free fetal DNA. In particular, I helped designing and evaluating multiple rounds of pilot experiments while mentoring a Masters student and closely collaborating with a post-doctoral researcher in Lajos Haracska's research group at the Institute of Genetics. Based on the results, we plan to carry on the project to refine the methodology.
** Summary of progress: transfer of knowledge
*** Graduate class on computational genomics
In Spring 2015, I held a graduate course at the Szeged University, entitled "Informatikai módszerek a genomikában" (Computational methods in genomics), with the participation of 3 doctoral students in Computer Science. The course material was developed in Hungarian, and covered a basic introduction to genomics, as well as contemporary methods for assembly, annotation, comparison and variation analysis. The material was posted regularly on the class website at http://szegedinfogenom2015.wordpress.com.
*** Hands-on genome annotation course
In Spring 2016, I taught a university course on computer-aided genome annotation for biology majors at the University of Szeged. The class was quite popular (attracted 36 students in 2 sessions, including undergraduates at the university and graduate students in the Biological Research Centre's programs). My main objective was to provide hands-on training mixing biology (genomics, molecular genetics, and cellular biology) with bioinformatics skills (including basic Linux literacy, programming, use of Web services and appropriate software).
For this class, we sequenced two strains of Agrobacteria, assembled their genomes and annotated their genes and other features. Each week, we discussed a particular bioinformatics problem or biological aspect, coupled with the adequate computer tools and mathematical techniques. The class was held in a computer laboratory, so that the students - working in pairs - can have hands-on experience with the techniques, while performing actual research activities (i.e. annotating and interpreting the genomes). The class notes (in Hungarian) are available at the site https://szagenann2016.wordpress.com. As a didactic experiment, I mounted the course with a dedicated "genome wiki" (custom bilingual Mediawiki backed by MySQL, where students added their observations to articles on annotated genes) and genome browser (JBrowse): these are available from the course web server at running on Amazon Web Services. I found that the students' work was remarkably good. The students felt that the course helped them acquire the basic bioinformatics competences (based on surveys at the beginning and the end of the course, asking their self-assessment in different skills).
I am in the process of finalizing the genome assemblies and annotations for public release.