PPT-Bacteriophage Gene Clustering and Phylogeny

Nicholas Celms San Diego State University Funded in part by NSF 0827278 UBM Interdisciplinary Training in Biology and Mathematics 1 Goal Build a method for making taxonomic groupings of bacteriophages. Khansa. . Bukhari. Maryum. . Zeb. . History and Definition. Frederick . Twort. (1915) and Felix . d'Herelle. (1917) were the first to recognize bacteriophage.. In the 1930s and after words virologists utilized these viruses as model systems to investigate many aspects of virology. Yvonne. . Lin. . AP. . Bio. . 2. a.k.a. Phages. Bacterial . VIRUS. Attacks, infects, and replicates within bacteria. Discovered. . by. . Frederick. . Twort. . (Great. . Britain, 1915). Species specific – named after the group or species it infects. Beth . Benas. Rizwan. . Habib. Alexander . Lowitt. Piyush. . Malve. Contents. What is Gene Clustering?. Two or more genes that code for the same or similar products. Two different processes for duplication of original genes via: . Phylogenies. The process of evolution produces a pattern of relationships between species. . As . lineages evolve and split and modifications are inherited, their evolutionary paths diverge. . This . Phylogeny. The evolutionary history of a species or group of species. . Convergent Evolution. A process in which species from different evolutionary branches may come to resemble each other if they live in similar environments and natural selection favored similar adaptions.. and Physical Interaction . Datasets. Manikandan Narayanan, Adrian Vetta, Eric E. Schadt, Jun Zhu. PLoS Computational Biology 2010. Presented by: Tal Saiag. Seminar in Algorithmic Challenges in Analyzing Big Data* in Biology and . Systematics. Phylogeny. Phylon. = tribe, . geny. . = genesis or origin. The evolutionary history of a species or a group of related species.. Investigating the Tree of Life. Phylogeny: the evolutionary history of a species or group of species. Welkin Pope. SEA-PHAGES In . Silico. Workshop. , 2014. Virion structural and assembly genes. , i.e. those encoding proteins that are either components of virion particles or assist in their formation. These include genes encoding the . Welkin Pope. SEA-PHAGES Bioinformatics Workshop, . 2016. Virion structural and assembly genes. , i.e. those encoding proteins that are either components of virion particles or assist in their formation. These include genes encoding the . Machine . Learning . 10-601. , Fall . 2014. Bhavana. . Dalvi. Mishra. PhD student LTI, CMU. Slides are based . on materials . from . Prof. . Eric Xing, Prof. . . William Cohen and Prof. Andrew Ng. Tandy Warnow. The University of Illinois at Urbana-Champaign. Brief history. We met in 1992, when I was working in the Discrete Algorithms Group at Sandia National Labs.. I moved to the University of Pennsylvania in 1993, then to the University of Texas at Austin in 1999. No papers yet. Johanne Ahrenfeldt . PhD Student. Overview. What is Phylogeny? . How has it been used in the past?. Advantages of WGS based phylogeny. - Vibrio . cholerae. . case. BREAK. How are we using it?. CSI phylogeny & . Log. 2. transformation. Row centering and normalization. Filtering. Log. 2. Transformation. Log. 2. -transformation makes sure that the noise is independent of the mean and similar differences have the same meaning along the dynamic range of the values.. . Streptomycetaceae. Alan Ward. Motivation. Streptomyces . taxonomy. 16S. Whole genome sequencing. A bigger 16S phylogeny. Where is the diversity. The type strains.