Yulia Newton yulia.newton@gmail.com Ph.D. in Bioinformatics and Biomolecular Engineering candidate University of California Santa Cruz M.S. in Bioinformatics and Biomolecular Engineering University of California Santa Cruz B.S. in Computer Science with minor in Mathematics San Jose State University

Background

Previous Research

• Classification of human centromeric sequences - Spring 2012
  Completed this project as a part of rotating in the Haussler Lab under the guidance of Dr. Karen Hayden, postdoc, and Distinguished Professor David Haussler. Published in Genome Research ("Centromere reference models for human chromosomes X and Y satellite arrays", Miga et al.).


• Discovery of Master Regulators in Basal vs. Luminal Breast Cancer - Winter 2012
  Completed this project as a part of rotating in the Stuart Lab under the guidance of Professor Josh Stuart. Presented the results of this work during the poster session at the 20th International Conference on Intelligent Systems for Molecular Biology (ISMB), July 2012


• Evidence of biased gene conversion in 1000 genomes trio data - Fall 2011
  Completed this project as a part of rotating in the Green Lab under the guidance of Professor Richard Green. Presented the results of this work during the poster session at the Biomedical Computation at Stanford conference (BCATS) in November, 2011

• Building and visualizing drug interaction networks. Was able to predict previously unknown drug interactions using the resulting network. I presented the results of this project in a porster presentation at The California State University Program for Education and Research in Biotechnology (CSUPERB) in January, 2011.
• Developed prokaryotic gene predictor for Escherichia coli genome using Hidden Markov Models.
• Developed global protein aligner using Needleman-Wunsch algorithm and local protein aligner using Waterman-Smith algorithm. For an alignment of a set of transmembrane proteins, computed custom PAM30, PAM50, PAM120, and PAM150 transmembrane substitution matrices.
• Implemented a genome assembler using De Bruijn graphs.
• Performed statistical analysis of microarray expression data for ten healthy patients and ten patients affected by Muscular Distrophy. The results revealed heavy up-regulation of genes TUBB6 and COL1A2 in MD patients. This finding has been confirmed in the literature.

Publications, Conferences, Posters and Presentations

• "Linear sequence models of human centromeric DNA" publication, Genome Research, January 2014
• "Discovery of master regulators in basal breast cancer" poster presentation at the 20th International Conference on Intelligent Systems for Molecular Biology (ISMB), July 2012
• "Evidence of biased gene conversion in 1000 genomes trio data" poster presentation at the Biomedical Computation at Stanford conference, November 2011
• "Building and visualizing compound-target interaction networks" poster presentation at the refereed symposium The California State University Program for Education and Research in Biotechnology, January 2011

Awards

• Spring 2012 - Awarded recognition of exemplary academic achievement by the Dean of College of Science at San Jose State University for the academic year 2010-2011.
• Spring 2011 - Awarded recognition of exemplary academic achievement by the Dean of College of Science at San Jose State University for the academic year 2009-2010.
• Summer 2010 - Was one of only ten students selected from the whole Computer Science and Computer Engineering departments to spend July and part of August of 2010 studying various computational topics at The School of Business and Engineering Vaud (HEIG-VD) in Yverdon-les-Bains, Switzerland.

Graduate-level courses completed

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