State University Computer Science

Location:

Seattle, WA

Posted:

March 08, 2016

Contact this candidate

Resume:

Myron Peto

503-***-****

*********@*******.***

https://www.linkedin.com/in/mpeto

Relevant Skills/Experience

o10+ years of experiences in applied data science, bioinformatics, computational biology and next-generation DNA sequence.

oWorked with Intel to design 200+ node cluster specific to the needs of the cancer research community at OHSU.

oActively collaborating with CS group at UCLA and Intel to improve genomics software used to process and analyze DNA sequencing.

oSkilled in machine learning and modeling of complex biological phenomena.

o8+ years experience in the health care industry. Deep background in genetics, molecular biology, cancer genetics and genomics.

oProgramming languages: C/C++, perl, Galaxy, Condor, SGE, unix scripting, python, R, FORTRAN, SQL scripting, HADOOP.

Employment History

Oregon Health Sciences University (OHSU), Portland, OR, 6/2011-Present

Senior Research Associate I process and analyze next-generation DNA sequence data. In this capacity I call mutations in cancer samples, both exome and whole genome. Those mutations can be used to characterize tumor types and can also be used to inform treatment options for cancer patients. I also collaborate with computer scientists to work on improvements in bioinformatics tools for processing DNA sequence data. I present my work to disparate groups with diverse backgrounds and manage many projects simultaneously. I use perl, R, Galaxy, C/C++, python, unix scripting, condor queue manager.

Kaplan, Portland, OR, 3/2010-2011

MCAT instructor I taught courses that prepared students to take the MCAT, the GRE and the SAT. This involved reviewing content in biology, physics, chemistry and organic chemistry. I tutored

Waldorf College, Forest City, IA 1/2010-2011

Adjunct Professor I taught several online genetics courses.

Iowa State University/USDA, Ames, IA 10/2007-10/2009

Post-doctoral scientist Research focusing on the soybean genome, including aiding in the final assembly of the scaffolds, inferring ancestral states of the genome, and comparing the soybean genome against other sequenced plant genomes. I used machine learning techniques to discover patterns in nucleosomic DNA. Advisor was Randy Shoemaker.

Iowa State University, Ames, IA 8/2002-8/2007

Pre-doctoral fellow Research focusing on the relationship between amino acid sequence and 3-D protein structure. I used reduced lattice models of proteins to discover traits of designable protein structures – those that are more likely to be found by natural selection. I used machine-learning tools to classify and predict which sequences are likely to fold to designable structures. Advisor was Robert Jernigan.

OHSU, Portland, OR, 7/2000-7/2002

DBA Planned, maintained, and phased out various database applications, implemented procedures for better maintenance of the server group, setup various Oracle environments for classes and applications, applied patches and helped move forward with an 11i upgrade

Microsoft Inc., Issaquah, WA, SQL Server DBA 2/1999-5/1999

Database Inc., Seattle, WA, SQL Server DBA 7/1998-2/1999

Education

2002–2007 Ph.D in Bioinformatics and Computational Biology, Iowa State University

Thesis: “Studies of protein designability using reduced models”

Advisor: Robert Jernigan

1989-1994 BS in Biochemistry, University of Washington, Seattle

Publications

“A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes”

TCGA Publishing

Nature Communications (In Submission)

“Patient-specific factors influence somatic variation patterns identified by whole genome sequencing of independent tumors from von Hippel-Lindau disease”

Suzi Fei et. al.

Cancer Discovery (In Submission)

“A Comprehensive Multicenter Comparison of Whole Genome Sequencing Pipelines using a Uniform Tumor-normal Sample Pair”

Ivo Buchhalter et. al.

Nature Communications (In submission)

“Gauging NOTCH1 Activation in Cancer Using Immunohistochemistry”

Michael Kluk, et. al.

PLOS One (2013)

“Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences”

Myron Peto, David Grant, Randy C. Shoemaker, and Steven B. Cannon

Advances in Bioinformatics (2010)

“Genome sequence of the palaeopolyploid soybean”

Jeremy Schmutz, http://www.nature.com/nature/journal/v463/n7278/abs/nature08670.htmlet. al.

Nature (2010)

“Using machine learning algorithms to classify binary hydrophobic/polar protein sequences folding to highly-designable and poorly-designable structures”

Myron Peto, Andrzej Kloczkowski, and Robert L. Jernigan

BMC Bioinformatics (2008)

“Shape-dependent designability studies of lattice proteins”

Myron Peto, Andrzej Kloczkowski, and Robert L. Jernigan

J. Phys.: Condens. Matter (2007)

“Computer generation and enumeration of compact conformations within simple geometries on the 2D triangular and 3D fcc lattices”

Myron Peto, Andrzej Kloczkowski, Taner Sen, and Robert L. Jernigan

J. Chem. Phys. (2007)

Conference/Symposium Presentations

-NSF InTrans report (April 2015 short talk) Title: “Comparing alignments of an exome sample on accelerated and traditional architecture”

-NSF InTrans report (Oct 2014 short talk) Title: “Sequence alignment/assembly space.”

-NSF InTrans report (July 2014 short talk) Title: “Introduction to Cancer

genetics/sequencing”

-TCGA Scientific Symposium (May 2014 Poster Presentation) Title: “Profiling and Comparing two DNA Sequence Alignment Pipelines”

-Plant and Animal Genome XVII (Jan 2009 Poster Presentation) Title: “Repeat Array Characterization of the Soybean Genome”

-12th Biennial Molecular and Cellular Biology of the Soybean Conference (2008 Poster presentation) Title: “Applying small-scale genomic signatures as an aid in assembling soybean linkage groups”

-Plant and Animal Genome XVI (Jan 2008 20 minute talk) Title: “Syntenic Regions of the Soybean Genome”

-MCCMB 2007 (Moscow Conference on Computational Molecular Biology) (20 minute talk) Title: “Using machine learning algorithms to classify designable and non-designable binary H/P protein sequences”

-The 2006 ISMB Conference on Intelligent Systems in Fortaleza, Brazil (Poster presentation) Title: “Protein Designability in the 2-D Triangular Lattice Model ”

-The Workshop on Structure and Function of Biomolecules in Poznan, Poland (Poster presentation) Title: same as above

-The 2006 Biophysics Conference in Salt Lake City, Utah (Poster presentation)

Teaching Experience

-I taught several online genetics courses for Waldorf College.

-I taught MCAT, GRE and SAT prep courses for Kaplan

-I was a teaching assistant (TA) for “Fundamentals of Genome Informatics” for which I designed the homework, came up with a course project, generated exams, did all the grading, and lectured when needed.

-I was a TA for the summer Bioinformatics Institute (2006) where I led lab sessions and helped with the administration of the program.

-I was a TA for a year for a beginning algorithms course in the computer science department. In this context I led recitations, designed exam problems, graded homework, and lectured when necessary.

Rotation Labs

-Dr. Eulenstein: Inverse protein folding (IPF) – tested sequences designed against the real sequences to see where problem spots were and/or improvements could be made. Tested buried and exposed residues, residues in the heme pocket of a globin protein, and also residues of each of the 20 amino acids

-Dr. Andreotti: Searched for likely candidates for a proline switch from a likely motif

-Dr. Dobbs: Classified software that estimates the domain boundaries for a given protein sequence

References

Dr. Paul Spellman

********@****.***

6N020 CLSB, OHSU

2730 SW Moody Ave

Portland, OR 97201

503-***-****

Dr. Jason Cong (Collaborator)

****@**.****.***

UCLA Computer Science Department