Curriculum Vitae

Scott J. Emrich

Current Address

Department of Computer Science and Engineering

University of Notre Dame

*** *********** ****, ***** ****, IN 46556

Phone: 574-***-****; Email: abo1as@r.postjobfree.com

Homepage: http://www.nd.edu/~semrich

Education

2007 Ph.D. Bioinformatics and Computational Biology Iowa State University

2002 B.S. Biology and Computer Science Loyola College in Maryland

Academic Experience

Academic Appointments

University of Notre Dame

8/2007{present Assistant Professor, Dept. of Computer Science and Engineering

International

Indian Institute of Technology (IIT), Bombay

Fall 2006 Visiting Scholar, Kanwal Rekhi School of Information Technology

Affiliations

2008-present Eck Institute for Global Health, University of Notre Dame

Honors and Awards

2010 Invited and participated in 2010 Indo-American Frontiers of Engineering Symposium,

National Academy of Engineering

2008 Iowa State University Zaffrano Prize for Graduate Research

2007 Iowa State University Research Excellence Award

2006 Electrical and Computer Engineering Research Excellence, Iowa State University

Invited Presentations

2/15/12 Challenges and opportunities of non-model informatics

CANGS bioinformatics conference, Las Vegas, NV

3/17/11 Ecoinformatics: Algorithms and challenges

Invited seminar, Michigan State University

1/27/11 Scalable computing for ecoinformatics

Invited bioinformatics seminar, Indiana University Bloomington

6/21/10 Challenges of modern bioinformatics

Invited Panelist, Emerging Computational Methods for the Life Sciences workshop, HPDC'10

6/11/10 Bioinformatics for arthropod gene discovery. 4th Annual Arthropod Genomics Sympo-

sium, Kansas City, MO.

10/14/09 Enabling, cost-effective bioinformatics analysis for arthropod genomics, 1st

International

Workshop on Information Systems for Insect Pests, Rennes, France, November 2009 (joint

INIRA/INRA workshop).

3/2/09 Sequencing your favorite genome for $1000

Invited Seminar, Biomedical Research Workshop

University of Notre Dame

2/20/09 Recent advances inAn. gambiae genome analysis

Invited talk, African Virtual Conference on Bioinformatics (Afbix '09)

4/10/08 Lean on me: Comparative Anopheles genomics

Invited Seminar, Workshop on Interdisciplinary Biomedical Research

University of Notre Dame and Indiana University School of Medicine

3/26/07 Maize genome assembly on IBM BlueGene/L

Invited Seminar, Animal Breeding and Genetics

Iowa State University

10/18/06 Massively parallel plant genomics

Invited Seminar, Interdepartmental Plant Physiology

Iowa State University

1/12/04 A strategy for assembling the maize genome

Plant & Animal Genome XII Bioinformatics Workshop, San Diego CA

External Support

Current

F. Collins (PI): VectorBase: An NIAID Bioinformatics Resource Center for Invertebrate

Vectors of Human Pathogens. National Institutes of Health. $14,671,665 (5 years; Emrich

scientific manager and co-PI, 50% effort)

P. Clark (PI): Synonymous Codon Usage as a Predictive Tool for Disease Susceptibility,

$9600. Indiana Clinical and Translational Sciences Institute.

Course Experience

CSE40532/60532 Bioinformatics Computing, Fall 2008 + 2010

{ developed from scratch

CSE20212 Fundamentals of Computing, Spring 2008{2012

{ Outcomes based on Prof. Flynn's previous version but lectures redone

CSE40833/60833 Introduction to Parallel Algorithms and Programming, Fall 2007 + 2009

{ Text based on comprehensive lecture notes by Prof. Aluru at ISU, otherwise redeveloped

Current Graduate Students

Shawn O'Neil PhD candidate; joined 2009 (Schmidt Fellow, Global Health Fellow)

Andrew Rider PhD candidate; joined 2008 (Global Health Fellow; coadvised with Nitesh

Chawla)

Wei Zhang PhD in progress; joined 2010

Irena Lanc PhD in progress; joined in 2009

Andrew Thrasher PhD in progress; joined in 2009

Lauren Assour PhD in progress; joined in 2010

(Naughton Fellow, coadvised by Ken Wolfe at Trinity College Dublin)

Rory Carmichael MS in progress; joined 2011

Undergraduate Research Assistants

Brian KachmarckSummer 2010{present

Paul Baranay

Summer 2010{presentTheses Supervised

2011 Allison A.P. Regier

"A flexible comparative genomics framework for integrating heterogeneous sequence data"

Doctoral Thesis, Computer Science and Engineering, University of Notre Dame

2010 Benjamin Drda

"Hive: an alignment tool for distributed systems"

Honors Thesis. Undergraduate Engineering Honors, University of Notre Dame

2009 Michael R. Olson

"New methods for assembly and validation of large genomes"

Master's Thesis, Computer Science and Engineering, University of Notre Dame

2008 Allison A.P. Regier

"Challenges in working with draft genomes,"

Master's Thesis, Computer Science and Engineering, University of Notre Dame

Graduate Student Alumni

Alison Regier 2007{2011 (Presidential Fellow); currently a research scientist at WashU

(St. Louis)

Michael Olson 2007{2009 ; currenly software architect for CenterX

Undergraduate Research Alumni

Pengqui Cheng (Tsinghua) 2011

Sicong Zhang (Tsinghua) 2011

Benjamin Drda2007{2010

Steven Bohlson2009 (Indiana University - South Bend)

University Service

University2011{presentCo-director, Genomics and Bioinformatics Core Facility (GBCF)

2008{2011 Director, Bioinformatics Core Facility (BCF)

Departmental Committees

2007{2010 Graduate Studies Committee

2008{present Curriculum Committee

Student Committees

CSE: Scott Christley (2008 PhD), Chris Moretti (2010 PhD), Ryan Kennedy (2010 PhD), Darcy

Davis (2011 PhD), Ryan Connaughton (2011 PhD), Li Yu, James Gentile

Biology: Jenica Abrudan, Changde Cheng, Masha Unger, Derrick Parker, Jihyun Won

Outside chair: 1 former student (AME), 4 collaborative (Biology), 4 university request

Service at Iowa State University

2006 BCB Graduate Curriculum Committee, which redesigned the PhD core curriculum in

bioinformatics and computational biology.

Professional Memberships

International Society for Computational Biology (ISCB)

Association for Computing Machinery (ACM)

Institute of Electrical and Electronics Engineers (IEEE)

External Service Activities

Steering Committee Member

2010{2012 Arthropod Genomics Symposium

Program Chair

2012 Emerging Computational Methods for the Life Sciences workshop

ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC)

2011 Parallel Bio-Computing Workshop

International Conference on Parallel Processing and Applied Mathematics

Program Committee Member

2011{2012 IEEE International Conference on Computational Advances in Bio and medical

Sciences

(ICCABS)

2010{2011 IEEE International Conference on Cloud Computing Technology and Science

(CloudCom)

2009{2012 International Conference on Bioinformatics and Computational Biology (BiCoB)

2009{2012 Using Emerging Parallel Architectures for Computation Science Workshop

International Conference on Computational Science

2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine

2011 ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC)

2010 Workshop on Parallel Programming and Applications on Accelerator Clusters, IEEE

Cluster

2007{2011 Parallel Bio-Computing Workshop

International Conference on Parallel Processing and Applied Mathematics

2009, 2011 International Conference on Contemporary Computing, Applications

2008-2009 IEEE/ACM Supercomputing (SC), Applications

2008 HICOMB Workshop, IEEE International Parallel and Distributed Processing Symposium

(IPDPS)

2008 ACS/IEEE International Conference on Computer Systems and Applications (AICCSA)

Tutorials

2007 Computational Problems in Maize Genomics

International Conference on Computational Systems Bioinformatics (CSB)

2006 Exploring Computational Biology with a Massively Parallel

High Performance Computing Environment

International Conference on Intelligent Systems for Molecular Biology (ISMB)

Professional Committees

Education Committee

International Society for Computational Biology (ISCB)

Recent reviewer for the following journals:

Bioinformatics

Nucleic Acids Research

BMC Bioinformatics

BMC Genomics

Heredity

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