Computer Science Assistant

***F Weill Hall *********@*******.***

Ithaca, NY 14853 ******@****.***.***

Matthew D. Rasmussen http://mattrasmus.com

Education

Massachusetts Institute of Technology

**** ****

Ph.D. in Computer Science

Supervisor: Assoc. Prof. Manolis Kellis

Thesis title: Methods and Analysis of Genome-scale Gene Family Evolution Across Multiple Species

GPA: 4.9/5.0

Massachusetts Institute of Technology

2004 2006

Masters of Science in Electrical Engineering and Computer Science

Supervisor: Assoc. Prof. Manolis Kellis

Thesis title: Probabilistic Framework for Genome-wide Phylogeny and Orthology Determination

Thesis earned the MIT William A. Martin Award for best M.S. thesis in the eld of Computer Science

GPA: 5.0/5.0

University of Minnesota

2000 2004

Bachelor of Science in Mathematics, Bachelor of Science in Computer Science

GPA: 3.872/4.0 (summa cum laude)

UMTYMP (University of Minnesota Talented Youth Math Program), Solar Vehicle Project

Research Experience

Cornell - Biological Statistics and Computational Biology

4/2011 Present Ithaca, NY

Postdoctoral Researcher

Developing models in phylogenetics and population genetics. Supervised by Assoc. Prof. Adam

Siepel.

MIT - Computer Science and Arti cial Intelligence

9/2010 4/2011 Cambridge, MA

Postdoctoral Researcher

Integrated computational models from phylogenetics and population genetics. Supervised by

Assoc. Prof. Manolis Kellis.

MIT - Computer Science and Arti cial Intelligence

2004 2010 Cambridge, MA

Masters Thesis, Ph.D. Thesis

Developed phylogenomic algorithms for analyzing gene duplications and losses in multiple mam-

malian, fungal, and y genomes. Supervised by Assoc. Prof. Manolis Kellis.

Yahoo Research Labs

Summer 2004 Pasadena, CA

Research Intern

Developed prototypes of personalized web search, parallel PageRank, clustered search, and

sparse matrix and graph visualization tools. Supervised by Dr. Leonid Zhukov.

Bioinformatics Summer Institute at University of Minnesota

Summer 2003 Minneapolis, MN

Research Intern

Developed a bootstrap clustering algorithm for use on E. coli microarray data using MANOVA.

University of Minnesota - Computer Science Department

2002 2004 Minneapolis, MN

Undergraduate Research Assistant

Developed gCLUTO, a graphical interface to Prof. George Karypis s CLUTO data clustering library.

Army High Performance Computing Research Center

Summer 2002 Minneapolis, MN

Research Intern

Wrote a frontend and visualizations for the CLUTO data clustering library.

University of Minnesota - Computer Science Department

Spring 2002 Minneapolis, MN

Undergraduate Research Assistant

Wrote C and Perl programs for classifying genes by regulatory sequences in promoters regions.

Publications

1. Wu, Rasmussen, Bansal, Kellis. TreeFix: statistically informed gene tree error correction using species trees.

Systematic Biology, accepted.

2. Choi, Rasmussen, Hubisz, Gronau, Stanhope, Siepel. Replacing and additive horizontal gene transfer in Strep-

tococcus. Molecular Biology and Evolution. 2012.

3. Rasmussen, Kellis. Uni ed modeling of gene duplications, losses, and coalescence using a locus tree. Genome

Research. 2012.

4. Bergwitz, Rasmussen, DeRobertis, Wee, Sinha, Chen, Huang, Perrimon. Roles of Major Facilitator Superfamily

Transporters in Phosphate Response in Drosophila. PLoS One. 2012.

5. Wu, Rasmussen, Kellis. Evolution at the sub-gene level: gene architecture rearrangements in the Drosophila

phylogeny. Molecular Biology and Evolution. 2011.

6. Lindblad-Toh, Garber, Zuk, Lin, Parker, Washietl, Kheradpour, Ernst, Jordan, Mauceli, Ward, Lowe, Holloway,

Clamp, Gnerre, Alfoldi, Beal, Chang, Clawson, Cuff, Di Palma, Fitzgerald, Flicek, Guttman1, Hubisz, Jaffe, Jun-

greis, Kent, Kostka, Lara, Martins, Massingham, Moltke, Raney, Rasmussen, Robinson, Stark, Vilella, Wen, Xie,

Zody, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Worley, Kovar, Muzny, Gibbs,

Baylor College of Medicine Human Genome Sequencing Center, Warren, Mardis, Weinstock, Wilson, Genome

Institute at Washington University, Birney, Margulies, Herrero, Green, Haussler, Siepel, Goldman, Pollard, Peder-

sen, Lander, Kellis. A high-resolution map of evolutionary constraint in the human genome based on 29 eutherian

mammals. Nature. 2011.

7. Rasmussen, Kellis. A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction. Molecular Biology

and Evolution. 2010.

8. Organ, Rasmussen, Baldwin, Kellis, and Edwards. A Phylogenomic Approach to the Evolutionary Dynamics of

Gene Duplication in Birds. In Evolution After Gene Duplication. (Eds.) K. Dittmar and D. Liberles. Wiley & Sons.

2010.

9. Butler, Rasmussen, Lin, Santos, Sakthikumar, Munro, Rheinbay, Grabherr, Forche, Reedy, Agra oti, Arnaud,

Bates, Brown, Brunke, Costanzo, Fitzpatrick, de Groot, Harris, Hoyer, Hube, Klis, Kodira, Lennard, Logue,

Martin, Neiman, Nikolaou, Quail, Quinn, Santos, Schmitzberger, Sherlock, Shah, Silverstein, Skrzypek, Soll,

Staggs, Stans eld, Stumpf, Sudbery, Thyagarajan, Zeng, Berman, Berriman, Heitman, Gow, Lorenz, Birren, Kel-

lis, Cuomo. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459: 657-662.

2009.

10. Lin, Deoras, Rasmussen, Kellis. Performance and Scalability of Discriminative Metrics for Comparative Gene

Identi cation in 12 Drosophila Genomes. PLoS Comput Biol. 2008.

11. Rasmussen, Kellis. Accurate gene-tree reconstruction by learning gene- and species-speci c substitution rates

across multiple complete genomes. Genome Research 17: 1932-1942. 2007.

12. Stark, Lin, Kheradpour, Pederson, Parts, Carlson, Crosby, Rasmussen, Roy, Deroas, Ruby, Brennecke, FlyBase

curators, Berkeley Drosophila Genome Project, Hodges, Hinrichs, Caspi, Paten, Park, Han, Maeder, Polansky,

Robson, Aerts, vanHelden, Hassan, Gilbert, Eastman, Rice, Weir, Hahn, Park, Dewey, Pachter, Kent, Haussler,

Lai, Bartel, Hannon, Kaufman, Eisen, Clark, Smith, Celniker, Gelbart, Kellis. Discovery of functional elements in

12 Drosphila genomes using evolutionary signatures. Nature 450: 219-232. 2007.

13. Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature

450: 203-218. 2007.

14. Rasmussen, Deshpande, Karypis, Johnson, Crow, and Retzel. wCLUTO: A Web-Enabled Clustering Toolkit.

Plant Physiology. 2003.

15. Rasmussen and Karypis. gCLUTO: An interactive clustering, visualization, and analysis system. University of

Minnesota Technical Report #04-021. 2004.

Talks

1. 9/2012. Genome Sciences, University of Washington. Seattle, WA.

Bayesian Models for Genome-wide Analysis of Phylogenies and Populations.

2. 9/2012. Fred Hutchinson Cancer Research Center. Seattle, WA.

Bayesian Models for Genome-wide Analysis of Phylogenies and Populations.

3. 11/2011. Guest lecturer for BTRY 4840/6840 Computational Genomics. Cornell, NY.

Gene trees and species trees.

4. 11/2011. Guest lecturer for 6.878/6.047 Computational Biology. MIT, MA.

Phylogenetics, Population Genetics, and Genomes.

5. 12/2010. NIMBioS Working Group: Inferring Patterns and Processes of Gene Diversi cation by Reconciling

Gene Trees and Species Trees. Knoxville, TN.

Gene families undergoing duplications, losses, and coalescence.

6. 11/2010. Guest lecturer for 6.878/6.047 Computational Biology. MIT, MA.

Phylogenetics, Population Genetics, and Genomes.

7. 6/2010. Bertinoro Computational Biology. Bertinoro, Italy.

Reconciliation of duplications, losses, and coalescence.

8. 2/2010. MBI: Inference in Stochastic Models of Sequence Evolution. Ohio State, OH.

Bayesian reconstruction of gene families.

9. 11/2009. Guest lecturer for 6.878/6.047 Computational Biology. MIT, MA.

Algorithms for Phylogenomics.

10. 7/2009. Quest for Orthologs. Wellcome Trust Sanger Institute, Hinxton, UK.

Ef cient Bayesian Reconstruction and Reconciliation of Thousands of Gene Family Phylogenies Across Multiple

Complete Genomes.

11. 4/2007. Genome Analysis Program. Broad Institute of MIT and Harvard, MA.

Phylogenomics of mammalian, y, and fungal genomes.

12. 10/2005. Meetings on Genome Informatics. Cold Spring Harbor Laboratory, NY.

Multiple genome phylogeny for ortholog and paralog detection.

Teaching Experience

6.878/6.047 and 6.895/6.085 Computational Biology: Genomes, Networks, Evolution

Fall 2006, 2008 MIT

Teaching Assistant

Developed course materials including lectures, homework assignments, midterms, and nals. Led

weekly recitations.

Univeristy of Minnesota - Institute of Technology Center for Education (ITCEP)

Summer 2003 MN

Teaching Assistant

Worked with gifted middle and high school students for several math, science, and engineering

summer programs at the University of Minnesota. Responsibilities included teaching and tutoring.

Software Developed

DLCoal (Duplications, Losses, and Coalescence) - Phylogenetic software.

http://compbio.mit.edu/dlcoal

SPIMAP (SPecies Inferred Maximum A Posteriori Reconstruction) - Phylogenetic software.

http://compbio.mit.edu/spimap

SPIDIR (SPecies Inferred DIstance-based Reconstruction) - Phylogenetic software.

http://compbio.mit.edu/spidir

gCLUTO - Graphical clustering toolkit

http://glaros.dtc.umn.edu/gkhome/views/cluto; http://mattrasmus.com/umn/gcluto

SUMMON - Scienti c visualization prototyping and scripting library.

http://mattrasmus.com/summon

KeepNote - Cross-platform note-taking and organization software.

http://keepnote.org

Honors & Awards

Cornell Center for Comparative and Population (3CPG) Genomics Fellowship (2011)

William A. Martin Award for best M.S. thesis in the eld of Computer Science (2006)

Ruth L. Kirschstein National Research Service Award (2004-2007)

Barry M. Goldwater Scholarship (2003)

CRA Outstanding Undergraduate Award, Honorable Mention (2003) Frank Louk Scholarship (2003) Lando Scholarship

(2002), Ella Thrope Math Scholarship (2001, 2002, 2003), Math Undergrad Scholarship (2001), Iron Range Scholarship

(2001), IT Honors Undergraduate Research Assistant Scholarship (2001), Minnesota Technology, Inc. Scholarship

(2001, 2002)

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