Lucas D. Ward

Postdoctoral Associate
Computational Biology Group
Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology
32 Vassar St., 32-D526
Cambridge, MA 02139
luke ward at mit dot edu

Links: Twitter - LinkedIn - Facebook - Google Scholar



I am a postdoctoral researcher in Manolis Kellis's computational biology group at MIT. I have a long-standing interest in the evolution of regulatory DNA and how regulatory sequences vary among individuals, and I am currently exploring the relationship between cross-mammalian conservation, human diversity, and epigenetic marks. My graduate work was completed in Harmen Bussemaker's regulatory genomics lab at Columbia, where I studied regulatory evolution in yeast and transcription factor colocalization in yeast and fly, earning my Ph.D. in biology in 2010. My dissertation and defense are available to download. I completed a B.S. in chemistry with specialization in biochemistry from the University of Virginia in 2004.

I enjoy teaching. For two summers, I taught a physics course for premed students in Columbia's SMDEP program; the materials I developed are here (please let me know if you are interested in using them) and a selection of my teaching evaluations are here. My experience also includes helping to design a new personal genomics seminar at MIT, and serving as a teaching assistant for the summer undergraduate research program at Columbia, bioinformatics programming lab sections at Columbia and CSHL, and a biology and evolution course for non-majors at Columbia.

When I studied clarinet, my teachers were Marguerite Levin, Steve Barta, Paul Cigan, and Nancy Garlick, and I have played in CUSO and CUO. I am always interested in opportunities to play; you can listen to my portfolio here

Curriculum Vitae

Research Interests

My background spans both experimental molecular biology and comparative and functional genomics of model organisms and humans. I am currently interested in the sequences in the human genome that dictate tissue-specific chromatin structure and gene expression: their evolution on the mammalian lineage, their patterns of variation among human populations, and the phenotypic diversity they generate.

Publications

2012

Ward LD and Kellis M. Interpreting noncoding genetic variation in complex traits and human disease. Nature Biotechnology, 30: 1095-1106.

Ward LD and Kellis M. Evidence of abundant purifying selection in humans for recently-acquired regulatory functions. Science, 337: 1675-78.

The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature, 489: 57-74.

Ward LD and Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. (Database is here.) Nucleic Acids Res., 30: D930-4.

2011

Lindblad-Toh K, Garber M*, Zuk O*, Lin MF*, Parker BJ*, Washietl S*, Kheradpour P*, Ernst J*, Jordan G*, Mauceli E*, Ward LD*, Lowe CB*, Holloway AK*, Clamp M*, Gnerre S*, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, and Kellis M. A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478: 476-82.

The ENCODE Project Consortium. A user's guide to the Encyclopedia of DNA Elements (ENCODE). PLos Biology, 9: e1001046.

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, and Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473: 43-49.

2010

Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, and van Steensel B. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell, 143: 212-24.

2008

Ward LD and Bussemaker HJ. Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics, 24: i165-71.

2007

Bussemaker HJ, Ward LD, and Boorsma A. Dissecting complex transcriptional responses using pathway-level scores based on prior information. BMC Bioinformatics, 8: S6.

Bussemaker HJ, Foat BC, and Ward LD. Predictive modeling of genomewide mRNA expression: from modules to molecules. Ann. Rev. Biophys. Biomol. Struct., 36: 329-47.

2006

Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, and van Steensel B. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA., 103: 12027-32.

Presentations

2012

Poster, RECOMB-Regulatory Genomics, San Francisco, CA

Poster, ASHG, San Francisco, CA

Talk, Washington University Department of Psychiatry, St. Louis, MO

Poster, CSHL-Biology of Genomes, Cold Spring Harbor, NY

Talk, Wellcome Trust annual meeting on Genomic Disorders, Hinxton, UK

2011

Poster, ASGH/ICHG, Montreal, QC

Talk, Connecticut College Department of Chemistry, New London, CT

Poster, CSBB annual meeting on Systems Biology of Human Disease, Boston, MA

Poster, ENCODE-modENCODE Consortia Meeting, Arlington, VA

Poster, CSHL-Biology of Genomes, Cold Spring Harbor, NY

2010

Poster, RECOMB-Regulatory Genomics, New York, NY

Poster, CSHL-Systems Biology, Cold Spring Harbor, NY

2008

Talk, ISMB, Toronto, ON

Poster, CSHL-Biology of Genomes, Cold Spring Harbor, NY

2007

Talk, RECOMB-Regulatory Genomics, Cambridge, MA

Poster, CSHL-Systems Biology, Cold Spring Harbor, NY

Teaching

2012

Guest Lecture, Course 6.878: Computational Biology
MIT Department of Electical Engineering and Computer Science, Cambridge, MA

2012

Guest Lecture, OEB 275r: Phylogenomics, Comparative Genomics and Adaptation
Harvard University Department of Organismal and Evolutionary Biology, Cambridge, MA

2012

Teaching Assistant, Course 6.881: Computational Personal Genomics
MIT Department of Electical Engineering and Computer Science, Cambridge, MA

2009

Teaching Assistant, CHBC W4510: Molecular Systems Biology
Columbia University Department of Biological Sciences, New York, NY

2008-2009

Physics Instructor, Summer Medical and Dental Education Program
Columbia University Medical Center, New York, NY

2006-2007

Section Head, Summer Undergraduate Research Fellowship
Columbia University Department of Biological Sciences, New York, NY

2006-2007

Teaching Assistant, Integrated Data Analysis for High-Throughput Biology (summer course)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

2006

Teaching Assistant, BIOL W3037/4037: Bioinformatics of Gene Expression
Columbia University Department of Biological Sciences, New York, NY

2005

Teaching Assistant, BIOL C1015: Molecular Biology and Evolution for Nonscientists.
Columbia University Department of Biological Sciences, New York, NY

Awards

2008

ISMB Outstanding Student Paper Award
Awarded anually in memory of Ian Lawson Van Toch

2006

James Howard McGregor prize for teaching
Columbia University Department of Biological Sciences

Research Experience

2010-present

Postdoctoral Associate, Massachusetts Institute of Technology, Cambridge, MA
Laboratory of Manolis Kellis, CSAIL
Integrative analysis of human population genetic and functional epigenomics data.

2005-2010

Graduate Research Assistant, Columbia University, New York, NY
Laboratory of Harmen Bussemaker, Department of Biological Sciences
Biophysical and evolutionary modeling from high-throughput sequence, expression, and binding data.

2005

Rotation Student, Columbia University, New York, NY
Laboratory of Iva Greenwald, Department of Biochemistry
Genetics of cell-cell signaling in C. elegans. Performed genetic crosses and microscopy supporting a project studying the SEL-2 protein.

2004

Rotation Student, Columbia University, New York, NY
Laboratory of Virginia Cornish, Department of Chemistry
Chemical biology. Performed organic syntheses relating to the development of a novel protein-labeling technique.

2003

Summer Student, New York University, New York, NY
Laboratory of Joel Belasco, Department of Microbiology
Protein-mediated mRNA degradation pathways. Performed RNA-binding assays on a variant of HIV-1 Rev protein being used for structural studies.

2002-2003

Undergraduate Research Assistant, The University of Virginia, Charlottesville, VA
Laboratory of Ann Beyer, Department of Microbiology
Assisted with cytological studies of hnRNPs in D. melanogaster.

2002

Summer Student, National Institute of Standards and Technology, Rockville, MD
Laboratory of Gary Gilliland, CARB (now Institute for Bioscience and Biotechnology Research)
Perfomed crystallization screens on hypothetical proteins from H. influenzae.

1999

Summer Student, U.S. Naval Research Laboratory, Washington, DC
Laboratory of Matthew Mauro, Center for Biomolecular Science and Engineering
Cloned and purified engineered E. coli thioesterase vesicles.

1998

Summer Student, Connecticut College, New London, CT
Laboratory of Bruce Branchini, Department of Chemistry
Assisted in subcloning supporting a site-directed mutagenesis study of firefly luciferase.

Education

2010

Ph.D., Biological Sciences, Columbia University, New York, NY
Advisor: Harmen J. Bussemaker
Thesis: Biophysical and evolutionary genomic analysis of non-canonical transcription factor binding

2007

M.Phil., Biological Sciences, Columbia University, New York, NY

2006

M.A., Biological Sciences, Columbia University, New York, NY

2004

B.S., Chemistry, University of Virginia, Charlottesville, VA
Specialization in Biochemistry (A.C.S.)
Completed B.A. program in Music, awarded High Distinction

Skills

Programming: Perl, R/Bioconductor
Molecular biology: Basic molecular cloning techniques in E. coli and S. cerevisiae, protein purification, screening for protein crystallization, light and confocal microscopy in C. elegans, immunohistochemistry in D. melanogaster

Professional Societies

Sigma Xi
National Postdoctoral Association
National Association of Gay and Lesbian Scientists and Technical Professionals
American Association for the Advancement of Science
International Society for Computational Biology

Community

Peer Advocate, GHAP/Columbia University Health Services (2007-2010)
Judge, NYC and NYS Science and Engineering Fairs (2007-2009)
Graduate Editor-in-chief, Columbia Undergraduate Science Journal (2007)
Clarinetist, Columbia University Orchestra (2005-2009)