Sumaiya

Nazeen
77 Massachusetts Avenue, 32-G570
Ph.D. Candidate in EECS Cambridge, MA 02139
Computer Science and Artificial Intelligence Laboratory (CSAIL) Email: nazeen@mit.edu, Ph: +1 (857) 206-2195
Massachusetts Institute of Technology (MIT) Website: http://nazeen.csail.mit.edu/

Education

Ph.D. in Computer Science Fall 2014 – Present

Massachusetts Institute of Technology (MIT) CGPA: 5.00/5.00
Computation and Biology Group
Department of Electrical Engineering & Computer Science (EECS)
Advisor: Professor Bonnie Berger, Ph.D.
Thesis: Computational Methods for Functional Interpretation of
Diverse Omics Data
Minor: Corporate Finance (MIT Sloan School of Management)

S.M. in Computer Science 2012 – 2014
Massachusetts Institute of Technology (MIT) CGPA: 5.00/5.00
Computation and Biology Group
Department of Electrical Engineering & Computer Science (EECS)
Advisor: Professor Bonnie Berger, Ph.D.
Thesis: Integrative analysis of heterogeneous genomic datasets to
discover genetic etiology of autism spectrum disorders

B.Sc. in Computer Science & Engineering 2011
Bangladesh University of Engineering & Technology (BUET) CGPA: 4.00/4.00
Algorithm Engineering, Design & Analysis Group (AlEDA) Rank: 1/138 (CSE)
Department of Computer Science & Engineering (CSE)
Advisor: Professor M Sohel Rahman, Ph.D.

Current Research Interests

• Role of Microbiome in Human Health and Diseases

• Integrative Omics Analyses for Complex Human Diseases
• Personalized Medical Omics

Areas of interest: Machine Learning, Combinatorial Optimization

Selected Honors and Awards

• Ludwig Center Molecular Oncology Graduate Fellowship, 2015-16

Koch Institute of Integrative Cancer Research, MIT, USA
• International Fulbright Science & Technology Fellowship, 2012-15
Bureau of Educational and Cultural Affairs (ECA), U.S. Department of State
• Prime Minister’s Gold Medal, 2011 (for outstanding results in the Bachelor’s level)
University Grants Commission, Bangladesh
• Chancellor’s Award, BUET, 2011 (for securing highest CGPA in the University)
Bangladesh University of Engineering & Technology (BUET), Bangladesh
 • Departmental Gold Medal, 2011 (highest CGPA in the Department of CSE, BUET)
Bangladesh University of Engineering & Technology (BUET), Bangladesh
• Dean's List award in every year of undergraduate studies at BUET, 2006-10
Bangladesh University of Engineering & Technology (BUET), Bangladesh
• University Merit Scholarship in all semesters at BUET, 2006-10
Bangladesh University of Engineering & Technology (BUET), Bangladesh

Publications

JOURNAL PUBLICATIONS:

[1] Nazeen, S., Yu, Y. W., and Berger, B. Carnelian uncovers hidden functional patterns across diverse study
populations from whole metagenome sequencing reads. (under review at Genome Biology)

[2] Nazeen, S.†, Palmer, N.P.†, Berger, B., and Kohane, I.S. Integrative analysis of genetic datasets reveals a shared
innate immune component in autism spectrum disorder and its co-morbidities. Genome Biology, 17:1(2016) 228
(† Co-first authors)

[3] Moosa, T.M., Nazeen, S. †, Rahman, M.S., and Reaz, R. †, Inferring Strings from Cover Arrays, Discrete
Mathematics, Algorithms and Applications, 5.02 (2013) 1360005 (Author names in alphabetical order)

[4] Nazeen, S., Rahman, M.S., and Reaz, R. †, Indeterminate String Inference Algorithms, Journal of Discrete
Algorithms, 10 (2012) 23-34

CONFERENCE PROCEEDINGS/TALKS:

[5] Nazeen, S. and Berger, B. Carnelian: alignment-free functional binning and abundance estimation of
metagenomic reads. ECCB 2018. Applications Track. Athens, Greece (2018)

[6] Moosa, T.M., Nazeen, S., Rahman, M.S., Reaz, R., Linear Time Inference of Strings from Cover Arrays using a
Binary Alphabet. Rahman and Nakano (eds.) WALCOM 2012. LNCS, vol. 7157, pp. 160-172. Springer, Heidelberg
(2012)

POSTERS AND ABSTRACT SUBMISSIONS:

[8] Nazeen, S., Singh, R., Berger, B.A., LAPRAS: An integrative model incorporating heterogeneous datasets to
discover genetic etiology of autism spectrum disorder, ISMB/ECCB, Dublin, Ireland (2015) (one of the 36 posters
selected for oral presentation among ~600 accepted posters)

[9] Nazeen, S., Berger, B.A., Integrative Analysis of Multiple Gene Expression Studies Reveals Genes and Pathways
involved in Alteration of Steroidogenesis in Polycystic Ovary Syndrome (PCOS), ECCB, Strasbourg, France (2014)

INVITED TALKS:

[1] Nazeen, S. Uncovering hidden functional patterns across diverse study populations from whole metagenome
sequencing reads with Carnelian. ACM-BCB: Workshop on Microbiomics, Metagenomics, and
Metabolomics, September 2019 (forthcoming)

[2] Nazeen, S. Carnelian: enhanced functional profiling for whole genome metagenomics. Frontiers in Microbiota
Interactions Symposium, Harvard Medical School, 2018
[3] Keynote Speech at the Workshop on Women Empowerment through ICT: Higher Studies, Research and
Career, Road to Grad Schools Abroad: Guidelines & Advices, Bangladesh University of Engineering &
Technology, Dhaka, Bangladesh, June 2014

Research and Teaching Experience

• Research Assistant at MIT Computation and Biology Group under supervision of Prof. Bonnie Berger,
September 2013 – Present
• Remote Associate Researcher, Broad Institute of MIT and Harvard, Cambridge, MA, USA, January 2013 –
Present
• Teaching Assistant to Prof. Bonnie Berger, 18.418: Topics in Computational Molecular Biology, Spring
2017
• Research Assistant (Rotation) at MIT Computation and Biology, Computational Genomics, and
Computational Biology Groups under supervision of Prof. Bonnie Berger, Prof. Manolis Kellis, and Prof.
David K. Gifford, September 2012 – August 2013
• Lecturer at Department of Computer Science and Engineering, Bangladesh University of Engineering
and Technology, March 2011 – August 2012
• Associate Sub-project Manager, Enhancement of Graduate Studies Facilities for the Department of CSE,
BUET, Higher Education Quality Enhancement Project, AIF Round-II (A project aided by World Bank), 2012

Membership and Social Affiliations

• Member, International Society for Computational Biology, February 2014 – Present

• Member, Association for Computing Machinery, 2018 – Present
• EECS Departmental Representative, Graduate Women at MIT (GWAMIT), September 2013 – June 2019
• Advisor, Bangladeshi Students Association at MIT (MIT BSA), June 2016 – June 2019
• President, Bangladeshi Students Association at MIT (MIT BSA), June 2015 – May 2016
o was awarded “Engineering Community Award” by Office of Multicultural Programs at MIT
• Member, International Students Council at MIT (Representative for Bangladesh), June 2015 – May 2016
• Co-President, Graduate Women’s Group in EECS, MIT (GW6), January 2015 – December 2015
• Treasurer, Bangladeshi Students Association at MIT (MIT BSA), June 2013 – May 2015
o was awarded “Organization of the Year Award” by Office of Multicultural Programs at MIT
• Vice President, Bangladeshi Students Association at MIT (MIT BSA), September 2012 – May 2013
o was awarded “Excellence in Programming Award” by Office of Multicultural Programs at MIT
• Member, Holy Cross College Alumni Association

Extracurricular Activities

• 1st Runner Up, EECS GSA Logo Design Competition, MIT (2014)
• Volunteer for MIT GSC Orientation Events (2013)
• Instructor for Special Sunday School at Parkside Elementary School, Atlanta, GA (2013)
• 1st Runner Up, Women's Singles Badminton Tournament, CSE Day'07 organized by Department of CSE,
BUET, 2007
• 1st Runners Up, Science Fair, 27th National Science & ICT Week, Tejgaon - Ramna Thana Zone, Dhaka
Division, 2004
• 2nd Runners Up, Quiz Competition, Josephite Festival organized by St. Joseph High School & College, 2004

References available upon request.