Education
M.S./Ph.D. in Computer Science
Concentration: Computational & Systems Biology
B.S. in Biology and Computer Science, summa cum laude
Senior Thesis, Awarded Highest Honors: "Formatt: Correcting Protein Multiple Structural Alignments by Sequence Peeking" [pdf]
› All Coursework:
Computer Science
- Intro to Comp. Sci.
- Data Structures
- Web Programming
- Computer Architecture
- Programming Languages
- Intro to Machine Learning
- Protein Bioinformatics
- Stochastic Search & Genetic Algorithms
- Algorithms
- Advanced Algorithms
- Computation Theory
- Computational Biology
- Directed Study
- Senior Honors Thesis
Other
- Advanced Power Yoga
- Muscle Conditioning
Biology
- Intro to Biotechnology
- General Genetics
- Cells & Organisms
- Organisms & Populations
- Human Genetics
- Microbiology
- Plant Physiology
- Evolutionary Ecology
- Seminar in Molecular Biology & Genetics
- Independent Research
Chemistry
- Chemistry I
- Chemistry II
Math
- Calculus I
- Calculus II
- Calculus III
- Calculus IV
- Discrete Math
Language/Culture (English, French, Arabic)
- Intro to Literature
- Writing in the Professions
- Expository Writing
- The Social Web
- Human Sexual Behavior
- Elementary French II
- Intermediate French I
- Arabian Nights
Art
- Creative Writing: Fiction
- Early Islamic Art
- Adobe Photoshop
Religion
- Intro to Philosophy & Religion
- The Literary Qur'an
- Intro to Hinduism
Honors, Awards, & Fellowships
The purpose of the NSF Graduate Research Fellowship Program (GRFP) is to help ensure the vitality and diversity of the scientific and engineering workforce in the United States. The program recognizes and supports outstanding graduate students who are pursuing research-based master's and doctoral degrees in fields within NSF's mission. The GRFP provides three years of support for the graduate education of individuals who have demonstrated their potential for significant achievements in science and engineering research. The ranks of NSF Fellows include individuals who have made transformative breakthroughs in science and engineering research and have become leaders in their chosen careers and Nobel laureates.
The Wu Fellowships are Princeton's most prestigious award for graduate study in engineering and are made to new graduate students who demonstrate the potential to be world leaders in their fields in the 21st century. Wu Fellows are awarded four years of full financial support, including full tuition and a premium stipend. In addition, the award provides funds that can be used by the student for research expenditures and for travel to international professional conferences.
Google hopes to encourage women to excel in computing and technology and become active role models and leaders in the field. Google Anita Borg Memorial Scholarships are awarded to a group of female undergraduate and graduate students based based on the strength of each candidate's academic background and demonstrated leadership. Scholarship recipients will each receive a $10,000 award for the upcoming school year.
The Neubauer Scholars Program was founded in 2000 by Joesph Neubauer (E'63). The program was established to encourage intellectually gifted young men and women who have the initiative, curiosity, and drive to become future scholars and campus leaders at Tufts. At its heart, the program intends to enhance the scholars' ability to engage in critical thinking and to help them mature into future leaders in their chosen professions. While the intellectual climate at Tufts will greatly contribute to the enrichment of these scholars, their presence on campus, reciprocally, will enhance the intellectual climate of the Tufts community at large.
When students begin the application process, the Admissions Department identifies and recruits Neubauer Scholars to Tufts. The Neubauer Scholarship replaces students' federal and university loans with grant money for four years of undergraduate education, and awards a grant of $3500 to be used toward research expenses and academic enrichment opportunities.
The James Schmolze Prize is awarded annually to a graduating senior who has demonstrated excellence in computer science studies.
The Prize Scholarship of the Class of 1882 honors an undergraduate student with great potential for intellectual leadership and creativity. This prize was founded in the name of his class by Dr. Arthur Winslow Peirce, A'82, Litt.D'99.
The Audrey Butvay Gruss Science Award is awarded annually to a Tufts undergraduate who has demonstrated outstanding academic achievement in any of the sciences, and includes a $2500 scholarship prize. This award was established in 1992 by Audrey Butvay Gruss, an alumna of Jackson College.
The objective of the Distributed Research Experiences for Undergraduates (DREU) is to increase the number of women and underrepresented groups entering graduate studies in the fields of computer science and engineering. This highly selective program matches promising undergraduate women and underrepresented groups with a faculty mentor for a summer research experience at the faculty member's home institution. Students are directly involved in a research project and interact with graduate students and professors on a daily basis.
The goal of the Multidisciplinary Research Opportunities for Women (MRO-W) initiative is to involve undergraduate students in collaborative, multidisciplinary research creating and using cyberinfrastructure, and to allow women computer science undergraduates to investigate applications of computer science to other areas in which they may have an interest and to serve as a catalyst for forming new multidisciplinary partnerships. Teams of undergraduates from both computing and non-computing fields will work during the academic year and potentially the following summer at their home institutions. The women students will each receive a stipend of $3,000 for their work during the academic year and $4,000 during the summer. Each project may also request up to $1,500 to be used for special equipment, travel, or supporting materials.
- Unfortunately, the MRO-W program is no longer accepting applications.
- More information about the MRO-W program (2008-2010)
The Bioinformatics Summer Institute program provides an opportunity for exceptionally talented students who are interested in pursuing a career in bioinformatics to participate in a comprehensive research and learning experience.
Students will partake in an extensive 3-week education program consisting of courses bridging molecular life sciences and computer sciences to achieve a common goal. They will then have a unique opportunity to work with leading scientists and subsequently apply their knowledge towards a mentored state-of-the-art research project of their choice for the following 7-8 weeks.
- Unfortunately, the SoCalBSI program is no longer accepting applications.
- More information about the SoCalBSI program (2003-2009)
Research & Work Experience
Investigating the evolution of transcriptional regulatory networks through analysis of variation in Cys2-His2 zinc finger genes in Drosophila sp. and primates.
› "Formatt: Correcting Protein Multiple Structural Alignments by Sequence Peeking"
Abstract.
We present Formatt, a multiple protein structural alignment program that also takes sequence similarity into account when constructing alignments. We show that Formatt is superior to Matt, a purely geometric structural aligner, based on objective measures (e.g. Staccato Seq and Str scores). Advantages in core length and RMSD that Matt, a flexible structural aligner, has as compared to other multiple structural alignment programs is preserved.thesis · paper · poster 1 · poster 2 · presentation
› "Cataloging Retrocopies for Retrotransposition Model"
Abstract.
Existing retrocopy-identification algorithms are fine-tuned for specific genomes and rely heavily on annotation information, making extensive and sensible retrocopy comparison between species difficult. We present here an annotation-independent algorithm for identifying retrogenes, retropseudogenes, and chimeric genes in any animal genome, and summarize some major difficulties in identifying retrocopies in a large-scale study.webpage · paper · poster
› "Modeling the Neuro-mechanical Control of a Soft-Tissue Organism"
Abstract.
The intrinsic non-linear properties of soft materials make the control of an entirely soft-bodied robot difficult and computationally expensive. We demonstrate the accuracy of using PhysX, a fast physics rendering engine, to create a virtual model of the neuro-mechanical control of a SoftBot. We then present methods utilizing genetic algorithms to evolve a solution, representing the firing of the nervous system, that elicits locomotion in the model. webpage · paper
› "Discovery of Novel Metabolic Types of Bacterial Micro-compartments"
Abstract.
Bacterial micro-compartments (BMCs) in prokaryotes are analogous to organelles in eukaryotes in that they compartmentalize related proteins to increase the efficiency of metabolic processes. We present a pipeline to discover new BMCs in the ocean and human gut metagenomes. We first search for BMC shell protein domains, and then cluster neighboring (i.e. encapsulated) proteins by metabolic function. Potentially two novel BMC types were discovered.presentation
Set up a secure database containing all clinical and research reports for all drugs produced or under testing.
› "Identification of Genes Involved in Expansion of Chromosomal Repeat in E. coli"
Abstract.
A particular strain of E. coli with a damaged lac operon has the ability, when grown on lactose-minimal plates, to amplify its damaged operon 100s of times in a poorly-understood process known as "gene amplification," producing enough partially-defective protein to survive. We systematically knocked out various genes and measured subsequent bacterial vitality, in order to identify genes such as recN with a significant effect on gene amplification. paper
Peer-Reviewed Publications
Nadimpalli, S., Daniels, N., Cowen, L. (2011). "Formatt: Correcting Protein Multiple Structural Alignments by Sequence Peeking." Proceedings of the 2011 ACM Conference on Bioinformatics, Computational Biology, and Biomedicine. 2:315-319. [pdf]
Presentations, Posters, & Panels
Panelist: Graduate School Application Process and Visit Experience
Poster: "Formatt: Correcting Protein Structural Alignments by Sequence Peeking" [png]
Oral Presentation: "Formatt: Correcting Protein Structural Alignments" [mov]
Student Volunteer
Poster: "Taking a Peek at the Seq: Improving Matt Protein Structural Alignments by Considering Sequence Homology" [png]
Poster: "Cataloging Animal Retrocopies: An Annotation-Independent Methodology" [png]
Teaching Experience
TA for CS40: Machine Structure & Assembly Language Programming (Fall 2009)
TA for CS80: Programming Languages (Spring 2010)
Attended lectures, assisted in labs, held office hours (~10-18 hours/week), and graded assignments.
HHMI ARRAYS Project Programmer & Instructor
Analyzed Illumina sequencing output to discover new soil microbes, and taught bioinformatics seminars to Somerville High students about gene sequencing, alignment algorithms, and BLAST.