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Noah Daniels
PhD. Candidate
Tufts University
Summary
I am a Ph.D. candidate in the Computer Science department at Tufts University. I am working on various problems in computational biology (particularly protein structure prediction and remote homology detection).
My research interests include computational biology, machine learning, algorithms, graph theory, and trying to make the intractable tractable.
In the past, I have been involved with several interesting companies including Analog Devices, IntrinsiQ, Panjiva, andPatientsLikeMe.
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Education
Tufts University
School of Liberal Arts
Bachelor of Science,
Computer Science
(Jan 1999 - May 2001)
Tufts University
Graduate School of Engineering
Master of Science,
Computer Science
(Sep 2002 - Dec 2006)
Tufts University
Graduate School of Engineering
Doctor of Philosophy,
Computer Science
(Jan 2009 - Dec 2012)
Work Experience
Course head & lecturer
Tufts University
Reworked curriculum and taught semester-long course "Exploring computer science," for non-computer science majors. Avera course evaluation 4.6/5.0, instructor evaluation 4.8/5.0.
Research Assistant
Tufts University
(Jan 2009 - Dec 2012)
Doctoral research in computational biology (mostly protein remote homology detection). Software implementations in Ruby, C, and Haskell. Supervised and mentored undergraduate and more junior graduate students.
Director of Data Analysis
Panjiva, Inc.
(Nov 2006 - Jul 2008)
• Responsible for designing and implementing entire architecture, using PostgreSQL and Ruby on Rails, for warehousing, processing, and analyzing US Customs import data.
• Designed and implemented a ratings platform for overseas suppliers, including novel methodolo- gies for determining factors such as customer loyalty and specialization.
• Developed strategy for expanding existing business model across additional industries.
• Designed and implemented a rule-based system for anomaly detection to flag suspicious suppliers.
• Developed Ruby on Rails back-end tied into data warehouse, production data push system, and search engine using Ferret.
• Contributed to Ruby on Rails front-end web interface, including sophisticated AJAX and other Javascript functionality and data visualization.
• Implemented and refined numerous string comparison algorithms, such as Damerau-Levenshtein, Jaro-Winkler, and SoftTFIDF in Ruby and C for corporate approximate record matching.
• Co-authored a provisional patent application (currently pending).
• Collaborated in interviewing and hiring process to build technology team.
Vice President — Research
IntrinsiQ Financial, LLC
(Oct 2004 - Mar 2007)
• Designedandimplementedanartificialneuralnetwork(regression)learningsystemforforecasting the oncology pharmaceutical revenues based on internal usage data. Developed a web interface, in Ruby on Rails, for running and automating pdf output of forecasting reports.
• Performed quantitative analysis and research in the oncology pharmaceutical marketplace, ap- plying machine learning and statistical techniques.
• Designed and implemented a neural network learning system, in Ruby, C, and SQL, for au- tomating the monthly ’scrubbing’ of patient line-of-therapy data previously performed by trained oncology nurses.
• Maintained and enhanced a Java-based application for processing XML data from oncology sites into a data warehouse.
• Collaborated in interviewing and hiring process to build analytics team.
Senior Software Systems Engineer
Analog Devices, Inc.
(Jun 2001 - Oct 2004)
• Supported a large (100+ systems) Unix network centered around a microchip testing and probing operation.
• Implemented Cfengine for centralized management of all Unix systems, improving standardiza- tion of system configurations.
• Led the development of a system for automation of data uploads to a legacy manufacturing database. Designed and implemented fail-safe upload mechanism and data parser in Perl, and managed all aspects of the project.
• Managed several large Perl-based software projects including automation of a software release process.
• Collaborated with engineers from other departments on the development of IS systems, including worldwide test data automation, DNS migration, and system utilization tracking.
• Taught a Perl programming class to engineers at Analog.
• Supervised and mentored one direct report.
Achievements
- Research assistant, Tufts University (Jan 2009 - Dec 2012)
General
Publication Summary
Couch A, Daniels N (2001). The Maelstrom: Network Service Debugging via "Ineffective Procedures", Pro- ceedings of LISA 2001, San Diego, CA.
Zhou W, Wu W, Palmer N, Mower E, Daniels N, Cowen L, Blumer A (2003). Microarray Data Analysis of Survival Times of Patients with Lung Adenocarcinomas Using ADC and K-Medians Clustering, Proceedings of CAMDA 2003, Durham, NC.
Brady A, Maxwell K, Daniels N, Cowen L (2009). Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways, PLoS One 4(4): e5364.
Daniels N, Kumar A, Cowen L, Menke M (2010). Touring Protein Space with Matt, Bioinformatics Research and Applications. Lecture Notes in Computer Science, 2010, Volume 6053/2010, 18-28
Daniels N, Kumar A, Cowen L, Menke M (2011). Touring Protein Space with Matt, IEEE/ACM Trans Comput Biol Bioinform. 2011 Apr 1
Nadimpalli S, Daniels N, Cowen L (2011). Formatt: Correcting Protein Multiple Structural Alignments by Sequence Peeking, Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Aug 2011
Books
Other Publications
