Computer Science Medical

Sanmitra Bhattacharya

*** ******** ****, ******: 785-***-****

Contact

Apt 6, e-mail: ********-************@*****.***

Information

Iowa City, Iowa 52246 http://www.cs.uiowa.edu/ sbhttcha/

Natural Language Processing, Text Mining, Web Mining, Data Mining, Data Analytics, Information

Research

Retrieval, Statistical Modeling and Analysis, Health Informatics, Bioinformatics.

Interests

PhD in Computer Science (Graduate Certificate in Health Informatics),

Education

University of Iowa, Iowa City, Iowa, USA May 2014(expected)

BTech in Computer Science and Engineering,

West Bengal University of Technology, Kolkata, West Bengal, India August 2008

Bhattacharya S, Cantor MN: “Analysis of Eligibility Criteria Representation in Industry-standard

Selected

Clinical Trial Protocols” Journal of Biomedical Informatics, Volume 46, Issue 5, October 2013, pp.

Publications

805-813, ISSN 1532-0464, doi: 10.1016/j.jbi.2013.06.001

Toldo L, Bhattacharya S, Gurulingappa H: “Text Analytics for the Detection of Drug Safety Events

from Case Reports.” Drug Safety Journal, Volume 35, Issue 1, 2012. pp. 1197-1198.

Bhattacharya S, Tran H, Srinivasan P: “Discovering Health Beliefs in Twitter.” In Proceedings of

AAAI 2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text;

Nov 2-4, 2012; Arlington, Virginia, USA.

Bhattacharya S, Srinivasan P: “A Semantic Approach to involve Twitter in LBD Efforts.” In

Proceedings of The First International Workshop on the role of Semantic Web in Literature-Based

Discovery (SWLBD 2012), The IEEE International Conference on Bioinformatics and Biomedicine

(BIBM 2012); Oct 4-7 2012; Philadelphia, PA, USA.

Bhattacharya S, Toldo L: “Question Answering for Alzheimer Disease using Information Retrieval.”

In Proceedings of Question Answering for Machine Reading Evaluation Lab, Conference and Labs of

the Evaluation Forum (CLEF) 2012 ; September 17-20 2012 ; Rome, Italy.

Yang C, Bhattacharya S, Srinivasan P: “Lexical and Machine Learning approaches toward Online

Reputation Management.” In Proceedings of RepLab, Conference and Labs of the Evaluation Forum

(CLEF) 2012 ; September 17-20 2012 ; Rome, Italy.

Toldo L, Bhattacharya S, Gurulingappa H: “Automated Identification of Adverse Events from Case

Reports using Machine Learning.” In Proceedings of Computational Methods in Pharmacovigilance,

24th European Medical Informatics Conference (MIE 2012); August 26th -29, 2012; Pisa, Italy.

Bhattacharya S, Tran H, Srinivasan P, Suls J: “Belief Surveillance with Twitter.” In Proceedings

of Fourth ACM Web Science Conference (WebSci 2012); June 22-24, 2012; Northwestern University,

Evanston, IL, USA.

Bhattacharya S, Ha-Thuc V, Srinivasan P: “MeSH: a window into full text for document sum-

marization.” Proceedings of the 19th Annual International Conference on Intelligent Systems for

Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011);

Vienna, Austria. Bioinformatics 2011 27: i120-i128.

Arighi CN, Roberts P, Agarwal S, Bhattacharya S, Cesarini G, Chatr-aryamontri A, Clematide

S, Gaudet P, Giglio MG, Harrow I, Huala E, Krallinger M, Leser U, Li D, Liu F, Lu Z, Maltais L,

Okazaki N, Perfetto L, Rinaldi F, Saetre R, Salgado D, Srinivasan P, Thomas PE, Toldo L, Hirschman

L, Wu CH: “BioCreative III interactive task: an overview.” BMC Bioinformatics 2011, 12(Suppl 8):S8

Lu Z, Kao H-K, Wei C-H, Huang M, Liu J, Kuo C-J, Hsu C-N, Tsai RT-H, Dai H-J, Okazaki

N, Cho H-C, Gerner M, Solt I, Agarwal S, Liu F, Vishnyakova D, Ruch P, Clematide S, Rinaldi

F, Bhattacharya S, Srinivasan P, Liu H, Torii M, Matos S, Campos D, Verspoor K, Livingston

KM, and Wilbur WJ: “The gene normalization task in BioCreative III.” BMC Bioinformatics 2011,

12(Suppl 8):S9

Bhattacharya S, Tran H, Srinivasan P: “Data-driven methods for SMS-based FAQ retrieval.” Pro-

ceedings of Forum for Information Retrieval Evaluation (FIRE 2011),In Multilingual Information

Access in South Asian Languages. Lecture Notes in Computer Science. Springer Berlin Heidelberg,

2013. (pp. 104-118).

Bhattacharya S, Harris C, Mejova Y, Yang C, Srinivasan P: “The University of Iowa at TREC

2011: Microblogs, Medical Records and Crowdsourcing.” In Proceedings of the 20th Text Retrieval

Conference (TREC 2011); Gaithersburg, MD, USA.

Bhattacharya S, Sehgal AK and Srinivasan P: “Online Gene Indexing and Retrieval for BioCreative

III at the University of Iowa.”, In Proceedings of BioCreative III (2010); Bethesda, MD, USA.

Bhattacharya S, Sehgal AK and Srinivasan P: “Cross-species Gene Normalization at the University

of Iowa.”, In Proceedings of BioCreative III (2010); Bethesda, MD, USA.

Pfizer, Inc., New York City, New York, USA

Professional

Experience

Summer Intern (R & D)/Clinical Informatics and Innovation May 2013 – August 2013

Built a knowledge management framework to facilitate collaboration in internal research using nat-

ural language processing (NLP) techniques on Pfizer’s internal SharePoint repositories. Used graph

visualization techniques for building networks around colleagues and their research interests.

Merck KGaA, Darmstadt, Germany

Summer Intern (Knowledge Management) May 2012 – August 2012

Developed system for identification of adverse drug reactions from case reports using text analyt-

ics and semantic web technologies. Also developed an automated question-answering system for

Alzheimer’s Disease using various information retrieval and NLP techniques. Results from these

researches have been published in the Journal of Drug Safety and the Conference and Labs of the

Evaluation Forum.

Pfizer, Inc., New York City, New York, USA

Summer Intern (R & D)/Biomedical Informatics May 2011 – August 2011

Developed methods for standardization of eligibility criteria representation in Pfizer’s internal clin-

ical trial protocols. The results of this research has been published in the Journal of Biomedical

Informatics.

The University of Iowa, Iowa City, Iowa, USA

Research Assistant January 2010 – present

Actively lead/participated in research on biomedical text mining, information retrieval and public

health informatics based on traditional data resources and contemporary social media data. Also

participated in NSF-funded collaborative research projects employing various text mining techniques

for leveraging critical information from the Gene and Plant Ontology annotations.

The University of Iowa, Iowa City, Iowa, USA

Teaching Assistant August 2009 – December 2009

Taught undergraduate courses in Computer Organization, Assembly Language Programming and

Fundamentals in Computing. Assisted students in discussion sections and Help-Lab.

Sysgen Solutions Technologies Private Limited, Kolkata, India

Summer Intern May 2007 – August 2007

Designed an online in-house doctor and patient registration system with front-end and database

design, performance testing and report generation using Crystal Report. This project served as the

basis for my Bachelor’s Thesis.

Programming : Perl, Java, R, C, Linux shell scripting, SQL, CGI, HTML/CSS, ASP, JSP, Java Script.

Computing

Skills

Database Systems : MySQL, PostgreSQL.

Indexing & Searching : Linguamatics I2E, LUXID, ProMiner, Lemur/Indri, large dataset processing,

social media retrieval (webpages, blogs, Twitter, Facebook).

Data Mining : Weka, KNIME, RapidMiner.

Natural Language Processing : Text/HTML/XML parsing, stemming, POS tagging, phrase extrac-

tion, named entity recognition, etc.

Ontologies : UMLS, ICD-9/10 CM, SNOMED-CT, MeSH, Entrez, etc.

Health Informatics, Principles of Public Health Informatics, Bioinformatics, Bioinformatics Tech-

Graduate

niques, Computational Genomics, Web Mining, Knowledge Discovery, Algorithms, Database Sys-

Courses

tems.

Arthur Collins Scholarship (2011-12) from Rockwell Collins and UI for academic excellence.

Awards

Nominated for the Howard Hughes Medical Institute (HHMI) International Student Research Fel-

lowship 2012 by the University of Iowa (one of 400 nationwide).

Travel Grant from the Executive Council of Graduate and Professional Students (ECGPS), UI for

attending SWLBD/BIBM 2012.

Travel Fellowship from the International Society for Computational Biology (ISCB)/National Science

Foundation (NSF) for attending ISMB/ECCB 2011.

International Student Travel Award from International Programs, University of Iowa to attend

ISMB/ECCB 2011.

Travel grant to attend General Architecture for Text Engineering (GATE) workshop in Montreal,

Quebec, Canada.

Reviewer of the Journal of the National Cancer Institute (JNCI), Journal of Medical Internet Research

Activities

(JMIR), Bioinformatics and Biology Insights (BBI).

Program Committee Member of FIRE 2012.

Reviewer of Medicine 2.0, World Congress on Social Media, Mobile Apps, Web 2.0 2012.

Reviewer of ISMB 2012.

Student Volunteer at ISMB/ECCB 2011.

Member of the Association for Computing Machinery (ACM), Institute of Electrical and Electronics

Engineers (IEEE), Association for the Advancement of Artificial Intelligence (AAAI).

Webmaster of The University of Iowa Cricket Club (UICC).

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