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  Peer-reviewed Publications


2018

WWWPhD
A More Decentralized Vision for Linked Data

Axel Polleres, Maulik R. Kamdar, Javier D. Fernandez, Tania Tudorache, and Mark A. Musen

Workshop on Decentralizing the Semantic Web at the 17th International Semantic Web Conference, Monterey, October 2018

In this deliberately provocative position paper, we claim that ten years into Linked Data there are still (too?) many unresolved challenges towards arriving at a truly machine-readable and decentralized Web of data. ... Read More

 Download  |   Vision Statement

WWWPhD
Mining the Web of Life Sciences Linked Open Data for Mechanism-Based Pharmacovigilance

Maulik R. Kamdar

The Web Conference (PhD Symposium Track), Lyon, April 2018

The vision of the Semantic Web has stimulated the development of Web-scale architectures for discovering implicit associations from multiple heterogeneous data and knowledge sources. In biomedicine, ... Read More

 Download  |   Poster

M3CRNN
MRI to MGMT: Predicting Methylation Status in Glioblastoma Patients Using Convolutional Recurrent Neural Networks

Lichy Han* and Maulik R. Kamdar*

23rd Pacific Symposium on Biocomputing, Big Island of Hawaii, January 2018

Glioblastoma Multiforme (GBM), a malignant brain tumor, is among the most lethal of all cancers. Temozolomide is the primary chemotherapy treatment for patients diagnosed with GBM. The methylation status of the ... Read More

 Download  |   Pubmed  |   Code  |   Application  |   Poster

PolygOnto
Analyzing user interactions with biomedical ontologies: A visual perspective

Maulik R. Kamdar, Simon Walk, Tania Tudorache and Mark A. Musen

Journal of Web Semantics, March 2018

Biomedical ontologies are large: Dozens of ontologies in the BioPortal repository contain thousands or even hundreds of thousands of entities. The development and maintenance of such large ontologies ... Read More

 Article  |   Slides  |   Code  |   Poster  |   Application  | BEST POSTER AWARD | INVITED TALK


2017

Mecha
Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud

Maulik R. Kamdar, and Mark A. Musen

American Medican Informatics Association Annual Symposium, Washington, November 2017

Adverse drug reactions (ADR) result in significant morbidity and mortality in patients, and a substantial proportion of these ADRs are caused by drug--drug interactions (DDI). Pharmacovigilance ... Read More

 Download  |   Slides  |   Visualization  | DISTINGUISHED PAPER AWARD

Bionic
BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

Maulik R. Kamdar, Simon Walk, Tania Tudorache and Mark A. Musen

16th International Semantic Web Conference, Vienna, October 2017

BiOnIC is a catalog of aggregated statistics of user clicks, queries, and reuse counts for access to over 200 biomedical ontologies. BiOnIC also provides anonymized sequences of classes accessed ... Read More

 Download  |   Data  |   Slides  |   Application  | BEST STUDENT PAPER AWARD | NSF TRAVEL AWARD

PhLeGrA
PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data

Maulik R. Kamdar and Mark Musen

26th World Wide Web Conference, Perth, April 2017

Integrated approaches for pharmacology are required for the mechanism-based predictions of adverse drug reactions that manifest due to concomitant intake of multiple drugs. These approaches ... Read More

 Download  |   ACM Library  |   Slides  |   Code  |   Poster  |   Visualization  | BEST POSTER AWARD


2016

Systematic Analysis
A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies

Maulik R. Kamdar, Tania Tudorache and Mark Musen

Semantic Web – Interoperability, Usability, Applicability, February 2016

Reusing ontologies and their terms is a principle and best practice that most ontology development methodologies strongly encourage. Reuse comes with the promise to support the semantic interoperability ... Read More

 Article  |   Slides  |   Code  |   Poster  |   Data  |   Visualization  | BEST POSTER AWARD | INVITED TALK

PRISM
PRISM: A Data-driven Platform for Monitoring Mental Health

Maulik R. Kamdar* and Michelle Wu*

21st Pacific Symposium on Biocomputing, Big Island of Hawaii, January 2016

Neuropsychiatric disorders are the leading cause of disability worldwide and there is no gold standard currently available for the measurement of mental health. This issue is exacerbated ... Read More

 Download  |   Slides  |   Code  |   Application  |   Pubmed  |   Video  | NIH/NLM TRAVEL AWARD


2015

Ebola-KB
An Ebola Virus-centered Knowledge Base

Maulik R. Kamdar and Michel Dumontier

Database: The Journal of Biological Databases and Curation, April 2015

Ebola Virus (EBOV), of the family Filoviridae viruses, is a NIAID category A, lethal human pathogen. It is responsible for causing the Ebola Virus Disease (EVD) that is a severe hemorrhagic fever ... Read More

 Article  |   Code  |   Pubmed  |   Poster  |   Data  |   Visualization

TermReuse
Investigating Term Reuse and Overlap in Biomedical Ontologies

Maulik R. Kamdar, Tania Tudorache and Mark Musen

6th International Conference on Biomedical Ontology, Lisbon, July 2015

We investigate the current extent of term reuse and overlap among biomedical ontologies. We use the corpus of biomedical ontologies stored in the BioPortal repository, and analyze three types of reuse ... Read More

 Download  |   Slides  |   Poster  |   Data  |   Code  |   Visualization  | BEST POSTER AWARD


2014

LSLODRoadmap
A Roadmap for Navigating the Life Sciences Linked Open Data Cloud

Ali Hasnain, Syeda Sana e Zainab, Maulik R. Kamdar, Qaiser Mehmood, Claude N. Warren, Jr, Qurratal Ain Fatimah, Helena F. Deus, et al.

4th Joint International Semantic Technology Conference, Chiang Mai, November 2014

Multiple datasets that add high value to biomedical research have been exposed on the web as a part of the Life Sciences Linked Open Data (LSLOD) Cloud. The ability to easily navigate through these datasets ... Read More

 Download  |   Website  |   Visualization

Big Linked Cancer Data
Big Linked Cancer Data: Integrating Linked TCGA and PubMed

Muhammad Saleem, Maulik R. Kamdar, Aftab Iqbal, Shanmukha Sampath, Helena F. Deus and Axel-Cyrille Ngonga

Web Semantics: Science, Services and Agents on the World Wide Web, October 2014

The amount of bio-medical data available on the Web grows exponentially with time. The resulting large volume of data makes manual exploration very tedious. Moreover, the velocity at which this data ... Read More

 Article  |   Code  |   Demo

LinkedPPI
LinkedPPI: Enabling Intuitive, Integrative Protein-Protein Interaction Discovery

Laleh Kazemzadeh, Maulik R. Kamdar, Oya D. Beyan, Stefan Decker and Frank Barry

4th Workshop on Linked Science at the 13th International Semantic Web Conference, Riva Del Garda, October 2014

Understanding the dynamics of protein-protein interactions(PPIs) is a cardinal step for studying human diseases at the molecular level. Advances in "-omics" technologies has resulted in a deluge of biological data ... Read More

 Download  |   Demo

Linked Biomedical Dataspace
Linked Biomedical Dataspace: Lessons Learned integrating Data for Drug Discovery

Ali Hasnain, Maulik R. Kamdar, Panagiotis Hasapis, Dimitris Zeginis, Claude N. Warren, Jr., Helena F. Deus, Dimitrios Ntalaperas, et al.

13th International Semantic Web Conference (In-use Track), Riva Del Garda, October 2014

The increase in the volume and heterogeneity of biomedical data sources has motivated researchers to embrace Linked Data (LD) technologies to solve the ensuing integration challenges and enhance information ... Read More

 Download  |   Demo

GenomeSnip
GenomeSnip: Fragmenting the Genomic Wheel to augment discovery in cancer research

Maulik R. Kamdar, Aftab Iqbal, Muhammad Saleem, Helena F. Deus and Stefan Decker

7th Conference on Semantics in Healthcare and Life Sciences, Boston, February 2014

Cancer genomics researchers have greatly benefited from high-throughput technologies for the characterization of genomic alterations in patients. These voluminous genomics datasets when supplemented with ... Read More

 Download  |   Slides  |   Code  |   Demo  | BEST PAPER AWARD

ReVeaLD
ReVeaLD: A user-driven domain-specific interactive search platform for biomedical research

Maulik R. Kamdar, Dimitris Zeginis, Ali Hasnain, Stefan Decker and Helena F. Deus

Journal of Biomedical Informatics, February 2014

Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical ... Read More

 Article  |   Slides  |   Code  |   Pubmed  |   Poster  |   Video  |   Demo  | BEST POSTER AWARD

Reactome
The Reactome pathway knowledgebase

David Croft, Antonio F. Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani Garapati, Marc Gillespie,

Maulik R. Kamdar, Bijay Jassal, Steven Jupe, Lisa Matthews, Bruce May, Stanislav Palatnik, Karen Rothfels, Veronica Shamovsky, et al.

Nucleic Acids Research (Database Issue), January 2014

Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human ... Read More

 Article  |   Pubmed  |   Demo


2013

LinkedTCGA Dashboard v1
Fostering Serendipity through Big Linked Data

Muhammad Saleem, Maulik R. Kamdar, Aftab Iqbal, Shanmukha Sampath, Helena F. Deus and Axel-Cyrille Ngonga

Semantic Web Challenge in the 12th International Semantic Web Conference, Sydney, October 2013

The amount of bio-medical data available over the Web grows exponentially with time. The large volume of the currently available data makes it difficult to explore, while the velocity at which this data changes and ... Read More

 Download  |   Slides  |   Code  |   Poster  |   Demo  | BIG DATA PRIZE |   WALL STREET JOURNAL

exAFP-C28 Protein
Identification of an extracellular antifungal protein from the endophytic fungus Colletotrichum sp. DM06

Prabuddha Dey, Maulik R. Kamdar, Santi M. Mandal and Mrinal K. Maiti

Protein and Peptide Letters, February 2013

An extracellular antifungal protein of 28 kDa (exAFP-C28) was identified from an endophytic fungus Colletotrichum sp. DM-06. After purification, the MIC value of exAFP-C28 against Candida albicans, a well-known ... Read More

 Article  |   Slides  |   Pubmed

  Awards

Remote Student Teaching Excellence Award (BIOMEDIN 210) - Stanford University
2018
NSF Travel Award (PhLeGrA-M) - 1st US Semantic Technologies Symposium (US2TS)
2018
Distinguished Paper Award (PhLeGrA) - American Medical Informatics Association Symposium (AMIA)
2017
Best Paper Award (BiOnIC) - 16th International Semantic Web Conference (ISWC)
2017
NSF Travel Award (BiOnIC) - 16th International Semantic Web Conference (ISWC)
2017
Best Poster Award (VisIOn) - Biomedical Informatics Training Program Retreat
2017
Best Poster Award (PhLeGrA) - Biomedical Informatics Training Program Retreat
2016
NIH/NLM Travel Award (PRISM) - 21st Pacific Symposium on Biocomputing (PSB)
2016
Best Poster Award (Term Reuse) - Biomedical Informatics Training Program Retreat
2015
Best Paper Award (GenomeSnip) - 7th Conference on Semantics in Healthcare and Life Sciences (CSHALS)
2014
Semantic Web Challenge Winner (Big Data Prize) - 12th International Semantic Web Conference (ISWC)
2013
Best Project Award (Hospital Finder) - 10th Summer School on Ontology Engineering and the Semantic Web (SSSW)
2013
Best Poster Award (ReVeaLD) - 10th Summer School on Ontology Engineering and the Semantic Web (SSSW)
2013
Google Summer of Code (Reactome Pathway Summary Visualization) - Genome Informatics
2012
Honourable Mention in Technology - Indian Institute of Technology, Kharagpur
2012
Best Outgoing Student (Technology) - Meghnad Saha Hall of Residence, IIT Kharagpur
2012
Google Summer of Code (HTML5 Canvas based Pathway Visualization Tool) - Genome Informatics
2011
Google Summer of Code (HTML5 Support to Drupal 7) - Drupal
2010
Xavierite Super Award - St. Xaviers High School, Ahmedabad
2007

  Book Chapters

Open Data Ireland: Data Audit Report

Richard Cyganiak, Maulik Kamdar, Fadi Maali, Deirdre Lee and Stefan Decker

Open Data Ireland Support Project, 2014

 Download  |   Launch Article

  Posters

BMI Retreat 2017
Analyzing User Interactions with Biomedical Ontologies: A Visual Perspective

Maulik R. Kamdar, Simon Walk, Tania Tudorache and Mark Musen

BMI Retreat, September 2017

 Download

BMI Retreat 2016
Mining the Life Sciences Linked Open Data Cloud: An Application to Discover Drug-Adverse Reaction Associations

Maulik R. Kamdar and Mark Musen

BMI Retreat, September 2016

Gordon Research Conference on Advanced Health Informatics, September 2015

 Download

BMI Retreat 2015
Extracting Similar Flavors in the Spaghetti of Biomedical Ontologies

Maulik R. Kamdar, Tania Tudorache and Mark Musen

BMI Retreat, September 2015

 Download

Ebola Poster
An Ebola-centered Knowledge Base

Maulik R. Kamdar and Michel Dumontier

Bio-X Interdisciplinary Initiatives Seed Grant Symposium, February 2015

 Download

CS 231N
MRI to MGMT: Predicting Drug Efficacy for Glioblastoma Patients

Lichy Han and Maulik Kamdar

CS 231N Poster Presentation, June 2017

 Download

CS 224D
Bridging the Usability-Expressivity Gap in Biomedical Data Discovery

Maulik R. Kamdar

CS 224D Poster Presentation, June 2016

 Download

CS 224W
Predicting Transcription Factor Complexes Using Similarities in Genomic Motifs

Lichy Han, Maulik Kamdar and Daniel Kim

CS 224W Poster Presentation, December 2015

Big Data in Biomedicine Conference, May 2016

 Download

BMI210 Poster
Bioinformatics Search

Lichy Han, Winn Haynes, Maulik Kamdar and Alejandro Schuler

BMI 210 Poster Presentation, March 2015

Big Data in Biomedicine Conference, May 2015

 Download

CS229 Poster
Visualizing Personalized Cancer Risk Prediction

Maulik R. Kamdar

CS 229 Poster Presentation, December 2014

 Download

Reveald Poster
ReVeaLD: A user-driven domain-specific interactive search platform for biomedical research

Maulik R. Kamdar, Dimitris Zeginis, Ali Hasnain, Stefan Decker and Helena F. Deus

10th Summer School on Ontology Engineering and the Semantic Web,
Cercedilla, July 2013

 Download

  Selected Talks

Analyzing User Interactions with Biomedical Ontologies: A Visual Perspective

Invited Talk at the International Semantic Web Conference (ISWC 2018) - October, 2018

A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies

Invited Talk at the International Semantic Web Conference (ISWC 2018) - October, 2018

A Web-based Integration Framework over Heterogeneous Biomedical Data and Knowledge Sources

Stanford Biomedical Informatics Program Defense Talk - 7 June, 2018

Mining the Web of Life Sciences Linked Open Data for Mechanism-Based Pharmacovigilance

The Web Conference 2018 - 24 April, 2018

Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud

American Medican Informatics Association Annual Symposium (AMIA 2017) - 7 November, 2017

BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

16th International Semantic Web Conference (ISWC 2017) - 24 October, 2017

Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data

26th World Wide Web Conference (WWW 2017) - 4 April, 2017

PRISM: A Data-driven platform for Monitoring Mental health

Pacific Symposium on Biocomputing - 6 January, 2016

Investigating Term Reuse and Overlap in Biomedical Ontologies

International Conference on Biomedical Ontology - 29 July, 2015

Current advances to bridge the usability-expressivity gap in semantic search (and visualizing linked data)

Protege Friday Research Seminar - 3 April, 2015

ReVeaLD (a Real-time Visual Explorer and Aggregator of Linked Data)

DERI Friday Research Seminar - 5 April, 2013

  Other Projects

Regulating energy consumption by discerning occupant state

CS 221 Project, September-December 2015

 Read More

Pharmacogene Information for MGMT

BIOMEDIN 244 Project, September-December 2016

 Read More

Deciphering gene regulation networks in cancer

BIOMEDIN 217 Project, January-March 2015

 Read More

SNPedia Information for Rs841853

Gene 210 Project, March-June 2015

 Read More

CKAN Modules - Data.gov.ie theme and Data request

Data.gov.ie, March-May 2014

 Read More  |   Code  |   Demo

ViMeASpaTeA

Visualizing.org Challenge: Visualizing Meteorites

 Read More  |   Code  |   Demo  |   CHROME EXPERIMENT

Hospital Finder Application

10th Summer School on Ontology Engineering and the Semantic Web,
Cercedilla, July 2013

 Read More  |   Code  |   Video  | BEST PROJECT AWARD

Drupal Modules - Google Charts, Extended HTML and RGraph

Digital Enterprise Research Institute, Galway, July 2011
Google Summer of Code, August 2010

 Read More  |   Code

Bazaar - Woodstock and Forex

Kshitij: The Annual Techno-Management Symposium of IIT Kharagpur, 2009-10

Mess Online Management System (MOMS)

Meghnad Saha Hall of Residence, 2009-10