Computational Systems Biology & Bioinformatics

REFEREED PUBLICATIONS
36new 2017 Huey Eng Chua, Sourav S Bhowmick, Jie Zheng

TROVE: A User-friendly Tool for Visualizing and Analyzing Cancer Hallmarks in Signaling Networks

Bioinformatics, Oxford Univ Press.

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35new 2017 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg

Synergistic Target Combination Prediction From Curated Signaling Networks: Machine Learning Meets Systems Biology and Pharmacology

To appear in Methods, Elsevier Science (Invited Paper)

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34 Aug 2017 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg

TINTIN: Exploiting Target Features for Signaling Network Similarity Computation and Ranking

In the Proceedings of 8th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2017)

ACM Press, Boston, USA

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33 May 2017 Sourav S Bhowmick, Boon-Siew Seah Summarizing Biological Networks

Springer Verlag, ISBN 978-3-319-54620-9, Pages: 146.

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32 Dec 2016 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, and C Forbes Dewey, Jr

TENET: A Machine Learning-based System for Target Characterization in Signaling Networks

In the Proceedings of 16th IEEE Conference on Data Mining (IEEE ICDM 2016)

IEEE CS, Barcelona, Spain (Demo)

 Acceptance Rate: -
31 Dec 2016 Boon Siew Seah, Sourav S Bhowmick, Huey Eng Chua, Mengxuan Chen, and C Forbes Dewey, Jr

FacetsViewer: A Tool for Multi-faceted Decomposition of Complex Networks

In the Proceedings of 16th IEEE Conference on Data Mining (IEEE ICDM 2016)

IEEE CS, Barcelona, Spain (Demo)

Video

 Acceptance Rate: -
30 Oct 2016 Huey Eng Chua, Sourav S Bhowmick, Zheng Jie, Lisa Tucker-Kellogg

TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks

In the Proceedings of 7th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2016)

ACM Press, Seattle, USA

Software

 Acceptance Rate: 47/112
29 Oct 2016 Shital K Mishra, Sourav S Bhowmick, Huey Eng Chua, Zheng Jie

Predictive Modeling of Drug Effects on Signaling Pathways in Diverse Cancer Cell Lines

In the Proceedings of 7th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2016)

ACM Press, Seattle, USA

 Acceptance Rate: 47/112
28 March 2016 Sourav S Bhowmick, Boon Siew Seah

Clustering and Summarizing Protein-Protein Interaction Networks: A Survey

IEEE Transactions on Data and Knowledge Engineering (TKDE), 28(3), IEEE CS

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27 Oct 2015 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, C F Dewey, Jr

TENET: Topological Feature-based Target Characterization in Signaling Networks

Bioinformatics, 31(20), Oxford Univ Press.

Technical Report

Software

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26 January 2015 Shital K Mishra, Sourav S Bhowmick, Huey Eng Chua, Fan Zhang, Jie Zheng

Computational Cell Fate Modelling for Discovery of Rewiring in Apoptotic Network for Enhanced Cancer Drug Sensitivity

BMC Systems Biology, 9:S4, Biomed Central.

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25 Oct 2014 Boon-Siew Seah, Sourav S Bhowmick, C. Forbes Dewey, Jr.

DiffNet: Automatic Differential Functional Summarization of dE-MAP Networks

Methods (IF 4.15), 69, Elsevier Science (Invited Paper)

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24 Sep 2014 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg

One Feature Doesn’t Fit All: Characterizing Topological Features of Targets in Signaling Networks

In the Proceedings of 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2014)

ACM Press, Newport Beach, California, USA

 Acceptance Rate: -
23 Sep 2014 Boon-Siew Seah, Sourav S Bhowmick, C. Forbes Dewey, Jr.


DualAligner: A Dual Alignment-based Strategy to Align Protein Interaction Networks

Bioinformatics (IF 5.32), 30(18), Oxford Univ Press

Software

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22 Jan 2014 Sourav S Bhowmick, Huey Eng Chua, Jie Zheng

INGOT: Towards Network-driven In Silico Combination Therapy

In the Proceedings of 1st International Conference on Big Data and Smart Computing (BigComp 2014)

IEEE CS, Bangkok, Thailand (Invited Paper)

 
21 Nov 2012 Boon-Siew Seah, Sourav S Bhowmick, C. Forbes Dewey, Jr.

FACETS: Multi-faceted Functional Decomposition of Protein Interaction Networks

Bioinformatics (IF 5.47), 28(20), Oxford Univ Press

Software

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20 Oct 2012 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, C. F. Dewey, Jr

STEROID: In Silico Heuristic Target Combination Identification for Disease-Related Signaling Networks

In the Proceedings of 3rd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2012)

ACM Press, Orlando, Florida, USA

Extended version

 Acceptance Rate: 20.7%
19 Sept 2012 L. Venkatraman, Ser-Mien Chia, B. C. Narmada, Jacob K White, Sourav S Bhowmick, C. Forbes Dewey, Jr., Peter So, Lisa Tucker-Kellogg, Hanry Yu

Plasmin Triggers a Switch-like Decrease in Thrombospondin-Dependent Activation of TGF-beta1

Biophysical Journal, 103(5), Elsevier Science (IF 4.22)

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18 Mar 2012 Boon-Siew Seah, Sourav S Bhowmick, C F Dewey,Jr, Hanry Yu

FUSE: A Profit Maximization Approach for Functional Summarization of Biological Networks

BMC Bioinformatics, 13(S3), Biomed Central (IF 3.03)

(Special Issue on Best Papers of ACM BCB 2011)

17 Jan 2012 Huey-Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, Qing Zhao, C F Dewey, Hanry Yu

In Silico Identification of Endo16 Regulators in the Sea Urchin Endomesoderm Gene Regulatory Network

In the Proceedings of 2nd ACM SIGHIT International Health Informatics Symposium

ACM Press, Miami, Florida, USA

 Acceptance Rate: 25.4%
16 Jan 2012   Huey-Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, Yingqi Wang, C F Dewey, Hanry Yu

PANI: An Interactive Data-Driven Tool for Target Prioritization in Signaling Networks

In the Proceedings of 2nd ACM SIGHIT International Health Informatics Symposium

ACM Press, Miami, Florida, USA (Demo)

Video

 
15 Jan 2012 Boon-Siew Seah, Sourav S Bhowmick, C F Dewey, Hanry Yu

FUSE: A System for Data-Driven Multi-Level Functional Summarization of Protein Interaction Networks

In the Proceedings of 2nd ACM SIGHIT International Health Informatics Symposium

ACM Press, Miami, Florida, USA (Demo)

Video

 
14 2011 L Venkatraman, Huipeng Li, C. F. Dewey, J. K. White, Sourav S Bhowmick, Hanry Yu, Lisa Tucker-Kellogg

The Steady States and Dynamics of Urokinase-mediated Plasmin Activation In Silico and In Vitro

Biophysical Journal, 101(8), Elsevier Science (IF 4.2)

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13  Aug 2011 Boon-Siew Seah, Sourav S Bhowmick, C F Dewey, Jr, Hanry Yu  

FUSE: Towards Multi-Level Functional Summarization of Protein Interaction Networks

In the Proceedings of 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2011)

ACM Press, Chicago, USA

Best Paper Award

 Acceptance Rate: 19%
12 Aug 2011 Huey-Eng Chua, Sourav S Bhowmick, Qing Zhao, L Tucker-Kellogg, C F Dewey, Jr, Hanry Yu

PANI: A Novel Algorithm for Fast Discovery of Putative Target Nodes in Signaling Networks

In the Proceedings of 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2011)

ACM Press, Chicago, USA (Short)

Extended version

 
11

March

2010

W.-X. Zhang, Lisa Tucker-Kellogg, B.C. Narmada, L. Venkatraman, S. Chang, Y. Lu, Nancy Tan, J. White, C. F. Dewey, S S Bhowmick, Peter So, S Shen, Hanry Yu

Cell Delivery Therapeutics for Liver Regeneration

Advanced Drug Delivery Reviews (ADDR)
62(7-8), Elsevier Science (IF 8.3)

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10 Jan 2010 L Venkatraman, Hanry Yu, Sourav S Bhowmick, C F Dewey, Jr, L Tucker-Kellogg

The Steady States and Dynamics of Urokinase Mediated Plasmin Activation

In the Proceedings of 15th Pacific Symposium of Biocomputing (PSB 2010)  Hawai, USA.

 
9 Apr 2010 Yang Song, Sourav S Bhowmick

BIDEL: An XML-based System for Effective Fast Change Detection of Genomic and Proteomic Data
In the Proceedings of 15thInternational Conference on Database Systems for Advanced Applications (DASFAA 2010)
Springer Verlag, Tsukuba, Japan (Demo paper)

 
8 Apr 2007 Y Song, S S Bhowmick, C F Dewey

BioDIFF: An Effective Fast Change Detection Algorithm for Biological Annotations
In the Proceedings of 12th International Conference on Database Systems for Advanced Applications (DASFAA 2007)
Springer Verlag, Bangkok, Thailand

Acceptance rate 18.7%
7 Feb 2005 Yang Song, S S Bhowmick, S K Madria Bio2X: A Rule-based Approach to Semi-automatic Transformation of Semistructured Biological Data to XML
Data and Knowledge Engineering Journal (DKE)
52(2): pp. 249-271, Elsevier Science
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6 Nov 2004 Song Yang, S S Bhowmick

BioDiff: An Effective Fast Change Detection Algorithm for Genomic and Proteomic Data
In the Proceedings of the 13th ACM International Conference on Information and Knowledge Management (ACM CIKM 2004)
Springer Verlag, Beijing, China (Poster Paper)

 
5 Nov 2003 S S Bhowmick, Vivek Vedagiri, Amey Laud

HyperThesis: The gRNA Spell on the Curse of Bioinformatics Applications Integration
In the Proceedings of the 12th ACM International Conference on Information and Knowledge Management (ACM CIKM 2003)
ACM Press, New Orleans, USA

Acceptance rate 15%
4 Sep 2003 S S Bhowmick, Dadabhai T Singh, Amey Laud

Data Management Issues in Metaboloinformatics - Issues and Challenges
In the Proceedings of the 14th International Conference on Database and Expert Systems Applications (DEXA 2003)
Springer-Verlag, Prague, Czech Republic

 
3 Mar 2003 S S Bhowmick, Pedro Cruz, Amey Laud

XomatiQ: Living with Genomes, Proteomes, Relations and a Little Bit of XML
In the Proceedings of the 19th IEEE International Conference on Data Engineering (ICDE 2003)
IEEE Computer Society, Bangalore, India

 
2 Aug 2002 A Laud, S S Bhowmick, P Cruz, D T Singh, G Rajesh

The gRNA: A Highly Programmable Infrastructure for Prototyping, Developing and Deploying Genomics-Centric Applications
In the Proceedings of the 28th International Conference on Very Large Data Bases (VLDB 2002)
Morgan Kauffmann, Hong Kong, China

 
1 Jun 2002 S S Bhowmick, Pedro Cruz, A Laud

Warehousing and Querying Biological Data using the gRNA
In the Proceedings of the International Workshop on Bioinformatics (in conjunction with ISMIS 2002)
Lyon, France

 

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