About me

I am currently a Scientist at the Systems Biology Institute, Tokyo. Before this I was a post-doctoral fellow at INRIA, Rennes with the SUMO Team and INRIA, Saclay with the Lifeware Team.
Before INRIA I was a post-doctoral researcher at the Laboratory for Disease systems modeling, RIKEN Center for Integrative Medical Sciences, Japan with Prof.Hiroaki Kitano. I got my PhD in Computer science under the supervision of Prof P.S. Thiagarajan from the Department of computer science, School of computing, National University of Singapore.
My core interests lies at the cross roads of computational and complex systems. I have worked on both applied and basic research in employing large-scale data analytics, machine learning, text mining and dynamic modeling techniques for deeper understanding of complex systems in bio-medicine, health-care and related areas.

Research Interests

My current research interests are mainly focused on using computational methods for understanding biological systems. More specifically,

Computational systems biology - I am interested in building computational models describing the dynamics of biological systems (both at the intracellular and at the multi-scale setting) and in developing novel and efficient algorithms for analyzing them. I work closely with biologists as an integral part of my research to study important pathways implicated in diseases such as Cancer.

Text analytics and natural language processing - I am interested in using natural language processing and machine learning strategies to harness the power of existing literature and knowledge to contextualize and help enhance our understanding of these biological systems

Probabilistic systems and formal verification - I am interested in studying probabilistic systems such as Markov chains, dynamic Bayesian networks etc., as abstraction schemes for the dynamics of large scale models. I am also interested in the development of novel algorithms using formal verification techniques, such as model checking and their application to understanding biological systems.

Omics and big data analysis - I am interested in the computational analysis of high-dimensional large scale experimental data arising from high-throughput experiments such RNA-seq, flow cytometry etc., and developing ways formulating novel biological hypotheses automatically. I am also interested in integrating such analysis to focused modeling studies.

Publications

Book chapters


Takeshi Hase, Samik Ghosh, Sucheendra K. Palaniappan and Hiroaki Kitano. Cancer Network Medicine. Network medicine: Complex Systems in Human Disease and Therapeutics, Harvard University Press, ISBN 9780674436534, 2017.

Published Articles


Gregory J. Baker, P.S. Thiagarajan, Sucheendra K. Palaniappan, Stephanie H. Davis, Jodene K. Moore and Peter K. Sorger A flow-based immunoprofiling strategy for interrogating system-wide leukocyte composition in response to glioblastoma Cancer Res July 1 2017 (77) (13 Supplement) 1678; DOI: 10.1158/1538-7445.AM2017-1678

Sucheendra K. Palaniappan, Francois Bertaux, Matthieu Pichené, Gregory Batt, Eric Fabre and Blaise Genest Abstracting Biological Pathways using Information theory measures: A case study of Apoptosis Pathway February 2017, Oxford Bioinformatics

Sucheendra K. Palaniappan, Matthieu Pichené, Gregory Batt, Eric Fabre and Blaise Genest A Look-ahead Simulation Algorithm for DBN Models of Biochemical Pathways. Hybrid Systems Biology (HSB2016), Grenoble, France.

Michael Spranger, Sucheendra K. Palaniappan, Samik Ghosh. Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway. BioNLP 2016, Berlin, Germany.

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Harold F. G omez, Jens Hahn, Tuure Hameri, Denis Kazakiewicz, Ilya Kise- lev, Vincent Knight-Schrijver, Christian Kn upfer, Matthias K onig, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Jan- nis Uhlendorf, Thawfeek M Varusai, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, and Falk Schreiber. Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering. Volume: 63, Issue: 10, Oct. 2016

Bing Liu, Qian Liu, Lei Yang, Sucheendra K. Palaniappan, Ivet Bahar, P.S. Thiagarajan and Jeak L Ding. Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways. Science Signaling. Vol9, Issue 436, pp. ra70, 2016

Michael Spranger, Sucheendra K. Palaniappan, Samik Ghosh. Extracting Biological Pathway Models From NLP Event Representations. Proceedings of the ACL 2015 Workshop on Biomedical Natural Language Processing (BioNLP’15)

Benjamin M. Gyori, Daniel Paulin, Sucheendra K. Palaniappan. Probabilistic verification of partially observable dynamical systems. arXiv preprint arXiv:1411.0976, 2014.

Sucheendra K. Palaniappan, Benjamin M. Gyori, Bing Liu, David Hsu, P.S. Thiagarajan. Statistical model checking based calibration and analysis of bio-pathway models. In Proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 13, Austria, 2013.

Hagiescu Andrei, Bing Liu, R. Ramanathan, Sucheendra K. Palaniappan, Zheng Cui, Bipasa Chattopadhyay, P.S. Thiagarajan, and Weng-Fai Wong. GPU Code Generation for ODE-Based Applications with Phased Shared-data Access Patterns. ACM Transactions on Architecture and Code Optimization, 10(4):1-19 (2013).

Sucheendra K. Palaniappan and P.S. Thiagarajan. Dynamic Bayesian networks: A factored model of probabilistic dynamics. In Supratik Chakraborty and Madhavan Mukund, editors, ATVA2012, volume 7561 of Lecture Notes in Computer Science, pages 17-25. Springer, 2012.

Sucheendra K. Palaniappan, S Akshay, Bing Liu, Blaise Genest, and P.S. Thiagarajan. A hybrid factored frontier algorithm for dynamic Bayesian networks with a biopathways application. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 9(5):1352–1365, October 2012.

Bing Liu, Hagiescu Andrei, Sucheendra K. Palaniappan, Bipasa Chattopadhyay, Zheng Cui, Weng-Fai Wong, and P.S. Thiagarajan. Approximate probabilistic analysis of biopathway dynamics. Bioinformatics, 28(11):1508-1516, 2012.

Chuan H. Koh, Sucheendra K. Palaniappan, P.S. Thiagarajan, and Limsoon Wong. Improved statistical model checking methods for pathway analysis. BMC Bioinformatics, 13(Suppl 17):S15, Dec 2012.

Sucheendra K. Palaniappan, S. Akshay, Blaise Genest, and P.S. Thiagarajan. A hybrid factored frontier algorithm for dynamic Bayesian network models of biopathways. In Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB 11, pages 35-44, New York, NY, USA, 2011.

Conference abstracts/ Posters


Matthieu Pichene, Sucheendra K. Palaniappan, Eric Fabre, Gregory Batt, Blaise Genest. Efficient Analysis of Multi-level Biological Systems Using Abstraction Poster in the 5th International Workshop on Hybrid Systems Biology (HSB2016), 2016.

Sucheendra K. Palaniappan, Francois Bertaux, Matthieu Pichene, Eric Fabre, Gregory Batt, Blaise Genest. Approximating the dynamics of the Hybrid Stochastic-Deterministic Apoptosis pathway. Poster in the 13th International Conference of Computational Method in System Biology (CMSB15), 2015.

Bing Liu, Qian Liu, Sucheendra K. Palaniappan, Ivet Bahar, P.S. Thiagarajan and Jeak L Ding. TLR3-TLR7 Pathway Crosstalk Confers Innate Immune Memory and Homeostasis. Integrative Systems Biology Symposium, Pittsburgh, US. 2015.

Hagiescu Andrei, Bing Liu, R. Ramanathan, Sucheendra K. Palaniappan, Zheng Cui, Bipasa Chattopadhyay, P.S. Thiagarajan, and Weng-Fai Wong. GPU Code Generation for ODE-Based Applications with Phased Shared-data Access Patterns. The 9th International Conference on High-Performance and Embedded Architectures and Compilers (HiPEAC), Vienna, Austria (2014)

Bing Liu, Qian Liu, Sucheendra K. Palaniappan, Ivet Bahar, P.S. Thiagarajan and Jeak L Ding. Mathematical Modeling Reveals a Synergistic Mechanism of Toll-like Receptor Pathways. In the 8th q-bio Conference on Advancing Predictive Modeling of Cellular Regulation (q-bio), Santa Fe, US (2014).

Thesis


Sucheendra K. Palaniappan. Probabilistic verification and analysis of bio-pathway dynamics. PhD Thesis (2013).

Grants, Honors, Awards

Conferred with the VTU Gold Medal by the then President of India - Dr APJ Abdul Kalam (2007)
Conferred with the PES Gold Medal by the Minister of Higher Education, Karnataka, India (2006)
NUS Graduate research Scholarship (2008 - 2012)
INRIA Postdoctoral Fellowship (2015-2016)
Travel Grant - the Volkswagen whole-cell modeling summer school in Rostock, Germany (2016)

Professional Services

Served on the Program Committee for Workshop on Formal Methods for Biological and Biomedical Systems. FMBBS16
Reviewer for Elseiver Methods.
Reviewed articles for ACM-BCB2011, LNCS Transactions on Petri Nets and Other Models of Concurrency (ToPNoC), CMSB-2013, Bio-PPN-2013
Was a co-organizer for The 3rd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, 2011.

Talks

Discrete Stochastic Abstraction of Biological Pathway Dynamics: A case study of the Apoptosis Pathway.Symbiose seminars, January 2016, INRIA, Rennes
Approximating the dynamics of the Hybrid Stochastic-Deterministic Apoptosis pathway Journe nationale du groupe de travail BIOSS, November 2015, Paris.
Computational Systems biology INRIA foundation seminars, October 2015, Rennes.
Systems biology of Atopic dermatitis: A Computational paradigm, RIKEN center for Intergrative Medical Sciences (IMS) seminar series, February 2014, Yokohama.
Probabilistic verification and analysis of biopathway dynamics, Sony computer science labs (SonyCSL), July 2013, Tokyo.
Parameter estimation of bio-pathway models using statistical model checking, Korea-Singapore Workshop on Bioinformatics and NLP, February 2013, Singapore.
Improved Statistical Model Checking Methods for Pathway Analysis 11th International Conference on Bioinformatics (InCoB2012), October 2012, Thailand.
A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Network Models of Biopathways, 9th International Conference on Computational Methods in Systems Biology(CMSB2011), September 2011, Paris, France.
DBN approximation of ODE dynamics, Inference on DBNs INRIA Parisian location, September 2011, Paris, France. A Hybrid Factored Frontier algorithm for Dynamic Bayesian Networks. The 3nd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, Apr 2011, Singapore.
Probabilistic Verification of Biological pathway Dynamics, The 2nd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, Feb 2010, Tokyo, Japan.