Ayshwarya Subramanian

Research Fellow

Department of Biostatistics

655 Huntington Avenue
Building II, Room 451
Boston, MA 02115

About

I am a postdoctoral fellow at the Department of Biostatistics and my advisor is Dr. Curtis Huttenhower. I am also affiliated with the Broad Institute of MIT and Harvard.

I am interested in understanding the relationship between the human gut microbiome, environmental factors and host genetics in complex diseases like Inflammatory Bowel Disease (IBD) and colorectal cancer. I primarily design and develop computational biology tools to mine large metagenomics datasets  to infer disease associations.

I completed my Ph.D in Biological Sciences in the Computational Biology concentration from Carnegie Mellon University in 2013. My dissertation established a computational phylogenetic framework for inferring tumor evolution.

Publications

Peer-reviewed Journal Articles

  1. Subramanian A, Shackney S, Schwartz R. Novel multisample scheme for inferring
    phylogenetic markers from whole genome tumor profiles. IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1422-31. doi: 10.1109/TCBB.2013.33. PubMed PMID: 24407301; PubMed Central PMCID: PMC3830698. (Pubmed)
  2. Subramanian A, Shackney S, Schwartz R. Inference of tumor phylogenies from
    genomic assays on heterogeneous samples. J Biomed Biotechnol. 2012;2012:797812.
    doi: 10.1155/2012/797812. Epub 2012 May 13. PubMed PMID: 22654484; PubMed Central PMCID: PMC3359715. (Pubmed)
  3. Tolliver D, Tsourakakis C, Subramanian A, Shackney S, Schwartz R. Robust
    unmixing of tumor states in array comparative genomic hybridization data.
    Bioinformatics. 2010 Jun 15;26(12):i106-14. doi: 10.1093/bioinformatics/btq213.
    PubMed PMID: 20529894; PubMed Central PMCID: PMC2881397. (Pubmed)
  4. Adithi M, Kandalam M, Ramkumar HL, Subramanian A, Venkatesan N, Krishnakumar S. Retinoblastoma: expression of HLA-G. Ocul Immunol Inflamm. 2006 Aug;14(4):207-13. PubMed PMID: 16911982. (Pubmed)

Peer-reviewed Conference Papers

  1. Subramanian A, Shackney S, Schwartz R. Novel multi-sample scheme for inferring phylogenetic markers from whole genome tumor profiles. Proceedings of the 8th International Symposium on Bioinformatics Research and Applications (ISBRA) 2012, Dallas, TX, USA, May 21-23, 2012. Bioinformatics Research and Applications. Lecture Notes in Computer Science Volume 7292, 2012, pp 250-262. (Oral Presentation). (Link)
  2. Subramanian A, Shackney S, Schwartz R. Inference of tumor phylogenies from genomic assays on heterogeneous samples. BCB ’11 Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB) 2011. Pages 172-181. (Oral Presentation). (Link)
  3. Tolliver D, Tsourakakis C, Subramanian A, Shackney S, Schwartz R. Robust unmixing of tumor states in array comparative genomic hybridization data. Intelligent Systems for Molecular biology (ISMB) 2010. (Oral Presentation).

Book Chapter

Ayshwarya Subramanian, Stanley Shackney and Russell Schwartz. Tumor Phylogenetics in the NGS Era: Strategies, Challenges, and Future Prospects. Next Generation Sequencing in Cancer Research 2013, pp 335-357. (Link)

Invited Talks

  1. Ayshwarya Subramanian and Russell Schwartz. Reference-free inference of single cell tumor phylogenies. 4th Computational Advances in Next Generation Sequencing (CANGS) Workshop 2014. IEEE-ICCABS 2014, Miami Beach, FL. 06/02/2014.
  2. Ayshwarya Subramanian. Inferring tumor progression using computational phylogenetics. MIT CSAIL, Boston, MA. 08/22/2013.
  3. Invited Panelist. ACM Women in Bioinformatics Panel. ACM-BCB 2011, Chicago, IL.