Ayshwarya Subramanian

Research Fellow

Department of Biostatistics

About

I am a postdoc at the Department of Biostatistics at Harvard Chan and the Department of Biostatistics and Computational Biology at DFCI. My advisor is Dr. Rafael Irizarry. I am also affiliated with the Broad Institute of MIT and Harvard.

My current research seeks to understand sources of bias and technical variability in DNA and RNA sequencing data. I also work on specific problems in host-microbe interactions and tumor biology. My PhD dissertation sought to understand tumor evolution by applying computational phylogenetics to genomic datasets. I completed my Ph.D in Biological Sciences in the Computational Biology concentration from Carnegie Mellon University in 2013.

Publications

Peer-reviewed Journal Articles

  1. Subramanian A, Schwartz R. Reference-free inference of tumor phylogenies from single-cell sequencing data. BMC Genomics. 2015;16 Suppl 11:S7.
  2. 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)
  3. 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)
  4. 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)
  5. 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

Subramanian A, Shackney SE and Schwartz R. 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.