Ayshwarya Subramanian

Ayshwarya Subramanian

Computational Biologist | Single Cell Genomics

Publications

Google Scholar

Publons

† Shared first-authorship

‡ Shared second-authorship.

Pre-prints/Under review

[1] Subramanian A†, Alperovich M†, Yang Y and Li Bo. Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics. bioRxiv 2021.10.27.466176; doi: https://doi.org/10.1101/2021.10.27.466176. in revisions.

[2] Subramanian A†, Vernon KA†, Zhou Y† et al. Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution. bioRxiv 2021.05.30.446342; doi: https://doi.org/10.1101/2021.05.30.446342. in revisions.

[3] Subramanian A†,Vernon KA†, Slyper M, Waldman J, et al. RAAS blockade, kidney dis- ease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells. 2020. bioRxiv doi: https://doi.org/10.1101/2020.06.23.167098

[4] Mangani D,Subramanian A‡,Huang L‡ et al. A TCF1-driven regulatory network determines homeostatic versus pathogenic Th17 cell state. in revisions.

[5] Wilder A, Supple M,Subramanian A et al. Historical processes shape contemporary extinction risk in placental mammals. in revisions.

Peer-reviewed Journal Articles

  1. Kaur G, Porter C.B.M., Ashenberg O, Lee J, Riesenfeld S.J., Hofree M, Aggelakopoulou M, Subramanian A, et al. 2021. Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade. Nat Commun. 2022 Jul 29;13(1):4398. doi: 10.1038/s41467-022-32171-w. PMID: 35906236.
  2. Zhang Y, Bhosle A, Bae S, McIver L, Accorsi E, Thompson K, Arze C, Wang Y, Subramanian A, et al. Identifying Novel Bioactive Microbial Gene Products in Inflammatory Bowel Disease. Nature 2022 (in press).
  3. Eraslan G†, Drokhlyansky E†, Anand S‡, Fiskin E‡, Subramanian A‡, et al. Single-nucleus cross-tissue molecular reference maps to decipher disease gene function. bioRxiv 2021.07.19.452954; doi: https://doi.org/10.1101/2021.07.19.452954. Science 2022.
  4. Marshall JL†, Noel T†, Wang QS†, Bazua-Valenti S†, Chen H†, Murray E, Subramanian A et al. High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways. bioRxiv 2021.10.10.463829; doi: https://doi.org/10.1101/2021.10.10.463 iScience. 2022.
  5. Tang R, Acharya N, Subramanian A, et al. Tim-3 adapter protein Bat3 acts as an en- dogenous regulator of tolerogenic dendritic cell function. Science Immunology. 2022 Mar 11;7(69):eabm0631. doi: 10.1126/sciimmunol.abm0631. Epub 2022 Mar 11. PMID: 35275752.
  6. Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, et al. Multivariable Association Discovery in Population-scale Meta-omics Studies. PLoS Compu- tational Biology. 2021 Nov 16;17(11):e1009442. doi: 10.1371/journal.pcbi.1009442. PMID: 34784344.
  7. Biancalani T, Scalia G, Buffoni L, Avasthi R, Lu Z, Sanger A, Tokcan N, Vanderburg CR, Segerstolpe A, Zhang M, Avraham-Davidi I, Vickovic S, Nitzan M, Ma S, Subramanian A, et al. Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram. Nature Methods. 2021 Nov;18(11):1352-1362. doi: 10.1038/s41592-021-01264-7. Epub 2021 Oct 28. PMID: 34711971
  8. Delorey TM†, Ziegler CGK†, Heimberg G†, Normand R†, Yang Y†, Segerstolpe A†, Abbondanza D†, Fleming SJ†, Subramanian A†, et al. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021 Apr 29. doi: 10.1038/s41586-021-03570-8. Epub ahead of print. PMID: 33915569.
  9. Muus C†, Luecken MD†, Eraslan G†, Sikkema L†, Waghray A†, Heimberg G†, Kobayashi Y†, Vaishnav ED†, Subramanian A†, et al. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine. 2021 Mar;27(3):546-559. doi: 10.1038/s41591-020-01227-z. Epub 2021 Mar 2. PMID: 33654293.
  10. Kost-Alimova M, Sidhom EH, Satyam A, Chamberlain BT, Dvela-Levitt M, Melanson M, Alper SL, Santos J, Gutierrez J, Subramanian A et al. A High-Content Screen for Mucin-1-Reducing Compounds Identifies Fostamatinib as a Candidate for Rapid Repurposing for Acute Lung Injury. Cell Reports Medicine. 2020 Oct 29;1(8):100137. doi: 10.1016/j.xcrm.2020.100137. PMID: 33294858; PMCID: PMC7691435.
  11. Marjanovic ND, Hofree M, Chan JE, Canner D, Wu K, Trakala M, Hartmann GG, Smith OC, Kim JY, Evans KV, Hudson A, Ashenberg O, Porter CBM, Bejnood A, Subramanian A, et al. Emergence of a High-Plasticity Cell State during Lung Cancer Evolution. Cancer Cell. 2020 Aug 10;38(2):229-246.e13. doi: 10.1016/j.ccell.2020.06.012. Epub 2020 Jul 23. PMID: 32707077; PMCID: PMC7745838.
  12. Subramanian A†, Sidhom EH†, Emani M†, Vernon K, Sahakian N, Zhou Y, Kost-Alimova M, Slyper M, Waldman J, Dionne D, Nguyen LT, Weins A, Marshall JL, Rosenblatt-Rosen O, Regev A, Greka A. Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation. Nat Commun. 2019 Nov 29;10(1):5462. doi:10.1038/s41467-019-13382-0. PMID: 31784515; PMCID: PMC6884507.
  13. Korthauer K†, Kimes PK†, Duvallet C ‡, Reyes A‡, Subramanian A‡, Teng M, Shukla C, Alm EJ, Hicks SC. A practical guide to methods controlling false discoveries in computational biology. Genome Biol. 2019 Jun 4;20(1):118. doi: 10.1186/s13059-019-1716-1. PMID: 31164141; PMCID: PMC6547503.
  14. Kalluri AS, Vellarikkal SK, Edelman ER, Nguyen L, Subramanian A, Ellinor PT, Regev A, Kathiresan S, Gupta RM. Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations. Circulation. 2019;140(2):147–163. doi:10.1161/CIRCULATIONAHA.118.038362
  15. Baryawno N, Przybylski D, Kowalczyk MS, Kfoury Y, Severe N, Gustafsson K, Kokkaliaris KD, Mercier F, Tabaka M, Hofree M, Dionne D, Papazian A, Lee D, Ashenberg O, Subramanian A, Vaishnav ED, Rozenblatt-Rosen O, Regev A, Scadden DT. A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia. Cell. 2019;177(7):1915–1932.e16. doi:10.1016/j.cell.2019.04.040
  16. Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A, Lochhead P, Joshi AD, Ivey KL, Khalili H, Brown GT, DuLong C, Song M, Nguyen LH, Mallick H, Rimm E, Izard J, Huttenhower C, Chan AT. Stability of the human faecal microbiome in a cohort of adult men. Nat Microbiol. 2018 Mar;3(3):347-355.PMID: 29335554
  17. Subramanian A and Schwartz R. Reference-free inference of tumor phylogenies from single- cell sequencing data. BMC Genomics. 2015;16 Suppl 11:S7. PMID: 26576947
  18. Subramanian A, Shackney S, Schwartz R. Novel multi-sample scheme for inferring phyloge- netic markers from whole genome tumor profiles. IEEE/ACM Trans Comput Biol Bioinform. 2013 Apr 23. PMID: 24407301
  19. Subramanian A, Shackney S, Schwartz R. Inference of tumor phylogenies from genomic assays on heterogeneous samples. J Biomed Biotechnol. 2012; 2012:797812. PMID:22654484
  20. 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. PMID:20529894
  21. 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. PMID: 16911982

Peer-reviewed full-length Conference Papers

  1. Subramanian A and Schwartz R, “Reference-free inference of tumor phylogenies from single- cell sequencing data,” 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Miami, FL, 2014, pp. 1-1. Oral Presentation
  2. Subramanian A, Shackney S, Schwartz R. Novel multi-sample scheme for inferring phyloge- netic markers from whole genome tumor profiles. Proceedings of the 8th International Sym- posium 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.
  3. Subramanian A, Shackney S, Schwartz R. Inference of tumor phylogenies from genomic assays on heterogeneous samples. ACM-BCB, Chicago, IL, August 01 - 03, 2011. BCB ’11 Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM- BCB). pp 172-181. Oral Presentation.
  4. Tolliver D, Tsourakakis C, Subramanian A, Shackney S, Schwartz R. Robust unmixing of tu- mor states in array comparative genomic hybridization data. Intelligent Systems for Molecular biology (ISMB) 2010. Oral Presentation.

Book Chapter

  1. Subramanian A, Shackney S, Schwartz R. “Tumor phylogenetics in the Next Generation Sequencing era: Strategies and Challenges.” Applications of Next Generation Sequencing in Cancer Research. 2013

Ph.D. Dissertation

  1. Subramanian A, “Inferring tumor evolution using computational phylogenetics” (2013). Dis- sertations. 275.