† co-first, * co-corresponding, ^mentee, ‡ equal contributionPreprints/in submission
Ding Q, Wu Y^, Torlai Triglia E, Gommerman JL, Subramanian A, Kuchroo VK, Rothstein DM. TIM-4 Identifies Effector B Cells Expressing An IL-23-Driven Proinflammatory Cytokine Module That Promotes Immune Responses. bioRxiv 2023.09.22.558524; doi: https://doi.org/10.1101/2023.09.22.558524. in review.
Kimura K†, Subramanian A† et al. Cooperation of the immune checkpoint molecule Tim3 and TGF-b pathway in microglial homeostasis and activation. in revisions.
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.
Pita-Juarez Y, Karagkouni D, Kalavros N, ..., Subramanian A et al. A single-nucleus and spatial tran- scriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. bioRxiv doi: 10.1101/2022.10.27.514070. PMID: 36324805.
Subramanian A†, Vernon KA†, Slyper M, Waldman J, et al. RAAS blockade, kidney disease, 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.
Peer-reviewed Journal Articles
2024
27. Transcription factor TCF1 binds to RORγt and orchestrates a regulatory network that determines homeostatic Th17 cell state.
Mangani D, Subramanian A‡, Huang L‡,…, Kuchroo V, Anderson A. Immunity 2024.
26. Neuropeptide signaling orchestrates T cell differentiation.
Hou, Y., Sun, L., LaFleur, M.W.,… Subramanian A,…, Regev A*, Sharpe A*, Kuchroo V.* Nature. 2024.
25. Protective role for kidney TREM2high macrophages in obesity- and diabetes-induced kidney injury.
Subramanian A†*, Vernon KA†, Zhou Y†*,…, Clatworthy M, Regev A, Greka A*. Cell Reports. 2024.
2023
24. Historical processes shape contemporary extinction risk in placental mammals.
Wilder A†, Supple M†, Subramanian A, Mudide A^,…, Zoonomia Consortium, Ryder OA, Shapiro B. Science. 2023.
23. Identification of a protective microglial state mediated by miR-155 and interferon-g signaling in a mouse model of Alzheimer’s disease.
Yin Z, Herron S, Silveira S, Kleemann K, Gauthier C, Mallah D, Cheng Y, Margeta MA, Pitts KM, Barry JL, Subramanian A,…,Ikezu S, Ikezu T, Butovsky O. Nature Neuroscience. 2023.
2022
22. Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics.
Subramanian A†,*, Alperovich M†,^, Yang Y and Li Bo. Genome Biology. 2022.
21. Single-nucleus cross-tissue molecular reference maps to decipher disease gene function.
Eraslan G† , Drokhlyansky E†, Anand S‡, Fiskin E‡, Subramanian A‡,…, Rozenblatt-Rosen O, Ardlie KG, Regev A. Science 2022.
20. Discovery of bioactive microbial gene products in inflammatory bowel disease.
Zhang Y, Bhosle A, Bae S, McIver L, Accorsi E, Thompson K, Arze C, Wang Y, Subramanian A,…, Krueger A, Huttenhower C, Franzosa EA. Nature. 2022.
19. Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function.
Tang R, Acharya N, Subramanian A,…, Aviv Regev, Ana C Anderson, Vijay K Kuchroo . Science Immunology. 2022.
18. Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade.
Kaur G, Porter C.B.M., Ashenberg O, Lee J, Riesenfeld S.J., Hofree M, Aggelakopoulou M, Subramanian A,…,Rozenblatt-Rosen O, Regev A, Fugger L. Nature Communications. 2022.
17. High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways.
Marshall JL†, Noel T†, Wang QS†, Bazua-Valenti S†, Chen H†, Murray E, Subramanian A,…,Macosko EZ, Chen F, Greka A. iScience. 2022.
2021
16. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.
Delorey TM†, Ziegler CGK†, Heimberg G†, Normand R†, Yang Y†, Segerstolpe A†, Abbondanza D†, Fleming SJ†, Subramanian A†,…,Villani AC, Rozenblatt-Rosen O, Regev A. Nature. 2021.
15. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus C†, Luecken MD†, Eraslan G†, Sikkema L†, Waghray A†, Heimberg G†, Kobayashi Y†, Vaishnav ED†, Subramanian A†,…, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network. Nature Medicine. 2021.
14. Multivariable Association Discovery in Population-scale Meta-omics Studies.
Mallick H, Rahnavard A, McIver LJ ,…, Subramanian A,…, Franzosa EA, Bravo HC, Huttenhower C. PLoS Computational Biology. 2021.
13. Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram.
Biancalani T, Scalia G, Buffoni L,…, Subramanian A,…, Zhuang X, Macosko EZ, Regev A. Nature Methods. 2021.
2020
12. A High-Content Screen for Mucin-1-Reducing Compounds Identifies Fostamatinib as a Candidate for Rapid Repurposing for Acute Lung Injury.
Kost-Alimova M, Sidhom EH, Satyam A,…, Subramanian A ,…,Tsokos GC , Shaw JL, Greka A. Cell Reports Medicine. 2020.
11. Emergence of a High-Plasticity Cell State during Lung Cancer Evolution.
Marjanovic ND, Hofree M, Chan JE,…, Subramanian A,…,Jacks T, Regev A, Tammela T. Cancer Cell. 2020.
2019
10. Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation.
Subramanian A†, Sidhom EH†, Emani M†,…, Rosenblatt-Rosen O, Regev A, Greka A. Nature Communications. 2019.
9. A Practical Guide to Methods Controlling False Discoveries in Computational Biology.
Korthauer K†, Kimes PK†, Duvallet C‡, Reyes A‡, Subramanian A‡,…,Shukla C, Alm EJ, Hicks SC. Genome Biology. 2019.
8. Single cell analysis of the normal mouse aorta reveals functionally distinct endothelial cell populations.
Kalluri AS, Vellarikkal SK, Edelman ER, Nguyen L, Subramanian A ,…, Regev A, Kathiresan S, Gupta RA. Circulation. 2019.
7. A cellular taxonomy of the bone marrow stroma in homeostasis and leukemia demonstrates cancer-crosstalk with stroma to impair normal tissue function.
Baryawno N, Przybylski D, Kowalczyk MS,…, Subramanian A,…, Rozenblatt-Rosen O, Regev A, Scadden DT. Cell. 2019.
2018 and before
6. Stability of the human faecal microbiome in a cohort of adult men.
Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A,…,Izard J, Huttenhower C, Chan AT. Nature Microbiology. 2018.
5. Reference-free inference of tumor phylogenies from single-cell sequencing data.
Subramanian A and Schwartz R. BMC Genomics. 2015.
4. Novel multi-sample scheme for inferring phylogenetic markers from whole genome tumor profiles.
Subramanian A, Shackney S, Schwartz R. IEEE/ACM Trans Comput Biol Bioinform. 2013.
3. Inference of tumor phylogenies from genomic assays on heterogeneous samples.
Subramanian A, Shackney S, Schwartz R. J Biomed Biotechnol. 2012.
2. Robust unmixing of tumor states in array comparative genomic hybridization data.
Tolliver D, Tsourakakis C, Subramanian A, Shackney S, Schwartz R. Bioinformatics. 2010.
1. Retinoblastoma: expression of HLA-G.
Mohan A, Kandalam M, Ramkumar HL, Subramanian A, Venkatesan N, Krishnakumar S. Ocul Immunol Inflamm. 2006.