Ayush Raman
Statistical Epigenomics Postdoc Associate
Broad Institute
Dana Farber Cancer Institute
Massachusetts General Hospital, Harvard Medical School
I am a Postdoc Associate at Broad Institute of MIT and Harvard and affiliated with Dana Farber Cancer Institute & MGH, Harvard Medical School. I am working with the labs of Martin Aryee and Alex Meissner to understand the dynamics of gene regulation using single-cell genomics.
I earned my Ph.D. in Quantitative and Computational Biosciences at the Baylor College of Medicine, where I worked with Zhandong Liu and Huda Zoghbi focused on batch effects in NGS datasets, reproducibility & meta-research, and also worked with Kunal Rai in the field of the cancer epigenomics. Prior to my Ph.D. studies, I worked as a Bioinformatics Scientist at the Institute for Systems Biology, Seattle.
I completed my MS in Computational Biology from Carnegie Mellon and did my undergrad at Vellore Institute of Technology, where I earned B.Tech in Bioinformatics.
I am currently on the job market!
- Epigenetics and Gene Expression
- Statistical Analysis
- Machine Learning
- Computational Biology
- Single Cell Analysis
PhD in Quantitative and Computational Biosciences, 2018
Baylor College of Medicine
MS in Computational Biology, 2009
Carnegie Mellon University
BTech in Bioinformatics, 2006
Vellore Institute of Technology
Recent News
- 10-2022: Review manuscript on Computational methods to explore chromatin state dynamics got published in Briefings in Bioinformatics
- 07-2021: Dual-omics protocol manuscript for profiling of methylome and transcriptome in single cell got published in Nature Protocols
- 07-2021: Manuscript on enhancer reprogramming in MPNST tumors got published in Acta Neuropathologica
- 05-2021: Manuscript on enhancer subtypes in colorectal cancer got published in Gut.
- 03-2021: Commentary article on my experience as a research parasite in GigaScience
- 12-2020: Eliana Hechter Memorial Award, Broad Institute
- 06-2020: MCBIOS Young Scientist Excellence Postdoc Award
- 01-2020: Junior Research Parasite Award for Rigorous Secondary Data Analysis
Selected Publications
- H Gu†, AT Raman† et al. Smart-RRBS for single cell methylome and transcriptome analysis. Nature Protocols (2021)
- E Orouji†, AT Raman†, AK Singh† et al. Chromatin State Dynamics Confers Specific Therapeutic Strategies in Enhancer Subtypes of Colorectal Cancer. Gut (2021)
- Veena Kochat†, AT Raman†, et al. Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state. Acta Neuropathologica (2021)
- AT Raman†, AE Pohodich†, YW Wan, HK Yalamanchili, HY Zoghbi, Z Liu. Apparent bias towards long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations. Nature Communications (2018)
- H Yi†, AT Raman†, H Zhang, G Allen and Z Liu. Detecting hidden batch factors through data-adaptive adjustment for biological effects. Bioinformatics (2018)
†Co-first authorship