I am a Staff Scientist at LRBGE, CCR, NCI. I am currently working with the labs of Dan Larson and Shalini Oberdoerffer to understand the role of RNA modifications and splicing factors in gene expression. I did my Postdoc at Broad Institute of MIT and Harvard and Dana Farber Cancer Institute on the dynamics of gene regulation using single-cell genomics. I worked with the labs of Martin Aryee and Alex Meissner.
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 with late Ilya Shmulevich. 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.
Here is the summary of my research.
- Epigenetics and Gene Expression
- Statistical Analysis
- Machine Learning
- Computational Biology
- Single Cell Analysis
Postdoc in Computational Epigenomics
Broad Institute of MIT and Harvard, DFCI/MGH/HMS
PhD in Quantitative and Computational Biosciences
Baylor College of Medicine
MS in Computational Biology
Carnegie Mellon University
BTech in Bioinformatics
Vellore Institute of Technology
Recent News
- 04-2024: Moved to NCI, NIH to start as Staff Scientist
- 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