Academic Profile

Dr. Amartya Sanyal joined NTU as Nanyang Assistant Professor in School of Biological Sciences (SBS) in 2014. The laboratory of Dr. Sanyal is interested in understanding the chromatin basis of transcriptional regulation during cellular state transitions. The laboratory employs high-throughput genomics, genome-editing and imaging techniques in combination with bioinformatics and computational approaches to understand structure-function relationship of chromatin in various model organisms. The ultimate goal is to decipher systems-level understanding of complex relationships between genome architecture, gene transcription and, chromatin and epigenetic features in normal development and disease. Prior to this position, Dr. Sanyal worked at the University of Massachusetts Medical School, Worcester, MA, USA for his postdoctoral training. During his postdoctoral tenure, he was actively involved in the ENCODE (ENCyclopedia Of DNA Elements) project. Dr. Sanyal’s work has been published in leading research journals and is highly cited. Recently, his group has reported the first gapless chromosome-level genome assembly and chromatin contact map of the pathogenic yeast, Candida tropicalis.

Keywords: 3D chromatin organization; Epigenetics; Gene expression; Cancer; Liver biology; Bioinformatics; Computational Biology

Ph.D. (2008) Indian Institute of Science, Bangalore, India
M.Sc. (2002) Banaras Hindu University, Varanasi, India
B.Sc. (2000) University of Calcutta, Kolkata, India
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Asst Prof Amartya Sanyal (No longer with NTU)
Nanyang Assistant Professor, School of Biological Sciences

The main focus of our research is to understand 3D genome organization inside the nucleus and its impact on transcriptional regulatory code during development, differentiation and disease using variety of model organisms. Please visit Sanyal Lab webpage (

Human genome is organized in highly complex conformations inside the nucleus. How this three-dimensional organization of chromatin affects gene regulation is largely unknown. We are trying to decipher the regulatory mechanisms of cell- and tissue-specific gene expression in relation to 3D chromatin architecture, epigenetic mechanisms (chromatin modifications) and binding of trans-acting factors to understand various biological processes in normal and disease conditions.
  • Khalil AIS, Muzaki SRBM, Chattopadhyay A*, Sanyal A*. (2020). Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines. BMC Bioinformatics, 21, 506.

  • Guin K, Chen Y, Mishra R, Muzaki SRBM, Thimmappa BC, O’Brien C, Butler G, Sanyal A*, Sanyal K*. (2020). Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres. eLIFE, 9, e58556.

  • Khalil AIS, Khyriem C, Chattopadhyay A*, Sanyal A*. (2020). Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes. BMC Bioinformatics, 21(1), 147.

  • Sreekumar L, Jaitly P, Chen Y, Thimmappa BC, Sanyal A, Sanyal K. (2019). Cis- and trans-chromosomal interactions define pericentric boundaries in the absence of conventional heterochromatin.. Genetics, 212(4), 1121-1132.

  • Hong R, Lin B, Lu X, Lai LT, Chen X, Sanyal A, Ng HH, Zhang K, Zhang LF. (2017). High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration. Scientific Reports, 7, 45460.