Sasi Arunachalam, PhD

Department of Computational Biology &
Cancer Biology Program
Comprehensive Cancer Center
St Jude Children’s Research Hospita
l Memphis, TN 38105, USA


I am a wet-lab biologist transitioned into computational biology & bioinformatics. As a bioinformatic scientist, I gained valuable research experience working from top cancer institutes. I have analyzed diagnostic, relapsed and clinical trials pediatric cancer patient samples for clinical biomarker discovery. I analyzed 800 non-cancer patient samples (including childern) to illuminate the potential precursors of blood cancers which was published in blood cancer discovery and this research was highlighted in many science magazines and news. I have more than three years of experience on next generation sequence analysis such as RNA seq, WES, WGS, SNP, fusion genes and structural variants.

I currently lead and aggregate genomic and clinical data for various pediatric cancers In Gabriella Miller Kids First project at St Jude children research hospital. This project is ongoing in various institutes to collect vast amount of pediatric cancer biomarker. The goal of the Gabriella Miller Kids First Pediatric Research Program (Kids First) is to uncover new insights into the biology of childhood cancer and structural birth defects, including the discovery of shared genetic pathways between these disorders. I have working efficiency in Python, R, Shell scripts, Scikit-learn (Machine Learning in Python), Linux-based high-performance computing environments and various bioinformatics tools /software.

Research Interest

His research interest includes: Data driven biological discoveries, Genomics personalized medicine, Bioinformatics and biomarker discovery.

Scientific Activities


1. Feusier JE, Arunachalam S, Tashi T, Baker MJ, VanSant-Webb C, Amber Ferdig, et al. Large-scale identification of clonal hematopoiesis and mutations recurrentin blood cancers. Blood Cancer Discov. 2021; 2(3): 226-237. doi: 10.1158/2643-3230.bcd-20-0094
2. Evrard YA, Srivastava A, Randjelovi J, Doroshow JH, Dean DA, Morris JS, et al. Systematic establishment of robustness and standards in patient-derived xenograft experiments and analysis. Cancer Res. 2020; 80: 2286-2297. doi: 10.1158/0008-5472.CAN-19-3101
3. Ma X, Arunachalam S, Liu Y.Applications of probability and statistics in cancer genomics. Quant Biol. 2020; 8: 95-108. doi: 10.1007/s40484-020-0203-8
4. Rusch M, Ding L, Arunachalam S, Thrasher A, Jin H, Macias M, et al.XenoCP: Cloud-based BAM cleansing tool for RNA and DNA from Xenograft. Biorxiv. 2019; 16: 53. doi: 10.1101/843250
5. Mandelker D, Kumar R, Pei X, Selenica P, Setton J, Arunachalam S, et al. The landscape of somatic genetic alterations in breast cancers from CHEK2 germline mutation carriers. JNCI Cancer Spectrum. 2019; 3(2): pkz027. doi: 10.1093/jncics/pkz027
6. Pareja F, Lee JY, Brown DN, Piscuoglio S, Gularte-Mérida R, Selenica P, et al. The genomic landscape of mucinous breast cancer. J Natl Cancer Inst. 2019; 111(7): 737-741. doi: 10.1093/jnci/djy216
7. Vaden RM, Guillen KP, Salvant JM, Santiago CB, Gibbons JB, Pathi SS, et al. A cancer-selective zinc ionophore inspired by the natural product naamidine A. ACS Chem Biol. 2019; 14(1): 106-117. doi: 10.1021/acschembio.8b00977
8. Madsen MJ, Knight S, Sweeney C, Factor R, Salama M, Stijleman IJ, et al. Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genome-wide significant breast cancer locus at 12q15. Cancer Epidemiol Biomarkers Prev. 2018; 27(6): 644-652. doi: 10.1158/1055-9965.EPI-17-0887
9. Goswamee P, Arunachalam S, Mehta S, Nasim R, Gunning WT, Giovannucci DR. Gastro-enteropancreatic neuroendocrine tumor cell dynamics in liver microvasculature. Microsc Microanal. 2015; 21(3): 655-665. doi: 10.1017/S1431927615000392
10. Arunachalam S, Zhelay T, Giovannucci DR. Molecular and Functional characterization of non-voltage operated calcium entry in gastrointestinal neuroendocrine tumor cells. Int J Physiol Pathophysiol Pharmacol; 2010; 2(2): 125-136.
11. Bechtel JM, Wittenschlaeger T, Dwyer T, Song J, Arunachalam S, Ramakrishnan SK, et al. Genomic mid-range in homogeneity correlates with an abundance of RNA secondary structures. BMC Genomics. 2008; 9: 284. doi: 10.1186/1471-2164-9-284
12. Arunachalam S, Brady SW, Ma X. Spatial heterogeneity in diffuse intrinsic pontine gliomas treated with a PDGFR inhibitor. AACR Abstract. 20201.
13. Roberts KG, Brady SW, Gu Z, Shi L, Pounds S, Pei D, et al. The genomic landscape of childhood acute lymphoblastic leukemia. ASH Blood. 2019; 124(Supplement_1): 649.
14. Arunachalam S, Nasim R, Giovannucci D. Development of an Organotypic system to image metastasis of carcinoid tumors in situ. Paper presented at: 54th Annual Meeting of the Biophysical Society; 2010; Long Beach, CA, USA.
15. Zheley T, Arunachalam S, Howard M, Giovannucci D. STIM and ORAI mediated Calcium entry in gastroenteropancreatic neuroendocrine Tumor (GEPNET) cell lines. Paper presented at: 39th Annual meeting of Society for Neuroscience; 2009; Chicago, Illinois, USA.
16. Arunachalam S, Zhelay T, Al-Jibonry H, Koehler K, Giovannucci DR. The role of store operated calcium entry (SOCE) in human neuroendocrine tumor. Paper presented at: 52nd Annual Meeting of the Biophysical Society; 2008; Long Beach, CA, USA.