Anand Mayakonda

Bioinformatics and Cancer Genomics

About Me

Hello there! Thank you for visiting my resume. I am Anand and, I am a post-doc researcher working on the Genomics and Epigenomics of myeloid and lymphoid malignancies. My research interests are in the biology of leukemia, MRD, clonal evolution, and PROTACs. Technically, I am most skilled in R, some of Python and Rust.



maftools is an R package for analysing data from large-scale cancer genome projects. This package attempts to summarize, analyze, annotate and visualize MAF files in an efficient manner either from TCGA sources or any in-house studies.


Methrix is an R package for fast and flexible DNA methylation analysis. It reads bedGraph files from bisulfite sequening results and aggregates them into coverage/beta value matrices. It supports both in-memory and on-disk h5 arrays.


Ever tried working with TCGA mutation datasets? It’s a real pain in the posterior. Well, this package tries to mitigate the issue by providing pre-compiled, curated somatic mutations from 33 TCGA cohorts along with relevant clinical information for all sequenced samples (from Broad Firehose and TCGA MC3 Project)


somaticfreq is a command line tool written in C which facilitates to get a quick overlook of known somatic hot-spots from tumor BAM files in a matter of minutes, without spending hours on variant calling and annotation.




2014 - 2017

I worked as a Research Assistant in Prof. Phillip Koeffler’s lab, on genomic landscape of various hematological cancers (AML, APL, B-ALL) during primary and relapse stages of the disease. I assisted post-doctoral research fellows and clinicians in WGS/WXS data analysis/interpretation.


Junior Research Fellow

2012 - 2013

I worked as a Junior Research Fellow in Dr. Nishant KT’s lab. I was involved in analysis of whole genome sequencing data generated from over 100 yeast tetrads during meiosis phase. We measured crossover and gene conversion events by looking at exchange of SNPs and effect of point mutation in MSH4/5 gene on recombination rate.



PhD-Cancer EpiGenomics

2018 - 2021

For my thesis, I worked on the Genetics and Epigenetics of T-Cell Acute Lymphoblastic Leukemia. I used DNA-methylation and changes in histone marks (H3K27ac/H3K4me3/H3K4me1) to study normal T-cell and thereby T-ALL development. You can find my dissertation here.



2010 - 2012

During my thesis, I analyzed publically available mRNA microarray data from over 20 human tissues and showed that human testicular transcriptome shares similarities with stem cells.



2006 - 2010

During my thesis, we took silk work pupae, crushed them, fractionated them, extracted fatty content, and converted it into Biofuel! It was a cool project (but the whole lab stinked of dead and dried worms for 6 months). We even won second place in a state-level competition.

A Little More About Me

Alongside my interests in Academic research you can also find me on Biostars. My other hobbies are,

  • Reading: checkout my bookshelf on goodreads
  • Running: checkout my runs on strava