Anand Mayakonda

Bioinformatics and Cancer Genomics

About Me

Hello there! Thank you for visiting my resume. I am Anand and, I am a bioinformatics research group leader at DKFZ/KiTZ. My research interests include cancer genomics, population genetics, and tool development for open-source genomics research.

Projects

maftools

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.

trackplot

trackplot is an R is an ultra-fast, simple, and minimal dependency R script to generate IGV style track plots (aka locus plots), profile plots, and heatmaps from bigWig files.

somaticfreq

somaticfreq is a command line tool written in C that facilitates getting 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.

methrix

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

TCGAmutations

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)

TCGAmutations

Do you like Data Visualization and Rstats? This project demonstrates the usage of base R graphics (along with code and datasets) to generate visually appealing plots, without any dependencies whatsoever. I also tweet plots @baseRgraphics. Make sure to follow there for updates :)

Experience

DKFZ,KiTZ - Heidelberg

Bioinformatics research group leader

2023 - Present

Genomics of childhood cancers (primarily neuroblastoma)

Arcensus diagnostics

Bioinformatician

2022 - 2023

I am responsible for clinical whole genome sequencing analysis, identifying genetic risk factors, and implementing standardized workflows and statistical models (for ethnicity prediction, variant prioritization, in-house biobanks, etc).

CSI-Singapore

Bioinformatician

2014 - 2017

I worked as a lead bioinformatician for Prof. Phillip Koeffler’s lab. A few projects I worked on include deciphering the genomic landscape of hematological cancers (AML, APL, B-ALL), and tumoral heterogeneity in Lung cancer. I assisted post-doctoral research fellows and clinicians in WGS/WXS data analysis/interpretation.

IISER-TVM

Junior Research Fellow

2012 - 2013

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

Education

DKFZ-Heidelberg

PhD-Cancer EpiGenomics

2018 - 2021

I worked on the Genetics and Epigenetics of T-Cell Acute Lymphoblastic Leukemia for my thesis. I used DNA-methylation and changes in histone marks (H3K27ac/H3K4me3/H3K4me1) to study normal T-cell and T-ALL development. You can find my dissertation here. You can find my 20 min thesis defense PowerPoint here.

I2IT-Pune

MS-Bioinformatics

2010 - 2012

For 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.

VTU-Belagavi

BE-Biotechnology

2006 - 2010

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

A Little More About Me

Alongside my research interests, you can also find me on Biostars. Follow me on baseRgraphics Twitter handle where I tweet pretty plots created using pure base graphics without any dependencies.

My other hobbies are,

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