Santhilal Subhash

Interested in addressing problems in molecular

biology using computational approaches

Introduction

Interests (Postdoc: Erikssonlab)

Keen to address molecular mechanisms involved in disease prognosis by integrating datasets from various high-throughput techniques. My current postdoctoral project work involves identifying somatic mutations in the vascular wall of age-related cardiovascular disease (CVD).

Ph.D. research work (Kandurilab)

I have experience in the field of cancer, noncoding RNAs, epigenetics, and chromatin biology. During my Ph.D., I worked with transcriptome (nascent and stable RNAs), chromatin immunoprecipitation (DNA and RNA), and genome (methylome) based high-throughput sequencing datasets. By analyzing genome-wide chromatin profiles, I have proposed distinct mechanisms of active and repressive chromatin-associated RNA molecules. Moreover, with an integrative approach using chromatin and transcriptome datasets of mammalian gametes, early-late developmental stages, somatic, and cancer tissues, I have identified a unique set of sperm-specific long noncoding RNAs (lncRNAs) having a role in multiple cancer. Additionally, using the nascent RNA sequencing approach and PAN-cancer datasets (transcriptome and methylome) from The Cancer Genome Project (TCGA), I have identified cell-cycle associated oncogenic and tumor suppressor lncRNAs in multiple cancers.


Current Position & Affiliation

POSTDOCTORAL RESEARCHER

December 15, 2020-present.

Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden.

Lab Head: Prof. Maria Eriksson.

Research: Evaluating somatic mutation load in differentiated progenitor cells using single-cell approach to find cell type specific mutational hotspots.

Profile: https://staff.ki.se/people/sansub


Education

Ph.D. IN MEDICAL SCIENCE

July 2014 – December 2020.

Department of Medical Biochemistry & Cell Biology, University of Gothenburg, Sweden.

Title: Chromatin and transcriptome-based integrative approaches to profile functional long noncoding RNAs.

Ph.D. Supervisor: Prof. Chandrasekhar Kanduri

Co-supervisors: Prof. Erik Larsson Lekholm and Dr. Tanmoy Mondal.

Access Thesis: http://hdl.handle.net/2077/66195


BACHELOR OF TECHNOLOGY (B.Tech.) IN BIOINFORMATICS

Mar 2004 - May 2008.

SRM university (Chennai, Tamil Nadu, India).


Experience

START-UP

Xandrax Pharma AB

August 2020-present

Role: Deputy Board member

Objective: Long noncoding RNA to treat and diagnose cancer and other diseases and disorders.

TEACHING INSTRUCTOR

May 2017 - June 2018.

Department of Medical Biochemistry & Cell Biology, University of Gothenburg.

Supervisor and course organizer: Prof. Chandrasekhar Kanduri and Dr. Marcela Davila (Head of Bioinformatics Core Facility, Sahlgrenska Academy)

•Designing course materials for ChIP-seq in a Ph.D. level course Bioinformatics in Genomics.

•Teaching ChIP-seq analysis.

•Supervising the practical sessions.

BIOINFORMATICIAN (RESEARCH ASSISTANT)

July 2012 - June 2014.

Department of Medical Biochemistry & Cell Biology, University of Gothenburg.

Lab Head: Prof. Chandrasekhar Kanduri.

•Benchmarking transcriptome analysis pipelines.

•Analyzing RNA-seq datasets from cancer patients.

•Implementing advance visualization methods on analyzed results.


Tools and Research Networks

GeneSCF: Developer

Biostars: Moderator

LabWorm: Moderator

RELISH: Curator


Expertise

Analyzing sequencing datasets: RNA-seq (bulk & single-cell), ChIP- seq, MBD-seq, MEDIP-seq, ChRIP-seq and HiC- seq.

Hypothesis generation: Addressing important scientific questions.

Experimental designing: Suggesting wet lab experiments, replicate and comparison designs.

Developing tools: Making tools and pipelines to approach scientific problems.

Data visualization: Present informative data or results using advanced visualization techniques.

Computational skills: PERL, R language, BASH scripting, HTML, CSS, Java script and SQL.


Grant and funding

SWEDISH SOCIETY FOR MEDICAL RESEARCH (SSMF)

Type: Post-doctoral research in medical science.

Grant amount: 2,340,000 SEK

Period: July 2021- june 2023


ROYAL SWEDISH ACADEMY OF SCIENCES

Type: Postdoctoral project grant for research in Biosciences.

Grant amount: 100,000 SEK

Period: April 2021- April 2022

Project: The contribution of somatic mutations to mis-regulated regulation of LINE elements in aging.


Patents

•Long non-coding RNA in cancer (Approved 16/620700; USA).

•Cancer treatment and diagnosis involving lincRNA (Filed: 2050536-8; Sweden).