Santhilal Subhash

Interested in addressing problems in molecular

biology using computational approaches

Introduction

Current postdoc work (Prof. Maria Eriksson lab)

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). In addition to that, I am analyzing single-cell RNA-seq datasets from chronic kidney disease (CKD) and Hutchinson-Gilford progeria syndrome related mouse model.

Ph.D. research work (Prof. Chandrasekhar Kanduri lab)

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

Project: Identification of somatic mutations in the vascular wall – new risk factors and targets for age-related cardiovascular disease.



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 (online 16/620700; USA).

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