Santhilal Subhash

Introduction

Current postdoc work (Semir Beyaz lab)

My primary objective is to explore the molecular mechanisms influencing disease prognosis through the integration of data from diverse high-throughput techniques. Presently, my research focuses on unraveling the complexity of endometrial cancer biology by investigating single-cell datasets obtained from both patients and patient-derived organoids. This involves studying immune-cancer crosstalk, with the goal of improving treatment modalities for endometrial cancer patients.

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 

March 02, 2022-present. 

Cancer Center, Cold Spring Harbor Laboratory, New York, USA.

Lab Head: Prof. Semir Beyaz.

Research: This postdoctoral research work involves analyzing single-cell datasets from patient derived organoids and tumor dataset. Focus of this research includes how different diets and microbiome influences immune system in cancer patients.

Profile: https://facultyprofiles.cshl.edu/santhilal.subhash 

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.

POSTDOCTORAL RESEARCHER 

December 15, 2020-February 24, 2022. 

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

Lab Head: Prof. Maria Eriksson.

Research: This postdoctoral research work involved identifying somatic mutations in the vascular wall of age-related cardiovascular disease (CVD). In addition to that, I analyzed single-cell RNA-seq datasets from chronic kidney disease (CKD) and Hutchinson-Gilford progeria syndrome related mouse model.

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

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).