Deepankar Chakroborty

Deepankar Chakroborty

PhD student (Turku Doctoral Programme of Molecular Medicine)

University of Turku

Turku Bioscience

Hi!!

I am Deepankar, but I usually go by the shorter version: “Deep”. I am a PhD student enrolled at the University of Turku in Finland. I am actively involved in several projects, predominantly in the field of Cancer Genetics, which are aimed at understanding molecular mechanisms of different human cancers and identifying opportunities for developing targeted therapeutics.

During my PhD, I developed a new high-throughput screen to discern activating mutations in kinases by constructing a cDNA library encompassing all possible point-mutations in the said kinase. So far, the screen has been used to study the EGFR family of RTKs (EGFR, HER2, HER3, and HER4) and identify activating mutations and assess their druggability with various TKIs. Using my screening workflow I am also investigating therapeutic resistance to ERBB-targeted inhibitors.

I have also developed a collection of webtools using R and shiny, some of which are hosted at https://eleniuslabtools.utu.fi.

Here’s a shorter version of my CV (PDF).

Interests
  • Kinases & Kinase inhibitors
  • Receptor Tyrosine Kinases
  • Mutations in EGFR family
  • Targeted therapeutics
  • Therapeutic resistance
  • Predictive biomarkers
Education
  • PhD in Medical Biochemistry and Genetics, 2015 - now

    University of Turku, Finland

  • MSc in Bioinformatics, 2014

    University of Turku, Finland

  • B.Tech in Biotechnology, 2012

    Amity University, India

Experience

 
 
 
 
 
University of Turku
PhD student
Jan 2015 – Present Turku, Finland

Conducting Functional Genetics research at the laboratory of Prof. Klaus Elenius. My responsibilities included:

  • Planning and conducting Functional Genetics experiments
  • Mammalian cell culture & dose-response analysis (Kinase inhibitors)
  • Analysis of next-generation sequencing data
 
 
 
 
 
University of Turku
Research Assistant
Jun 2014 – Dec 2014 Turku, Finland
While working at the laboratory of Prof. Klaus Elenius. I cloned and tested some retroviral mammalian expression constructs. I also evaluated different methods of random mutagenesis.
 
 
 
 
 
Turku Centre for Biotechnology
Master’s thesis student
Nov 2013 – May 2014 Turku, Finland
Under supervision of Prof. Laura Elo, my project was to investigate an embryonic stem cell marker and its interaction partners in gene expression datasets from different cancer types.
 
 
 
 
 
Turku Centre for Biotechnology
Summer Internship
Jun 2013 – Jul 2013 Turku, Finland
During the internship (supervised by Prof. Laura Elo) my primary task was mining cancer databases (like Oncomine, GEO, ArrayExpress, etc.) and summarizing the data by performing bioinformatics analyses.

Recent Publications

Quickly discover relevant content by filtering publications.
Identification of Predictive ERBB Mutations by Leveraging Publicly Available Cell Line Databases
Identification of Predictive ERBB Mutations by Leveraging Publicly Available Cell Line Databases
L1TD1 - a prognostic marker for colon cancer
L1TD1 - a prognostic marker for colon cancer
An unbiased in vitro screen for activating epidermal growth factor receptor mutations
An unbiased in vitro screen for activating epidermal growth factor receptor mutations

Patents

L1TD1 as predictive biomarker of colon cancer
Identification of gene signature predicting positive prognosis in colon cancer using gene expression data.

Funding

Personal Grants

University of Turku Graduate School
Turku Doctoral Program of Molecular Medicine (2020)
University of Turku Graduate School
Turku Doctoral Program of Molecular Medicine (2019)
University of Turku Graduate School
Turku Doctoral Program of Molecular Medicine (2015)

Conferences

American Association for Cancer Research, Annual meeting, 2019

View poster - AACR 2019

Travel Grant

  • Syöpäjärjestöt Travel grant
  • TuDMM Travel grant
  • LIFESPAN research program, Turku Travel grant
American Association for Cancer Research, Annual meeting, 2018

View poster - AACR 2018

Travel Grant

  • Turku Doctoral programme for Molecular Medicine
  • LIFESPAN research program, Turku
EMBO course: Non-neuronal Optogenetics workshop

View poster - EMBO 2016

Travel grant

  • Turku Doctoral programme for Molecular Medicine
  • Reagent & Experiments covered by EMBO.
  • Accomodation (partial) sponsored by EMBO partners.

Hobbies

Photography

I ❤️ Primes!

🏊‍♂️
Swimming

Swim & Snorkel

Scripting

Shell, R, Python

Interests

‘Always happy to discuss these’

🎬
TV shows

The Office, Dark, Chuck

💶
Money

Equities, ETFs, #Essentialism

🕶️
Digital Privacy

Pihole, DNS resolvers, FOSS

Contact

  • Tykistökatu 6 A, Turku, Värsinäis-Suomi FI-20520