Ashis Saha

Ashis Saha

Principal Scientific Researcher

Genentech, Inc

About me

I am a computatonal researcher at Genentech, Inc. working with Christian Hammer. I closely work with fellows in the department of Human Genetics and the department of Cancer Immunology. Earlier, I completed my Ph.D. under supervision of Dr. Alexis Battle in the Department of Computer Science at Johns Hopkins University, USA.

As a computational biologist, I try to connect Computer Science with Biology by developing biologically-informed computational methods. I incorporate biological insights into the computational models so that the outcomes are interpretable. In my current research, I investigate the roles of genetic variants in the development and evolution of tumors in order to identify and enhance understanding of novel therapeutic targets and biomarkers. I leverage various kinds of biological data from both public consortia and clinical trials in cancer immunology.

I primarily use R for my research. I also use Python, Matlab and C/C++ whenever required. I care about efficient coding and reproducible research.

Interests

  • Expression Quantitative Trait Loci (eQTL)
  • Cancer immunology
  • Translational Genomics
  • Single-cell
  • Gene Regulatory Networks

Education

  • PhD in Computer Science, 2021

    Johns Hopkins University, USA

  • MSc in Computer Engineering, 2013

    Korea University, South Korea

  • BSc in Computer Science and Engineering, 2007

    Bangladesh University of Engineering and Technology, Bangladesh

Experience

 
 
 
 
 

Principal Scientific Researcher

Genentech, Inc.

May 2021 – Present South San Fransisco, USA

I analyze biological data and apply statistical and machine learning methods in order to identify and enhance understanding of novel therapeutic targets and biomarkers. Here, my responsibilities include:

  • Analyzing large-scale genome-wide association studies (GWAS) in cancer immunology clinical trial cohorts and real world data.
  • Analyzing the roles of immunogenetic variations in determining survival and adverse events in cancer patients.
  • Investigating the impact of inherited genetic variation on tumor evolution and mutational patterns.
  • Performing integrated analyses of multidimensional molecular data sets to better understand anti-tumor immune responses.
 
 
 
 
 

Qualifying Project Developer

Langmead Lab, Johns Hopkins University

Jun 2019 – Jun 2020 Baltimore, USA
With Dr. Ben Langmead, I studied the application of sketch data structures in computational genomics. We showed that the conservative count-min sketch consistently provides more accurate estimates than the regular count-min sketch. We also developed two sketch algorithms – offline count-min sketch and offline conservative count-min sketch – that visit the k-mers multiple times to improve estimates.
 
 
 
 
 

Research Assistant

Battle Lab, Johns Hopkins University

Sep 2014 – Apr 2021 Baltimore, USA

At the Battle Lab, I worked to develop and use computational methods to understand, analyze and interpret gene regulation in humans. Here, my responsibilities included:

  • Improving accuracy and interpretability of co-expression networks,
  • Studying regulation of transcription and splicing using bulk and single-cell RNA-seq,
  • Establishing best practices for co-expression and trans-eQTL analysis,
  • Uncovering genetic effects on gene expression across diverse human tissues as part of two big consortia (GTEx and eQTLGen) and other collaborations, and
  • Mentoring junior lab members.
 
 
 
 
 

Research Assistant

Data Mining and Information Systems Lab, Korea University

Sep 2011 – Jul 2014 Seoul, South Korea

At DMIS lab, my responsibility was to

  • Develop methods to find disease-causing pathways or co-expressed genes using microarray gene expression profiles, and
  • Create tools to visualize and interpret gene interactions.
 
 
 
 
 

Software Engineer

Vizrt Bangladesh

Nov 2009 – Aug 2011 Dhaka, Bangladesh
Vizrt creates leading-edge content production tools for the digital media industry. As a Scrum Master of the Media Asset Management (MAM) application team, I designed and developed a media logger tool to annotate scenes in a video. As a developer of the Escenic Widget Framework team, I developed templates for displaying contents on a publication page.
 
 
 
 
 

Senior Software Engineer

Structured Data Systems Limited

Jun 2007 – Oct 2009 Dhaka, Bangladesh
Structured Data Systems Limited is an offshore branch of AfriGIS, a geographic information based company in South Africa. I designed and developed the javascript API framework for their map services.

Recent Publications

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(2020). Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis. In Nature Genetics (Accepted).

PDF Dataset

(2020). Novel Aggregative trans-eQTL Association Analysis of Known Genetic Variants Detect Trait-specific Target Gene-sets. In medRxiv.

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(2020). Network reconstruction for trans acting genetic loci using multi-omics data and prior information. In bioRxiv.

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(2020). ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study. In medRxiv.

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(2020). The architecture of brain co-expression reveals the brain-wide basis of disease susceptibility. In bioRxiv.

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(2019). Imputed gene associations identify replicable trans‐acting genes enriched in transcription pathways and complex traits. In Genetic Epidemiology.

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(2015). iCOSSY: An online tool for context-specific subnetwork discovery from gene expression data. In PLOS ONE.

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Extracurricular Activities

Badhan (a voluntary blood donors' organization)

Badhan has been a defining chapter for me. I have been an active volunteer for the organization since 2002. I served Badhan in different capacities including as the President of Badhan, Buet Zone in 2005. I am now a central adviser of the organization. So far I donated blood ~30 times (lost counting). The above photo was taken while donating platelets in 2010.

Photography

I’m a hobbyist photographer. Birds and wild animals especially attract me. You are welcome to visit my 500px profile to see a few of my photographs.

Travel

States and National parks I visited

I love traveling. My target is to visit every state and every national park in USA. So far I visited 31 states and 12 national parks. The pins in the above map show the states (blue pins) and national parks (red pins) I visited until September 2018.

Camping

A water-color painting by my lovely wife.

Hiking

From one of my most favorite hikes at the Old Rag Mountain, VA.

Reading Books

Reading books is one of my favorite leisure activities. The above picture shows some of my favorite popular science books I read in 2019. You are welcome to visit my goodreads profile.