Summary
Overview
Work History
Education
Skills
Interests and Hobbies
Timeline
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Sakina Saif

Needham,MA

Summary

Detail-oriented bioinformatics scientist with expertise in genomics, molecular biology, programming and data analysis tools. Skilled at working independently and collaboratively. Strong network of Key Opinion Leaders for enabling business solutions and capabilities.

Overview

20
20
years of professional experience

Work History

Sr. Bioinformatics Scientist

Cellarity
02.2020 - Current
  • Process multimodal single molecule and bulk RNA-seq data to profile baseline and perturbed differences in gene expression.
  • Perform thorough QC and analyze key metrics to communicate and deliver to stakeholders.
  • Ingest, organize and process external datasets for hypothesis generation and integration with internal data.
  • Develop and upgrade Bash, Python and R scripts for various bioinformatics pipelines and methods.
  • Interact with AWS and Saturn cloud computing resources for data processing and storage.
  • Read literature and monitor new products and pipelines to lead evaluation pilots in a methodical and timely manner, independently and collaboratively.
  • Identify process redundancies, and provide scientific and technical expertise for potential automated and scalable solutions.
  • Mentor new team members in best practices for applying bioinformatics workflows, fostering a culture of continuous improvement.
  • Maintain clear documentation for projects and analyses with attention to detail.

Data Scientist, Bioinformatics

AstraZeneca Pharmaceuticals
07.2014 - 01.2020
  • Processed whole genome and exome sequencing datasets to identify high confidence mutations, leading to translating discoveries into clinic for lung and breast cancers.
  • Analyzed pre-clinical and early-phase clinical trial datasets to understand the role of variants in resistance to targeted therapies, leading to addressing cancer progression despite standard of care therapies.
  • Developed and maintained Bash pipelines which executed best-practice Python workflows using multiprocessing.
  • Presented analysis findings and QC metrics in a clear, concise manner using visualizations that informed executive decision-making processes.
  • Identified technology vendors and implemented POC and data management solutions for growing business needs using data-driven approaches.
  • Collaborated cross-functionally with stakeholders, ensuring alignment on project goals.

Bioinformatics Analyst II

The Broad Institute
06.2004 - 06.2014
  • Generated genome assemblies for identifying polymorphism using assembler algorithms to aid large scale microbial comparative genomics analysis that contributed to many peer-reviewed publications.
  • Performed rigorous quality control checks on large datasets, ensuring reliable results during downstream analyses.
  • Developed a 16S rRNA pipeline to identify and compare microbial diversity in complex and environmental microbiome datasets.
  • Collaborated with principal investigators to identify actionable metagenomic insights for their microbial research projects.
  • Analyzed sequence information for validating shRNA clones for The RNAi Consortium library of human and mouse genes.
  • Contributed to grant proposals by generating preliminary data analysis and QC results, supporting successful funding applications.
  • Presented data at relevant conferences and published high-impact articles in peer-reviewed journals, showcasing significant achievements in genomics research.

Education

Masters Certificate - Bioinformatics

Brandeis University
Waltham, MA
06.2010

Master of Science - Biotechnology

Worcester Polytechnic Institute
Worcester, MA
05.2004

Master of Science - Biology

Science College
Jabalpur, India
04.2002

Skills

  • Platforms - Linux, AWS, Jupyter, Saturn
  • Datatypes - Single cell/nuclei, Bulk, HASH, Targeted, scGenotyping, ATAC, WGS, WES
  • Troubleshooting and Problem-Solving
  • Organization and Time Management
  • Languages - Bash, Python, R, SQL
  • Technologies - 10X, Illumina, PacBio, Nanopore, Smart-Seq
  • Communication and Critical Thinking
  • Supervision and Leadership

Interests and Hobbies

  • Yoga and Strength Training
  • Board and Card Games
  • Cooking and Bollywood Dancing

Timeline

Sr. Bioinformatics Scientist

Cellarity
02.2020 - Current

Data Scientist, Bioinformatics

AstraZeneca Pharmaceuticals
07.2014 - 01.2020

Bioinformatics Analyst II

The Broad Institute
06.2004 - 06.2014

Masters Certificate - Bioinformatics

Brandeis University

Master of Science - Biotechnology

Worcester Polytechnic Institute

Master of Science - Biology

Science College

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Sakina Saif