Hello! I am Morteza M.Saber . Bioinformaticien and Biologist.
I am a Senior bioinformatician with more than 10 years of experience researching on various genomic and proteomic projects with the aim of developing companion diagnostics for medically important conditions such as Cancer. Areas of focus:
- Next-generation sequencing
- Machine learning
- Big data analysis
- Population genomics
- Genome-wide association study (GWAS)
Professional Skills
Python (Scripting, Big data analysis & visualization)
I have been programming in Python for biological big data analysis for more than 10 years and possess extensive experience writing python codes for parsing and analyzing various types of Genomics, transcriptomics, proteomics and epigenomics data. I also have professional experience in data visualization using matplotlib, seaborn and plotly libraries.
Next-Generation Sequencing data analysis
During my PhD studies, I have worked on multiple aspects of genomic and transcriptomic next generation sequencing data analysis including read filtering, trimming, reference mapping and variant calling. During my post-doctoral fellowship, I extended my next generation sequencing data experience to haploid microbial genomes. To do so, I have mastered dozens of well-known and widely used NGS analysis libraries including TRIMMOMATIC, BWA, SAMTOOLS, GATK, VARSCAN, PYBEDTOOLS, PYSAM, CD-HIT, ARTEMIS, etc.
Machine learning
I have developed multiple machine learning models for prediction of phenotype using genomics and clinical data both in human and microorganisms, using several well-known libraries including scikit-learn, KERAS and TPOT libraries. In addition, during my work at MIMS, I have contributed to the development of a comprehensive AI workflow to identify genomics bio-markers for accurate prediction of treatment outcome in cancer patients.
Workflow design
I have extensive experience designing bioinformatic pipelines using Snakemake workflow management tool. Leveraging snakemake, I have developed a software, named BacGWASim , for simulation of genomic and pheontypic data that is publicly available and maintained on Github platform. I have also contributed to the development of multiple bioinformatic workflows during my work at ROCHE and MIMS companies.
High-performance computing & Linux
During my PHD and POST-DOC studies and my work at industry, I have performed extensive big data analysis only feasible on High-performance computing (HPC) systems such as DDBJ computer clusters, ComputeCanada, CalculQubec and private computer clusters. Performing data analysis on HPCs requires mastery on LINUX operating system which I obtained during over 10 years of work and reasarch as bioinformatician.
Version control (GIT)
To maintain all of the code repositories including my developed tools, I extensively use GIT version control system. Maintaining and updating code repositories using GIT is also part of my daily tasks in ROCHE and MIMS companies.
Apr. 2014 -Mar. 2017
Department of Biological Science, Graduate School of Science,
University of Tokyo
Advisor Prof. Naruya Saitou
Prof. Saitou laboratory
Thesis topic: Computational and experimental analysis of evolutionary changes at Hominidae and
Hominoidea specific coding and conserved non-coding genomic elements
Sep. 2009 - Sep. 2011
Department of biological Science, Graduate School of Sceince,
University of Tarbiat Modares
Advisor Prof. Mehrdad Behmanesh
Prof. Behmanesh laboratory
Thesis topic: Investigation of CYP2C19 allele and genotype frequencies in Iranian population using
experimental and computational approaches.
Sep. 2005 –Jun. 2009
Department of biological Science, Graduate School of Science,
University of Isfahan
The main focus was on the cellular and molecular biology covering the theoretical, experimental and computational research aspects.
2022:
| Date | Type | Publication |
|---|---|---|
| Dec. 2022 | Journal |
A Creasy-Marrazzo, Morteza.M. Saber, M Kamat, LS Bailey, F Qadri, KB Basso, BJ Shapiro, EJ Nelson Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in Vibrio cholerae under anaerobic conditions Microbial Genomics, Volume 8, Issue 12 (link) |
2020:
| Date | Type | Publication |
|---|---|---|
| Nov. 2020 | Conference |
Morteza.M. Saber, Maxwell Libbrecht, Leonid Chindelevitch and B. Jesse Shapiro, Do machine learning predictors of microbial phenotype from genotype identify causal variants? Machine Learning In Computational Biology conference (MLCB), Vancouver, Canada, 2020 (pdf) |
| Jun. 2020 | Journal |
Inès Levade, Morteza M. Saber, et al, Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study The Journal of Infectious Diseases, jiaa358, https://doi.org/10.1093/infdis/jiaa358 (link) |
| Mar. 2020 | Journal |
Morteza.M. Saber, and B. Jesse Shapiro, Benchmarking genome-wide association study (GWAS) methods using simulated bacterial genotypes and phenotypes Microbial Genomics. 2020 Mar;6(3). doi: 10.1099/mgen.0.000337. (link) |
2017:
| Date | Type | Publication |
|---|---|---|
| Aug. 2017 | Journal |
Morteza.M. Saber, et al. , The hominoid-specific gene DSCR4 is involved in regulation of human leukocyte migration Accepted for publication in journal of GENES & GENETIC SYSTEMS, 2017 (link) |
| Sep. 2017 | Journal |
Morteza.M. Saber and Naruya Saitou, Silencing effect of Hominoid highly conserved non-coding sequences on embryonic brain development Genome Biology and Evolution, 9(8):2037-2048, 2017 (link) |
2016:
| Date | Type | Publication |
|---|---|---|
| Jul. 2016 | Journal |
Morteza.M. Saber, Isaac Adeyemi Babarinde, Nilmini Hettiarachchi and Naruya Saitou , Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences Genome Biology and Evolution, 8(7):2076-2092- July 2016. (link) |
| Dec. 2016 | Journal |
Morteza.M. Saber and Naruya Saitou, Evolution of coding and noncoding genomic sequences shared by humans and great apes GENES & GENETIC SYSTEMS 91 (6), 345-345 (link) |
2014:
| Date | Type | Publication |
|---|---|---|
| Feb. 2014 | Journal |
Morteza.M. Saber, Mohammadali Boroumand, Mehrdad Behmanesh M , Investigation of CYP2C19 allele and genotype frequencies in Iranian population using experimental and computational approaches Thrombosis research, 133(2):272-5 (link) |
| Date/location | Conference | Presentation title |
|---|---|---|
| 2020. Oaxaca, Mexico | Mathematics and Statistics of Genomic Epidemiology |
Do machine learning predictors of microbial phenotype from genotype identify causal variants? |
| 2020. Vancouver, Canada | Machine Learning In Computational Biology conference (MLCB) |
Do machine learning predictors of microbial phenotype from genotype identify causal variants? |
| 2020. Quebec, Canada | Society of molecular biology and evolution (SMBE) |
Benchmarking genome-wide association study (GWAS) methods using simulated bacterial genotypes and phenotypes |
| 2016. Shizuoka, Japan | Genetic Society of Japan symposium |
Evolution of coding and non-coding genomic sequences shared by humans and great apes |
| 2015. Tokyo, Japan | Evolutionary society of Japan symposium |
Global discovery of Hominidae-specific unique genomic elements in human genome |
| 2015. Vienna, Austria | Society of molecular biology and evolution (SMBE) |
Hominidae-specific coding and conserved non-coding genomic sequences |
| 2014. Jeju island, South korea | Korea, China, Japan Bioinformatics Training program |
Toward deciphering hominoid-specific genomic changes which determine their specific phenotypes |
| 2011. Tehran, Iran | National congress of biotechnology |
Investigation of CYP2C19 allele and genotype frequency in Iranian population using computational and experimental approaches |
Work Experiences
Develop computational tools to analyze and evaluate next generation sequencing data
- Create tools and methods to streamline computational analysis needed for assay development.
- Perform bioinformatic analysis required for writing white paper on various products.
- Create tools and methods to analyze next generation sequencing data analysis.
- Support regulatory presubmission and submission activities.
- Generate testing framework and modular pipeline for development.
- Contribute to new algo evaluation and implementation into analysis workflows.
- Support Bioinformatic analysis required for Assay Development activities.
Application of GWAS and machine learning techniques to identify cancer biomarkers using genomics and proteomics data.
- Provide templates for data visualization for the interface and the documentation.
- Develop methods for integrating heterogeneous Omics data.
- Create tools and methods to analyze next generation sequencing data analysis.
- Maintain MIMs common core bioinformatics libraries.
- Report Quality Assurance and Tests on bioinformatic, biostatistic and machine learning pipeline.
- Create appropriate documentation including the precise description of MIMS bioinformatic workflows.
- Mentor junior team members.
Post-doctoral researcher in Bioinformatics
Collaboration between Department of Biological Sciences at University of Montreal and Department of Computer Sciences at Simon Fraser University
Application of machine learning and deep learning techniques in deciphering the genomic elements underlying antibiotic resistance
- Extending BacGWASim simulation tool. The main objective is to develop bacterial genotype-phenotype simulation tool scalable to the needs of artificial intelligence techniques .
- Benchmarking methods of artificial intelligence. The main objective is to benchmark machine learning and deep learning techniques in their power to identify genetic determinants of antimicrobial resistance.
Post-doctoral researcher in Bioinformatics
Department of Biologcial Sciences at University of Montreal
Application of Genome-Wide Association study techniques in deciphering the genomic elements underlying antimicrobial resistance in bacterial pathogens
- Benchmarking methods of microbial GWAS. Evaluating and benchmarking the power and accuracy of Genome-wide assotiation study (GWAS) methods in discovering the genomic elements underlying microbial phenotypes
- Developing BacGWASim simultion tool. A novel tool for bacterial genotype-phenotype simulation
Post-doctoral researcher in Bioinformatics
Department of Electrical Engineering and Bioscience at University of Waseda
Application of Population and comparative genomics techniques in deciphering the role of human noncoding RNAs in cancer
- Investigating the role of human non-coding RNAs in etiology of cancer. Investigating the role of long non-coding RNAs in etiology of cancer using population, comparative and evolutionary genomics
Experimental and computational genomics research assistant
Department of Biological sciences at University of Tokyo
Identification and characterization of genomic elements underlying unique evolutionary charcteristics of humans and Great apes
- Application of routine wetlab techniques including Human Bone marrow cell culturing, Plasmid and Genomic DNA extraction, Transfection, etc.
- Application of evolutionary, comparative, population genomics and phylogenomics in investigating the role of conserved noncoding genomic elements in human evolution
- Application of genetic engineering assay and microarray data analysis in investigating the role of hominoid-specific de-novo origniated protein coding gene, Down Syndrome Critical region of 4 (DSCR4)
Teaching bioinformatics, population genetics and evolutionary genomics
- Teaching Bioinformatics and population genetics to undergraduate students
Morteza, joined my lab as post-doctoral researcher and his considerable accomplishments speak to his incredible productivity and stellar work
ethic. He built up a substantial expertise over his years in the lab. He developed, validated and applied genome-wide
association studies (GWAS) to bacterial genomes.Morteza was also a pioneer in the lab, in terms of benchmarking the use of machine-learning
(ML) approaches to microbial GWAS. He established himself as an expert in machine learning and high-performance computing, skills that
transferred well to his position as Senior Bioinformatics Scientist at the AI startup My
Intelligent Machines (mims.ai). Morteza was always a joy to work with, and was keen to assist
other lab members with his bioinformatics expertise. He is also a very clear communicator, both
in terms of writing and presenting. He works independently, but openly seeks feedback as
needed. Had it not been for another excellent career opportunity, I would have happily kept
Morteza in the lab for as long as possible!
In my lab as PhD student at the university of Tokyo and special collaborative researcher at National institute of Genetics of Japan, Dr, Saber made intriguing
discovery on novel noncoding and coding genomic elements in Hominoid by using pure computational evolutionary genomics approaches. His bioinformatics analysis on these
novel genomic elements further shed light on importance of noncoding regulatory elements in the evolution of Hominoid-specific phenotypes. Dr. Saber brough his work to
fruition in two papers published in the journal of Genome Biology and Evolution, which is leading journal on evolutionary genomics. The variety of analysis he conducted
for these papers, mainly performed on the supercomputer available at DNA Databank of Japan (DDBJ), attest to his deep understanding of evolutionary genomics, population
genetics, bioinformatics programming, Linux operating system and biostatistics. Dr. Saber is also excellent in writing research proposal proved by the fact that his proposal
on functional analysis of DSCR4 gene wone a competitive grant on 2016 awared by Japan Science Society, which he later conducted in RIKEN Nanomedical Engineering laboratory.
As Chief Scientist and Director of Nano Medical Engineering at RIKEN, which is one of the leading national
research centers in Japan, I accepted Morteza to do an internship course in my laboratory from October, 2015 to March, 2017.
His well-written research plan on functional analysis of a functionally unknown gene which he identified during his doctoral course in the University of Tokyo, received a competitive
research grant from Japan Science Society and he was able to complete the project within the specified time period in my laboratory. During his internship, he successfully
accomplished multiple scientific objectives. In computational biology research, which is his main specialty, he successfully conducted various analysis including NGS and microarray data processing, data normalization and differential
gene expression analysis. He accomplished majority of these objectives without requiring significant assistance and supervision, besides, in multiple occasions he also assisted members of my lab with his
computational and bioinformatics expertise in the analysis of Next Generation
Sequencing (NGS) and selection data.
Considering his performance, knowledge and intelligence, I believe that he possesses all the characteristics required for a strong researcher.
2016
In 2016, my research on identification and characterisation of Hominoid-specific genomic elements was chosen as research highlight of Department of population Genetics of National Institute of Genetics of Japan (NIG)
2015 - 2017
My research grant proposal entitled "Functional Analysis of DSCR4 Gene" won the 2015 Japan Science Society grant award
2013 - 2017
By passing written and oral examinations, I was awarded Japanese Government MEXT scholarship for completing my doctoral degree in University of Tokyo
2008
In two series of nation-wide written examinations across all Iranian universities, I was ranked 5th in academic olympiad of biology among 16,000 undergraduate students in biology
2008
In 2008, I obtained 1st rank in nation-wide written Master course entrance exam in Genetics and cellular and molecular biology conducted by ministry of science and technology of IRAN among more than 16000 participants.
2013
Biochemistry: 84%, Cell biology: 78%, Molecular biology and Genetics: 95%
2012
Quantitative section:84%, Verbal section: 50%
2020
2017
2014