Sahar Nohzadeh-Malakshah

*** ******* ***, ***#**

San Carlos, CA 94070

951-***-****

accaiq@r.postjobfree.com

OBJECTIVE Interested in Bioinformatics related positions where my multidisciplinary background in

Genomics and Computer Science could be utilized to develop innovative solutions for biological

problems.

EDUCATION Ph.D.

Major Field: Evolutionary Genomics

Minor Fields: Computational Biology & Crop Genomics Sep 2007– Dec 2012

Plant Biology, University of California, Riverside, GPA: 3.9/4

M.Sc.

Biotechnology Sep 2003 – Sep 2006

University of Tehran, GPA: 18/20

B.Sc.

Biotechnology Sep 1999 – June 2003

University of Tehran, GPA: 16.5/20

RESEARCH Integrated analysis of Human Next Generation Sequencing data including alignment and

EXPERIENCES genetic variation studies (single sample, multi-generational pedigree and de novo variant

calling) with different tools like BWA, NovoAlign, Seqalto, RTG, SOAP, GATK, Samtools,

PolyMutt

Develop pipelines necessary to compile, manage and evaluate complex biological data mostly

NGS data and create graphics for reporting

Determine the quality metrics (eg het/hom, Ti/Tv, ROC curves) for NGS data and improve the

analysis tools based on them

Validate the NGS analysis pipeline to find out the probable sources of errors and suggest sound

solutions accordingly

Transcriptome annotation improvement, gene expression quantification, motif finding

using RNA-Seq, ChiP-seq or microarray data

and ChiP-seq libraries) with

Evolutionary and conservation study of genes by the aid of synteny data, clustering, ..

Metagenomics Analysis of infectious diseases & strategic planning to commercialize the

related product

Cloud Computing using Amazon Web Services

Wet lab experience including Proteomics study by two-dimensional electrophoresis &

transcriptomics study by quantitative PCR

Some of the open source tools used: Samtools, Picard, VCFtools, IGV, BioPerl modules,

Bioconductor packages, SolexaQA (NGS reads quality control), MEME Suite (for motif

discovery), DAGchainer (for finding collinear regions in chromosomes), HMMER (software for

sequence homology search), ABySS (genome assembly tools)

WORK Bioinformatics Scientist at RealTimeGenomics (a fast-growing startup company in Bay

EXPERIENCES Area with it’s own pipeline for human NGS data analysis)-Feb 2013 till present

Internship at BinaTechnologies (a startup company in Bay Area with the focus on high

performance human NGS data analysis)-Fall 2012

Teaching Assistant at UC Riverside: Introduction to Genomics and Bioinformatics in

Fall 2008 & Spring 2012, Organismal Biology-Spring 2011

COMPUTER Programming: Proficient in Perl and BioPerl, R & Bioconductor, awk, working knowledge

SKILLS in Python, C++, SAS and SQL

Operating Systems: Linux (Linux clusters), Macintosh, Windows

All basic molecular and cell biology techniques

LAB SKILLS

Proteomics: High throughput differential expression analysis of proteins using two-

dimensional electrophoresis (and related softwares) and enzyme assay

PUBLICATIONS Cleary, J., Braithwaite, R., Gaastra, K., Hilbush, B., Inglis, S., Irvine, S., Jackson, A., Littin,

R., Nohzadeh-Malakshah, S., Shah, M, Rathod, M., Ware, D., Trigg, L. and De La Vega, F.

“Joint variant and de novo mutation identification on pedigrees from high-throughput

sequencing data”. BioRxiv (2014)

Nohzadeh-Malakshah, S. and Liu, R. “Refining microRNA Gene Boundaries in Cereals

Using RNA-Seq Data”. (Under review)

Nohzadeh-Malakshah, S. and Liu, R. “Evolution of Overlapping Genes and Nat-siRNAs

in Cereal Genomes”. (Under review)

Ellstrand, N., Heredia, S., Leak-Garcia, J., Heraty, J ., Burger, J., Yao, L., Nohzadeh-

Malakshah, S. and Ridley, C. “Crops gone wild: evolution of weeds and invasives from

domesticated ancestors” Evolutionary Applications, Vol 3 (2010), No. 5-6, pp. 494–504

Nohzadeh-Malakshah, S., Habibi M., Heidari, M., Hosseini Salakdeh,Gh. ”Proteomics

Reveals New Salt Responsive Proteins Associated to Rice Plasma Membrane”

Bioscience, Biotechnology, and Biochemistry, Vol. 71 (2007), No. 9 pp.2144-2154

RELEVANT Computational Method for Bimolecular Data, Advances in Bioinformatics and Genomics,

COURSES Introductory Data Structure and Algorithms, Intermediate Data Structure and Algorithms,

Biostatistics, Quantitative Genetics, Statistics for Biological Sciences

HONORS AND Five year Graduate Fellowship, University of California, Riverside

ACTIVITIES

Co-chair of Graduate Student Association (GSA) in the Department of Botany and Plant

Sciences, University of California, Riverside (2010-2011)

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