Anat Lavi-Itzkovitz, Ph.D.

Highly experienced and motivated bioinformatician with strong background in experimental biology. Expertise include R and Python programming, NGS analysis, pipeline development, MySQL and hands-on experience in molecular biology and biochemistry

Education

2014-2017 Postdoctoral Fellow at Bar-Ilan University, Faculty of Medicine/Engineering

2010-2012 Postdoctoral Fellow at the FAS center for Systems Biology, Physics Department,
Harvard University, Cambridge, USA

2005-2009 Ph.D. at the Weizmann Institute of Science, Department of Biological Chemistry

2002-2004 M.Sc. at Tel-Aviv University, Department of Biochemistry, magna cum laude

1999-2002 B.Sc. in Life sciences at Tel-Aviv University

Professional experience

Bioinformatician at Hazera seeds 2018-

• Lead and support global and internal R&D projects
• Develop analysis pipelines for NGS data
• Write scripts for data download, analysis, and statistics

Researcher at Augmanity Nano 2017-2018

• developed the bioinformatics pipeline for NGS analysis
• designed and managed MySQL database
• Developed customized Python script for drug discovery platform

Postdoctoral Fellow at Bar-Ilan University, Faculty of Medicine/Engineering 2014-2017

Supervisors: Dr. Meital Gal-Tanami and Prof. Gur Yaari Topic: Analysis of Next Generation Sequencing data from human liver cancer samples

• Developed a bioinformatic pipeline for analysis of genomic sequencing data
• Multivariate data analysis

Senior Researcher at Arthritis lab, Institute of Rheumatology, Tel-Aviv Sourasky medical 2013

• Lab research and management

Postdoctoral Fellow at Harvard University, FAS center for Systems Biology 2010-2012

Supervisor: Prof. Erel Levine Topic: sRNA regulation in bacteria and stem cell dynamics in C. elegans

• Data analysis
• MATLAB programming
• Provided technical expertise in Molecular biology, training students

PhD at Weizmann Institute of Science 2005-2009

Supervisor: Prof. Michael Fainzilber Topic: Network analysis and intercellular interactions of Necdin, a gene involved in a neurogenetic disorder in humans

• Used Molecular Biology and Biochemistry techniques, optimized protocols
• Characterized new protein interactions both experimentally and computationally
• Extensive experience with microscopy systems

Student instructor in Tel-Aviv University, Department of Biochemistry 2003-2004

Biochemistry lab course

MSc at Tel-Aviv University, Department of Biochemistry 2002-2004

Supervisor: Prof. Nathan Nelson Topic: Structural biology of membrane proteins over-expressed in bacteria

• Developed protocols for membrane protein purification
• Participated in patent writing

assistant at Tel-Aviv University, Department of Biochemistry 2002

Supervisor: Prof. Nathan Nelson Topic: The role of unit V in the function of V-ATPase in yeast

Research assistant at Tel-Aviv University, Department of Plant Sciences 2001

Supervisor: Prof. Nir Ohad Topic: The role of polycomb genes in tomato development

Technical skills

Computation and bioinformatics: Python, R, Linux, NGS analysis from both Illumina and Oxford Nanopore Technologies sequencing, Bash scripting, experience in cloud-based environment, Git repository, statistical data analysis, public databases (UCSC, Cosmic, Ensembl, HMP, dbSNP), microbiome analysis (MetaPhlAn, De Novo assembly tools), clustering analysis, biological network analysis (IntAct, VisANT), LaTeX.

Molecular Biology: Molecular cloning, Gateway cloning, site-directed mutagenesis, gel electrophoresis, PCR, qPCR, DNA and RNA purification from different organisms ‬‬‬‬‬‬‬‬‬‬‬‬‬‬

Biochemistry: Western Blots, SDS-PAGE, immunoprecipitation, recombinant protein expression and ‬‬‬‬‬‬‬‬‬‬purification (affinity purification, ion-exchange), sucrose gradient, protein- ‬‬‬‬‬‬protein interaction screen in yeast

Cell Biology: Cell culture, transfections, plant tissue culture and transformation, immunofluorescence, epifluorescence and ‬‬‬‬‬‬‬‬‬confocal microscopy and analysis, live cell imaging, RNAi, flow cytometry, ‬‬‬‬‬‬‬‬‬‬‬‬‬viability assays, C. elegans techniques

Publications and patents

1. Perez S., Kaspi A., Domovitz T., Davidovich A., Lavi-Itzkovitz A., Meirson T., Holmes J., Dai C., Huang C., Yu M., Chung R., Nimer A., El-Osta A., Yaari G., Stemmer S., Yu M., Haviv I., Gal-Tanamy M., “Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals”, PLoS genetics, 15 (6)

2. Perez S., Lavi-Itzkovitz A., Kaspi A., Davidovich A., Tover A., Livoff A., Solmonov E., El-Osta A., Yaari G., Stemmer S., Haviv I., Gal-Tanamy M., “High-resolution genomic profiling of liver cancer, linking etiology with epigenetic and mutation signature”, under revision in Hepatology ( shared first author)

3. Lavi-Itzkovitz A., Peterman N., Jost D*. and Levine E., “Quantitative effect of target translation on small RNA efficacy reveals a novel mode of interaction”, Nucleic Acids Research, 2014 Oct 29;42(19):12200-11

4. Peterman N., Lavi-Itzkovitz A. and Levine E., “Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity”, Nucleic Acids Research, 2014 Oct 29;42(19):12177-88

5. Lavi-Itzkovitz A., Tcherpakov M., Levy Z., Itzkovitz S., Muscatelli F. and Fainzilber M., “Functional Consequences of Necdin Nucleocytoplasmic Localization”, PLoS ONE, 7(3), e33786 (2012)

6. Nelson N., Lavi-Itzkovitz A., Leviatan S., “Soluble fusion proteins comprising heterologous polypeptides” U.S. Patent 7,989,183