Resume

• 1998

  PhD

  Genetics

• 1993

  BS

  Biochemistry

• Biochemistry

  Biotechnology

  Genetics

  Systems Biology

  Lifesciences

  R

  DNA

  Sequencing

  Computational Biology

  RT-PCR

  Bioinformatics

  Microarray Analysis

  Gene Prediction

  Cell Biology

  BioPerl

  Molecular Biology

  Molecular Genetics

  Bioconductor

  Genomics

  Science

  Plasticity regulators modulate specific root traits in discrete nitrogen environments

  Miriam L. Gifford

  Joshua A. Banta

  Manpreet S. Katari

  Jo Hulsmans

  Lisa Chen

  Daniela Ristova

  Daniel Tranchina

  Michael D. Purugganan

  Gloria M. Coruzzi

  Kenneth D. Birnbaum

  Plasticity regulators modulate specific root traits in discrete nitrogen environments

  WRKY1 mediates transcriptional regulation of light and nitrogen signaling pathways.

  Gloria M Coruzzi

  Robert A Martienssen

  W Richard McCombie

  Mariana Obertello

  Milos Tanurdzic

  Karen E Thum

  Ying Li and Indrani Mukherjee are co-first authors.

  The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants

  A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

  Molecular Basis of Disease Resistance in Banana Progenitor Musa balbisiana against Xanthomonas campestris pv. musacearum.

  Gloria M Coruzzi

  Dennis Shasha

  Rebecca S Davidson

  Juan M Cabello

  Lee Parnell Thompson

  Jonathan KelferL

  Felipe F Aceituno

  Steve D Nowicki

  VirtualPlant: a software platform to support systems biology research

  QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties

  Namikonga and Albert

  TCF7L1 Modulates Colorectal Cancer Growth by Inhibiting Expression of the Tumor-Suppressor Gene EPHB3

  Elena A Vidal

  Tomás C Moyano

  Gabriel Krouk

  Manpreet S Katari

  Milos Tanurdzic

  W Richard McCombie

  Gloria M Coruzzi

  Rodrigo A Gutiérrez

  Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots

  AA Myburg

  F Kapinga

  Inosthers Nzuki

  JV Bredeson

  QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii.

  VirtualPlant integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data. The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses.

  PNI Innovation: Phylogenomic Network Inference

  Constructed a machine-learning framework to infer correlation in a little-studied target species based on experiments in well-studied and fully-sequenced source species.\nDeveloped the pipeline of Phylogenomic Network Inference (PNI) Model on larger Expression Data using Java

  shell and parallel computing.

  Enabling individualized therapy for Prostate Cancer Patients

  Project: Enabling individualized therapy for Prostate Cancer Patients\n- Developed biomarker discovery pipeline using R for high-throughput gene expression and proteomic array data analysis. \n- Employed this tool to identify candidate biomarker signatures for separating aggressive vs. indolent prostate cancers

  using both supervised and unsupervised bioinformatics approaches.

  Katari

  Global Bioinformatics Solutions LLC

  New York University

  Cold Spring Harbor Laboratory

  While attending Stony Brook University for my Phd in Genetics

  my thesis advisor was W. R. McCombie at CSHL.\n\nImprove the Arabidopsis thaliana annotation by comparing to Brassica oleracea sequences.\n•\tWrote PERL scripts to automate and manage analysis of Brassica oleracea shotgun reads and used MySQL database to store results. \n•\tDesigned experiments to verify expression

  using RT-PCR

  of hypothetical genes (computationally predicted genes lacking experimental evidence) and genes not previously annotated in Arabidopsis.\n•\tIdentified 25 novel genes and detected expression for 43 hypothetical genes.\n\nVicogenta (VIewer and database for Comparing Genomes To Arabidopsis - http:/www.vicogenta.org/).\n•\tDatabase and Viewer based on the GMOD project (www.gmod.org).\n•\tProvides an interface to the database using common SQL queries.\n•\tWrote a Plugin (Vicogenta.pm) which allows user to go from Viewer to Database Interface.\n•\tDesigned to work with any GMOD database.\n•\tPublicly available at the above URL and used often by scientists at New York University and New York Botanical Garden.

  Cold Spring Harbor Laboratory

  Clinical Assistant Professor of Bioinformatics

  Enabling individualized therapy for Prostate Cancer Patients\n• In Collaboration with Dr. Alex Rai (Columbia University Department of Pathology)\n• Developed biomarker discovery pipeline using R for high-throughput gene expression and proteomic array data analysis. \n• Employed this tool to identify candidate biomarker signatures for separating aggressive vs. indolent prostate cancers

  using both supervised and unsupervised bioinformatics approaches.\n\nIdentification of Biomarkers for Brown Streak Disease susceptible in Cassava using Next-generation sequencing data\n• In collaboration with Morag Ferguson (ILRI

  Nairobi

  Kenya) \n• Identified differentially expressed genes in resistant and susceptible Cassava ecotypes by analyzing RNA-seq data from infected and un-infected leaves.\n• Identified candidate SNPs associated with resistance to virus by analyzing draft sequences from related Cassava ecotypes\n• Comparative genomics analysis of virus resistant relatives of Cassava to identify region of recent adaptations. \n\nInstructor for following Graduate level courses: \n• Biological Databases and Datamining (Weka

  R

  MySQL

  SQLite)\n• Programming for Biologists (Python)\n• Statistics in Biology(R)

  New York University

  Global Bioinformatics Solutions LLC

  Farmingdale

  NY

  Specializing in Data Management

  Data Integration

  Data Visualization

  and Analysis of High throughput Next-gen data.\n\nFormer Clients\n7/2011-10/2011\n- Client: Biotech Company based in Europe\n- Project: Statistical and Network analysis of Multivariate Microarray Gene expression data generated from a non-model organism.\n\n8/2010 - 4/2011\n- Client: IT Company in Texas\n- Project: Ideas on how to apply Semantic Web technology to Genomics research

  Owner

  VirtualPlant (Project Director): An integrated database and webserver that allows users to analyze their microarray results in the context of other publicly available functional genomic data.\n•\tDeveloped and currently maintain the VirtualPlant database in MySQL.\n•\tDatabase includes functional annotations such as Gene Ontology and Mips Funcat

  and biochemical pathways from databases such as KEGG and AraCyc

  which are used to create association between genes and their functions.\n•\tCreated a tool which automatically updates the database and is species non-specific.\n•\tCreated plugins to analyze microarrays

  create networks

  and perform functional over-representation analysis on Genes of interest.\n\nRNA-seq of Nitrogen treated Arabidopsis plants.\n•\tEvaluated tools for aligning Illumina reads to the Arabidopsis genome.\n•\tAdapted the GMOD database to store short read alignments and developed queries to generate expression data at the level of locus

  exon

  and user specified sequence intervals.\n•\tGenerate output in standard format to visualize data in common Genome viewers. \n\t\nRNA-seq analysis of ovule and sporophyll ESTs from Cycad and Ginkgo.\n•\tAssembly of reads generated by both

  ABI 3700 and Illumina

  using Velvet.\n•\tIdentification of genes differentially expressed in Ovule vs. Sporophyll\n•\tCreated pipeline to automate putative annotations of Unigenes created by Velvet and visualize results on Gbrowse.

  New York University

  Clinical Associate Professor - Biology

  NYU Bioinformatics Workshop for faculty and postdocs\t(Organizer and Instructor)\t\tLinux NGS\nBIOL-GA 1009: Biological Databases and Datamining \t(Graduate - Instructor)\t \tMySQL

  SQLite

  R

  Weka\nBIOL-GA 1007: Bioinformatics for Biologists \t\t(Graduate - Instructor) \t\tPython

  NGS

  Linux \nBIOL-GA 2031: Statistics in Biology\t\t\t(Graduate – Co-Instructor\t\tR

  Statistics\nBIOL-GA 1001: Bio Core I \t\t\t\t(Graduate - Co-Instructor) \tNGS\nBIOL-UA 103: Bioinformatics in Medicine and Biology \t(Undergraduate - Instructor) \tR

  Statistics\nBIOL-UA 124: Fundamentals of Bioinformatics \t\t(Undergraduate - Instructor)\tNGS\nBIOL-UA 038: Genome Biology \t\t\t\t(Undergraduate - Co-instructor) \tNGS\n

  New York University

  Postdoctoral Fellow

  Identify networks of nitrogen-regulated genes during seed development in Arabidopsis thaliana.\n•\tRe-designed the in-house hydroponic system allowing plant to complete life cycle.\n•\tDesigned and implemented a microarray experiment to identify nitrogen-regulated genes that are involved in seed development.\n•\tAnalyzed publicly available microarray data to identify networks that integrate seed development and nitrogen networks.

  New York University