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square Professional Skills:

  • MANAGEMENT: Coop students, graduate students, PhD, postdocs hiring and supervision (~20 years) and multiple institutional clinical study coordination and management (4 years)
  • NEXT-GENERATION SEQUENCING: deep technical expertise in the analysis of genomics (WGS and WES), transcriptomics (microarray, RNA-seq, scRNA-seq, miRNA), and proteomics (Olink, MS) datasets as well as their integration (multiomics). Familiar with the following tools: read alignments (BWA, STAR); transcript abundance estimation (Kallisto, Salmon, RSEM); somatic mutation calling (GATK, Mutect/Mutect2, Strelka, ISOWN)
  • PROGRAMMING: R, Java, Python, Perl, bash, html/CSS, PHP, JavaScript
  • SOFTWARE DEVELOPMENT: ISOWN
  • TEXT-MINING: text retrival and structure, sentiment analysis, genomic entity frequency calculation, wordclouds using pubmed.mineR, RISmed, wordcloud, tidytext, tm;
  • HIGH-THROUGHPUT DATA ANALYSIS: Pathway analysis (ORA, CROSSTALK, GSEA, SPIA, CAMERA, etc), Immune cell deconvolution (xCell, CIBERSORT, CellMix), Network analysis (CBDD, ChainRank, community clustering, network centralities), protein-protein networks (REACTOME, FunCoup, StringDB, BioPlex2, Barabasi, nWeb_IM network, Metabase from Clarivate), pathway knowledgebases (Reactome, KEGG, MSigDB)
  • DATA VISUALIZATION: RShiny, Rmarkdown, Dashboard, htmlwidgets (plot_ly, HighCharter, visNetwork, d3heatmap, DT, wordcloud2), Jupyter, Cytoscape
  • DATA RESOURCES: GEO, TCGA, ICGC, Human Protein Atlas (HPA), ExAC, dbSNP, COSMIC, ClinVar, PhosphoSitePlus, DrugBank, DGIdb, and many others
  • MOLECULAR BIOLOGY and BIOCHEMISTRY: strong background in biochemistry and molecular biology gained from eight years of wet-lab experience and leveraged by PhD in Biochemistry
  • DISEASE AREA FOCUS: working knowledge of biology (oncology, immunology, autoimmunity, osteoarthritis) and target identification
  • Firm grasp of modern statistical methods and machine learning techniques
  • DATABASE: mysql, some experience with Oracle, basic SQL
  • OTHER RELEVANT TOOLS: git/github, bitbucket, AWS, HPC, Google Analytics, enterprise software platform GENEDATA
  • TEACHING: bioinformatics workshop organization for broad research communities

square Keywords:

Drug target discovery using bioinformatics tools, biomarker identification, Machine Learning, R, Python, Rshiny, Reactome, protein pathways and networks, network biology.

square Contact me:

E-mail:
ikalats at gmail.com

square Publications:

Perform an automatic PubMed search of my publications


square My motto:

I hope my grandchildren
will think about cancer like
we think now about the Bubonic plague or smallpox.


Last updated: November 2020