Curriculum vitae

Contacts

e-mail: alexey.efanov@yahoo.com

+1-614-570-8264

Educational history

1999-2002: Ph. D in Molecular Biology, Koltzov Institute of Developmental Biology, Moscow, Russia Dissertation title: The expression of human neurotrophic genes in transgenic Drosophila lines.

2019-2022: Bellevue University, NE, US. MS in Data Science

2022- 2024: Johns Hopkins University, Sequence Analysis and Genomics, Post-Master’s Certificate

Professional training and appointments

1998-1999: Lab Assistant, Gene Biology Institute, Moscow, Russia

1999-2002: Ph.D Student, Koltzov Institute of Developmental Biology, Moscow, Russia

2002-2004: Postdoctoral Scientist, Gene Biology Institute, Moscow, Russia

2004-2015: Postdoctoral Researcher, The Ohio State University, Comprehensive Cancer Center, Columbus, OH, US

2015-2016: Research Associate, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US

2017-2018: Postdoctoral Fellow, Cleveland Clinic, Cleveland, Ohio, US

2018-2020: Project Scientist, Moores Cancer Center, San Diego, CA, US

2021-2024: Bioinformatician, Data Analyst, Koltzov Institute of Developmental Biology, Moscow, Russia (remote work).

Programming and Computer skills

Python, R, bash, awk, JavaScript, HTML, CSS, CGI (common gateway interface), regular expressions, SQL, git, GitHub, Anaconda, Jupyter lab, Ubuntu

• Data visualization
  Python: Matplotlib, Seaborn, Plotly, dash
  R: ggplot2, GGally, Plotly
• Data wrangling
  Python: Pandas, Numpy
  R: Caret, rpart
• Machine learning
  Python: Scikit-learn, statsmodels
  R: Caret, rpart
• Statistical, math packages
  Python: scipy, numpy, math, Sympy
  R
• Data mining
  Python: NumPy, Pandas, Scikit-learn, Matplotlib, Seaborn, pyspark, SciPy, NLTK, TensorFlow, Keras
  R: caret, dplyr, ggplot2, tm, igraph
• Microsoft Office (Word, PowerPoint, Excel)
  Excel:

  • math functions (ROUND, ROUNDUP, ROUNDDOWN, FLOOR, CEILING, INT, ...)
  • statistical functions (SUMIFS, COUNTIFS, AVERAGEIFS, MINIFS, MAXIFS, ...)
  • logical functions (AND, OR, IF, IFS, SWITCH, IFERROR)
  • text functions (CONCATENATE, CONCAT, TEXTJOIN, MID, LEFT, RIGHT, TRIM, PROPER, LOWER, UPPER, ...)
  • text to columns, flash fill
  • date and time functions (YEARFRAC, DAY, MONTH, NETWORKDAYS,...)
  • conditional formatting
  • sort, filtration, duplicates removal, slicers
  • VLOOKUP, HLOOKUP, MATCH, INDEX, INDIRECT
  • array functions and formulas
  • Pivot Tables, PivotCharts
  • Power Pivot (making models from several tables, making calculated columns and calculated fields using DAX (Data Analysis Expression) and so on)
  • Power Query (usage of M language to extract and transform data)
  • Power BI (making interactive graphs)

Web-design

HTML, CSS (cascading style sheets), JavaScript, CGI (common gateway interface)

Bioinformatics skills

Bulk RNA-seq, Single cell RNA-seq, Chip-Seq, DNA-seq, ATAC-Seq, Methyl-Seq

• fastq file generation: fastqc
• read's trimming: trimmomatic, cutadapt
• read mappers: STAR, bowtie2, BWA, Cell Ranger, HISAT2, Bismark
• working with SAM/BAM files: samtools
• count matrix generation: featureCounts, Cell Ranger
• count matrix analysis
• scRNA-seq: Seurat
• Bulk RNA-seq: DESeq2, edgeR
• GO and pathway analysis: clusterProfiler,enrichplot,goseq,ReactomePA
• SNPs and INDELs call, filtration, and annotation: Genomic Analysis Toolkit (GATK)

Bioconductor packges: IRanges, GenomicRanges, Homo.sapiens, Biostrings, BSgenome, Biobase, GEOquery, affy, genefilter, Rsamtools, GenomicAlignments, ArrayExpress, AnnotationDbi, Rsubread, ShortRead, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, GenomeInfoDb, ChIPseeker, UpSetR, ggupset, Herper, enrichplot, goseq, MSigDB, ReactomePA, DEseq2, edgeR, Seurat,rtracklayer, soGGi, ATACseqQC, BSgenome.Hsapiens.UCSC.hg19, pathview, gage, gageData, GO.db, GOstats, ballgown, GOfuncR, tximportData, biomaRt

Biopython

FACS skills:

Development of new flow cytometry-based assays.

• PNH platelets detection
• PNH reticulocytes detection

Cell cycle analysis by FACS using eDU, BrdU or DNA-binding dyes, such as PI, 7-AAD. Proliferation analysis by FACS using CFSE and other dyes.

Phospho-protein analysis by FACS and by xMAP technology Serum immunoglobulin and cytokine level analysis by FACS and xMAP technology.

Immunophenotyping (up to 9 markers simultaneously by FACS).

Apoptosis analysis by FACS using Annexin V, Mitoprobe DilC1 assays and other FACS (Fluorescence-activated cell sorting).

FACSVerse, Sony SH800, FACS Melody, LSR II, FACS Calibur, FACS Canto II, FACS Aria, Gallios, FC-500, xMAP( FACS-based technology), MAGPIX, Bio-Plex Bio-Rad 200, Bio-Rad ZE-5.

Molecular biology skills:

Generation of transgenic mice. Mouse genotyping, tail vein, abdominal, subcutaneous injections, and gavaging. Isolation of mouse tissues. Intracranial injections of cells.

Evaluation of mouse immune response by intravenous injection of KHL (keyhole limpet hemocyanin) or sheep red blood cells(SRBC) and following measuring of anti-KHL or anti-SRBC antibodies ELISA (Enzyme-Linked Immunosorbent Assay).

Luciferase assays.

Expression and purification of proteins in E coli Immunoprecipitation, Co-immunoprecipitation.

Calculation of colony forming units (CFU) of hematopoietic progenitor cells before treatment and after treatment using MethoCult. Calculation of the number of hematopoietic stem cells using LTC-IC.

Southern, Northern and Western Blotting, agarose electrophoresis and SDS-PAGE, isolation of a DNA fragment from the agarose gel.

PCR (polymerase chain reaction).

RT-PCR for miRNA and gene expression, primer design for reverse transcription and RT-PCR.

RT-PCR on the ViiA™ 7 Real-Time PCR System.

Cloning of genes, site-direct mutagenesis.

Maintaining mammalian cell lines both growing in suspension and adherent, transfection of mammalian cells with plasmids. Transfection of mammalian cell lines using AMAXA KIT on 4D-Nucleofector.

Isolation of human B-cells from the blood using CD19 beads, preparation of PBMC using ficoll. Test drugs in the system of cancer cells (labeled with green or other color) and PMBC. Gating the labeled population we can monitor apoptosis of the cancer cells using annexin V APC or Mitoprobe DilC1(can be seen in APC channel) assays.

Isolation of human PBMC using ficoll and beads. Isolation of human and mice’s macrophages and checking the macrophages’ response to different miRNA.

Testing new anti-cancer drugs on mammalian cell lines. Calculation of IC50.

Calculation of colony forming units (CFU) of hematopoietic progenitor cells before treatment and after treatment using MethoCult. Calculation of the number of hematopoietic stem cells using LTC-IC.

Generation of mammalian cells stably transfected with the gene of interest. Soft agar cell transformation assay.

Nanostring assay and data analysis.

Generation of recombinant adenoviruses and lentiviruses.

Gel filtration.

Affinity chromatography.

Confocal microscope.

List of publications

1. Gurnari C, Graham AC, Efanov A, Pagliuca S, Durrani J, Awada H, Patel BJ, Lichtin AE, Visconte V, Sekeres MA, Maciejewski JP. Frequency and perturbations of various peripheral blood cell populations before and after eculizumab treatment in paroxysmal nocturnal hemoglobinuria. Blood Cells Mol Dis. 2021 Mar;87:102528
2. Efanov A, Kelly LM, Liu P, Brenner AV, Little MP, Bogdanova TI, Evdokimova VN, Hatch M, Zurnadzy LY, Nikiforova MN, Yue NJ, Zhang M, Mabuchi K, Tronko MD, Nikiforov YE. "Investigation of the relationship between radiation dose and gene mutations and fusions in post-Chernobyl thyroid cancers". JNCI . 2018. Apr 1; 110(4):371-378
3. Efanov A, Zanesi N, Coppola F, Nuovo J, Bolon B, Croce CM. Human HMGA2 protein overexpressed in mice induces precursor T-cell lymphoblastic leukemia. Blood Cancer Journal. 2014. Jul 11(4).
4. Gaudio E, Paduano F, Ngankeu A, Lovat F, Fabbri M, Sun HL, Gasparini P, Efanov A, Peng Y, Zanesi N, Shuaib MA, Rassenti LZ, Kipps TJ, Li C, Aqeilan RI, Lesinski GB, Trapasso F, Croce CM. Heat shock protein 70 regulates Tcl1 expression in leukemia and lymphomas. Blood. 2013 Jan 10;121(2):351-9.
5. Gaudio E, Spizzo R, Paduano F, Luo Z, Efanov A, Palamarchuk A, Leber AS, Kaou M, Zanesi N, Bottoni A, Costinean S, Rassenti LZ, Nakamura T, Kipps TJ, Aqeilan RI, Pekarsky Y, Trapasso F, Croce CM. Tcl1 interacts with Atm and enhances NF-kB activation in hematological malignancies. Blood. 2012 Jan 5;119(1):180-7.
6. Santanam U, Zanesi N, Efanov A, Costinean S, Palamarchuk A, Hagan JP, Volinia S, Alder H, Rassenti L, Kipps T, Croce CM, Pekarsky Y. Chronic lymphocytic leukemia modeled in mouse by targeted miR-29 expression. Proc Natl Acad Sci U S A. 2010, 107(27):12210-5.
7. Efanov A, Zanesi N, Nazaryan N, Santanam S, Palamarchuk A, Croce CM and Pekarsky Y. CD5+CD23+ leukemic cell populations in Tcl1 transgenic mice show significantly increased proliferation and Akt phosphorylation. Leukemia. 2010, 24:970-5.
8. Efanov A, Palamarchuk A, (Alexey Palamarchuk and Alexey Efanov are equally contributed to the manuscript), Nazaryan N, Santanam U, Alder A, Rassenti L, Kipps T, Croce CM and Pekarsky Y. 13q14 deletions in CLL involve cooperating tumor suppressors. Blood. 2010, 115(19): 3916-3922.
9. Pekarsky Y, Palamarchuk A, Maximov V, Efanov A, Nazaryan N, Santanam U, Rassenti L, Kipps T, Croce CM. Tcl1 functions as a transcriptional regulator and is directly involved in the pathogenesis of CLL. Proc Natl Acad Sci U S A. 2008 105(50):19643-8.
10. Pekarsky Y, Santanam U, Cimmino A, Palamarchuk A, Efanov A, Maximov V, Volinia S, Alder H, Liu CG, Rassenti L, Calin GA, Hagan JP, Kipps T, Croce CM. Tcl1 expression in chronic lymphocytic leukemia is regulated by miR-29 and miR-181. Cancer Res. 2006 66(24):11590-3.
11. Palamarchuk A, Zanesi N, Aqeilan RI, Efanov A, Maximov V, Santanam U, Hagan JP, Croce CM, Pekarsky Y. Tal1 transgenic expression reveals absence of B-lymphocytes. Cancer Res. 2006, 66(12): 6014-7.
12. Palamarchuk A, Efanov A, Maximov V, Aqeilan RI, Croce CM, Pekarsky Y. Akt phosphorylates and regulates Pdcd4 tumor suppressor protein. Cancer Res. 2005 65(24):11282-6.
13. Palamarchuk A, Efanov A, Maximov V, Aqeilan RI, Croce CM, Pekarsky Y. Akt phosphorylates Tal1 oncoprotein and inhibits its repressor activity. Cancer Res. 2005, 65(11):4515-9.
14. Pavlova GV, Efanov AA, Bashkirov VN, Modestova EA, Mertsalov IB, Korochkin LI. Expression of genes coding NGF and BDNF human proteins in embryos of transgenic stocks of Drosophila melanogaster. Tsitologiia. 2002, 44(11):1104-8.
15. Pavlova GV, Efanov AA, Bashkirov VN, Modestova EA, Mertsalov IB, Korochkin LI. Expression of the human gdnf gene in a Drosophila melanogaster transgenic strain. Dokl Biochem Biophys. 2001, Jan-Feb;376:33-5.

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