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Molecular Biologist

Washington, District of Columbia, United States
November 27, 2018

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Rhishikesh R. Bargaje Ph.D.


Comprehensive experience with stem cell culture, cardiomyocyte and meso-endodermal differentiation of iPS cells, dedifferentiation of fibroblasts, small molecule screening, cell-based assays, automation, high-content imaging based screening, and flow cytometry

Extensive research experience with Single-cell gene expression analysis and integration of genome-level –omics datasets to study gene regulatory networks

Extensive molecular biology experience in designing and construction of vectors for miRNA expression, primer design, multiplexed PCR and RT-PCR based assays, immunohistochemistry, microscopy, high-content imaging based screening and next-gen sequencing methods



Stem Cell Translational Lab at NCATS, NIH, USA

Optimizing methods for cardiac and hepatic differentiation

Comprehensive characterization of automated hepatic differentiation 2018

Postdoctoral Fellow

Leroy Hood Lab at Institute for Systems Biology, USA

Identified cell fate trajectories during cardiomyocyte differentiation from iPSCs and formalized tipping points during differentiation in collaboration with team of computational biologists

Single-cell and bulk population gene expression analysis in terminally differentiated cell types using three different cutting edge single-cell technologies including drop-seq and Fluidigm

Systems-level analysis of progression of glioblastoma to identify disease-perturbed networks 2012-2018

Visiting Student for Training in Proteomics

John R. Yates Lab at The Scripps Research Institute, USA

Training in Proteomics

Identified targets for hsa-miR-34a and hsa-miR-29a using quantitative proteomics method – SILAC 2008

PhD Student

Beena Pillai Lab at Institute of Genomics and Integrative Biology, India

Analyzed transcriptomic, miRnomic and proteomic datasets in eukaryotic cells

Studied nucleosome positioning in mouse brain and liver 2006-2012


Trachana K., Bargaje R., Glusman G., Hood L. (2017) Taking Systems Medicine to Heart. Circulation Research 122

(9), 1276-1289.

Bargaje R., Trachana K., et. al., Huang S., Hood L. (2017) Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells. PNAS 114 (9), 2271-2276.

Bargaje R., Kumar M., Modak S. (2016) Consensus Phylogenetic trees of Fifteen Prokaryotic Aminoacyl-tRNA Synthetase Polypeptides based on Euclidean Geometry of All-Pairs Distances and Concatenation. bioRxiv doi:10.1101/051623.

Bargaje R.,, Yates J., Pillai B. (2012) Characterization of anti-apoptotic role of miRNAs, hsa-miR-34a and hsa- miR-29a by comparison of target finding approaches. PLoS ONE 7(8): e43243. 4411 Connecticut Ave NW, APT#201

Washington, DC 20008 +1-206-***-****

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Rhishikesh R. Bargaje Ph.D.

Bargaje R., et. al., Brahmachari V., Pillai B. (2012) Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. Nucl. Acids Res. 40(18): 8965-8978.

Modak S., Kumar M., Bargaje R. (2012) Molecular Phylogenetic Trees: Topology of Multiparametric Poly- Genic/Phenic Tree Exhibits Higher Taxonomic Fidelity than Uniparametric Trees for Mono-Genic/Phenic Traits. Evolutionary Biology: Mechanisms and Trends, 79-101.

Bargaje, R., Hariharan, M., Scaria, V., and Pillai, B. (2010) Consensus miRNA expression profiles derived from inter-platform normalization of microarray data. RNA 16(1): 16-25.

Ahluwalia, J.K., Hariharan, M., Bargaje, R., Pillai, B., and Brahmachari, V. (2009) Incomplete penetrance and variable Expressivity: Is there a microRNA connection? Bioessays 31(9):981-992 AWARDS AND FELLOWSHIPS

Best poster awards: “Genomeet–2012”, “Indian Proteomics conference: trends in translational proteomics–2011”.

Senior Research Fellowship, Aug 2008 – Aug 2011.

Travel fellowship to attend ‘Proteomics’ course at Cold Spring Harbor Laboratory, NY, USA; 2009.

Scholarship for ‘Training in Proteomics’, at The Scripps Research Institute, CA, USA; 2008.

Junior Research Fellowship, Aug 2006 – July 08.

Rajeshwar Pandey award for excellence in science, 2nd prize year 2003-04 in S. P. College, Pune. COMPUTER SKILLS

Programming in Python and R, acquainted with Linux.

Bioinformatics including gene expression data analysis, Next-Gen sequencing analysis, mass spectrometry data analysis, phylogenetics.


“Complex Systems Winter School” organized by Santa Fe Institute in Dec 2015.

“Gene Regulatory Networks for Development” course at Marine Biological Laboratories, MA, in Oct 2014.

Science and Communication Workshop organized by The Wellcome Trust/DBT India Alliance (Sept 2010).

‘Proteomics’, hands on course at Cold Spring Harbor Laboratory, NY, USA; in July 2009. EDUCATION, OUTREACH AND COMMUNICATION EXPERIENCE

Big Data Mentor Fall 2014 – Spring 2018

Valerie Logan Center for Education, Institute for Systems Biology STEP Fellow

Science Teaching Experience for Postdocs – University of Washington

Taught a seminars course – “BIO485A: Stem Cells and Gene Therapy” during winter quarter 2015


Ph.D., Biotechnology, Institute of Genomics and Integrative Biology (University of Pune) 2012 M.Sc., Zoology, University of Pune 2006

B.Sc., Zoology, S.P. College (University of Pune) 2004 4411 Connecticut Ave NW, APT#201

Washington, DC 20008 +1-206-***-****

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