BOGDAN TANASA, MD, PhD

Mountain View, CA

Phone: 858-***-****

Email: ad4pmp@r.postjobfree.com

LinkedIn: linkedin.com/in/bogdan-tanasa-8411923

Google Scholar: scholar.google.com/citations?user=1l8qSO4AAAAJ&hl=en SUMMARY OF QUALIFICATIONS:

• 12+ years of experience in bioinformatics and genomics, specializing in the study of disease mechanisms using NGS technologies (ChIP-seq, RNA-seq, GRO- seq, ChIRC-seq, ChIRP-seq, WGS, WES, scRNA-seq, scATAC-seq, Hi-C).

• Published 8 articles (including a first co-author article) in Nature and contributed to publications in other prestigious scientific journals such as Molecular Cell (3), Cell (1), Cell Metabolism (1), and PNAS (2).

• Extensive knowledge of bioinformatics, genomics, epigenomics, molecular and cellular biology, immunology, oncology, genetics, medicine, and neuroscience.

• Strong experience in machine learning and deep learning.

• Proficient in R, and Python.

• Excellent communication, organizational, and time-management skills.

• Strong analytical and problem-solving abilities with a focus on investigating complex problems.

TECHNICAL SKILLS :

• Analysis of NGS data: ChIP-seq, CUT&RUN, CUT&TAG, ChIRC-seq, ATAC-seq, ChIRP-seq, RNA-seq, small RNA-seq, GRO-seq, CLIP-seq, Drug-seq, Break-seq, 4C, 5C, Hi-C, SLAM-ITseq.

• Analysis of single-cell sequencing data: scRNA-seq, scATAC-seq.

• Analysis of whole genome sequencing data (SNV, INDEL, CNA / LOH, SV, MSI, mutational signatures, HRD, complex chromosomal rearrangements).

• Programming languages: R, Python, C, shell scripting.

• Machine learning and deep learning algorithms (R, Python).

• Workflow/pipeline development: CWL, Docker, AWS. EMPLOYMENT HISTORY :

Bristol Myers Squibb, Redwood City, CA: 06/2022 – 03/2024 Senior Scientist, Applied Bioinformatics

• Developed novel normalization methods for SNAP-ChIP and CUT&RUN analysis.

• Developed novel metrics to assess chromosome instability.

• Developed CWL-based workflows for SNAP-ChIP and CUT&RUN analysis. Stanford University, School of Medicine: 10/2018 – 11/2021 Research Engineer, Department of Ophthalmology

• Performed Hi-C and CUT&TAG data analysis to characterize the epigenetic landscape of retinal ganglion cells.

• Conducted scRNA-seq analysis to identify the disease trajectory in diabetic retinopathy.

• Performed SLAM-ITseq analysis of Muller glial cells in response to optic nerve injury.

Stanford University & University of California, San Francisco: 11/2015

– 09/2018

Software Developer, Department of Pediatrics, Hematology, and Oncology

• Responsible for setting up the analytical pipelines for the identification of SNV, CNA/LOH, and SV.

• Conducted WGS analysis of pediatric cancers.

University of California, San Diego, CA: 05/2013 – 10/2015 Postdoctoral Scholar, Computational Biology : Advisor: Dr. Michael Rosenfeld

• Conducted analysis of chromatin interactions of estrogen-responsive genes using techniques such as 4C, 5C, and Hi-C.

• Developed novel algorithms for the analysis and visualization of 5C interactions.

• Established the role of pasRNA (promoter antisense RNA) in transcriptional regulation.

The Scripps Research Institute, La Jolla, CA: 07/2006 – 04/2013 PhD Graduate Student, Computational Biology

PhD Thesis: Regulatory genomics : Advisor: Dr. Michael Rosenfeld

• Developed computational analysis pipelines for genomics data analysis, including ChIP-seq, ChIRP-seq, RNA-seq, small RNA-seq, GRO-seq, CLIP-seq, RIP-seq, Drug-seq, Break-seq, 3C, 4C, 5C, and Hi-C.

• Discovered novel small RNA species (riRNAs) that regulate mRNA stability.

• Identified novel RNAs (eRNAs) that regulate estrogen-dependent gene expression.

• Established the role of long noncoding RNAs in androgen-dependent gene expression.

• Elucidated the transcriptional regulatory roles of PHF8 and GPS2.

• Identified novel GWAS loci located in enhancers that provide susceptibility alleles for coronary artery disease.

University of California, San Diego, Department of Bioengineering: 08/2007 - 04/2008

Visiting Scholar : Advisor: Dr. Trey Ideker

• Identified tissue-specific pathways by integrating gene expression profiles and protein-protein interaction networks.

Massachusetts Institute of Technology (MIT) & Center for Cancer Research & Center for Blood Research, Harvard Medical School: 11/2003 – 05/2006

Postdoctoral Scholar, Immunology : Advisor: Dr. Anjana Rao

• Discovered T-cell ORAI1 calcium channels based on integrative approaches that consisted of RNAi-based screening and linkage analysis. National University of Singapore, Department of Computer Science: 07-12/2002

Visiting Student : Advisor: Dr. Gabriel Ciobanu

• Conducted computational modeling of T cell receptor signaling pathways. Research Institute of Molecular Pathology, Vienna, Austria: 09- 10/2001

Visiting Student : Advisor: Dr. Kim Nasmyth

• Investigated proteins involved in chromosome segregation. Romanian Academy, Institute for Computer Science, Romania: 12/2001

– 01/2003

Research Student : Advisor: Dr. Gabriel Ciobanu

• Developed computational models to study T cell receptor signaling pathways. EDUCATION

The Scripps Research Institute, La Jolla, CA

Ph.D. in Computational Biology, 08/2006 - 05/2013

• Thesis: Regulatory Genomics

"Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania M.D., 10/1997 - 09/2003

CERTIFICATES

• University of California, Irvine, Division of Continuing Education

• Certificate in Data Science, 2018-2020

• "Grigore C. Moisil" High School of Computer Science, Iasi, Romania

• Certificate in Computer Science, 1993-1997

BOOK CHAPTERS and REVIEWS

1. Heissmeyer V, Tanasa B, Rao A (2006). "Peripheral Tolerance of T Cells in the Mouse." In The Mouse in Biomedical Research, vol. 3, Elsevier. 2. Ansel MK, Djuretic I, Tanasa B, Rao A (2006). "Regulation of Th2 differentiation and the IL4 locus." In Annual Review of Immunology, 24:607-656. SELECTED PUBLICATIONS

1. Yang F*, Tanasa B*, Micheletti R, Ohgi KA, Aggarwal AK, Rosenfeld MG (2021).

"Shape of promoter antisense RNAs regulates ligand-induced transcription activation." Nature, 595(7867):444-449.

2. Sayles LC, Breese MR, Koehne AL, Leung SG, Lee AG, Liu HY, Spillinger A, Shah AT, Tanasa B, Straessler K, Hazard FK, Spunt SL, Marina N, Kim GE, Cho SJ, Avedian RS, Mohler DG, Kim MO, DuBois SG, Hawkins DS, Sweet-Cordero EA (2019).

"Genome-Informed Targeted Therapy for Osteosarcoma." Cancer Discovery, 9(1):46-63.

3. Cardamone MD, Tanasa B, Cederquist CT, Huang J, Mahdaviani K, Li W, Rosenfeld MG, Liesa M, Perissi V (2018). "Mitochondrial Retrograde Signaling in Mammals Is Mediated by the Transcriptional Cofactor GPS2 via Direct Mitochondria-to-Nucleus Translocation." Molecular Cell, 69(5):757-772. 4. Tan Y, Jin C, Ma W, Hu Y, Tanasa B, Oh S, Gamliel A, Ma Q, Yao L, Zhang J, Ohgi K, Liu W, Aggarwal AK, Rosenfeld MG (2018). "Dismissal of RNA Polymerase II Underlies a Large Ligand-Induced Enhancer Decommissioning Program." Molecular Cell, 71(4):526-539.

5. Zhang F, Tanasa B, Merkurjev D, Lin C, Song X, Li W, Tan Y, Liu Z, Zhang J, Ohgi KA, Krones A, Skowronska-Krawczyk D, Rosenfeld MG (2015). "Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program." Proceedings of the National Academy of Sciences USA, 112(5):1380-1385. 6. Cardamone D, Tanasa B, Chan M, Ohgi KA, Cederquist C, Andricovich J, Rosenfeld MG, Perissi V (2014). "Promoter-specific recruitment of PPARγ in adipocytes depends on GPS2-dependent stabilization of histone demethylase KDM4A/JMJD2." Cell Reports, 8(1):163-176.

7. Hu Q, Tanasa B, Trabucchi M, Li W, Zhang J, Ohgi KA, Rose DW, Glass CK, Rosenfeld MG (2012). "DICER- and AGO3-dependent generation of retinoic acid- induced DR2 Alu RNAs regulates human stem cell proliferation." Nature Structural & Molecular Biology, 19(11):1168-1175.

8. Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, Liu WT, Ohgi KA, Benner C, Garcia-Bassets I, Aggarwal AK, Desai A, Dorrestein PC, Glass CK, Rosenfeld MG

(2010). "PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression." Nature, 466(7305):508-512.

9. Lin C, Yang L, Tanasa B, Hutt K, Ju BG, Ohgi K, Zhang J, Rose DW, Fu XD, Glass CK, Rosenfeld MG (2009). "Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancers." Cell, 139(6):1069-1083. 10. Cardamone MD, Krones A, Tanasa B, Taylor H, Ricci L, Ohgi KA, Glass CK, Rosenfeld MG, Perissi V (2012). "A protective strategy against hyperinflammatory responses requiring the non-transcriptional actions of GPS2." Molecular Cell, 46(1):91-104.

11. Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Zhang J, Merkurjev D, Ohgi K, Song X, Kim HS, Oh S, Glass CK, Rosenfeld MG (2013). "Functional importance of estrogen receptor-regulated eRNAs for ligand-dependent gene transcriptional activation program." Nature, 498(7455):516-520.

12. Gwack Y, Sharma S, Nardone J, Tanasa B, Iuga A, Srikanth S, Okamura H, Bolton D, Hogan P, Feske S, Rao A (2006). "A genome-wide Drosophila RNAi screen identifies DYRK-family kinases as novel regulators of NFAT." Nature, 441(7093):646-650.

13. Yang L*, Lin C*, Jin C, Yang J, Tanasa B, Li W, Merkurjev D, Ohgi KA, Meng D, Zhang J, Evans CP, Rosenfeld MG (2013). "LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs." Nature, 500(7464):598- 602.

14. Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA (2011). "9p21 DNA variants associated with coronary artery disease impair interferon-γ signaling response." Nature, 470(7333):264-268.

15. Feske S, Gwack Y, Prakriya M, Srikanth S, Puppel S, Tanasa B, Hogan P, Lewis R, Daly M, Rao A (2006). "A mutation in Orai1 causes immune deficiency by abrogating store operated Ca2+ entry and CRAC channel function." Nature, 441(7090):179-185.

16. Jin C, Yang L, Xie M, Lin C, Merkurjev D, Yang JC, Tanasa B, Oh S, Zhang J, Ohgi K, Zhou H, Li W, Evans CP, Ding S, Rosenfeld MG (2014). "Drug-seq: An Approach to Identify the Genomic Targets of Chemicals Identified by Functional Phenotypic Screens." Proceedings of the National Academy of Sciences USA, 111(25):9235- 9240.

17. Heimbucher T, Liu Z, Bossard C, McCloskey R, Carrano AC, Riedel CG, Tanasa B, Klammt C, Fonslow BR, Riera CE, Lillemeier BF, Kemphues K, Yates JR III, O'Shea C, Hunter T, Dillin A (2015). "The Deubiquitylase MATH-33 Controls DAF-16 Stability and Function in Development and Longevity." Cell Metabolism, 22(1):151-163. 18. Li W, Hu Y, Oh S, Ma Q, Merkurjev D, Song X, Zhou X, Liu Z, Tanasa B, He X, Chen AY, Ohgi K, Zhang J, Liu W, Rosenfeld MG (2015). "Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation." Molecular Cell, 59(2):188-202.

19. Gökmen-Polar Y, Goswami CP, Toroni RA, Sanders KL, Mehta R, Sirimalle U, Tanasa B, Shen C, Li L, Ivan M, Badve S, Sledge GW Jr. (2014). "Gene Expression Analysis Reveals Distinct Pathways of Resistance to Bevacizumab in Xenograft Models of Human ER-Positive Breast Cancer." Journal of Cancer, 5(8):633-645. 20. Chang KC, Bian M, Xia X, Madaan A, Sun C, Wang Q, Li L, Nahmou M, Noro T, Yokota S, Galvao J, Kreymerman A, Tanasa B, Hu Y, Goldberg JL (2021).

"Posttranslational Modification of Sox11 Regulates RGC Survival and Axon Regeneration." eNeuro, 8(1).

21. Xia X, Yu CY, Bian M, Sun CB, Tanasa B, Chang KC, Bruffett DM, Thakur H, Shah SH, Knasel C, Cameron EG, Kapiloff MS, Goldberg JL (2020). "MEF2 transcription factors differentially contribute to retinal ganglion cell loss after optic nerve injury." PLoS One, 15(12).

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