Manager School

Sonali Patil

**** ***** ****** #**, *** Francisco, CA 94109. Ph: 847-***-****. Email: *********@*****.***

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Summary of PhD in Biomedical Sciences with over 5-years of academic training and over 4 years of industry work experience in

Qualifications the field.

• Strong understanding of the host immune responses and signaling pathways involved during viral infection.

• Mastered a broad array of molecular and biochemical techniques including single-cell single-molecule RNA

measurement using fluorescent in situ hybridization assay, droplet digital PCR, flow cytometry, imaging flow

cytometry (AMNIS), high-throughput siRNA targeting, FACs, qRT-PCR, DNA/RNA manipulation, proficiency

with fluorescence microscopy and image analysis tools

• Proven expertise at optimizing techniques and troubleshooting them to make them scalable

• Demonstrated ability to reconstruct biological networks based manual curation and using bioinformatics tools

• Successfully collaborated on projects with other labs within the institute and with groups outside.

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Education PhD in Biomedical Sciences, Icahn School of Medicine at Mount Sinai New York, 2008 - 2014

Thesis: Single cell interferon beta response variation with virus infection

Advisor: Stuart C. Sealfon

• M.S. in Computational Molecular Biology, University of Southern California, 2000 - 2002

• M.S. in Biochemistry, University of Pune, India 1995 - 1997

• B.S. in Chemistry, University of Pune, India 1993 - 1995

Research Icahn School of Medicine at Mount Sinai, New York Apr 2008- May 2014

Experience Research conducted during PhD program at department of Neurology, Icahn school of Medicine at Mount Sinai, New

York. Research topic: Study of single cell interferon-β responses in human primary immune cells to viral infection

and bacterial lipopolysacchride

• Optimized a single-molecule, single-cell fluorescent in situ hybridization assay for mRNA measurements in human

primary immune cells, in collaboration with Dr Sanjay Tyagi (New Jersey Medical School at Rutgers University)

• Optimized a protocol for using QX100™ Droplet Digital™ PCR System, in collaboration with

Dr. James G Wetmur (Icahn school of Medicine at Mount Sinai, New York) and QX100™ research team, to

measure mRNA copy number present in low abundance in cells

• Studied the infection efficiency of a influenza A virus H1N1 strains in mouse bone marrow derived and human

monocyte derived dendritic cells

• Optimized a protocol for efficient siRNA transfection of human monocyte derived dendritic cells

Bio-Informaticist Mar 2006- Jun 2008 Mount Sinai

Medical Center, Program for Research on Immune Modeling and Experimentation (PRiME), New York, NY

PRiME is funded by NIAID to develop data based models of human dendritic cells signaling response to pathogenic

viruses

• Developed a knowledge base of signaling network of dendritic cells in response to pathogens. For more details visit

- http://goo.gl/5aASb7

• Explored and evaluated different commercial and open source, pathway building tools such as Ingenuity,

Cytoscape, and CellDesigner

• Defined specifications to develop a web publishing tool for biological pathways "Biological Pathway Publisher

(BioPP)" that converted CellDesigner outputs to web formats. Subsequently published a paper see details in the

publication section.

• Evaluated and tested “BioPathwise”, a home grown software developed to build and stimulate biological networks.

• Analyzed existing Bio Ontologies (collaborated with the Computational Immunology group at Duke University led

Dr.Thomas B. Kepler) and data standards to represent experimental data like OBI, MIAME. Worked on modifying

the Cell type Ontology and developed data standards to describe cultured cells used for immunological research

Center for Global Health Technologies (CGHT), Apr 2005- Dec 2005

Kellogg School of Management, Northwestern University

CGHT is a non-profit partnership between Abbott Laboratories, Kellogg, and University of Wisconsin to develop point-

of-care AIDS diagnostic tests and their go-to market strategy in developing countries

• Researched potential technologies, such as use of p24 antigen to measure viral load and their general acceptance

among clinicians on suitability for detection of HIV

Senior Scientist and Manager (Curation Team, Diabetes type II) Aug 2002 – Mar 2005

Connexios Life Sciences Pvt. Ltd, Bangalore, India

Connexios is a Systems Biology based drug discovery startup (with ~40 people in 2005) and was focused on building a

pathway-based drug discovery platform; website: http://connexios.com/

• Managed a 6 member cross-functional team responsible for manually curating a knowledge base capturing

molecular pathways for Diabetes type II. Built a detailed project plan for the curation process and effectively

executed it for a year, one month ahead of schedule

• Studied ontologies like MeSH, UMLS, GO, and SNOMED to help create our proprietary knowledge base. Curated

literature sources (e.g. journal articles, abstracts, books) and standardized the information into the knowledge base

• Worked closely with the software development team to design, test and optimize the pathway database, and

authored the instruction manual

• Instrumented manual reconstruction process of Diabetes type II pathways based on journal articles screened from

PubMed, books, and other public databases

• Developed a metabolic disease drug database for cardiovascular disorders, Diabetes and Obesity to capture

molecular targets and labeled/off-label uses of a drug. Used this to predict affected pathways. Single-handedly

executed this as a proof of concept for the Diabetes knowledge base project

• Obtained unique exposure to the holistic view of R&D and the business aspects of being in a startup. Was promoted

twice in a period of less than three years from an Informatics Consultant to a Senior Scientist and then to Manager

(Curation Team, Diabetes type II)

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Wet lab & Wet lab skills: Fluorescent in situ hybridization assay, Fluorescence microscopy, RT-PCR, droplet digital PCR,

Computer Flow cytometry, Imaging flow cytometry (AMNIS), FACs, siRNA transfection, ELISA, Western blot, Molecular

Skills cloning, Primary human immune cells isolation from buffy coats, (Ficoll and MACS isolations), Mammalian cell

culture

• Software and bioinformatics tools: Matlab, Image J, Microscopy image analysis software MetaMorp and

AutoQuantX2, Flow cytometry data anlysis software FlowJo, CellDesigner, DAVID, Graphpad Prism, Adobe

illustrator

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Poster & Sonali Patil, “Studying the early dynamics of interferon-β response to Newcastle disease virus in human dendritic

Oral cells”. Oral presentation at annual pharmacology and systems biology departmental retreat 2012, Icahn school of

Presentations Medicine at Mount Sinai, NewYork

• Sonali Patil, Jeremy Seto, Ganesh Viswanathan, German Nudelman, Stuart Sealfon. “A knowledge base for human

dendritic cell signaling response to pathogens” Poster presentation at 3rd Annual summer School for Computational

Immunology 2008, Yale University

• Sonali Patil, Ganesh Viswanathan, Anamika Sarkar, Fernand Hayot, Avi Ma’ayan, Myung-June Park, Adolfo

Garcia-Sastre, Ravi Iyengar and Stuart C. Sealfon."Bioinformatics-based Dendritic Cell Signaling Network and

Modeling. " poster presentation at CIVIA meeting 2006, Icahn school of Medicine at Mount Sinai, NewYork

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Honors and Selected to participate in 3rd Annual Introductory School for Computational Immunology, Funded by NIAID Aug,

Awards 2008

• Selected to participate in the workshop on Infectious Disease Ontology at Cold Spring Harbor Laboratory,

Supported by The Burroughs Welcome Fund, Sep 2007.

• Selected to participate in the summer school on Biodefense Immune Modeling Summer School at Carnegie Mellon

University and University of Pittsburg, Funded by NIAID June 2006.

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Publications Sonali Patil, Miguel Fribourg, Yongchao Ge, Mona Batish, Sanjay Tyagi, Fernand Hayot, Stuart C. Sealfon.

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-b response to viral

infection. Sci Signal. 2015 Feb 10;8(363)

• Hartmann BM, Li W, Jia J, Patil S, Marjanovic N, Martínez-Romero C, Albrecht RA, Hayot F, García-Sastre A,

Wetmur JG, Moran TM, Sealfon SC. Mouse dendritic cell (DC) influenza virus infectivity is much lower than that

for human DCs and is hemagglutinin subtype dependent. J Virol. 2013 Feb;87(3):1916-8

• Bowles R, Patil S, Pincas H, Sealfon SC. Optimized protocol for efficient transfection of dendritic cells without cell

maturation. J Vis Exp. 2011 Jul 8;(53).

• Bowles R, Patil S, Pincas H, Sealfon SC. Validation of efficient high-throughput plasmid and siRNA transfection

of human monocyte-derived dendritic cells without cell maturation. J Immunol Methods. 2010 Dec 15;363(1):21-8

• Patil S, Pincas H, Seto J, Nudelman G, Nudelman I, Sealfon SC. Signaling network of dendritic cells in response to

pathogens: a community-input supported knowledgebase. BMC Syst Biol. 2010 Oct 7;4:137

• Viswanathan GA, Seto J, Patil S, Nudelman G and Sealfon SC. Getting Started in Biological Pathway Construction

and Analysis. PLoS Comput Biol. 2008 Feb;4(2).

• Ganesh A Viswanathan, German Nudelman, Sonali Patil, Stuart C Sealfon. BioPP: A Tool for Web-publication of

Biological Networks. BMC Bioinformatics 2007, 8:168

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