An overview of the oncology clinical trials network (CTNeT) which is being implemented throughout Texas.
The non-profit network is a first of its kind and combines the innovative science of Texas cancer centers with the expertise and resources of both academic and community oncologists throughout the state.
To learn more, visit www.ctnet.org
Epic EMR to OMOP CDM to Clinical Research Data Mart: an Unmaintained Road or ...Oksana Gologorskaya
Poster we presented at 2017 AMIA Joint Summits on Clinical and Translational Research Informatics.
In this research data delivery project, we explored a less traveled path of building a clinical data mart for a registry study on kidney transplant patients, based on the institutional instance of the EMR data, translated into the OMOP (Observational Medical Outcomes Partnership) common data model.
Remote presentation by Atul Butte at the NSTC Interagency Working Group on Biological Data Sharing on 2019-06-12.
The working group is charged by the National Science and Technology Council to develop a road map to enable robust sharing and maximize reuse of biological data, identifying opportunities for interagency coordination, and academic, industrial, and international partnerships. The workshop will bring together a diverse community of government, academic, and industrial stakeholders to identify key bottlenecks and challenges that interfere with the open exchange of information and to identify potential solutions that will accelerate biological science research.
An overview of the oncology clinical trials network (CTNeT) which is being implemented throughout Texas.
The non-profit network is a first of its kind and combines the innovative science of Texas cancer centers with the expertise and resources of both academic and community oncologists throughout the state.
To learn more, visit www.ctnet.org
Epic EMR to OMOP CDM to Clinical Research Data Mart: an Unmaintained Road or ...Oksana Gologorskaya
Poster we presented at 2017 AMIA Joint Summits on Clinical and Translational Research Informatics.
In this research data delivery project, we explored a less traveled path of building a clinical data mart for a registry study on kidney transplant patients, based on the institutional instance of the EMR data, translated into the OMOP (Observational Medical Outcomes Partnership) common data model.
Remote presentation by Atul Butte at the NSTC Interagency Working Group on Biological Data Sharing on 2019-06-12.
The working group is charged by the National Science and Technology Council to develop a road map to enable robust sharing and maximize reuse of biological data, identifying opportunities for interagency coordination, and academic, industrial, and international partnerships. The workshop will bring together a diverse community of government, academic, and industrial stakeholders to identify key bottlenecks and challenges that interfere with the open exchange of information and to identify potential solutions that will accelerate biological science research.
The Uneven Future of Evidence-Based MedicineIda Sim
An Apple ResearchKit study enrolled 22,000 people in five days. A
study claims that Twitter can be used to identify depressed patients. A computer program crunches genomic data, the published literature, and electronic health record data to guide cancer treatment. The pace, the data sources, and the methods for generating medical evidence are changing radically. What will — what should — evidence-based medicine look like in a faster, personalized, data-dense tomorrow?
- Presented as the 3rd Annual Cochrane Lecture, October 2015 in Vienna, Austria.
Atul Butte's presentation to the Association of Medical School Pediatric Department Chairs #AMSPDC on March 3, 2018.
Some pre-publication data slides have been removed from this deck.
The reality of moving towards precision medicineElia Stupka
How do we move towards precision medicine? How can we deliver on the big data in health promise? Who will be the enablers and players? Pharma, Big Tech, or newcomers?
2015 09-14 Precision Medicine 2015, London, Alain van GoolAlain van Gool
Outline of my view hoe personalized health(care) is more than just targeted medicines, also including personal motivation and actions towards disease prevention. It also outlines 4 key factors that should be in order for optimal personalized health(care): 1. start with patients first, 2. Accelerate translation research to application, 3. Copy best practice, 4. Spread the word.
The Uneven Future of Evidence-Based MedicineIda Sim
An Apple ResearchKit study enrolled 22,000 people in five days. A
study claims that Twitter can be used to identify depressed patients. A computer program crunches genomic data, the published literature, and electronic health record data to guide cancer treatment. The pace, the data sources, and the methods for generating medical evidence are changing radically. What will — what should — evidence-based medicine look like in a faster, personalized, data-dense tomorrow?
- Presented as the 3rd Annual Cochrane Lecture, October 2015 in Vienna, Austria.
Atul Butte's presentation to the Association of Medical School Pediatric Department Chairs #AMSPDC on March 3, 2018.
Some pre-publication data slides have been removed from this deck.
The reality of moving towards precision medicineElia Stupka
How do we move towards precision medicine? How can we deliver on the big data in health promise? Who will be the enablers and players? Pharma, Big Tech, or newcomers?
2015 09-14 Precision Medicine 2015, London, Alain van GoolAlain van Gool
Outline of my view hoe personalized health(care) is more than just targeted medicines, also including personal motivation and actions towards disease prevention. It also outlines 4 key factors that should be in order for optimal personalized health(care): 1. start with patients first, 2. Accelerate translation research to application, 3. Copy best practice, 4. Spread the word.
The changing face of digital: "Once upon a time…” & the power of storytellingHamish Anderson
How storytelling is coming back to shape the way we digest information
Take a look at how consumers are digesting information and the way which the internet is changing as a result.
See how story telling can break down information into digestible, easy to consume and share snippets that people connect with.
Ultimately, the question is Do you do what you’ve always done or what people want?
TCGC The Clinical Genome Conference 2015Nicole Proulx
Bio-IT World and Cambridge Healthtech Institute are again proud to host the Fourth Annual TCGC: The Clinical Genome Conference, inviting stakeholders impacting clinical genomics to share new findings and solutions for advancing the applications of clinical genome medicine.
This year's 3rd Annual TCGC: The Clinical Genome Conference, held June 10-12, 2014 in San Francisco, is a three-day event that weaves together the science of sequencing and the business of implementing genomics in the clinic. It uniquely illustrates the mutual influence of those areas and the need to therefore consider the needs, challenges and opportunities of both - from next-generation sequencing and variant interpretation to insurance reimbursement and electronic health records - throughout the entire research process.Learn more at http://www.clinicalgenomeconference.com
Join us in Boston this coming Fall to attend Cambridge Healthtech Institute's (CHI) 2nd Annual FAST: Functional Analysis & Screening Technologies Congress on November 17-19, 2014 and meet with a community of 250+ biologists, screening managers, assay developers, engineers and pharmacologists dedicated to improving in vitro cell models and phenotypic screening to advance drug discovery and development at 6 conferences: Phenotypic Drug Discovery (Part I & II), Engineering Functional 3D Models, Screening and Functional Analysis of 3D Models, Organotypic Culture Models for Toxicology and Physiologically-Relevant Cellular Tumor Models for Drug Discovery. Delegates have the opportunity to share insights in interactive panel discussions and connect during networking breaks. View innovative technologies and scientific research revolutionizing early-stage drug discovery in the exhibit/poster hall.
Dr. Ying Fang - Emerging swine disease diagnostics and characterization: conn...John Blue
Emerging swine disease diagnostics and characterization: connecting basic research to real-world applications - Dr. Ying Fang, Kansas State University, from the 2017 North American PRRS/National Swine Improvement Federation Joint Meeting, December 1‐3, 2017, Chicago, Illinois, USA.
More presentations at http://www.swinecast.com/2017-north-american-prrs-nsif-joint-meeting
1. Bryan Richard Soper, Ph.D.
San Francisco, CA • 415.265.6202 • brsoper@gmail.com
PROFILE
Specific knowledge of small molecule drugs and biologics in regards to mechanism of action,
clinical efficacy and adverse events, as well as the commercial marketplace
Experience mining big data and distilling relevant information for effective communication to
different target audiences
Highly collaborative and able to liaise easily with internal and external stakeholders
WORK EXPERIENCE
Medical Writer at Health Interactions Jan. 2016 – Present
Perform competitive intelligence contract work for Genentech/Roche
Develop content and presentation materials for competitive threat assessment
workshops to analyze competitor’s clinical trials and assess the potential efficacy and
probability of launch of therapies
Analyze the specificity/sensitivity of diagnostics, molecular and clinical features of
patient’s tumors, to render a quantitative assessment of a drug’s likelihood to achieve
frontline approval in a new indication that was missed by a panel of experts
Write quarterly reports and perform quality control on standard of care tables for five
Hematology / Oncology disease indications
PATENT
Bryan Soper (Sole Inventor and Assignee)
Patent number (France, U.K., Switzerland) : 1999668 Registered: Nov. 12, 2014
German patent number: 602007037897.4 Registered: Nov. 12, 2014
Japanese patent number: 5301424 Registered: June 28, 2013
International Application No. PCT/US2007/006563 Filed: March 15, 2007
Methods of Screening for and Mapping Phenotypic and Genotypic Variations in Cultured Cells
Employs a functional genomics means of discovering targets relevant to disease
Applicable in diseases capably modeled in single cells (e.g. cancer, HIV, Hep C)
Evaluates the value of a gene target against the current standard of care before
incurring the expense of therapeutic biologic or small molecule development
BIG DATA ANALYSIS
Meta-Analysis of Cancer Models and Clinical Outcomes 2010 –2011
Analyzed 324 pre-clinical treatments in 1455 experiments to test correlation to the
outcomes of 104 clinically tested treatments
Identified a dose-restricted set of data that demonstrates a statistically significant
correlation (r = -0.646, p = 0.002814) between pre-clinical experiments to phase 3
median overall survival benefit in patients
Meta-Analysis of Clinical Trial Outcomes 2012 – 2013
Analyzed 500 new investigational drugs in 1834 clinical trials listed on ClinicalTrials.Gov
to assess the need for new/better targets in non-small cell lung cancer (NSCLC)
Identified a mere 0.8% success rate in NSCLC phase 3 clinical trials in 12 years
2. BRYAN SOPER, PHD PAGE 2
ENTREPRENEURIAL EXPERIENCE
Business plan pitches 2005 – 2014
Secured meetings with leaders to pitch a business plan for drug development at:
o Roche (Head of Venture and Innovation, Jason Coloma)
o Gilead Sciences Inc. (Senior Director of Biology, Thomas Cihlar)
o Genomics Institute of the Novartis Research Foundation (Director, Peter Schultz)
o UCSF Comprehensive Cancer Center (Director, Frank McCormick)
o UCSF Center for AIDS Research (Co-director, Warner Greene)
RELATED EXPERIENCE
Innovation Accelerator Steering Committee member 2006 – 2008
RESEARCH EXPERIENCE
Postdoctoral Scholar 2007 – 2010
Staff Research Associate II 2006 – 2007
University of California, San Francisco - James McKerrow, Ph.D., M.D.
Employed patented method to identify new drug targets for HIV/AIDS, Leishmaniasis,
and Chagas disease
Investigated viral infection for transgenesis in the human parasite Schistosoma mansoni
Collaborated with Dr. Joseph DeRisi’s lab to identify endemic viruses by microarrays
Mentored students and peers by providing scientific direction and technical assistance
Initiated and organized a weekly meeting to provide scientific mentoring
Ph.D. Dissertation Research 1998 - 2005
Sloan-Kettering Institute - Kathryn V. Anderson, Ph.D.
Characterized pattern recognition receptors in the immune systems of flies and mice
Deleted a gene in mouse embryonic stem cells by homologous recombination to derive
a mouse deficient in a presumed pattern recognition receptor
Conducted genetic screens to identify genes involved in Drosophila innate immunity
Taught molecular genetics course as a graduate student instructor
EDUCATION
Ph.D., Molecular Biology 1998 - 2005
Cornell University, Weill Graduate School of Medical Sciences
Sloan-Kettering Institute, New York, NY
B.A., Molecular and Cell Biology emphasis in Genetics 1994 - 1997
University of California, Berkeley, CA
UC Berkeley MCB graduate with honors (1997)
California Alumni Leadership Scholar (1994-1997)
VOLUNTEER WORK
Head Soccer Coach (US Soccer Federation E License) 2013 - 2015
Coached mixed gender teams from U5-U7 beginner & returning leagues
Lead practices once to twice weekly for 2-3 teams during season
Parent Advisor for Early Childhood Education Steering Committee 2012 – 2014
3. BRYAN SOPER, PHD PAGE 3
CONGRESS PRESENTATIONS
B.R. Soper & K.V. Anderson. The role of Toll in distinguishing pathogens. Presented at 43rd
Annual Drosophila Research Conference. San Diego, CA, April 10-14, 2002. Abstract # 912
B.R. Soper & K.V. Anderson. Toll’s involvement in distinguishing pathogens. Presented at 42nd
Annual Drosophila Research Conference. Washington, DC, March 21-25, 2001. Abstract # 904
B.R. Soper & K.V. Anderson. Discovering Immunity: Identification of genes involved in
phagocytosis. Presented at 41st Annual Drosophila Research Conference. Pittsburgh, PA,
March 22-26, 2000. Abstract # 629
B.R. Soper, L. Sefton, T.W. Cline. A novel promoter for Sex-lethal?. Presented at 39th Annual
Drosophila Research Conference. Washington, DC, March, 1998.
TECHNICAL EXPERTISE/EXPERIENCE
DNA/RNA related
PCR, RT-PCR, quantitative PCR, cloning, plasmid construction, epitope tag fusions
Whole mount and single cell in-situ hybridizations
Southern/Northern blots
Comparative genomic hybridizations
Microarray analysis
RNA interference, siRNA, dsRNA
Animal related
Mouse husbandry, genotyping, tissue dissection and isolation of cell types
Single blastocyst isolations from timed pregnancies
Reverse perfusions, IP and tail vein injections
Protein related
Recombinant protein expression/purification
Enzymatic activity and drug screening inhibition assays
Western blots, SDS PAGE, ELISAs
Cell culture related
Culturing human, murine, rodent, insect, and embryonic stem cell lines
Homologous recombination to delete genes
Flow cytometry, FACS to isolate single cell clones and establish cell lines
Primary cell culture and viral transduction
Bone marrow isolation and derivation of dendritic cells and macrophages
Recombinant viral production for transduction
Microscopy related
Confocal, compound, dissecting, fluorescent microscopy
Live cell/animal imaging/video