Funding, Deals & Partnerships: BIOLOGICS & MEDICAL DEVICES; BioMed e-Series; Medicine and Life Sciences Scientific Journal – http://PharmaceuticalIntelligence.com
In an announcement televised on C-Span, President Elect Joseph Biden announced his new Science Team to advise on science policy matters, as part of the White House Advisory Committee on Science and Technology. Below is a video clip and the transcript, also available at
In Data Science, A Pioneer Practitioner’s Portfolio of Algorithm-based Decision Support Systems for Operations Management in Several Industrial Verticals: Analytics Designer, Aviva Lev-Ari, PhD, RN
An overview of Data Science as a discipline is presented in
On this landscape about IT, The Internet, Analytics, Statistics, Big Data, Data Science and Artificial Intelligence, I am to tell stories on my own pioneering work in data science, Algorithm-based decision support systems design for different organizations in several sectors of the US economy:
Images on 12/7/2019
Startups:
TimeØ Group – The leader in Digital Marketplaces Design
Concept Five Technologies, Inc. – Commercialization of DoD funded technologies
MDSS, Inc. – SAAS in Analytical Services
LPBI Group – Pharmaceutical & Media
Top Tier Management Consulting: SRI International, Monitor Group;
OEM: Amdahl Corporation;
Top 6th System Integrator: Perot System Corporation;
FFRDC: MITRE Corporation.
Publishing industry: was Director of Research at McGraw-Hill/CTB.
Northeastern University, Researcher on Cardiovascular Pharmacotherapy at Bouve College of Health Sciences (Independent research guided by Professor of Pharmacology)
Pioneering implementations of analytics to business decision making: contributions to domain knowledge conceptualization, research design, methodology development, data modeling and statistical data analysis: Aviva Lev-Ari, UCB, PhD’83; HUJI MA’76
Was prepared for publication in American Friends of the Hebrew University (AFHU), May 2018 Newsletter, Hebrew University’s HUJI AlumniSpotlight Section.
Aviva Lev-Ari’s profile was up on 5/3/2018 on AFHU website under the Alumni Spotlight at https://www.afhu.org/
On 5/11/2018, Excerpts were Published in AFHU e-news.
Science and technology bring tremendous value to society in years of life and quality of life, yet the public often perceives science as difficult, irrelevant or even threatening. Moreover, the inspirational and moving stories of scientists and innovators working around the world are often hidden or misrepresented in popular culture. Whose responsibility is it to communicate science and engage the public in supporting the scientific enterprise? Can everyone be a Champion of Science and what are the solutions to enlist and engage more champions of science across generations and geographies? How do we work together to enhance transparency, accessibility and relevance of science for everyone, everywhere? Can science become more inclusive and engage hearts and not only minds?
Join this exciting session as Johnson & Johnson announces the winners of the Champions of Science – BioGENEius Storytelling Challenge, and brings together other key stakeholders in a discussion about the importance of engaging the public to fall in love in science all over again.
Seema: We need to solve the problem of the lack of trust in scientists. Some of JNJ winners of their acheivement program went on to become Nobel Laureates. Arthur Horwich and Hans Ullrich won the Jannsen Award for discovering compounds that could refold proteins, including protein chaperones. Many diseases occur because of protein misfolding like neuro-degenerative diseases.
Seema: Great science going on in Africa. JNJ wanted to showcase the great science in Africa. they awarded four individuals with storytelling award (Emily).
Dr. Horwich: got interested in science early on. Worked on N terminal mitochondrial signal peptides. also then got interested in how proteins fold and unfold and refold since the 1950s. He had changed the thinking of how proteins are processed within cells and over many years he had worked on this.
Emily Wang: Parents and schoolteachers prodded her curiosity in biology. The impact of day to day work of scientists is arduous but the little things can lead to advances that may help people. If passionate and have a great mentor then can get a foot in the door. Worked at Stanford in the lab.
Dr. Mukherjee: He likes to cure diseases, physican first, scientist second, writer third but he doesn’t separate this. In older times scientists wrote to think and true today. How we visualize the word, or use our hands, is similar. He takes the word translational research very seriously. Can you say in one sentence how this will help patients in three years?
There are multitude ways of love for science.
Dr. Pinela: loved asking big question and loved storytelling but asking bigger questions. Moved from Columbia and moved to US; loved the freedom and government funding situation at that time. Need the training and mentorship so mentors are a very big aspect in innovation as it led her to entrepreneurship. We need to use technology to disrupt and innovate.
Nsikin: A lot of mentors nurture curiosity. People like to see them in that story of curiosity. That is how is bases the PBS science videos: did a study on engagement and people wants a morality, and a science identity (an inner nerd in all of us i.e. spark the interest). The feedback if they focus on this has been positive.
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Thriving at the Survival Calls during Careers in the Digital Age – An AGE like no Other, also known as, DIGITAL, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)
Thriving at the Survival Calls during Careers in the Digital Age – An AGE like no Other, also known as, DIGITAL
Author and Curator: Aviva Lev-Ari, PhD, RN
The source for the inspiration to write this curation is described in
Unlike that little cancer conference in Chicago last week, the BIO International convention is not about data, but about the people who make up the biopharma industry.
The meeting brings together scientists, board members, business development heads and salespeople, from the smallest virtual biotechs to the largest of pharmas. It allows executives at fledgling biotechs to sit at the same tables as major decision-makers in the industry — even if it does look a little bit like speed dating.
But it’s not just a partnering meeting.
This year’s BIO also sought to shine a light on pressing issues facing the industry. Among those tackled included elevating the discussion on gender diversity and how to bring more women to the board level; raising awareness around suicide and the need for more mental health treatments; giving a voice to patient advocacy groups; and highlighting the need for access to treatments in developing nations.
Four days of meetings and panel discussions are unlikely to move the needle for many of these challenges, but debate can be the first step toward progress.
I attended the meetings on June 4,5,6, 2018 and covered in Real Time the sessions I attended. On the link below, Tweets, Re-Tweets and Likes mirrors the feelings and the opinions of the attendees as expressed in real time using the Twitter.com platform. This BioTechnology events manifested the AUTHENTICITY of Careers in the Digital Age – An AGE like no Other, also known as, DIGITAL.
The entire event is covered on twitter.com by the following hash tag and two handles:
Part 2: Top 10 books to help you survive the digital age
From Philip K Dick’s obtuse robots to Mark O’Connell’s guide to transhumanism, novelist Julian Gough picks essential reading for a helter skelter world
Here are 10 of the books that did help me [novelist Julian Gough]: they might also help you understand, and survive, our complicated, stressful, digital age.
Marshall McLuhan Unbound by Marshall McLuhan (2005) The visionary Canadian media analyst predicted the internet, and coined the phrase the Global Village, in the early 1960s. His dense, complex, intriguing books explore how changes in technology change us. This book presents his most important essays as 20 slim pamphlets in a handsome, profoundly physical, defiantly non-digital slipcase.
Ubik by Philip K Dick (1969) Pure pulp SF pleasure; a deep book disguised as a dumb one. Dick shows us, not a dystopia, but a believably shabby, amusingly human future. The everyman hero, Joe Chip, wakes up and argues with his robot toaster, which refuses to toast until he sticks a coin in the slot. Joe can’t do this, because he’s broke. He then has a stand-up row with his robot front door, which won’t open, because he owes it money too … Technology changes: being human, and broke, doesn’t. Warning: Dick wrote Ubik at speed, on speed. But embedded in the pulpy prose are diamonds of imagery that will stay with you for ever.
The Singularity Is Near by Ray Kurzweil (2005) This book is what Silicon Valley has instead of a bible. It’s a visionary work that predicts a technological transformation of the world in our lifetime. Kurzweil argues that computer intelligence will soon outperform human thought. We will then encode our minds, upload them, and become one with our technology, achieving the Singularity. At which point, the curve of technological progress starts to go straight up. Ultimately – omnipotent, no longer mortal, no longer flesh – we transform all the matter in the universe into consciousness; into us.
To Be a Machine by Mark O’Connell (2017) This response to Kurzweil won this year’s Wellcome prize. It’s a short, punchy tour of transhumanism: the attempt to meld our minds with machines, to transcend biology and escape death. He meets some of the main players, and many on the fringes, and listens to them, quizzically. It is a deliberately, defiantly human book, operating in that very modern zone between sarcasm and irony, where humans thrive and computers crash.
A Visit from the Goon Squad by Jennifer Egan (2011) This intricately structured, incredibly clever novel moves from the 60s right through to a future maybe 15 years from now. It steps so lightly into that future you hardly notice the transition. It has sex and drugs and rock’n’roll, solar farms, social media scams and a stunningly moving chapter written as a PowerPoint presentation. It’s a masterpiece. Life will be like this.
What Technology Wants by Kevin Kelly (2010) Kelly argues that we scruffy biological humans are no longer driving technological progress. Instead, the technium, “the greater, global, massively interconnected system of technology vibrating around us”, is now driving its own progress, faster and faster, and we are just caught up in its slipstream. As we accelerate down the technological waterslide, there is no stopping now … Kelly’s vision of the future is scary, but it’s fun, and there is still a place for us in it.
The Meme Machine by Susan Blackmore (1999) Blackmore expands powerfully and convincingly on Richard Dawkins’s original concept of the meme. She makes a forceful case that technology, religion, fashion, art and even our personalities are made of memes – ideas that replicate, mutate and thus evolve over time. We are their replicators (if you buy my novel, you’ve replicated its memes); but memes drive our behaviour just as we drive theirs. It’s a fascinating book that will flip your world upside down.
Neuromancer by William Gibson (1984) In the early 1980s, Gibson watched kids leaning into the screens as they played arcade games. They wanted to be inside the machines, he realised, and they preferred the games to reality. In this novel, Gibson invented the term cyberspace; sparked the cyberpunk movement (to his chagrin); and vividly imagined the jittery, multi-screened, anxious, technological reality that his book would help call into being.
You Are Not a Gadget: A Manifesto by Jaron Lanier (2010) Lanier, an intense, brilliant, dreadlocked artist, musician and computer scientist, helped to develop virtual reality. His influential essay Digital Maoism described early the downsides of online collective action. And he is deeply aware that design choices made by (mainly white, young, male) software engineers can shape human behaviour globally. He argues, urgently, that we need to question those choices, now, because once they are locked in, all of humanity must move along those tracks, and we may not like where they take us. Events since 2010 have proved him right. His manifesto is a passionate argument in favour of the individual voice, the individual gesture.
All About Love: New Visions by bell hooks (2000) Not, perhaps, an immediately obvious influence on a near-future techno-thriller in which military drones chase a woman and her son through Las Vegas. But hooks’s magnificent exploration and celebration of love, first published 18 years ago, will be far more useful to us, in our alienated digital future, than the 10,000 books of technobabble published this year.All About Love is an intensely practical roadmap, from where we are now to where we could be. When Naomi and Colt find themselves on the run through a militarised American wilderness of spirit, when GPS fails them, bell hooks is their secret guide.
Part 3: A case study on Thriving at the Survival Calls during Careers in the Digital Age: Aviva Lev-Ari, UCB, PhD’83; HUJI, MA’76
On June 10, 2018
Following, is a case study about an alumna of HUJI and UC, Berkeley as an inspirational role model. An alumna’s profile in context of dynamic careers in the digital age. It has great timeliness and relevance to graduate students, PhD level at UC Berkeley and beyond, to all other top tier universities in the US and Europe. As presented in the following curations:
Professional Self Re-Invention: From Academia to Industry – Opportunities for PhDs in the Business Sector of the Economy
Pioneering implementations of analytics to business decision making: contributions to domain knowledge conceptualization, research design, methodology development, data modeling and statistical data analysis: Aviva Lev-Ari, UCB, PhD’83; HUJI, MA’76
Unemployment figures of PhDs by field of science are included, Ankita Gurao identifies the following four alternative careers for PhDs in the non-academic world:
Phase 2: Corporate Applied Research in the US, 1985 – 2005
Phase 3: Career Reinvention in Health Care, 2005 – 2012
Phase 4: Electronic Scientific Publishing, 4/2012 to present
These four phases are easily mapped to the four alternative careers for PhDs in the non-academic world. One can draw parallel lines between the four career opportunities A,B,C,D, above, and each one of the four phases in my own career.
Namely, I have identified A,B,C,D as early as 1985, and pursued each of them in several institutional settings, as follows:
A. Science Writer/Journalist/Communicator – see link above for Phase 4: Electronic Scientific Publishing, 4/2012 to present
B. Science Management – see link above for Phase 2: Corporate Applied Research in the US, 1985 – 2005 and Phase 3: Career Reinvention in Health Care, 2005 – 2012
C. Science Administration – see link above for Phase 2: Corporate Applied Research in the US, 1985 – 2005and Phase 4: Electronic Scientific Publishing, 4/2012 to present
D. Science Entrepreneurship – see link above for Phase 4: Electronic Scientific Publishing, 4/2012 to present
Impressions ofMy Days at Berkeley in Recollections: Part 1 and 2, below.
Recollections: Part 1 – My days at Berkeley, 9/1978 – 12/1983 –About my doctoral advisor, Allan Pred, other professors and other peers
The topic of Careers in the Digital Age is closely related to my profile, see chiefly: Four-phase Career,Reflections, Recollections Parts 1 & 2 and information from other biographical sources, below.
Corporate Applied Research in the US, 1985 – 2005 – Data Science at its BEST
Twenty years of top-tier management consulting and as a corporate executive. In the corporate world, I worked for Fortune 50, using the principles of Statistical Modeling, Economic Geography and of Industrial Organization Economics, every day.
1985-2005, worked at Director Level with Start-ups and Fortune 100 companies making presentations at the CEO Board Room level. Is reinventing work so that it works for the digital global economy. Consults and speaks to large and small groups. Lead webinars for universities, corporations and associations, and generally stir up conversation and inquiry on industry trends. Startups: TimeØ Group, Concept Five Technologies, Inc., MDSS, Inc.; Top Tier Management Consulting: SRI International, Monitor Group; OEM: Amdahl Corporation; Top 6th System Integrator: Perot System Corporation; FFRDC: MITRE Corporation. In the Publishing industry: was Director of Research at McGraw-Hill/CTB. Researcher on Cardiovascular Pharmaco-therapy at Bouve College of Health Sciences, Northeastern University.
In 4/2012, have launched LPBI Group. She is an Executive-Entrepreneur with high energy and passion. Followed by 6200 Biotech professionals on LinkedIn and Group Manager of three Groups on LinkedIn.
Cardiovascular pharmacology-therapy research, development of a combination drug therapy, 2006-2007, Northeastern University, with Prof. Paul Aburjaily, PharmD
In 2015, Margot Gerritsen, director of Stanford’s Institute for Computational and Mathematical Engineering, got tired of technical conferences that included no or few women speakers. “I always joke that this meeting was a revenge effect,” she said. “We wanted to showcase really amazing work that’s being done by women.”
Now, in its third year, the Women in Data Science conference included 17 women speakers and roughly 100,000 people listening on live stream or Facebook Live. More than 170 regional events in over 50 countries also featured their own panels of women speakers. Gerritsen, who is also a professor of energy resources engineering, said one reason for the meeting is to inspire women to enter and stay in the field of data science. “It’s still really tough for women not to feel a little isolated,” she said.
One outcome of the event has been lists of women worldwide who can speak about data science that are now regularly provided to meeting organizers looking for women speakers. “I would never have imagined that we would be reaching so many people,” Gerritsen said.
Women who attended the meeting reflected on their own experiences and the value of a community of inspiring women.
“As we have more women involved in data science and computer science and machine learning, companies can be shaped more by women. I think it’s always better to have a diverse perspective. Taking a different approach might lead to different conclusions or different innovations, both in terms of theory and in terms of products that are changing the way we live. More balanced input from both men and women would be beneficial for everyone.” —Lan Huong Nguyen, PhD candidate, computational and mathematical engineering
“I saw so many data science conferences where there were no female speakers or just one or two. I would ask the organizers why are there no women. One time they said, ‘Well, Margot, you couldn’t make it, so that’s why.’ At some point we said it is so hard to get existing conferences to change and we wanted to just totally cancel any argument that you cannot find excellent women. That first WiDS conference we live streamed because we thought it would be nice to try. It was such a success and we realized, ‘Oh my goodness, we are hitting something that people are so hungry for.’ But it is a bit pathetic we still have to do this in 2018. Honestly, there are so many fabulous women. At the start today I joked, ‘When you look at the program you see technical panels with really outstanding work by outstanding people and you may realize they are all women. We really tried to find some male data scientists but we just couldn’t find any.’” —Margot Gerritsen, PhD ’97, director of the Institute for Computational and Mathematical Engineering
“Lately I’ve been trying to find inspirational women and looking for a role model, especially in STEM fields. It’s good to see that you have all these opportunities and there are people doing interesting things. People like you. It opens up a world of opportunities. In my country when I was growing up, women were expected to enter fields of either education or medicine, but I didn’t find myself in either field. I was on a scholarship from a company to study geophysics, but beyond the technical expertise the job required I didn’t know what other things I could do. I think this meeting shows you what options you have out there and how far you can go. It makes me believe in myself more and what I could do and the difference I can make in the world when I see all these women making a difference.” —Fatimah Al-Ismail, PhD candidate, geophysics
“Data science occurred to me a year or so ago as a way to bring together the aspects I love about history with the skills I enjoy about math. Because the subjects I’m studying don’t lead directly into an application of data science, it was very cool this morning to see women applying data science in a range of ways and realizing how many options there are to be excited about. Over the next year, I will be writing a thesis on the way American media interpreted and potentially influenced the Tiananmen Square protests in 1989. I have been trying to figure out how to incorporate a data study or data visualization into that project. Being here today makes me much more comfortable about reaching out to people at Stanford and excited to talk and ask for advice.” —Emily Shaw, ’19, history and math
“The very first time I was in a group of women like this was as a speaker at the conference for undergraduate women in physics. For me, that first time speaking to a group of women was totally mind-blowing. It’s just such an interesting energy. It feels so warm. I’m in a field that is about 15 percent women. In fields like mine and in certain areas of tech, some women do persist, but it’s not like it’s just the best women. It’s the women who are willing to put up with a certain level of isolation, and that means we are losing a lot of good people. I love my life and I love my job and I love my work, and it’s an incredible privilege to think about the biggest questions that we have. I just wish there were people from a broader set of groups who were able to ask those questions. Those are really universal questions that matter to everybody.” —Risa Wechsler, associate professor of physics and of particle physics and astrophysics
“When I was doing my PhD, the joke was that if you told people you were a statistician, then it would end the conversation. That’s no longer the case. Now people are interested in statistics and data science and machine learning. It’s really fun to be part of a field that people appreciate and see a need for. I don’t think a conference like this would have been possible 5 or 10 years ago. It’s really wonderful to see enthusiasm for data science, and especially enthusiasm among young women today for data science. It’s so important for these young budding data scientists to have the opportunity to interact with people who are more senior in the field and to have role models. We’ve heard talks about how it’s important to take risks in your career. I think there are a lot of risk takers in that room, and it’s pretty inspiring.” —Daniela Witten, BS ’05, MS ’06, PhD ’10, associate professor of statistics and biostatistics, University of Washington
“My mom was a computational mathematician. It seemed normal to me growing up. Then as I grew older, I saw that it actually wasn’t that common. That’s why this meeting is so important for young girls to see these strong figures. Just to see so many strong women in the room together and know how that can encourage girls through the process is very important and powerful. I’ll be joining Amazon as a data science researcher, so it is encouraging to see people not only from academia but also in industry. It makes me feel more confident moving forward.” —Danielle Maddix, PhD candidate, computational and mathematical engineering
“When I first got interested in science, I really wasn’t aware that there was this disparity. I now realize that it’s such a big issue. It’s really important that there are events like this where you are inspiring other women to be interested in science and saying it’s OK. I have been working for the Institute for Computational and Mathematical Engineering and helping organize a list of potential speakers for this conference, and it’s been so exciting to read about all the women and their accomplishments. I’m interested in combining computer science with my bioengineering major, and I know those fields involve a lot of data science. That’s why I’m here. Seeing the speakers in person and seeing the passion they have about their fields and how far they’ve come is amazing. You can really feel the energy in the room.” —Bianca Yu, ’20, bioengineering
“I run the big math women’s group. As a grad student here I was a member of the mechanical engineering women’s group, and that was hugely important in my student experience. I tried to replicate that now that I’m a position to help. A lot of our women graduate students in math broadly speaking sometimes find themselves a little bit isolated, so we’re trying to build more of a sense of a community for them. They may be the only women in the research group or one of only a handful in their department or program. If we want to keep people in the pipeline, we don’t want them to be discouraged. I got really jazzed today when I got to sit in a room full of women in a technical meeting. Being here was a day of inspiration that I allowed myself in my really busy schedule.” —Alison Marsden, associate professor of pediatrics and of bioengineering
“One fact about Stanford Graduate School of Education is that it is extremely interdisciplinary, and there’s quite a lot of active research that’s quantitative in nature. So I took statistics and data science classes and economics along the way. It turns out that I had this very transferable skill set. I started out thinking it would be fun to do a summer internship at a tech company. Then I realized the work was amazing and I wanted to go for a full-time job. One of the really great things for women in industry is that there is a ton of momentum, especially around women in data science. Certainly there are fewer women in leadership positions. I’m very glad to be able to buck that trend, and hopefully that’s encouraging to others as well. Data science also has an advantage because it’s a new field, and people from different industries can enter. Some of those have more diversity, so it’s a natural advantage in creating a more diverse network.” —Elena Grewal, MA ’11, PhD ’12, head of data science, Airbnb
“I am not technical myself. I’m a marketing person. But I’m a data-driven marketing person and I worked in tech for a lot of years, so I am always looking for ways to push the envelope for women. I like the fact that we’re able to bring this to the world beyond Stanford. With regional events, we’re able to highlight women from those regions, so women who might not have other speaking opportunities have a platform from which to share their research and to share their work. We actually were really trying hard to be in Saudi Arabia last year and we did not quite get there. And then this year we ended up having three regional events in Saudi Arabia. These are amazing women who are speaking. I think it’s wonderful that even in a place where women don’t really have a voice, they have a voice through WiDS.” —Judy Logan, co-director, Women in Data Science conference
“I recall many times I was the only woman engineer in a team and rarely ever saw a woman role model. I’d love to see more women in engineering pursuing advanced degrees and going to the next stages in their careers. We were brainstorming at the Institute for Computational and Mathematical Engineering several years ago on what to do, and we thought to have real impact we need to show those role models and inspire the next generation so that they can say, ‘Oh, I see myself in that person.’ That was really missing. We decided to pilot a Women in Data Science conference. We had 6,000 people pick it up on live stream the first year, so that’s when we thought, ‘Aha, we hit a chord here and we could have a much bigger impact if we try to reach out across the world.’ The question is then what do you do with all that bubbled-up energy and inspiration. That’s the most exciting thing – to see women take action and pursue their dreams.” —Karen Matthys, MBA ’88, co-director, Women in Data Science conference
Data science, if judged as a separate science, exceeds its sisters in truth, breadth, and unity. DS finds truth better than any other science; the crisis in replicability of results in the sciences today is largely due to bad data analysis, performed by amateurs. As for breadth, a data scientist can contribute mightily to a new field with only minor cooperation from a domain expert, whereas the reverse is not so easy. And for utility, data science can fit empirical behavior to provide useful model where good theory doesn’t yet exist. That is, it can predict “what” is likely even when “why” is beyond reach.
But only if we do it right! The most vital data scientist skill is recognizing analytic hazards. With that, we become indispensable.
About John Elder:
John Elder, Ph.D., chairs America’s most experienced Data Science consultancy. Founded in 1995, Elder Research has offices in Virginia, Maryland, North Carolina, and Washington D.C. Dr. Elder co-authored 3 award winning books on analytics, was a discoverer of ensemble methods, chairs international conferences, and is a popular keynote speaker. John is occasionally an Adjunct Professor of Systems Engineering at the University of Virginia, and was named by President Bush to serve 5 years on a panel to guide technology for national security.
Dr. Elder’s keynote is not the only proof of PAW’s continued commitment to hosting the brightest, sharpest minds in data science and machine learning. When you attend PAW in Las Vegas this June you will witness only the the most inspirational keynotes and actionable workshops including:
Predictive Analytics World is the place to meet peers, new partners, and get up to speed on the industry’s latest developments and opportunities. The networking is like no other. Don’t miss the biggest PAW event to date.
Employment Trends in Biomedical – NIH Visualization Tool of Job Segmentation for Life Scientists
Reporter: Aviva Lev-Ari, PhD, RN
Led by Tammy Collins, Ph.D., director of the NIEHS Office of Fellows’ Career Development, team members collected detailed career outcomes for more than 900 NIEHS postdoctoral fellows over the past 15 years. Postdoctoral fellows, or postdocs, are scientists who have received their doctoral degrees and are participating in a program that offers additional training.
Lead author and NIEHS computer scientist Hong Xu analyzed the data using the R Project for Statistical Computing, a free online program that displays data using graphs and charts. Shyamal Peddada, Ph.D., former NIEHS head of the Biostatistics and Computational Biology Branch, served as key advisor. The study appeared online in the journal Nature Biotechnology, and is the first standardized method for categorizing career outcomes of NIEHS postdocs.
NIEHS supports research to understand the effects of the environment on human health and is part of NIH. For more information on environmental health topics, visit www.niehs.nih.gov. Subscribe to one or more of the NIEHS news lists to stay current on NIEHS news, press releases, grant opportunities, training, events, and publications.
Angella Schoellig — Roborts, Prof. University of Toronto, robots in predictable environments
Lorenz Meier — Vertical Technologies – Drones and safety – DB of flights
12:30
Lunch & Networking
2:00
Adapting to the reality of climate change
Lee Krevat, Sempra –
owns Wind Farms- managing a Grid with renewable energy. Variable – Wind technology wind is variable – if wind blows too much switch to diesel. 100% renewable for one hour on Islands
Growth area:
20 cents diesel, wind is 10 cents help the enviroment
mainland, not yet used, price diesel vs wind
Solar wind generation – next biggest Technology in Energy
and
Alex Tepper,Avetars
Robotics, Drones, AI and the Future of Energy – A start up incubator sponsored and funded by GE
RAIL – Predict derailments
OIL & GAS – corrosion is the enemy — knowledge of corosion progression – using AI algorithms
Growth area: Aviation
John Holdren – Harvard University – Government Role in ENERGY and Climate Change – Obama’s advisor Presidential CSO on Climate and energy
mitigation
adaptation
suffering – shortcomings of mitigation and adaptation
harm of business as usual
Efficiency standards during Obama Administration, assistance to other countries led to the Agreement in Paris 195 countirs — agreement to reduce emission. China and US declare cooperation on emission of gases into the environment.
PRESIDENT TRUMPS CALLED CLIMATE CHANGE A HOAX – proposed to cut energy R&D
All executive orders by Obama – were reverted by Trump
Innovations: Electricity from Solar increase and wind as well and batteries
Carbon capture and storage – technological challenge
Biofuel processing, liquid bio fuel
Nuclear innovations to nuclear waste
2100 – 5% on defense and 2% on the environment – model under estimate the contribution of innovations for the long run.
1000 businesses in deployment of technologies
Evelyn wang, MIT – Material Science – Sustainable energy – nano
material properties: superior properties of LOW DENSITIES
Light manipulation
membrane
CO2 capture
Technologies: Nnao, Thermoelectronics, energy and water
Solar 6% and wind 21%, biomass 5%voltaic
SOlar eneconversion
PHOVOLTAIC: SCALBALE, SOLID STATE, INTERMITTENT, PARTIAL SOLAR SPECTRUMrgy
Nanophotonics: Solar energy conversion: photo
Nano absorber – area ratio; Emitter: silicon and silicon – spectral approach
potential STPVs
Transportation using energy with emission
Power consumed by HVAC
Thermal Battery for Electric Vehicle: Adsorption Heating and Cooling
Desorption vs Adsoption: cooling vs Heating mode
High capacity adsobents – Zeolite MOF enhancing capacity heat and mass transport
Credential Stuffing Accounts Attacks – SONY was hacked and 93,000 Passwords stolen
Clip Farms at Google
BLACKFISH – identify Credential Stuffing Accounts Attacks, all invalid password are not valid to be used by cyber attackers again – that authentication is no longer valid
Multi Factors Authentications vs ease of use to Log In
Knowledge Basis – Probabilistic SYmbols – BlackFISH – technological advantage – iPhone stores a math formulation of characteristics of the finger print not the image of the fingure
Brain Computer Interaction (BCI) – maximum Privacy no voice involved like in SPeech
Voice, Motion Tracking, eye tracking
Human intentionality – a World without limitations
NASA is a client
consol technology for navigation, typing,
Problems: Add to glasses or as an Ear piece
the signal is ACTION POTENTIAL
latency differences between individuals
Non-invasive to invasive to capture signals
2:00 – 2:30 Capturing Our Imagination:: Evolution of Brain-Machine Interfaces
Mary Lou Jepsen, Openwater
Hosted by Antonio Ragalado, TR
Using functional MRI technology for a NEW device to scan emotions rather than medical diseases
HOLOGRAPHY of the Brain – liquid crystal display is like transistors on a chip
OPTICS – DISCONTINUITY of Moore’s law – high resolution like functional MRI
Holographic LCD – scattering material VOXEL detector – measure intensity of light, no resolution, consumer camera speed OK Inexpensive
Human body scattering
HAT and Bandage
2:30 – 3PM Future of Work – REWARD DISOBEDIENCE –
New Prize of $250,000 – Ethics and governance in AI at MIT Media lab
Reid Hoffman, Greylock Partners Founder LinkedIn
conversation with Joi Ito, MIT Media Lab
Tell the Truth
Media Lab — a Non-disciplinary place
Universities play a role in Social Justice
FEAR of AI:
For profit will own it all
stupid AI will govern
displace work
espionage
catalytic institute that will make a contribution to OPENNESS vs technological dominance
Joi Ito, MIT Media Lab: AI problems –
MUST be democratized – Now it is in the hands of very FEW
RISK SCORES can’t be contested in court because they are IP of for profit companies
Joi Ito, MIT Media Lab at MIT do good to Society vs make the most of money which the majority are doing
AUTONOMICH vs autonomous agents, said Joi Ito, MIT Media Lab – Hoffman: Design goals more symbiotic: Scaling, more productive, Season 2 launched today
Design principle – LEARNING vs EDUCATION, Joi Ito, MIT Media Lab
Hoffman on AI Technologies
shaping it to avoid catastrophic negatives
provide a public good via participation
3:00
Break & Networking
3:30 – 4 Big Problems, Big Data Solutions
Deb Roy, MIT media Lab
Tweets and News, Washington Post – Tracking tweets from US on Politics related to the Elections
National memory on Guns, Immigrations
Debate brief from tweets and News rooms
topic classifier, Campaign finance, SHARE OF COVERAGE IN NEWS, SHARED OF VOICE ON TWITTER
deep neural network training algorithms
Passion Gap: cut data on Twitter – Trump supporters exhibited x2 fold energy vs the Democratic candidate
How does Media flow: Sanders, Clinton, Trump – each is a Media Source
Truth, Trust, Attention – Fact checking
If Trust the source then I believe it is True
Public Opinion: The Politics of Resentment in Rural WI – Katherine Cramer
Listening Networks: Human- Human Interaction: Media sharing network – change week by week – the MOST innovative methodology developed to date for Public Opinion – presentation by
Deb Roy, MIT media Lab – using deep Neural network training
main stream
conservative
liberal activist
Health Indicators:
Shared attention
Shared Reality
Varied Perspective – surface under-heard voices
3:30 – 4
Meet the Innovators Under 35
1. Svenja Hinderer, Germany
Valve – development of Tissues, biochemical properties
signaling molecules
mechanical strength – physiological
Attrach stem cells – proper matrix formation
Functional implants
2. Viktor Adalsteinsson
Cancer Precision medicine – Liquid biopsy – tumor mutations
Emerging STAR in Molecular Biology, Synthetic Virology and Genomics: Clodagh C. O’Shea: ChromEMT – Visualizing 3D chromatin structure
Curator: Aviva Lev-Ari, PhD, RN
On 8/28/2017, I attend and covered in REAL TIME the CHI’s 5th Immune Oncology Summit – Oncolytic Virus Immunotherapy, August 28-29, 2017 Sheraton Boston Hotel | Boston, MA
I covered in REAL TIME this event and Clodagh C. O’Shea talk at the conference.
On that evening, I e-mailed my team that
“I believe that Clodagh C. O’Sheawill get the Nobel Prizebefore CRISPR
11:00Synthetic Virology: Modular Assembly of Designer Viruses for Cancer Therapy
Clodagh O’Shea, Ph.D., Howard Hughes Medical Institute Faculty Scholar; Associate Professor, William Scandling Developmental Chair, Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies
Design is the ultimate test of understanding. For oncolytic therapies to achieve their potential, we need a deep mechanistic understanding of virus and tumor biology together with the ability to confer new properties.
orthogonal capsid functionalization technologies (RapAd) and
replication assays that have enabled the rational design, directed evolution, systematic assembly and screening of powerful new vectors and oncolytic viruses.
Clodagh O’Shea’s Talk In Real Time:
Future Cancer therapies to be sophisticated as Cancer is
Targer suppresor pathways (Rb/p53)
OV are safe their efficacy ishas been limited
MOA: Specify Oncolytic Viral Replication in Tumor cells Attenuate – lack of potency
SOLUTIONS: Assembly: Assmble personalized V Tx fro libraries of functional parts
Adenovirus – natural & clinical advantages
Strategy: Technology for Assmbling Novel Adenovirus Genomes using Modular Genomic Parts
BS, Biochemistry and Microbiology, University College Cork, Ireland PhD, Imperial College London/Imperial Cancer Research Fund, U.K. Postdoctoral Fellow, UCSF Comprehensive Cancer Center, San Francisco, U.S.A
NIH announced its sixth class of Medical Research Scholars Program (MRSP) – 42 Students, 48% Females and 8 Minority Students
Reporter: Aviva Lev-Ari, PhD, RN
The National Institutes of Health has selected 42 talented and diverse students, representing 35 U.S.-accredited universities, for the sixth class of its Medical Research Scholars Program (MRSP). The MRSP received a record number of applications during the 2017-2018 application cycle. The 42 selected participants consist of 39 medical, two dental, and one veterinary student; 48 percent are female and eight individuals are from underrepresented minority groups. There are five second year, 35 third, and two fourth year students in the class; six of the 42 have had previous NIH research experience. The accepted scholars begin their MRSP fellowship in July/August of this year.
“These 42 scholars represent some of this country’s most promising future biomedical researchers and academic leaders.”
—Frederick P. Ognibene, M.D., Director, Office of Clinical Research Training and Medical Education, NIH Clinical Center
The MRSP is co-sponsored by the NIH and other partners via contributions to the Foundation for the NIH.
The 42 participants for the 2017-2018 NIH MRSP include:
Mairead Baker, Loyola University of Chicago, Stritch School of Medicine
Fatima Barragan, Michigan State University, College of Human Medicine, East Lansing
Jennifer Bayly, Rutgers, Robert Wood Johnson Medical School, Piscataway, New Jersey
Jacqueline Boyle, University of Illinois College of Medicine at Peoria
Rebecca Breese, the University of North Carolina at Chapel Hill School of Medicine
Sonny Caplash, the University of Connecticut School of Medicine, Farmington
Katherine Chen, the University of California, Irvine, College of Medicine
Sophie Claudel, Wake Forest University School of Medicine, Winston-Salem, North Carolina
Shavonne Collins, Meharry Medical College, Nashville
Shazia Dharssi, Johns Hopkins University School of Medicine, Baltimore
Joshua Diamond, the University of Virginia School of Medicine, Charlottesville
Youssef Elnabawi, Tufts University School of Medicine, Boston
Joseph Featherall, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
Kathleen Fenerty, Indiana University School of Medicine, Indianapolis
Samuel Gold, State University of New York, Downstate Medical Center College of Medicine, Brooklyn
Morgan Graves, Georgetown University School of Medicine, Washington, D.C.
Jacob Groenendyk, Washington University School of Medicine, St. Louis
Russ Guidry, Louisiana State University School of Medicine, New Orleans
Graham Hale, Jefferson Medical College of Thomas Jefferson University, Philadelphia
Christopher Hampton, the University of Connecticut School of Medicine, Farmington
Belen Hernandez, Colorado State University College of Veterinary Medicine, Fort Collins
Christopher Hogden, the University of Iowa College of Dentistry, Iowa City
Tommy Hu, Pennsylvania State University College of Medicine, Hershey
Eileen Hu-Wang, Northwestern University The Feinberg School of Medicine, Chicago
Sahar Khan, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
Alyssa Kosturakis, the University of Texas School of Medicine at San Antonio
Jason Lau, the University of Massachusetts Medical School, Worcester
Andrew Lum, Tufts University School of Dental Medicine, Boston
Uchenna Okoro, the University of Michigan Medical School, Ann Arbor
Kristen Pan, the University of Cincinnati College of Medicine
Priya Patel, Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo
Grant Randall, the University of Missouri – Kansas City School of Medicine
Corinne Rauck, the University of Cincinnati College of Medicine
Kareem Rayn, State University of New York, Downstate Medical Center College of Medicine, Brooklyn
Isabelle Sanchez, the University of Illinois College of Medicine at Chicago
Aakash Sathappan, the University of California, San Diego, School of Medicine
Clayton Smith, Georgetown University School of Medicine, Washington, D.C.
Dattanand Sudarshana, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
Enock Teefe, Chicago Medical School at Rosalind Franklin University of Medicine and Science
Alison Treichel, Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo
Fernando Vazquez, Dartmouth Medical School, Hanover, New Hampshire
Jeannette Yu, Duke University School of Medicine, Durham, North Carolina
Top 50 Women in CRISPR : Women in CRISPR, Legal Status of Inventions and Declaration of the Heroes in CRISPR
Curator: Aviva Lev-Ari, PhD, RN
2.1.5.6 Top 50 Women in CRISPR : Women in CRISPR, Legal Status of Inventions and Declaration of the Heroes in CRISPR, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair
Part 2: UPDATED – Status “Interference — Initial memorandum” – CRISPR/Cas9 – The Biotech Patent Fight of the Century: UC, Berkeley and Broad Institute @MIT
1, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
2Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
*Correspondence: lander@broadinstitute.org
Three years ago, scientists reported that CRISPR technology can enable precise and efficient genome editing in living eukaryotic cells. Since then, the method has taken the scientific community by storm, with thousands of labs using it for applications from biomedicine to agriculture. Yet, the preceding 20-year journey—the discovery of a strange microbial repeat sequence; its recognition as an adaptive immune system; its biological characterization; and its repurposing for genome engineering—remains little known. This Perspective aims to fill in this backstory—the history of ideas and the stories of pioneers—and draw lessons about the remarkable ecosystem underlying scientific discovery.
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Mangold, M., Siller, M., Roppenser, B., Vlaminckx, B.J.M., Penfound, T.A., Klein, R., Novak, R., Novick, R.P., and Charpentier, E. (2004). Synthesis of group A streptococcal virulence factors is controlled by a regulatory RNA molecule. Mol. Microbiol. 53, 1515–1527. Marraffini, L.A., and Sontheimer, E.J. (2008). CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845. Medawar, P. (1968). Lucky Jim (New York Review of Books), March 28, 1968. Miller, J.C., Tan, S., Qiao, G., Barlow, K.A., Wang, J., Xia, D.F., Meng, X., Paschon, D.E., Leung, E., Hinkley, S.J., et al. (2011). A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 29, 143–148. Mojica, F.J.M., and Garrett, R.A. (2012). Discovery and Seminal Developments in the CRISPR Field. In CRISPR-Cas Systems, R. Barrangou and J. van der Oost, eds. (Berlin, Heidelberg: Springer Berlin Heidelberg), pp. 1–31. Mojica, F.J.M., Juez, G., and Rodrı´guez-Valera, F. (1993). Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites. Mol. Microbiol. 9, 613–621. Mojica, F.J.M., Ferrer, C., Juez, G., and Rodrı´guez-Valera, F. (1995). Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol. Microbiol. 17, 85–93. Mojica, F.J.M., Dı´ez-Villasen˜ or, C., Soria, E., and Juez, G. (2000). Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol. Microbiol. 36, 244–246. Mojica, F.J.M., Dı´ez-Villasen˜ or, C., Garcı´a-Martı´nez, J., and Soria, E. (2005). Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174–182. Moscou, M.J., and Bogdanove, A.J. (2009). A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501–1501. 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Sharma, C.M., Hoffmann, S., Darfeuille, F., Reignier, J., Findeiss, S., Sittka, A., Chabas, S., Reiche, K., Hackermu¨ ller, J., Reinhardt, R., et al. (2010). The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464, 250–255. Siksnys, V., Gasiunas, G., and Karvelis, T. (2012). RNA-directed DNA cleavage by the Cas9-crRNA complex from CRISPR3/Cas immune system of Streptococcus thermophilus. U.S. Provisional Patent Application 61/613,373, filed March 20, 2012; later published as US2015/0045546 (pending). Sontheimer, E., and Marraffini, L. (2008). Target DNA interference with crRNA. U.S. Provisional Patent Application 61/009,317, filed September 23, 2008; later published as US2010/0076057 (abandoned). Sorek, R., Kunin, V., and Hugenholtz, P. (2008). CRISPR–a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6, 181–186. Sternberg, S.H., and Doudna, J.A. (2015). Expanding the Biologist’s Toolkit with CRISPR-Cas9. Mol. Cell 58, 568–574. Travis, J. (2015). GENETIC ENGINEERING. Germline editing dominates DNA summit. Science 350, 1299–1300. Urnov, F.D., Miller, J.C., Lee, Y.-L., Beausejour, C.M., Rock, J.M., Augustus, S., Jamieson, A.C., Porteusm, M.H., Gregory, P.D., and Holmes, M.C. (2005). Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646–651. van der Oost, J., Westra, E.R., Jackson, R.N., and Wiedenheft, B. (2014). Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat. Rev. Microbiol. 12, 479–492. Wright, A.V., James, K., Nun˜ ez, J.K., and Doudna, J.A. (2016). Biology and applications of CRISPR systems: Harnessing nature’s toolbox for genome engineering. Cell 164, this issue, 29–44. Zetsche, B., Gootenberg, J.S., Abudayyeh, O.O., Slaymaker, I.M., Makarova, K.S., Essletzbichler, P., Volz, S.E., Joung, J., van der Oost, J., Regev, A., et al. (2015). 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Evolution and Ecology – microbial diversity – Plant Biology
Research in my lab is driven by an interest in understanding how photosynthetic microorganisms perceive and evolve in response to environmental stressors, such as light, nutrients and viral attack.We work both with model organisms and with cyanobacteria in naturally occurring communities. Recently,we have started to develop synthetic biology-inspired approaches to use in cyanobacteria.
The study system for this project is an aquifer adjacent to the Colorado River in Rifle, Colorado, USA.Research addresses knowledge gaps related to the roles of subsurface microbial communities in biogeochemical cycling. Given the link between the carbon cycle and global climate change, a particular interest in this work is the impact of microorganisms on carbon compounds buried in the terrestrial subsurface, both through respiration and carbon fixation.
5
Denis
Bauer
Commonwealth Scientific and Industrial Research Organisation (CSIRO)
Dr. Denis Bauer is the team leader of the transformational bioinformatics team in CSIRO’s ehealth program. Her expertise is in high throughput genomic data analysis, computational genome engineering, as well as Spark/Hadoop and high-performance compute system.
The Blancafort laboratory focuses on the development of novel approaches to target cancers that are currently refractory to treatment and associated to poor outcome, such as triple negative breast cancers and ovarian cancers. At present, there are no targeted approaches to combat these tumors with chemotherapy and radiation the only treatment options. The laboratory generates novel functionalised molecules able to specifically target these tumors with minimal toxicity to normal cells. Our emphasis is in advanced stage metastatic tumors, which quasi invariably develop resistance. Ultimately we wish to revert the behavior of metastatic cells by sensitizing these treatment resistant tumors to chemotherapy regimes.
Our research relates to the field of Molecular Infection Biology. We are overall interested in understanding the molecular mechanisms governing physiology-, virulence- and infection-associated processes in Gram-positive bacterial pathogens. We use a combination of genetic, genomic, molecular, biochemical, physiological and cell infection approaches to study mechanisms of gene expression at the transcriptional and post-transcriptional level in horizontal gene transfer, adaptation to stress, physiology or virulence. In particular, we do research on CRISPR, the adaptive immune system that protects bacteria against invading genetic elements; the small regulatory RNAs that interfere with bacterial pathogenicity; protein quality-control that regulates bacterial adaptation, physiology and virulence; and the mechanisms of bacterial recognition by immune cells.
I am a bioethicist with an interdisciplinary background in medical biotechnologies, ethics and philosophy. I am a tenured Lecturer (the UK equivalent to Assistant Professor) in Bioethics & Society in the Department of Global Health & Social Medicine (formerly, Social Science, Health & Medicine) at King’s College London, where I direct the Master’s in Bioethics & Society.
Our group has a long-standing interest in RNA metabolism, with a particular focus on the molecular mechanisms of eukaryotic RNA transport and degradation.
The main research goal of our laboratory is to develop high-throughput transgene technologies for common wheat (Triticumaestivum L.) and maize (Zea mays) and other major crops to satisfy the needs of crop improvement and gene discovery.
Nowadays, we are mainly focusing on novel artificial DNA binding domains, the TALE repeats (transcription-activator like effector) and CRISPR/Cas9 system. We use the CRISPR/Cas or TALE as nucleases (TALEN) to study DNA repair in mammalian cells as well as DNA probes to study genome dynamics (see Repeated DNA sequences and chromatin).
Dr. Gomez-Ospina was born and raised in Medellin, Colombia. She began her undergraduate studies in petroleum engineering at the Universidad Nacional de Colombia before moving to Colorado. She double majored at the University of Colorado Boulder, completing her bachelor’s degree in Molecular Cellular and Developmental Biology as well as Biochemistry. She graduated summa cum laude and wrote an honors thesis entitled “Role of the quiescent center in the regeneration of the root cap in Zea Mays.” She then completed her combined MD, PhD at Stanford Medical School, where her PhD work focused on understanding the novel functions of voltage-gated calcium channels. Her PhD thesis, “The calcium channel CACNA1C gene: multiple proteins, diverse functions,” was published in Cell. After completion of her dual degrees, she did her preliminary year in internal medicine at Santa Barbara Cottage hospital before starting residency in Dermatology at Johns Hopkins Hospital. She completed residency in Medical Genetics at Stanford Hospital and clinics. She is currently doing her post-doctoral research with Dr. Matthew Porteus in Pediatric Stem Cell transplantation, where she is developing a genome editing strategy in stem cells as a curative therapy for metabolic diseases. In addition to her research, Dr. Gomez-Ospina is a clinical instructor in Medical Genetics. For her clinical practice she sees patients with suspected genetic disorders, and is also in charge of the enzyme replacement service for lysosomal storage disorders at Lucile Packard Children’s hospital. She has been the lead author in research studies in The New England Journal of Medicine, Cell, Nature Communications, and American Journal of Medical Genetics.
Bacterial infectious diseases are a major cause of mortality worldwide. The rise in antibiotic resistant infections, coupled with the sharp decline in the discovery of new and clinically useful classes of antibiotics, underscores an urgent need for alternative strategies to combat bacterial infections. Small noncoding RNA pathways have recently been recognized as important regulators of bacterial pathogenesis, and the challenge lies in gaining a detailed understanding of these processes. My research uses the tools of biochemistry and molecular genetics to unravel the mechanisms of small RNA-mediated pathways and enable the development of novel anti-microbial therapeutics.
Rachel is a co-founder of Caribou Biosciences and has been President and CEO since its inception. She has a research background in CRISPR-Cas biology, and is also a co-founder of Intellia Therapeutics. In 2014, she was named by Forbes Magazine to the “30 Under 30” list in Science and Healthcare, and in 2016, Fortune Magazine named her to the “40 Under 40” list of the most influential young people in business. Rachel is an inventor on several patents and patent applications covering multiple CRISPR-derived technologies, and she has co-authored scientific papers in high impact journals characterizing CRISPR-Cas systems. Rachel earned an A.B. in Biological Sciences from Harvard College, and received a Ph.D. in Molecular and Cell Biology from the University of California, Berkeley.
Around 10-20% of kidney disease is inherited. In children with kidney disease, this is closer to 50% although in many instances, the disease-causing mutation is unknown, therefore limiting treatment options. In our research group, we investigate the genes required for normal kidney development and what happens as a result of genetic or environmental damage during development. This knowledge is used to try to recreate kidney stem cells. We have developed methods for generating mini-kidneys from human stem cells that represent models of the human organ. We hope to use these mini-kidneys to screen drugs for kidney toxicity, as models with which to understand kidney disease, to generate cells for the treatment of kidney disease and eventually to bioengineer replacement organs.
Research Interest: The global threat of multi-drug resistant bacteria urgently demands alternatives to conventional antibiotics. Two promising alternatives to traditional antibiotics are bacteriophage (phage) therapy and inhibitors of bacterial cell-cell communication, known as quorum sensing (QS). Bacteria in high cell density maximally engage in QS. These cells are particularly vulnerable to phage infections, which could rapidly spread and kill the population. QS-control of antiphage activities would enable bacteria to specifically activate defenses when they are at the highest risk of infection. I am investigating to what extent bacteria use QS to regulate their antiphage defenses. Whereas QS-inhibitory compounds are generally studied for their capacity to inhibit bacterial virulence, I will study whether they additionally have the ability to increase the vulnerability of pathogenic bacteria to phages.
The ability to program naïve cells or to reprogram differentiated cells into particular fates will open the door to the discovery of novel therapeutics for diseases such as diabetes. The goal of my lab is to understand the fundamental principles that govern the identity of a cell, and to use these principles to manipulate cell fates for regenerative medicine. In pursuit of this goal, we employ a variety of approaches including cellular programming and reprogramming through gene transduction, directed differentiation of embryonic stem (ES) cells, chemical screening, mouse genetics, adult tissue injury and regeneration, and tissue/cell transplantation.
Human chromosomes are constantly assaulted by challenges to their integrity as a result of either environmental agents that damage DNA or from normal DNA metabolism. The failure to repair damaged DNA faithfully is ultimately responsible for many human diseases, especially cancer. This laboratory focuses on the repair of 1 particular lesion in DNA, the double-strand break (DSB). DSBs arise from agents, such as ionizing radiation, and can also occur spontaneously during DNA replication. Our emphasis is on repair of DSBs by homologous recombination, with a particular interest in the role of homologous recombination in maintaining genetic stability. Understanding the repair of DSBs is not only important for basic science and health concerns, but also impacts on molecular genetic manipulations of mammalian genomes
Josephine Johnston is an expert on the ethical, legal, and policy implications of biomedical technologies, particularly as used in human reproduction, psychiatry, genetics, and neuroscience.
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Helene
Jousset-Sabroux
The Walter and Eliza Hall Institute for Medical Research
High Throughput Screening – Technology Development
The screening laboratory offers a wide range of expertise gained from both industrial and academic backgrounds, resulting in a professional ability to develop high capacity cellular or biochemical assays. We offer liquid handling robotics, plate readers and computing programs to increase the scale and speed of assays, and leverage automation to quickly assess the activity of a large number of compounds.
My role within the group is to develop and assess novel mouse models of colorectal cancer, using colonoscopy techniques that are very similar to patient surveillance in humans. In addition, I am developing an in vitro method of growing mouse and human stem cells from the colon with their associated connective tissue. This will allow us to further investigate these support cells in normal growth and cancer. Both systems will be directly therapeutically relevant, allowing us to assess preclinical targeting of molecular pathways relevant to colorectal cancer.
A diverse range of RNA:protein, RNA:RNA and protein:protein interactions occur at the level of transcription and translation as well as post-transcriptional modifications. RNA:protein interactions are particularly interesting not only because they play important functional roles in assembly and biological processes, but also because the rules of their interactions are still poorly understood owing to the scarce structural data. Unlike DNA molecules, RNA can fold into a range of structures for interacting with proteins and small molecules. We hope, by providing exceptionally detailed images of the molecular events along the assembly and functional pathways, to unveil the underlying basis for assembly and functions involving RNA and partner proteins.
My area of expertise is in machine learning and applied statistics for computational biology. I’m interested in both methods development as well as application of methods to enable new insight into basic biology and medicine.
We are developing the computational methods for the design (SSC), analysis (MAGeCK), hit prioritization (NEST), and visualization (VISPR) of genome-wide CRISPR screens. We are also using this technology to identify key genes in breast and prostate tumor progression and drug resistance. We also develop CRISPR screen platforms to understand the functions of enhancers and long-noncoding RNAs, and identify synthetic lethal gene pairs in cancer that leads to optimized cancer precision medicine.
All prokaryotic cells have to fend off foreign genetic elements like for instance viruses. To do that they have developed several different defence strategies. The recently discovered new defence strategy is the so called prokaryotic immune system also called CRISPR/Cas (CRISPR: clustered regularly interspaced short palindromic repeats, Cas: CRISPR-associated). It is adaptive, since cells can become immune against new invaders and it is heritable, since the information about the invader is stored in the genome. The CRISPR/Cas system consists of clusters of repetitive chromosomal DNA in which short palindromic DNA repeats are separated by spacers, the latter being sequences derived from the invader. In addition, a set of proteins, the Cas proteins, is involved in this defence reaction. We are investigating the CRISPR/Cas system in the halophilic archaeon Haloferax volcanii. Haloferax encodes a type I-B CRISPR/Cas system with eight Cas proteins and three CRISPR RNAs.
The Maxwell lab studies the phages that infect and kill the human bacterial pathogens Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. Infections caused by these bacteria create a significant disease burden, and the increasing incidence of antibiotic resistant infections caused by these pathogens is one of our most serious health threats.
Targeted Genome-editing Across Highly Diverged Nematode Species. Thwarted by the lack of reverse genetic approaches to enable cross-species comparisons of gene function, we established robust strategies for targeted genome editing across nematode species diverged by 300 MYR. In our initial work, a collaboration with Sangamo BioSciences, we used engineered nucleases containing fusions between the DNA cleavage domain of the enzyme FokI and a custom-designed DNA binding domain: either zinc-finger motifs for zinc-finger nucleases or transcription activator-like effector domains for TALE nucleases (TALENs). In those experiments, we allowed the DNA double-strand breaks to be repaired imprecisely by non-homologous end joining (NHEJ) to create mutations in precise locations.
The Genome Engineering and IPSC Center (GEiC) was formed by the consolidation of two pre-existing cores, the Genome Engineering Center and the Induced Pluripotent Stem cell (iPSC) core, both established by the Department of Genetics in the past few years. These two Centers were established to facilitate functional genomic studies through the use of patient-derived iPSCs and the generation of modified cells and organisms using genome editing technologies.
The allocation of cells to a specific lineage is regulated by the activities of key signalling pathways and developmentally regulated transcription factors. The focus of our research is to understand the influence of signalling and transcription factors on differentiation during early human development.
We are also developing genetic technologies for identifying and gaining genetic control of neuronal subtypes to determine their characterize their roles in neural circuits. Working with the laboratories of Jill Wildonger and Melissa Harrison, we recently adapted the CRISPR/Cas9 system for use in Drosophila. CRISPR is a novel technique that is revolutionizing genome engineering. Developed from bacteria where the CRISPR/Cas9 system functions in acquired immunity, CRISPR technology enables highly efficient and specific editing of targeted genomic sequences – opening the door to routine genome engineering. The many applications of CRISPR technology include modifying the genomes of model organisms to probe gene function, conferring disease resistance to agricultural organisms, and correcting disease-causing mutations in humans. We are capitalizing on this advance to develop novel genome engineering approaches that overcome current technological limitations to understanding neural circuits. Visit our flyCRISPR and flyCRISPR Optimal Target Finder sites for more details on our genome engineering work.
Bacteria and their cognate viruses, known as bacteriophages, are in a constant battle for survival. Among many mechanisms that bacteria possess to defend against bacteriophage infection, one of the most widespread and sophisticated is the CRISPR-Cas system. Setting CRISPR-Cas apart from other defence systems is the fact that it is an adaptive immunity system: one that can acquire the ability to target newly encountered invaders in a sequence-specific manner. Although much has been uncovered about the targeting mechanisms of CRISPR-Cas systems, very little is known about how they select and capture genetic snapshots of bacteriophages for later use as guides for the “seek and destroy” machinery. I leverage biochemical and structural biology approaches to investigate the CRISPR-Cas adaptation process in detail.
Our laboratory studies the molecular genetic basis of human diseases, particularly Usher syndrome, the leading cause of combined deafness and blindess, and other diseases of the eye and ear.
Wenning has been focusing on and exploring into genetic engineering technologies in her entire professional career. Her association includes Monsanto Biosciences, Pharmacia Corporation, Pfizer Incorporated and the Jackson Laboratory. She currently directs the Genetically Engineered Models group of Biogen, leveraging into genetic engineering to advance drug discovery pipeline for Biogen. Over the years, she acquired extensive knowledge and experience in design and creation of genetically engineered models, using random transgenesis, conventional gene targeting as well as CRISPR/Cas9 technology.
Protein-nucleic acid interactions are key to fundamental life processes such as DNA replication, transcription, recombination, and protein synthesis. Deciphering the mechanism of protein-nucleic acid interactions is invaluable for understanding human disease pathways and infections. The primary focus of my lab is to characterize protein-DNA/RNA interactions structurally, biochemically, and biophysically. The immediate emphasis is the study of the recently discovered bacterial and archaeal immune system, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR is an RNA-based adaptive immune system that inactivates foreign DNA/RNA entering the cell, based on the sequence similarity of small RNAs, called CRISPR RNA (crRNA) to the invading genetic element. The process requires several proteins called CRISPR associated (Cas) proteins. The CRISPR/Cas9 system has revolutionized the genome editing field due to the ease with which targeted double-stranded DNA breaks can be achieved in cells, using a guide RNA and Cas9 protein. The long-term goals of my laboratory are to understand the role of CRISPR/Cas system in pathogenicity and virulence of bacteria, characterize the mechanism of adaptation of bacteria to phage infection, and to determine the signaling mechanisms of the CRISPR/Cas system. We incorporate molecular biology, biochemistry, X-ray crystallography, and additional biophysical tools to characterize these protein-nucleic acid interactions.
RNA-protein (RNP) complexes are central to many fundamental processes of gene regulation and genome maintenance in all kingdoms of life. The RNA components of these molecular machines often carry out diverse functions, acting as guide, template, scaffold, or catalyst. Despite this versatility, RNAs require protein partners to function, and the interactions that form between these components often dictate the overall activity of the RNP complex. Our lab is interested in understanding the molecular mechanisms underlying the function of RNPs from diverse cellular pathways. To that end, we combine a broad range of biochemical, structural and cellular tools to study RNA and protein structure, interactions and function.
The Shariat Lab research interests are in prokaryote small RNA regulation and function, specifically in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). These elements are present in nearly half of all sequenced bacterial genomes and comprise several unique short sequences, called spacers, which are interspaced by conserved direct repeats. Spacers are derived from exogenous nucleic acids, such as bacteriophage genomes and plasmids. The spacers are transcribed into CRISPR RNAs (crRNAs), which are subsequently targeted to complementary nucleic acids, resulting in degradation of the target. Due to acquisition of new spacers, CRISPRs provide a remarkably dynamic adaptive immune system in both bacteria and archaea.
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Bettina
Schmid
Deutsches Zentrum fur Neurodegenerative Erkankungen
Our group uses the advantages of the zebrafish, Danio rerio, as an in vivo model system to address some of the unresolved questions in Alzheimer’s disease, Parkinson’s disease, Frontotemporal Lobar Degeneration (FTLD), and Amyotrophic lateral Sclerosis (ALS).
The ability of V. cholerae to prevent phage predation is critical for its evolutionary fitness and epidemic potential. In turn, as obligate bacterial parasites, phages must co-evolve to overcome this resistance or they will face extinction. Our research is aimed at understanding the bacterial immunity and opposing phage immune evasion strategies at play in this dynamic co-evolutionary arms race. We use comparative genomics and complementary molecular approaches to identify and experimentally validate such strategies in disease associated phage and V. cholerae isolates.
High Throughput Screening – Technology Development
The Victorian Centre for Functional Genomics (VCFG) at Peter Mac offers biomedical researchers Australia-wide the ability to perform novel discovery-based functional interrogation all genes in the genome, or selected boutique collections using multiple platforms including CRISPR/cas9, small interfering RNA (siRNA), micro RNA (miRNA) and long non-coding RNA (lncRNA) and short hairpin RNA (shRNA).
The focus of research in the Van Eck laboratory is biotechnological approaches to the study of gene function and crop improvement. For our studies, we apply several genetic engineering strategies to two major food crops: potato and tomato. The development of biotechnological techniques has made it possible to design and introduce gene constructs into plant cells and recover plants that express the introduced genes. Genes of interest to us have the potential to strengthen a plant’s resistance to disease, improve fruit characteristics, and enhance nutritional quality.
I am a biologist with a broad interest in host-parasite interactions, from an evolutionary, ecological and molecular perspective. Currently I work as a Marie-Curie fellow in the lab of Professor Angus Buckling on the evolution of immunity against virus infections in Pseudomonas bacteria. My PhD research at the Laboratory of Virology, Wageningen University (the Netherlands) focused on manipulation of host insect behaviour by baculoviruses, insect-specific viruses that cause lethal disease in caterpillars.
The overall goal of work in our laboratory is to understand how complex behaviors are modulated by external chemosensory cues and internal physiological states. The lab takes a multi-disciplinary approach spanning cell biology, genetics, neurobiology and behavior. Our early focus has been to study how the brain interprets olfactory signals in the environment that signal food, danger, or potential mating partners. We have been studying these problems in three model organisms: the fly, the mosquito and the human. The majority of the early work in the laboratory was carried out in the genetically tractable vinegar fly, Drosophila melanogaster, which displays a rich repertoire of chemosensory behaviors despite having a nervous system with only 100,000 neurons. In this animal, we have studied the functional neuroanatomy of the olfactory system, how this system perceives sex pheromones, and the structure and function of the insect odorant receptors.
As the rapid development in plant genomics research identifies more genes, their functional analysis relies on strategies such as complementation, overexpression, or gene silencing. Plant genetic transformation is a critical technology required in the application of these strategies.
My lab combines population genomics with laboratory-based genetic and genomic experimental techniques to study the evolutionary ecology of microbial populations. We take a comparative approach, examining interactions within and between species using wild strains from natural populations isolated across spatial and temporal scales. Currently we are working on two critical forces that define the evolutionary process in all organisms: host-virus co-evolution and recombinational gene flow. We have a particular interest in how the unique biology of organisms in the Archaeal domain is reflected in genome architecture and how the CRISPR-Cas immune system functions in microbial populations.
Susan’s current project focuses on colorectal cancer. This is the second most common cancer type in Australia, costing us over $1 billion dollars annually. There are minimal effective treatments for advanced disease. The lab has recently identified a new stem cell that gives rise to a layer of cells that support the intestinal lining. We are investigating whether similar support cells can promote the formation of colorectal cancer from cells lining the intestine, and if we can prevent it using a new therapeutic approach.
Luhan is leading the effort to eradicate PERVs from the porcine genome and engineer human compatibility in porcine cells. She previously developed the highly programmable genome-engineering tool, CRISPR/Cas9, for use in mammalian cells, and pioneered the first isogenic human stem cell lines to model human diseases at the tissue level. She was named among the “30 Under 30” in Science and Healthcare by Forbes Magazine (2014) and was a laureate of the “Young Entrepreneur Initiative” competition (2014). Luhan holds B.S. degrees in Biology and Psychology from Peking University and a Ph.D. in Human Biology and Translational Medicine from Harvard Medical School.
CRISPR-Cas is a RNA-guided, genetic interference pathway in prokaryotes that enables acquired immunity against invasive nucleic acids. Nowadays, CRISPRs also provide formidable tools for facile, programmable genome engineering in eukaryotes. Cas9 proteins are the “effector” endonucleases for CRISPR interference; and have recently begun to be also recognized as important players in other aspects of bacterial physiology (e.g. acquisition of new spacers into CRISPRs, endogenous gene regulation, and microbial pathogenesis, etc.).My laboratory is broadly interested in CRISPR biology and mechanism. We will use Neisseria species as our model system, and E. coli and human cells as additional platforms. We employ complementary biochemical, microbiological, genetic and genomic approaches. We are also interested in working with the broader scientific community to develop and apply novel CRISPR-based tools to tackle diverse biological questions.
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Amandeep Kaur
Aashir Awan, Phd
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Alan F. Kaul, PharmD., MS, MBA, FCCP
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David Orchard-Webb, PhD
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