I'm the author of Airpocalypse, a medical thriller


Welcome to the digital era of biology (and to this modest blog I started in early 2005).

To cure many diseases, like cancer or cystic fibrosis, we will need to target genes (mutations, for ex.), not organs! I am convinced that the future of replacement medicine (organ transplant) is genomics (the science of the human genome). In 10 years we will be replacing (modifying) genes; not organs!


Anticipating the $100 genome era and the P4™ medicine revolution. P4 Medicine (Predictive, Personalized, Preventive, & Participatory): Catalyzing a Revolution from Reactive to Proactive Medicine.


I am an early adopter of scientific MOOCs. I've earned myself four MIT digital diplomas: 7.00x, 7.28x1, 7.28.x2 and 7QBWx. Instructor of 7.00x: Eric Lander PhD.

Upcoming books: Airpocalypse, a medical thriller (action taking place in Beijing) 2017; Jesus CRISPR Superstar, a sci-fi -- French title: La Passion du CRISPR (2018).

I love Genomics. Would you rather donate your data, or... your vital organs? Imagine all the people sharing their data...

Audio files on this blog are Windows files ; if you have a Mac, you might want to use VLC (http://www.videolan.org) to read them.

Concernant les fichiers son ou audio (audio files) sur ce blog : ce sont des fichiers Windows ; pour les lire sur Mac, il faut les ouvrir avec VLC (http://www.videolan.org).


Two human genomes per hour at Europe's largest DNA sequencing centre: Wellcome Trust Sanger Institute (UK+US)

10 Breakthrough Technologies

http://www.technologyreview.com/lists/technologies/2014/


"Facebook a sleeping giant in terms of impact it could have in healthcare"

Doctors 2.0™ & You on June 5-6th at the beautiful Cité Internationale Universitaire of Paris!

Berci Mesko, MD: "I cannot wait to reach a point where everyone can access the data of their own genome and use it accurately in their health management or when prescribing therapies. A few days ago, Illumina announced the $1,000 genome, now I’m waiting for the $100 genome."

"Editing DNA to eliminate genetic conditions now a reality"



Assessing the risks of Synthetic Biology in Europe






A variation around Craig Venter's "My greatest fear is us not using the technology" in his book "Life At The Speed Of Light".

Catherine Coste, Blog: "Ethics, Health and Death 2.0", certificate in genomics (MIT). I'm a genomic geek with strong social media skills.

When some French modern renaissance woman with medium sized intelligence is trying to come to terms with traditional medicine and some "organ-specialist" surgeons in the era of digital biology and precision "genomic" medicine... Wanting to talk about the Hippocratic Oath, she is raving about some hypocritical oak instead... She also talks about "twinkering" with her own genome -- "everybody stands back, I'm doing sciences!"

Also, she speaks about some "23 or me" company. Did you know that in France, it is forbidden by law that any French citizen asks -- on his or her own initiative -- for his or her own genome to be sequenced? It is punished by prison and a fine (cf. recent French bioethics laws)... French citizens are cut from their own genome. Hence, California-based 23andMe company becomes "23orMe". Exception culturelle française.

The EU scientific committee is currently assessing the risks of Synthetic Biology. Interesting experience for both technical and non-technical reasons. People might have developed some perspective on the subject and public perceptions via their own experience. Have such questions ever gotten into that in any kind of depth? Particularly the public sentiments? This is the kind of stuff this talk show is dealing with...


"Assessing the risks of Synthetic Biology in Europe from Cath Coste on Vimeo.

Presence of the Illumina "super-duper sequencing machines" worldwide:


MIT Digital class "The Secret of Life": "This is a class every biology teacher should take!"





Genomic and Precision Medicine: UCSF MOOC (started April 14, 2014)

https://www.coursera.org/course/genomicmedicine




Creative Writing: Future Learn's New MOOC starting April 28!


https://www.futurelearn.com/courses/start-writing-fiction

William Shih (Harvard) Part 1-3: Nanofabrication via DNA Origami

"A UCLA engineer is turning smartphones into pocket-sized medical testing labs."

US healthcare system is broken. Google using big data to "solve death"; 23andMe using big data to "solve health"

"The Google of Spit"
"With 23and­Me, Wojcicki wants to do with DNA what Google did for data—because, after all, DNA is data."

"Anne Wojcicki is CEO of a company she co-founded called 23andMe (so named for the number of chromosomes in human DNA) that could help forestall that legacy—could 'solve health,' as she puts it—by collecting the genetic information of a critical mass of humans on the planet.

Anne launched her company with the conviction, which happens to be the conviction of many of her friends and peers, that health care in America is broken, inefficiently treating the sick while insufficiently supporting the well, and that, enabled by the power of Big Data, Silicon Valley can fix it—accelerating to light speed the development of drugs and therapies by harvesting unprecedented insights from a reservoir of the nation’s genes.

By last fall, 23andMe had extracted and analyzed DNA from 650,000 people, making it one of the biggest genetic banks in the world. That was when the Food and Drug Administration stepped in. 23andMe was performing what it regarded as a medical test without its approval and without the oversight of any doctor, the FDA said, and until Wojcicki could demonstrate that those tests would inflict no harm, she was ordered to retreat from her quest to hoover up the world’s DNA.

But Wojcicki is undeterred. With 23and­Me, she wants to do with DNA what Google did for data—because, after all, DNA is data. Want to compare huge numbers of people with hereditary Parkinson’s disease against people who carry a gene for Parkinson’s but are healthy? Here’s a database of millions: All a researcher needs to do is create the algorithm. Want to look at genetic variances among people with very complex diseases, like diabetes, or Alzheimer’s, or coronary-artery disease? 23andMe can isolate disease groups and scrutinize the genotypes within them. Want to figure out why a tiny number of folks taking a certain multiple-sclerosis drug also get blood clots? Cull the patients from the database, email them a questionnaire, and compare answers. And then there are those connections algorithms might make between genes and health that humans hadn’t even thought to ask about.

These results might efficiently steer scientists toward especially promising targets for research, and the resulting discoveries—drugs, surgical procedures, nutritional information, eyeglasses, sunscreen—might then be marketed back to individuals who 23andMe already knows are predisposed to osteo­arthritis or hereditary blindness or melanoma. It’s a vision of seamless scientific research that is also a business—like, say, Google—tempting you with products the data engine has already discerned you need."

http://nymag.com/news/features/23andme-2014-4/?mid=gp_nymag

"How genetic variants can guide successful treatments must become part of routine medical practice and records"

Eric Topol MD's interview with Sid Mukherjee, author of "Emperor of All Maladies"

Not a scientist? Become one in four months with MIT 7.00x MOOC: "The Secret of Life", starting June 17, 2014. Enrol now, it's free!

MIT MOOC 7.00x "The Secret of Life"?! What's that?? To answer your question, here's the best read I was able to find:
This course will be live in June 2014! Enrol now!

https://www.edx.org/course/mitx/mitx-7-00x-introduction-biology-secret-1768#.U1eeLVfSmVq

Now, about my own experience: becoming gene savvy in four months?! How do you do that?

Healthcare consumers will need to become increasingly savvy regarding their genes...



Not a scientist? Become one in four months with MIT 7.00x MOOC: "The Secret of Life"
 (PDF Doc, 4 pages).


==> Software Tools that are being used for MIT Genomics courses: see here


Amazing!! With the help of this really "Awesome Sreenshot" software, I've been able to print each and every screen/page, with all the problem sets and midterm and final exams, including correction! 101 documents that will come in handy whenever I will feel like I need to review some or all of this stuff that gave me so much fun and challenge -- and that I came to love ;-)

"San Diego heart of digital health innovation"

"IBM's Watson Supercomputer May Soon Be The Best Doctor In The World"


Puttin On The Ritz - Irving Berlin - Pomplamoose

"Genome Sequencing Brings Hope to La Jolla Teen"


Every time I get to see Lilly Grossman's compelling story and updates on the net -- loved her book: "The girl they thought they never knew", by the way -- I get... slightly emotional. I admire her a lot -- her and her family. They are truly extraordinary people. Inspiring. As a genomic geek, I DO hope that Lilly's condition will be improved thanks to precision (genomic) medicine. My heart goes out to this family... Go Lilly!!!!!!!!!

A big fan of yours :-)

"Print your own 50-cent microscope - Retraction of Malaria"


http://www.nytimes.com/2014/04/22/science/science-tools-anyone-can-afford.html?ref=science

"Homo innovaticus"

Massimo Banzi's key note at "The First Day of Tomorrow", Paris, April 18 - 2014






The First Day of Tomorrow Conference in Paris - April 18, 2014

PROGRAM (PDF Doc.)

The First Day of Tomorrow Conference in Paris - April 18, 2014:

==> a few snapshots


Many thanks to Xavier Duportet for making this (slightly disruptive) event come true in Paris! Oh, and you might wanna check on Twitter...
And the winner is...






No doubt the IBM Watson will be interested in Google Deep Mind (and vice-versa)...




Documenting all the way from Organ Donation to CRISPR!

"Man tries to CrowdFund 3D Printed Kidney on Indiegogo"


The future of lab testing: Theranos Inc. and Archimej Technology

https://www.facebook.com/ArchimejTechnology
http://www.theranos.com

Erratum: instead of Terranos, read Theranos.

She's "The Voice"! Pomplamoose "I Feel Good"



https://www.youtube.com/user/PomplamooseMusic
http://www.patreon.com

"Edico Genome Aims at Data Processing Bottleneck in Whole Genome Sequencing"

"By mounting Edico’s proprietary Dragen processor on a standard computer expansion bus (similar to a graphics processing card) that is dedicated for genomics processing, van Rooyen says Edico’s technology could be installed in any next-generation sequencing machine—and would reduce the time needed to map a genome from 20 hours to 20 minutes.  (...) Van Rooyen says the underlying innovation of Edico’s technology is in the way the company implemented the genome-mapping algorithm, incorporating data compression techniques into a Field Programmable Gate Array (FPGA), a processor that is configured for specialized use after it is manufactured. (...) The company already is moving its design to a standard ASIC (Application Specific Integrated Circuit) processor, which typically can be mass-produced at low cost. (...) Van Rooyen’s commercialization plan calls for mounting the Dragen processor on cards that have been customized to work with specific genome sequencing machines, such as Illumina’s HiSeq X Ten. (...) By using Edico’s technology, van Rooyen says a facility using Illumina’s HiSeq X Ten machines to sequence 150 human genomes every three days would be able to save $6 million over a four-year period. (...) That would make it easier for hospitals and other healthcare providers to use genome sequencing to better diagnose heart disease, inflammatory disease, prenatal disease, and other conditions."

https://twitter.com/EdicoGenome
"With the arrival of next-generation gene sequencing machines like the Illumina (NASDAQ: ILMN) HiSeq X Ten, medicine has been moving to develop new ways of using genomic data to treat patients. Last month, for example, J. Craig Venter unveiled plans to sequence the entire genome of every patient entering the UC San Diego Moores Cancer Center as an initial goal for his latest startup, Human Longevity Inc.
At the same time, though, it’s becoming clear that generating genomic data for thousands of cancer patients involves working with very large numbers—and that means a wave of new opportunities for innovation are emerging as genomics and Big Data come together. One startup moving to catch this wave is Edico Genome, a San Diego startup founded last year to fix a bottleneck in the way the data being generated by the HiSeq X Ten and other next-generation sequencing machines is processed.
Edico has developed a specialized computer processor for ordering the readout of nucleotides—A, C, T, or G—from short segments of DNA generated by next-generation sequencing technology so they align with a reference genome. It’s a process that genomics specialists refer to as 'mapping.'
It is a Big Data problem. The human genome consists of roughly 3.2 billion nucleotide base pairs (made of that four-letter alphabet of DNA) that encode between 20,000 and 25,000 genes."

Tim Gardner, Riffyn: "The industrial revolution of genetic engineering"

The industrial revolution of genetic engineering: synthetic biology. Let's start building the future! Tim Gardner's Keynote at The First Day of Tomorrow 2014 Paris, April 18. Twitter: . The application of industrial measurement systems is the next frontier in Synthetic Biology. Next frontier in synthetic biology: applying industrial measurement & quality, even during the research process. #Gardner #Riffyn. 3D printing of stem cells.
"Hi Catherine, I noticed that you posted my talk from the FDOT conference on youtube. I am flattered and appreciative that you enjoyed it. But for many reasons I do not want the presentation on youtube. Would you mind removing the post? Perhaps we can have a chance to meet in person at some event the future. And perhaps there will soon be a presentation I don't mind posting on youtube! Thanks in advance for your understanding." All the best, Timothy Gardner

"More signs of digital-biological convergence: IBM's nano medicine efforts on HIV, TB, MRSA, cancer"


"Deep Mind" & "Her"



Richard Feynman: "What I cannot create, I do not understand"



http://subrealism.blogspot.fr/2011/04/what-i-cannot-build-i-cannot-understand.html

"Scientists on Track to Assemble 3D Printed 'Bioficial' Heart"

The First Day of Tomorrow in Paris, April 18/19-2014


#FDOT14

"The First Day of Tomorrow, during which 1,300 attendees from 20+ countries will meet in Paris around 40+ tech and startup superstars and 25 mind-blowing semifinalists... YES, we're getting excited!
A few key pieces of info we'd like to share:

#1  Our program is finalized, please find it attached & join us on Friday at 9:00 @Cité des Sciences, where a nice breakfast will be waiting for you, ahead of Joël de Rosnay welcome speech at 9:30
Venue details: 

Cité des Sciences et de l'Industrie

Congress Center

30, avenue Corentin Cariou

75019 Paris

France

#2   There is no such thing as a tech event without a rocking party, so let's meet at the Trabendo on Friday at 23:00, right after the conference, to celebrate on the best French groovy tunes!
Use the partaaay code on our Eventbrite page to get a free access to the party!
#3  On Saturday, meet the FrenchTech Safarithe First Day of Tomorrow's little brother  an amazing opportunity to discover the innovation places in Paris. 3D-printing, Arduino, Bio-hacking... welcome to our tech edition of Easter!"

Barthélémy Kiss
COO
Hello Tomorrow Challenge

Coursera MOOC "Epigenetic Control of Gene Expression" Univ of Melbourne starting on April 28th

https://www.coursera.org/course/epigenetics

On epigenetics: "The Epigenetic Control of Gene Expression course will start on the 28th of April, 2014. In case you'd like to brush up a little on genetics before we start, and you haven't had a chance to take another one of the genetics MOOCs available, you could take a look at this resource."
http://publications.nigms.nih.gov/thenewgenetics/index.html

"You may also like to watch some short animations that cover transcription and translation, and one which specifically goes into epigenetics and X chromosome inactivation, which we'll cover in the course."
http://www.wehi.edu.au/education/wehitv/dna_central_dogma_part_1_-_transcription/
http://www.wehi.edu.au/education/wehitv/dna_central_dogma_part_2_-_translation/
http://www.wehi.edu.au/x_inactivation_and_epigenetics/

"AlloMap: 11-gene (blood RNA) signature for monitoring rejection after cardiac transplant"

Much less painful than post-transplant biopsy ( for monitoring rejection after cardiac transplant) for heart and/or renal transplant patients!
https://d396qusza40orc.cloudfront.net/genomicmedicine/McCarthy-GenomicMedicineADecade.pdf
https://d396qusza40orc.cloudfront.net/genomicmedicine/McCarthy-GenomicMedicineADecade.pdf

"Well, choose me!"


https://www.facebook.com/catherine.coste

"Let me be your star" -- Bombshell/Smash, the Musical

=> Download audio file here.   

Audio files on this blog are Windows files ; if you have a Mac, you might want to use VLC (http://www.videolan.org) to read them.

Or: you can download MP3 version of audio file here.


Lyrics




https://twitter.com/cathcoste

Bioinformatics: Network visualization of programming language influence

"Genome:" A Magazine About Science and Medicine, Written for Patients



"The Underappreciated Ties Between Art and Innovation"

"Can law, ethics, keep up with technology?"

Love sequencing? Love DNA? Support collaborations and ethical data sharing tools for genetics!"

In France: laws that forbid the genomic sequencing of citizens on their own initiative. Will the French be forced to buy their own genome from the Chinese?

The Chinese will not *buy* French people's genome; they will *sell* it to them instead...

https://twitter.com/cathcoste


Illumina: "1 terabase in 6 days = 10 human genomes in 6 days" (Tb: 10 to the twelfth base pairs)

When we talk about next-gen gene sequencing, we talk about the amount of genetic sequence data, expressed in base pairs (bp). The growth has been exponential, and it is not gonna stop!
Base pairs (bp) < kilo base pairs (Kb: thousands of bp) < megabases (Mb: millions of bases)... up to 1 terabase (Tb: 10 to the twelfth bp)!
http://nextgenseek.com/2014/04/illuminas-new-v4-reagent-kits-for-hiseq-to-enable-1tb-per-run/
 By the way, there are no Illumina HiSeq® in Europe...

"Brain imaging can help doctors tell when a patient is more likely to recover"

http://time.com/63928/study-new-technique-predicts-consciousness-of-brain-damaged-patients/

"Read about DNA barcoding, CRISPR genome editing tools, hacking lab equipment, biomimicry and more"



Monsieur Doctissimo va-t-il créer son MOOC sur la médecine de précision (génomique) en français ?

Patrick Drahi investit 10 millions d'euros dans les MOOC via Mines-Télécom ; Laurent Alexandre, le fondateur de Doctissimo, va-t-il lui aussi créer son MOOC en génomique ? 

https://www.facebook.com/laurent.alexandre.96
https://www.edx.org/course/mitx/mitx-7-qbwx-quantitative-biology-1714#.U05BjFc9-IfIl

Hacking medicine, then cancer, then... death.



https://twitter.com/hackmedmit

Still a long way to go, though...

"Connaissez-vous le centre Inria-Microsoft Research à Palaiseau? Cloud, modélisation coeur et cerveau"

"Genome editing for all"


http://www.nature.com/nbt/journal/v32/n4/full/nbt.2879.html?WT.mc_id=TWT_NatureBiotech

"Cambridge Company Creates iPad-Sized Tech to Diagnose Diseases in Real-Time "

"Challenging routine medical dogma"

"Replacing a defective gene with a correct sequence to treat genetic disorders" + "Living organ regenerated for first time"


"Are Hackathons the Future of Medical Innovation? 'Doctors are Luddites in white coats'"

http://www.slate.com/articles/business/crosspollination/2014/04/medical_hackathons_is_this_the_future_of_health_care_innovation.html

"Synthetic DNA origami as interface for boolean logic and programming in vivo"

"Time to change disease classification from symptoms to the pathophysiology causing bio-mechanisms"


"Frenchwoman’s organs keep three Indians alive"

http://timesofindia.indiatimes.com/india/Frenchwomans-organs-keep-three-Indians-alive/articleshow/33633852.cms

"The Chemistry of Life" edX MOOC Course Now live!

"Creating new ideas at the interface between chemistry and biology"...



"The Chemistry of Life"
Actually, I got started with this MOOC and so far I like it. I'll audit it... The joy of learning... Creativity in chemistry and biology... sounds like fun...

New MITx MOOC in Biology: "Quantitative Biology Workshop"

A workshop-style introduction to tools used in biological research. Discover how to analyze data using computational methods. (read more)

Course will start June, 12th. Inscriptions are open! 
https://www.edx.org/course/mitx/mitx-7-qbwx-quantitative-biology-1714#.U0gqrFc9-If



I will definitely audit that one...