The Snyder Lab

The Snyder Lab Humbly studying the source code of life. Visit http://snyderlab.stanford.edu/ Michael Snyder is the Stanford Ascherman Professor and Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine.

Dr. Snyder received his Ph.D. training at the California Institute of Technology with Norman Davidson and carried out postdoctoral training at Stanford University with Ronald Davis. He is a leader in the field of functional genomics and proteomics. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and currently carries out a variety of projects in the areas of genomics and proteomics both in yeast and humans. These include the large-scale analysis of proteins using protein microarrays and the global mapping of the binding sites of chromosomal proteins. His laboratory built the first proteome chip for any organism and the first high resolution tiling array for the entire human genome. The Snyder laboratory sequenced the first genome (Acinetobacter) using high throughput DNA sequencing technologies, and invented RNA-Sequencing and Paired End-Sequencing using these technologies. Dr. Snyder co-founded Protometrix (now part of Invitrogen), Affomix and Metagenomix. He is the recipient of the Connecticut Medal of Science and the Pioneer Award in Proteomics.

A new paper from our lab is attracting some press attention. Paper: http://journals.plos.org/plosbiology/article?id=10.1...
07/30/2018
Glucotypes reveal new patterns of glucose dysregulation

A new paper from our lab is attracting some press attention.

Paper: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005143

Press: https://health.usnews.com/health-care/articles/2018-07-24/blood-sugar-spikes-seen-in-seemingly-healthy-people https://www.thetimes.co.uk/article/concern-over-hidden-blood-glucose-surge-dmbddcxtt https://med.stanford.edu/news/all-news/2018/07/diabetic-level-glucose-spikes-seen-in-healthy-people.html

Author summary One in 10 individuals is affected by diabetes, a condition involving abnormal regulation of blood glucose. Currently, diabetes is assessed using single-time or average measurements of blood glucose, without consideration for how blood glucose fluctuates over time. We used continuous g...

A (partial) laboratory photo
07/30/2018

A (partial) laboratory photo

Principle investigator Michael Snyder with his student Reem Abdel-Haq, in a lab at Stanford School of Medicine on Friday...
11/12/2014

Principle investigator Michael Snyder with his student Reem Abdel-Haq, in a lab at Stanford School of Medicine on Friday, August 23, 2014. ( Norbert von der Groeben / Stanford School of Medicine )
COPYRIGHT:Norbert von der Groeben

 http://mendelspod.com/podcast/short-read-sequencing-not-task-characterizing-transcriptome-says-mike-snyder-stanford
09/11/2014
Short Read Sequencing Not Up to the Task of Characterizing Transcriptome Says Mike Snyder of...

http://mendelspod.com/podcast/short-read-sequencing-not-task-characterizing-transcriptome-says-mike-snyder-stanford

Today we launch the much anticipated series on The Rise of Long Read Sequencing with Mike Snyder, Professor of Genetics at Stanford. Mike has been working four years on what has become known as the “Snyderome” (Narccisome if you want to be nasty), looking at hundreds of thousands of his own molecula…

The Hive
09/04/2014

The Hive

Professor Mike Snyder is in da house! Looking forward for another amazing tech talk @netapp!

Mike Snyder presenting at The Hive!
09/04/2014

Mike Snyder presenting at The Hive!

A sequencing genome is now cheaper than a used car

108: Dr. Michael Snyder: Decoding the Human Genome to Potentially Predict Disease Risk
08/04/2014
108: Dr. Michael Snyder: Decoding the Human Genome to Potentially Predict Disease Risk

108: Dr. Michael Snyder: Decoding the Human Genome to Potentially Predict Disease Risk

108: Dr. Michael Snyder: Decoding the Human Genome to Potentially Predict Disease RiskJuly 23, 2014 by PBtSLeave a CommentPodcast: Play in new window | DownloadListen Free in iTunes Listen Free on Stitcher RadioDr. Michael Snyder is the Stanford Ascherman Professor, Chair of Genetics and the Directo…

Congrats Professor Mia's! We will MISS you!!!!
02/03/2014

Congrats Professor Mia's! We will MISS you!!!!

Thanksgiving Day Turkey Bowl 2013 was a success!!
12/04/2013

Thanksgiving Day Turkey Bowl 2013 was a success!!

Check out this great article on Michael Snyder and personalized medicine http://membercentral.aaas.org/blogs/depth/perso...
07/19/2013
Personalized medicine: AAAS members paving the way for gene-tailored medical care | AAAS...

Check out this great article on Michael Snyder and personalized medicine http://membercentral.aaas.org/blogs/depth/personalized-medicine-aaas-members-paving-way-gene-tailored-medical-care

Over the past three years, AAAS member Michael Snyder has become a guinea pig for his own research, volunteering to regularly draw blood so his Stanford lab could track his genomes. His genetic profile, called an iPop, or integrative personal omics profile, revealed that he had a high risk of develo...

04/15/2013

Let's say reading and analyzing the DNA of everybody on Earth is completed. (Which can be possible within our lifetime.) What do you want to do with the knowledge? Any interesting idea?

04/06/2013

Decompiling the sourcecode of life: Functional Genomics.

The long-lost body of Richard III, the last Plantagenet king of England, has finally been found and identified, thanks i...
02/04/2013
Car park skeleton is Richard III

The long-lost body of Richard III, the last Plantagenet king of England, has finally been found and identified, thanks in part to DNA testing. Researchers extracted and sequenced mitochondrial DNA from the skeleton's teeth and femur, then compared it to mtDNA from a surviving descendent of Richard's sister and confirmed a match.

http://www.bbc.co.uk/news/uk-england-leicestershire-21063882

A skeleton found beneath a Leicester car park is confirmed by archaeologists as that of English king Richard III.

01/22/2013
Where have I been?

I was never someone who blogged a great deal. But once or twice a month, I would put hand to keyboard and come up with something to talk about that is relevant to my favorite field of study: Genetics.
I have every intention to continue doing that. …

User-friendly, open-source personal genome pipeline
12/19/2012
User-friendly, open-source personal genome pipeline

User-friendly, open-source personal genome pipeline

Today, GenomeWeb wrote a piece on the STORMSeq pipeline (Scalable Tools for Open source Read Mapping), our newest project in the goal of enabling the public to explore their own personal genetic data. In this pipeline, users upload reads to Amazon S3 and start a webserver in Amazon EC2, where they can set parameters for read mapping and [...]

Trending
12/19/2012
Trending

Trending

On Election Day 2012, what's the number two trending hashtag? #ASHG2012 baby! We've arrived! twitter.com/mjcgenetics/st…— Michael James Clark (@mjcgenetics) November 7, 2012 Beating #Election2012 on Election Day in the US. Human genetics has made it, people. Step aside, Charlie Sheen.

Save the Square Watermelons
12/19/2012
Save the Square Watermelons

Save the Square Watermelons

NO on 37! Think about it, Californians. Are you telling me you can't figure this one out, @carighttoknow? #prop37 twitter.com/mjcgenetics/st…— Michael James Clark (@mjcgenetics) November 6, 2012 Also, I just realized I've had over 25,000 hits on this blog. Thanks for reading! I hope it's been useful and interesting!

"Why I Don’t Want to Know My Genome Sequence"
12/19/2012
"Why I Don’t Want to Know My Genome Sequence"

"Why I Don’t Want to Know My Genome Sequence"

"Why I Don't Want to Know My Genome Sequence"Kind of interesting to read this as someone who at least has his own exome sequenced and has learned a lot from it. It's kind of interesting to read it in contrast to my own post explaining why I wanted to sequence myself.It ends with a funny statement: An osteoarthritis mutation manifested itself as an inability to play an F chord at age 33. A p53 mutation and then another that bloomed in response to years of orthodontia X-rays gave me thyroid cancer a few years after I gave up the guitar. And I don’t need a genetic test to know I didn’t inherit my father and grandfather’s psychotic depression. Ron Crystal, even though he’s among the sequenced, has the right idea: don’t smoke, exercise, eat a healthy diet, and don’t worry about DNA sequences. That’s good enough for me – at least for now.This is one of those statements used to make one's self feel better about not doing something he or she wants to do. That's my feeling, at least.To be more specific, let's use myself.Sure, I could have lived my life thinking my borderline migranes were from caffeine withdrawel and my mother and not bothered to find out the exact mutations likely to cause it and therefore which drugs may actually have a beneficial effect on me. I could have. But I didn't.I could have lived my life thinking my intestinal issues were due to a bad diet or food allergies. Because clearly copious amounts of salad, low fat, low carb, low salt is a bad diet, right? And clearly my wife who eats the same things and has zero gastrointestinal issues is just lucky. Oh no, it must be food allergies. It couldn't possibly be that I inherited two mutations, one from each parent, that damage a particular gene already known to be causative for gastrointestinal problems (among a number of other things that I happen to have that most general practitioners wouldn't link together).I could have survived without knowing I have asthma. Maybe.I mean, go ahead and live in ignorance if that's your thing. If you're not interested in your own genetics, then fair enough. You're not alone. But it was damn reassuring to me, personally, to figure out exactly what genes are mutated and how those are causing conditions that negatively effect me.And I would say not only am I healthier, but I'm also more aware of my health. And that's a good thing. And that genetic information isn't going to expire.Anyway, let's not devalue our genetics this way. The fact that we don't know everything yet doesn't make the data itself less valuable. Yes, it will take effort to understand but then again, so does nearly everything about your health and life.I see it as a great thing.

Congrats to the team working to crack the wheat genome, who published in Nature this week!  Thanks to all the hybrid cro...
11/28/2012
New Slice of Wheat Genome Could Help Feed Growing Global Population | Observations, Scientific Ameri

Congrats to the team working to crack the wheat genome, who published in Nature this week! Thanks to all the hybrid crosses, plant genetics are fiendishly complex. It's a great achievement to have the basic structure mapped out.

Common wheat (Triticum aestivum) might seem as boring as the sliced bread it is baked into. But genetically, it is vexingly complex. Its genome is about six ...

Guess which profession needs drinking coffee the most?
11/14/2012

Guess which profession needs drinking coffee the most?

11/07/2012

The Snyder is at the 2012 ASHG meeting this year with 15 abstracts. Go forth and talk some serious science.

ASGH2012 Fail
10/31/2012
ASGH2012 Fail

ASGH2012 Fail

#ASHG2012 : Encouraging cloning by putting multiple highly interesting talks I want to see in concurrent sessions. twitter.com/mjcgenetics/st…— Michael James Clark (@mjcgenetics) October 31, 2012

10/24/2012
Eric Lander dancing to Gangnam Style

Snyder lab: mind-blown by MIT's Eric Lander (genomics pioneer and visionary). During his intro to biology class, he performs Gangnam Style dance. Gangnam Style is a South Korean dance music that went viral through Youtube this year. Maybe Dr. Snyder will respond with another dance?

Renowned geneticist and founder of the Human Genome Project dances to Gangnam Style during 7.012 lecture: Introductory Biology at Massachusetts Institute of ...

Misunderstood: Genetic tests and the people who don't understand them
10/22/2012
Misunderstood: Genetic tests and the people who don't understand them

Misunderstood: Genetic tests and the people who don't understand them

On Friday, I was made aware of a story about a boy in my town (Palo Alto, California) who was being transferred from his school to another school against his and his parents wishes. He didn’t do anything wrong and he didn’t want to leave. Instead, the administrators at his school made this decision based on genetic information they were given by the parents. Genetic information that they apparently did not understand fully.The StoryThe original story made a bit of a splash, with articles on major news sources. Here are a few links explaining the fiasco:The original article that exposed what happened.An official response from the superintendent of the school district.An SFGate article that exposes important facts about this case.The article I first heard about the story in.The basic story goes like this:A boy named Colman Chadam is being forced to transfer out of his current school in the middle of the school year because he carries mutations that cause cystic fibrosis (CF). CF is a relatively common yet fairly severe genetic condition. Kids with CF should not be in close proximity to one another because they can easily infect each other with respiratory infections. In other words, a school would not want two kids with CF in the same class, and would probably be justified in keeping them separated for their own health (though it’s unclear if forcing them to go to separate schools is even necessary).CF can be predicted genetically—we are aware of major CF mutations (in the CFTR gene) in the population and a standard genetic tests can identify them. But CF is typically diagnosed through a non-genetic test called a sweat test, and is otherwise a rather self-evident disorder because it is a serious condition. It affects one in twenty-five Caucasians. Moreover, the genetic tests are necessarily conclusive—one could carry mutations for the disease yet not have it.The thing is, Colman was apparently never diagnosed with CF. He has never displayed any symptoms of the disorder. Instead, according to the SFGate article, Colman was found to have mutations in CFTR that could potentially cause CF. But they haven’t for him.For whatever reason Colman had a genetic test including CFTR eleven years ago. It’s unclear in the articles I’ve found, but I’ve been told he’s likely to have tested positive for a sign of CF at birth and then had the genetic testing to confirm, but the disease never manifested later. So despite not having cystic fibrosis, his parents are aware that he carries mutations in the CFTR gene.And, probably without thinking that there could be serious ramifications for Colman, his parents told the school that he carries mutations for CFTR when they were asked to report any pertinent genetic information.The SFGate article discusses the progression from an innocuous bit of irrelevant “medical” information to Colman being transferred out of his school:“A few weeks into the school year at Jordan Middle School, school officials took note of Colman's medical history, information that eventually was shared with another Jordan parent whose two children have classic cystic fibrosis and are predisposed to chronic lung infections.”Can anyone else see some major problems with this little statement? First off, school officials were looking into this child’s medical history why, exactly? He does not have cystic fibrosis, so why was it being followed up so heavily by the administration? Second, his information should never have been shared with the other parent who has two kids with CF.Moreover, with one in twenty-five Caucasians carrying mutations for CF, there’s likely to be numerous children at the same school carrying CF mutations who are not being transferred because they never had any symptoms and they never had a genetic test. That’s one of the things that makes this action by the school so unreasonable.So I tried to think about how this could have happened.I think what probably occurred was that Colman’s parents reported his CFTR mutations just in the interest of being fully compliant with school rules that say, “Tell us everything (or else),” which most parents are probably familiar with.Then a nurse or administrator or someone (who hopefully had permission to see Colman’s records) who was familiar with cystic fibrosis (at least at the level of understanding that two kids with CF shouldn’t be in the same class) noted that Colman had CF mutations and misunderstood that to mean he has cystic fibrosis.I’m not sure whether the other parents were really informed or not (at least one article suggests they were—if they were, they shouldn’t have been). But what I can imagine is that in the interest of avoiding any potential problems (imagined or otherwise), they decided to transfer Colman out without really understanding that he does not have cystic fibrosis.There’s some pretty strong evidence of this in a letter from the superintendant that was posted on PaloAltoPatch. I’m pasting it below for posterity:“The Palo Alto Unified School District strives to meet the needs of all students and to ensure that a safe and welcoming learning environment is provided for all our students and staff. To be clear, this commitment includes caring for our students with medical needs.“At this time, our District serves students who are diagnosed with Cystic Fibrosis (CF), a serious medical condition that creates a need for our staff to observe strict protocols on cleanliness in order to help protect these students' fragile condition. I am proud that our staff energetically and compassionately works to observe the necessary protocols for these students. Further, I am proud that our staff thoughtfully embraces these, and all, students."A recent story that appeared in the San Francisco Chronicle addresses the distance -- the literal physical distance -- that must be constantly maintained between children with CF in order to avoid bacterial cross contamination. I want to stress that medical authorities clarify that CF is not a health threat to the general public (a theme that was touched on in the story), but it is a topic of concern for non-sibling children with CF.“As background, at the beginning of this school year, we became aware that students (not related) with CF were on the same middle school campus. Based on the advice of medical experts, who stress the need for non-sibling CF patients to constantly maintain a specific distance from each other, we thought it best to place the students at different campuses. Again, based on the advice of medical experts, this is the zero risk option, and most certainly helps our District deliver on its commitment to provide safe learning environments.“We asked the family of the student who is new to our District if they would consider moving their child to Terman Middle School. We asked because Board policy gives priority site choice to students who are established at a site, and the other students have been with our District for years. Sadly, it was this request that caused the controversy, and the media coverage.“I want to stress a few critical points.“First, at both of these schools the dedicated staff are stepping up and working to provide these students with excellent learning environments. We are grateful for their professionalism and compassion.“Second, we are education professionals, not medical experts. I assure you that we will take action based on recommendations from medical authorities. Expert advice will be balanced by the PAUSD Board policy that strictly instructs our District to ensure we provide a safe learning environment for all students. To be clear, our Board of Education places the highest priority on student safety, in all situations and in protecting the privacy interests of all students."Finally, we must be honest about the fact that we are talking about public schools, not medical facilities. We will strive to implement all health and safety protocols to help protect the health of these children; however, the harsh reality of a busy middle school campus, where students ranging in ages from 12 to 15 share a cafeteria, restrooms, the gym and locker room, a library and other settings, is that it might be virtually impossible to maintain a specified separation and sanitation protocols at all times. This reality is what made us gravitate to the separate campus option. CF is a life-threatening condition, and in this context, based on the information provided to us at the time by all parties, we believed that zero risk was the best course of action. We hoped that these families would agree.“This topic is understandably emotional for the families involved, and we will work with them to meet the needs of their children. However, I must again stress that we will follow the advice of medical experts, who we trust will help us understand the option that eliminates, if possible, all risks.”Sincerely,Charles F. Young, Ed.D.Associate Superintendent Education ServicesPalo Alto Unified School DistrictI feel that this letter clearly shows that at the very least, Dr. Young here was under the impression that Colman has cystic fibrosis. But he apparently does not. He carries mutations in CFTR, but he doesn’t have CF. Here’s another piece of evidence that Dr. Young and the other administrators are misinformed, thinking that carrying CFTR mutations is equivalent to having CF:“The administrators sought medical advice, Silverman said Thursday, which resulted in a recommendation from Dr. Carlos Milla, of Lucile Packard Children's Hospital, saying that, ideally, children with cystic fibrosis would attend separate schools.The recommendation was not based on knowledge of Colman's specific medical history, his parents and their attorney said prior to Friday's court appearance.”Why else would they seek medical advice about whether children with cystic fibrosis should attend the same school unless they thought that Colman actually ha

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of Life …is Life, amen. By Robert Magill The sole purpose of life, and therefore our only human purpose may simply be, life itself. That, upon reflection, would appear to be quite enough. The life force does have its urges though, lots of them, it would appear. After countless eons of self-replication along came sexual reproduction, life had apparently gotten to be in somewhat more of a hurry. Life then pursued bigger and better forms of itself as mobility, size, vision etc. ensued over time. Vision was very unique and a promising end in itself, but life appeared to desire a different platform with which to fully employ this new sense. Many prototypes came and went, and eventually on the scene appeared humankind complete with a newly acquired awareness. Did life, with this move, express desire for an ego to admire itself or, more positively, to express itself? Why else create a platform embellished with consciousness? Then, alas, something went very wrong with life’s dedicated pursuit of life? Human behavior. We know large portions of the recent history of our species and it's not very good. Considering our known history, can we begin to significantly amend our ways if life demands a timely accounting? So if and when life decides we have exhausted all possibility of further usefulness, and our excesses overwhelm life's other vital interests, do we then risk severance of the thread with life? Should not we begin to tug ever more gently at this tether to lessen our risk? Does life even care about the fate of us, its creature? Probably not, countless other species have traveled along on life's quest, prospered to a degree and vanished. Will we join them? Whence came then, this thing, this awareness, this brightness in the void, so cherished by life our very species could be made forfeit to preserve it? Perhaps it was the animal curiosity of some lumbering hominid possessed of sufficient cranial matter that chanced upon a source. The menu of vegetable suspects is quite large. The plants, cacti, mushrooms and vines that possess the chemical soups that have the ability, and perhaps desire to exert themselves aggressively when combined with suitable host brain, is legion. We currently regard these substances as “mind altering” but could they perhaps have been “mind creating” at some remote point in time? Students of psychedelic phenomenon have reported a tendency among this family of substances to exhibit a strong urge to promote its own agenda over the host consciousness at times. Life, in this way, may have introduced the initial spark of awareness in receptive hominid brains with suitable vegetable matter containing psychedelic chemical ingredients. Imagine the wonder this revelation surely produced in a previously unconscious world. The binges and quest for more light shows that followed in the still only partially illuminated minds of these creatures must have been incredible. Perhaps this initial visitation of consciousness onto a receptive human brain and the incredible awakening produced therein is responsible for the ongoing human quest for enlightenment. Our species has demonstrated a universal affinity for various visions, ecstasies and raptures and they have been zealously sought for millennia. Perhaps then, a racial memory of, and longing for a return to that original staggering event gives impetus to the universal spiritual quests we humans faithfully follow to this day. Of course it is possible life may now be providing itself with a non-life fallback to the dilemma posed by our misuse of awareness and consciousness. If humankind becomes suspect of probable catastrophic losses to many of its other progeny, life then may seek to substitute Artificial Intelligence for flawed human intelligence. We, ourselves, may rapidly be creating the instruments for our future replacement with life's resigned encouragement. Life may value this tediously acquired awareness beyond all measure. More the pity for humankind. These phenomena are unique on the planet; life, the life force and the awareness/consciousness of one primate species. What we regard as ultimate reality is simply the stories we tell ourselves and others combined with whatever actions humans are capable of accomplishing. Humanity must now learn to live with 5 Gigabit technology becoming a reality and should perhaps begin to wonder which future Gigabit number will be the one to provide the artificial intelligence and awareness deemed sufficient by the life force to render our kind redundant if it chooses to do so? 🙁
A perfect platform, Bioinformatics Congress 2017 to showcase your innovations. Paris hosts the most exhilarating event during November 13-14, 2017. All the groups(students/researchers/deans/heads/companies) are invited as speakers/delegates. Catch the early bird registration.