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Author: Brian Krueger, PhD | Views: 4749 | Comments: 0

Image courtesy of Shutterstock
If you’re an avid follower of popular science in today’s news media, you might have noticed a recurring theme. Genomics is everywhere. On an almost weekly basis, the New York Times, the New Yorker, Forbes and a myriad of other outlets are publishing stories with overly optimistic ledes about doctors and gene sequencers being replaced by apps and iPhone accessories. You would be forgiven if you thought genomics was “solved” and we’re 5 years out from creating a Star Trek inspired “tricorder” that near instantly sequences your genome and tells you, without equivocation, what malady is afflicting you and how exactly to overcome said disorder. The fact of the matter is that we’re not there yet, not by a long shot.

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Author: Brian Krueger, PhD | Views: 1347 | Comments: 1
Last by Ematiz Alom on Mar 08, 2015, 8:37am
The Advances in Genome Biotechnology conference starts tomorrow in Marco Island, FL. Twitter and the blogs have been a flurry of speculation about what the major vendors will present at this years’ meeting. In previous years we’ve seen the introduction of new, “disruptive” technologies such as the ion torrent platform, the Oxford Nanopore Minion and the PacBio RS. Like many, I have mixed emotions about this conference. It’s more CES than science. Given the history of the major announcements and where those products are now 3 and 5 years out it’s hard to get excited about a show stopper. While technically impressive, the MinIon is still mired in problems that were glossed over in the fanfare of the original announcement and PacBio is FINALLY starting to deliver on the promises it made eons ago. I should also mention my disappointment with Ion Torrent here. This is yet another company that made a major announcement at AGBT and failed spectacularly. Keith Robison thinks they still have a sho . . . More
Author: Brian Krueger, PhD | Views: 2050 | Comments: 0
Yesterday marked the kickoff of the JP Morgan Healthcare Conference in San Francisco. Following last years’ lead, Illumina once again used this platform as an opportunity to announce the release of a number of new products including 4 “New” sequencing systems ahead of the more scientifically focused Advances in Genome Biotechnology conference in February. At this same time in 2014, Illumina presented the HiSeq X ten sequencing system which is a system for population scale genomics composed of ten HiSeq X sequencers. Illumina touted this system’s reduced reagent price, increased speed, and expanded capacity. It has now taken much of the technology from this HiSeq X system and put it into two new lower tier models: the HiSeq 3000 and HiSeq 4000.

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Author: Brian Krueger, PhD | Views: 1626 | Comments: 0
If you're using the twitteroauth php library from Abraham Williams and trying to delete old tweets/retweets you need to construst the post() query as such:

$response = $connection->post('statuses/destroy/'.$tweetID, array()); ->Curl url output = statuses/destroy/$tweetID.json

This will NOT work:
$response = $connection->post('statuses/destroy/', array('id' => $tweetID)); -> Curl url output = statuses/destroy/.json

I hope others find this helpful.

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Author: Brian Krueger, PhD | Views: 2329 | Comments: 0
Illumina, the world leader in short read DNA sequencing, made a series of very big announcements yesterday at the JPMorgan Healthcare Conference. These developments have many sequencing labs around the world excited and worried all at the same time. The excitement comes from the fact that it appears on the surface that Illumina has broken the $1000 genome* barrier – the worry comes from the realization that only a few of us can afford it.

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Author: Cynthia McKelvey | Views: 8312 | Comments: 0
For over two decades, Shark Week on Discovery Channel has been raising awareness of one of the ocean's most mysterious and powerful predators. Discovery originally started Shark Week with the purpose to dispel myths about the dangers of sharks, and to heighten the public's respect for the creatures. However, this year, many fans have felt outraged that Discovery may be straying further away from the original purpose of Shark Week. This year, Discovery unveiled the faux-documentary, Megalodon: The Monster Shark That Lives.

Megalodon, for the record, are definitely, absolutely extinct. They were super-sized sharks that once roamed the oceans some 2 million years ago.

Relative size of Megalodon (red and grey) vs. human. Source.
The Discovery special, on the other hand, suggested an alternative. Megalodon still roams the oceans, somewhere off the coast of South Africa. The documentary looked and seemed like any other documentary about real life events (however fantastic.) It convinced 70% of viewers that Megalod . . . More
Author: Cynthia McKelvey | Views: 3438 | Comments: 0
This article is being published here with permission from The Synapse. It originally appeared in the Spring 2013 edition of The Synapse at Oberlin College.

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Author: Brian Krueger, PhD | Views: 3463 | Comments: 0
It's been a long run and we have a strong readership of the press releases but sadly I no longer have the time or the interest to continue posting press releases on the site.  My additional work commitments here at Duke have really limited the amount of time I can devote to this and grabbing the press releases every night/morning for an hour or two just became tedious.  I'd like to spend my free time doing more creative things so hopefully I'll give my neglected blog some attention over the next few months.

To those who have been loyal followers of the press releases: Thanks for your devotion and continued support.  It does pain me to stop posting the press releases knowing they are served to nearly a million visitors a month, but I just do not have the time or desire to continue these activities.  I will, however, continue to post/link to mainstream news stories and blog posts I find interesting, so keep an eye on twitter and the right hand column here on the blogs.  I'll be adding a "from the web section" shortly.

The blogs will still be here for anyone that would like to use them as an outlet.  Just send me an email or contact me on twitter!

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Author: Cynthia McKelvey | Views: 4440 | Comments: 2
Last by Cynthia McKelvey on Apr 30, 2013, 1:10pm
Last summer, I became inspired to write an article about the potential benefits of the club drug, MDMA, otherwise known as Ecstasy or Molly. The blog post got turned into an article for my alma mater's science magazine, The Synapse, and was published a few months ago. With permission, I am cross-posting it here.

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Author: Brian Krueger, PhD | Views: 12353 | Comments: 9
Last by Michael Schatz on Feb 26, 2013, 12:13am
Aside from the dubstep pumping out of the Roche and Agilent booths, the volume of AGBT has been somewhat muted. There was no grand offering of new hardware or over the top promises of sequencing genomes on what now appear to be vaporware USB thumb drives. This is my first in person experience of AGBT, so as a virgin it seems for the most part to be rooted in the science despite the ridiculous parties and “showgirl” casino nights. The atmosphere here is unlike any other science conference I’ve attended. It’s like the bastard child of a Gordon Conference and a Las Vegas Porn Convention. I really hope that the deep pockets of Sequencing Centers are more influenced by the science than the free dinner parties and alcohol, but I have pretty low confidence in humanity. Regardless, I think everyone in attendance today was overwhelmed by a stunning talk from PacBio and the dramatic advancements of their long read technology.

The PacBio talk came on the heels of what felt like a warm-up opening act from Jeremy Schmutz of the Hudson Alpha Institute. Schmutz has been working with a start-up that was recently acquired by illumina called . . . More
Author: Brian Krueger, PhD | Views: 4011 | Comments: 0
As the second day of AGBT kicked off, it became quite clear that this meeting would be dominated by medical genomics. There were a few talks sprinkled in about gut or sewer microbiomes but the vast majority of the talks the last two days have been on clinical genomic sequencing. This is fine by me since it’s exactly what we do in the Genomic Analysis Facility in Duke’s Center for Human Genome Variation. It’s really nice to see how other centers are approaching these problems. Unfortunately, this is one of the few opportunities we have to peek into each other’s operations.

Yesterday’s first talk was by Russ Altman of Stanford University. Russ has been a leader in the field of pharmacogenomics and he presented his work on developing the Pharmacogenomics Knowledgebase (PharmGKB, He led by saying, “Don’t ever give a talk about a website,” and in his case it was true because WiFi in the conference room was down for the majority of his talk. He urged the crowd to follow along on the website, but only those of us with a cell connection could join him. Russ pointed out the major drawbacks of using GWAS and SNP chips for obtaining information about pharmacoenomic associations and joined pretty much everyone else in saying that the standard t . . . More
Author: Brian Krueger, PhD | Views: 3555 | Comments: 2
Last by Brian Krueger, PhD on Feb 21, 2013, 11:42pm
Today I dusted off my luggage and headed down to the annual Advances in Genome Biology and Technology meeting in Marco Island, FL.  Historically, this meeting has been the Detroit Auto Show of Genomics where companies and labs release their beautiful shiny new products and methodologies.  In past years, attendees were showered with fireworks displays and epic swag bags.  The tone this year is palpably more mutated.  One only has to point to the display banners located on the AGBT presenter stage for evidence of this: banners for Bronze and Silver Sponsors appear to hang waiting for accompaniment by Gold and Platinum brethren…there’s even space allocated for them.  

Despite the tightened biotech purse strings, the event appears from the outset to be extremely well organized.  There could be a few more power outlets for those of us carrying a small fortune in lithium powered devices, but I guess I’ll manage.  And of course there’s no live streaming or any form of web enabled anything…but I can gripe about that in a long winded and whiny post next week.

The evening opened with a brief introduction with a description of some new meeting changes.  This is the biggest AGBT yet with over 800 attendees.  A new abstract selection committee was created . . . More
Author: Jordan Gaines | Views: 5177 | Comments: 1
Last by Sneha Mokashi on May 08, 2013, 2:08pm
My friend texted me something today that she thought I'd find interesting.

She had a meeting for work in an office she'd never entered before. Immediately as she entered the room, conflicting feelings of happiness and awkwardness washed over her.

The smell. It wasn't necessarily good or bad—just distinctive. And it didn't smell like anything in particular. All she knew was that it had an odor exactly like her boyfriend's dorm room when she was a freshman in college—something she hasn't experienced in five years—bringing back the paired feelings of excitement and nervousness that come with new relationships. And those of, well, being in a boy's stinky dorm room.

We've all experienced this at one time or another: a familiar perfume, a family recipe in the oven, the scent of a bonfire—they all bring back a flood of memories, momentarily whisking us away to re-live our past. But why does this happen?

One of animals' most primal senses is that of smell. If you look at a rat brain, the olfactory bulbs (the two little notches at the top) take up a significant portion of the total surface area. In the human brain, the piriform cortex (our primary olfactory cortex) is composed of three primitive layer . . . More
Author: Jordan Gaines | Views: 4479 | Comments: 1
Last by jimbot on Jan 28, 2013, 7:14pm
The weekend before Christmas, I was sucked into a giant, enticing vortex of craving and desire, stuck for hours with the inability to leave—my only limitation being my wallet.

In other words, I went to Target.

And—again, in other words—I was like a bull in a China shop.

Back in 2009, Target introduced new gigantic, plastic, Playskool-esque shopping carts. Maneuvering the aisles is like passing a car on a one-lane country road in a Hummer.

Of course they're ridiculously cumbersome, but it's all a trick on the Target executives' part—the bigger your cart, the more you can fit in there. You'll look silly hauling around a couple packages of pens and a box of tissues to the checkout counter, after all. Better head to the appliance section and fill it with a microwave or plasma TV.

In this second installment, we'll explore how stores betray our sense of sight, tricking us to buy stuff we really don't want or need.

Retailers have—quite creepily, actually—studied our every move. In fact, they've found that we like to shop counter-clockwise, and stores with their main entrance to the right side sell more than their counterparts with doors on the left.

They also like to welcome us . . . More
Author: Jordan Gaines | Views: 4210 | Comments: 1
Last by Brian Krueger, PhD on Dec 10, 2012, 9:46am
On the first day of Christmas my true love gave to me...

...a bunch of crap I really didn't need.

With just sixteen shopping days until Christmas, it's easy to get roped into buying things we might not actually have on our gift list.

Most times, we're conscious of our impulse purchases—there's a great sale on this! I'll use that later!

But sometimes reasons for our frivolous purchases are not so obvious to us. Don't feel too bad—store chains actually hire researchers to study our shopping patterns and take advantage of our weaknesses.

Our brains are endlessly fascinatingly organs—but sometimes they betray us. The following is the first post in a five-part series on how stores trick our senses into shelling out more money than we may intend.


Did you ever take the Pepsi Challenge?

For those unfamiliar (or living under a rock), the Pepsi Challenge was a campaign started by Pepsi back in the 1970s where Coca-Cola was pitted against Pepsi in a blind taste test by consumers.

When it was revealed that most Americans chose Pepsi over Coca-Cola, sales skyrocketed.

How they tricks us: We consumers like brands, and we're loyal to them.

It make sen . . . More
Author: Nick Fahrenkopf | Views: 1733 | Comments: 0
Day 4 was also a travel day so I didn’t get to see much of the conference. I spent time packing, checking out, and getting out of the city before rush hour set in. But I did want to write about one unexpected but interesting talk, and recap some culinary highlights of the trip (sorry, I love food!)

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Author: Nick Fahrenkopf | Views: 2637 | Comments: 0
To be honest, most of today I was preoccupied getting ready for my talk in the afternoon. But, to take my mind of it I still tried to attend talks. I feel like sometimes conferences are hit or miss. Sometimes you could walk into a 15 minute contributed talk and be blown away. But other times the 30 minute invited talks could be a literature review or incremental research. A lot of the talks I went to today were incremental talks. It was a lot of “the field is at point A and we’ve brought it to A + dA”. So I heard about thin film transistors which could be useful for wearable electronics, but I didn’t feel like it was anything new. I heard another nanowire sensor talk, but again, nothing revolutionary.

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Author: Nick Fahrenkopf | Views: 2548 | Comments: 0
Before I get started with my summary of Day 2, I need to vent a bit. As a presenter 99% of the time you are not loud enough to not use a microphone, so please don’t try to forgo it. Also, 99% of the time you will cover 1 slide per minute. So, a 15 minute presentation should not have 40 slides. You will never cover all of that material. Please rethink what point you want to get across. I’m constantly disappointed by folks who have the fly through their results due to poor planning. I’m also disappointed when chairs don’t stick to the schedule. There are multiple sessions all over the place so when I show up at 10:15 to see talk X and you just started talk X-1 because you’re running 15 minutes late, that means I can’t see X and still make it to the 10:30 talk in a different session. The times are more than a suggestion!

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Author: Nick Fahrenkopf | Views: 2333 | Comments: 0
Today was a travel day, but I was still able to attend a number of biomedical engineering talks which are personally interesting to me, and some talks on memristors, which some of my lab mates work on. I’ve explained elsewhere what a memristor is, but briefly it is a metal-insulator-metal material stack that has two resistance states (high and low). If that sounded like goobldy-gook to you, imagine a chunk of wood sandwiched in between two chunks of copper metal. Normally electricity won’t flow between the two chunks of copper through the wood (high resistance). In a memristor you can apply a high voltage to create a conductive path through the “wood” creating a low resistance state. This is useful for computers because it can be used as a memory device: high versus low translates to a 1 or a 0. If you make lots of these you have the memory chip that could be used in your computer or cell phone. These are better than what we have now because they take no power to maintain the data, and can be fabricated much smaller so you can store even more songs and apps on your phone.

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Author: Nick Fahrenkopf | Views: 2165 | Comments: 0
I was a little disappointed to see how little the MRS Fall Meeting was getting mentioned on Twitter, so I decided to summarize some of the cool things I learned day by day. Before I get started, though, why MRS? Materials research might not sound glamorous but without it we wouldn’t have the advanced electronics we have today. Indeed, work continues to advance the development of better, faster, cheaper electronic devices, but materials researchers also work on alternative energy (solar cells, fuel cells) and biomedical technology (stem cell engineering, diagnostic sensors). It is this broad array of topics that interests me, as well as the shear size of MRS. Monday night the poster sessions had over 500 posters. And there are different poster sessions on Tuesday, Wednesday and Thursday. I end up finding more interesting talks than I can actually attend. So, what I’d like to do is show you all a sample of some of the most interesting things that I’ve come across for the four days I’m at MRS.

Side note: If you find or know anyone else covering this conference please send them my way. I'm on Twitter @NanoBioNick

Update: You can read my day-by-day coverage here: . . . More