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Author: Brian Krueger, PhD | Views: 45459 | Comments: 12
Last by Brian Krueger, PhD on Jun 24, 2013, 8:39am
I’m totally late to this party. I spent the morning writing my rebuttal to DrugMonkey and Co, doing the news, and cranking out a few pesky experiments. Ah, to live the life, right? Anyway, I’ve noticed that all of the good topics are now taken so I have to scrub the bottom of the bucket. I think one of the most important decisions I made in my scientific career was when I decided where I wanted to go to graduate school. The factors that play ball in this game are numerous and obviously not the same for everyone, but here’s my rundown of all of the things I wish I knew before heading off to graduate school.

Not to be too bitter about my undergraduate experience or anything, but the graduate school preparation was horrendous. No one told me from the beginning, “If you want to go to graduate school, here’s the X, the Y and the Z.” This may all sound like common sense, but some of it is not and having someone tell me all about X, Y, and Z my freshman year would have been helpful.

Do grades matter?

YES. They matter as much as they do for your annoying pre-med classmates, especially if you want to go to a . . . More
Author: Brian Krueger, PhD | Views: 23248 | Comments: 6
Last by Mike Gruidl on Feb 22, 2013, 1:22pm
It's bound to happen in every lab. Someone is going to get distracted and for whatever reason a box full of tubes or tubes themselves are going to accidentally get dropped in the lab's liquid nitrogen container. A lot of people might say, "Screw it," and leave those samples on the bottom of the tank. This might be a good solution for some samples, but what happens when you drop half a rack of boxes to the bottom of your tank? And what happens when those boxes are full of very important cell lines that keep your lab running?

I don't want to admit it, but this is exactly what happened to me today. I was preparing an order for a collaborator and getting 5 of my cell lines out of liquid nitrogen storage. I was explaining to my summer students how to safely handle liquid nitrogen, always wear cryoprotective gloves, lift the rack slowly and be sure to drain all of the liquid nitrogen before handling the boxes, etc. I got the box I needed, and put the rack back in the tank while I was hunting for my cells. Unfortunately, I forgot to put the wire back in the rack that holds the boxes in place. When I went to put the box back that I was handling, I pulled the rack up and half the boxes were gone. "Oh, shit."

So now the rack doesn't fit in . . . More
Author: Brian Krueger, PhD | Views: 17572 | 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: 17828 | Comments: 136
Last by Isabel on Nov 26, 2010, 3:02pm
With the launch of this year’s “Rock Stars of Science” campaign, there’s been a lot of talk about how to best promote science. I’m no marketing guru, but I am a scientist. This latest campaign is better than last years', only because it’s more diverse, but I think it really misses the boat. Is the public really going to be inspired by a couple of pictures in GQ of scientists looking uncomfortable and over dressed in the presence of Rock Stars? The most appalling aspect of this campaign is that there is no highlight of the researchers or their science. There truly are some science all stars in this group, many of which are well spoken.

However, the Rock Stars of science pages in GQ only list the scientist’s name and title, while the “Rock stars” get a one or two sentence summary of how awesome they are for standing in on these pictures. What’s the real focus of this campaign? To promote Bret Michaels’ latest reality TV dreck? If a reader wants to actually understand why these scientists were chosen and what they’re doing to cure disease, they have to visit the website. I find it hard to believ . . . More
Author: Brian Krueger, PhD | Views: 16410 | 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: 16950 | Comments: 0
So I came across a movie about Stanislaw Burzynski and his controversial antineoplastons treatment. So I'm pretty sure you are scratching your head wondering what an antineoplaston is? Apparently Burzynski created this convoluted phrase to use instead of simply saying, its a peptide. But take it from top here gang. In 1968, Burzynski graduated from medical school at age 24 in Poland, at age ~25 he also received a doctorate in biochemistry, making him one of the country's youngest M.D., Ph.D. Are you kidding me, when did he start his MSTP training program at age 17? The claim to the Ph.D. is slightly dubious as the medical school at that time was not known to grant Ph.D.'s and faculty at the Medical Academy of Lubin report that Burzyinski only did one year of a lab research project while in medical school to receive this mystery doctorate. Also the guy never received any specialized training in cancer or cancer therapeutics. So flash forward to 1973, Burzynski has spent the past three years at Baylor COM working in a lab isolating peptides from rat brains. He receives his license and is able to practice medicine in the US and also gets a three year grant to study urinary pepti . . . More
Author: LabSpaces.net | Views: 8979 | Comments: 42
Last by Evie on Sep 21, 2010, 11:12am
Last night, I retweeted Genomic Repairman’s request for the twitterverse to sign up for an account at LabSpaces. He wanted users to join in on the discussions he was having in the group he created. We were greeted moments later by a tweet from DrugMonkey saying that THE Facebook for science is dead. Considering I just wrote a blog post on that exact topic, I found his tweet Ironic. The emphasis in that previous post being that there probably will never be ONE single social hub for scientists, but that doesn’t preclude the formation of multiple niche venues. Please excuse me while I get this out of my system:

(rant)What exactly is a FaceBook for science anyway? Is any site with a science spin, groups, a forum, and/or user profiles a “FaceBook.” If that’s the case, then there are hundreds of FaceBooks for science out there. I’d argue that the term is deprecated. Many sites employ social tool . . . More
Author: Brian Krueger, PhD | Views: 9784 | Comments: 13
Last by Brian Krueger, PhD on Feb 07, 2011, 10:23am
"This is the one thing you never want to mess around with. You'll wake up in the middle of the night crying like a baby and you'll have no idea why." These were the sage words of my undergraduate advisor, it's too bad they got discarded with everything else that I learned in undergrad.

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My scientific career has been filled with plenty of misadventures and screw ups. Most of them are really boring mistakes that didn't involve bodily harm, and only resulted in weeks of repeated work or extended nights in the lab re-preparing samples. Though, every good scientist has an epic fail story locked away in their skeleton closet. I think many of us go into science in the beginning thinking that we're unstoppable know it alls. That is until some event punches us in the gut to tell us, "Open your eyes and pay attention or else next time I'm going to aim a little lower and negatively affect your chances of reproduction."

When I was in undergrad, I worked on a bunch of projects ranging from ecology field studies to molecular biology projects in plants and fish. One of the last projects I worked on was one where we were trying to determine if fish bacterial infections could be transferred from mother to egg. This project involved c . . . More
Author: Angry Scientist | Views: 8188 | Comments: 3
Last by Moderates_Rule on Mar 26, 2013, 11:56am


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Author: Brian Krueger, PhD | Views: 7365 | 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, pharmGKB.org). 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: Angry Scientist | Views: 6402 | Comments: 12
Last by Carniwhore_hater on Apr 02, 2013, 4:11pm
Vegans, please STFU. I'm sick of you preaching to me about what I should and should not eat. I evolved canines for a reason and will eat anything that I damn well please.

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Author: Brian Krueger, PhD | Views: 6853 | 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: 6924 | 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: Brian Krueger, PhD | Views: 6187 | Comments: 1
Last by Evie on Dec 18, 2010, 11:17am
Yesterday there was some buzz over at Huffington Post about a stem cell cure for HIV. I first ran across the article via a link a friend of mine had posted on Facebook. The HuffPo piece is scant on details, so I’ll provide a quick run down on what’s going on here. But first, a lesson in HIV virology…

Human immunodeficiency virus (HIV) was first discovered in the 1980’s when gay men and IV drug users started turning up in hospitals with very odd opportunistic infections like Kaposi’s Sarcoma Herpes virus. These individuals had severely compromised immune systems and the original name given to the condition was gay related immunodeficiency disorder (GRID). The discovery of a viral cause of the disease came in 1983 from the labs of Luc Montagnier (recently won the Nobel Prize for this work) and Robert Gallo (recently didn’t win the Nobel Prize and is kind of pissed about it).

Genetic tests have shown that HIV originated in African monkeys and is related to a similar condition in monkeys called Simian Immunodeficiency Virus (SIV). It is thought that the virus was passed on to humans through the consumption of “bush meat” in sub-saharan . . . More
Author: Brian Krueger, PhD | Views: 7252 | 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: Angry Scientist | Views: 6245 | Comments: 3
Last by Mike Bramnik on Mar 26, 2011, 11:09pm


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Author: Brian Krueger, PhD | Views: 6480 | Comments: 0
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: 6269 | 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: LabSpaces.net | Views: 5156 | Comments: 0
I have finally added blogs to the website. Now you can write your own blogs that relate to the news stories on this site.

In the future (like later this week):

add RSS feeds for all bloggers blogs
Add blogger links to link to outside sources

When I get more time (and more server space):
Allow picture uploads and image hosting

Test out the blogs for me and let me know if you find any bugs. I'm always looking for good suggestions for improving the site!

-Brian . . . More
Author: Angry Scientist | Views: 5076 | Comments: 6
Last by JanedeLartigue on Oct 15, 2010, 12:42pm
24hrs or less to live. Gotta make the most of it!

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