Genomics:
Good news! Good news! Last week the Senate passed the Genetic Nondiscrimination Act (GINA). This week it was passed by the House. It only needs one signature and GINA will become law. For years, those of us who teach genetics have had to caution students about genetic testing. The biggest reason was the fear that having a genetic test would...
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Posted on May 1, 2008 3:51 PM • 6 Comments •
A potential link between lung cancer and human papilloma virus may make parents even more glad about vaccinating their children with Gardasil®. Not only are the children protected against viruses that commonly cause cervical cancer, they may be protected against some forms of lung cancer as well. The April 25th version of Nature News reports (1) that two viruses, HPV...
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Posted on April 27, 2008 5:50 PM • 10 Comments •
Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church fielded questions last night at a fascinating panel discussion on personal genomics at the University of Washington. We were fortunate to be in the audience. I'll share some of the questions and answers, in some cases shortened and paraphrased....
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Posted on April 24, 2008 10:41 AM • 9 Comments •
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different...
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Posted on April 17, 2008 8:00 AM • 2 Comments •
You can find out. Blaine Bettinger, the Genetic Genealogist has a fun little quiz....
Posted on April 9, 2008 5:30 PM • 0 Comments •
And so do you.
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Posted on April 4, 2008 12:45 PM • 21 Comments •
Goodbye desktop, we're off to see the web. Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve everything by using Linux. Others have convincingly demonstrated that Open Office...
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Posted on April 3, 2008 12:40 PM • 6 Comments •
A few months ago I posed some questions about the regulations that might oversee personal genomics companies (Who's your Daddy? and Step right up, get your very own DNA profile). Why?...
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Posted on April 2, 2008 1:59 PM • 6 Comments •
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA)...
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Posted on March 27, 2008 9:11 AM • 22 Comments •
One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies. I've been running into this uncertainty myself lately....
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Posted on March 17, 2008 2:05 PM • 3 Comments •
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found...
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Posted on March 13, 2008 6:42 PM • 0 Comments •
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned...
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Posted on March 12, 2008 12:50 PM • 35 Comments •
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA...
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Posted on March 11, 2008 12:00 PM • 6 Comments •
Here's a fun puzzler for you to figure out. The blast graph is here:...
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Posted on March 7, 2008 12:28 PM • 2 Comments •
The New England Journal of Medicine published a study yesterday showing that small changes in the DNA in the long arm of chromosome 16 are associated with autism. I met a teenager with autism last summer, when I attended family night at the Seattle Park and Rec summer camp program for kids with special needs. It's a fantastic program. The...
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Posted on January 10, 2008 12:00 AM • 13 Comments •
In which we're reminded that database searches are experiments, too. One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the database that you'll be using at a later time, sometimes...
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Posted on December 19, 2007 9:13 AM • 0 Comments •
How do you go about researching a genetic disease? This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio. A bit of background Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the...
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Posted on December 18, 2007 9:45 AM • 1 Comments •
If you like ham and bacon, you might be interested in this. GenomeWeb reports that researchers at the University of Barcelona have developed an assay that tests 46 SNPs and can be used to trace the origin of your pork dinner. According to GenomeWeb, the test identifies both the breed and origin of the animal. The university and the company...
Posted on December 6, 2007 1:00 AM • 2 Comments •
If we suspected a virgin birth, how could we prove it?
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Posted on December 3, 2007 9:00 AM • 13 Comments •
Drug stores branch out from pregnancy to paternity.
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Posted on November 26, 2007 12:07 PM • 12 Comments •
The genie is out of the bottle. Personal genomes are not just for Venter and Watson anymore. Three competing companies, 23andme, Decode, and Navigenics are betting that you want to do a little better than reading your horoscopes and playing with tea leaves. They think that you want to know something about your destiny and take control of your future....
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Posted on November 20, 2007 1:00 AM • 4 Comments •
Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread. Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used...
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Posted on November 14, 2007 4:04 PM • 9 Comments •
An evolution activity for the classroom.
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Posted on November 9, 2007 3:47 PM • 0 Comments •
Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome. Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out...
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Posted on October 28, 2007 2:24 PM • 0 Comments •
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles....
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Posted on October 26, 2007 2:20 PM • 0 Comments •
Welcome Bio256 students! This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a...
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Posted on October 21, 2007 4:30 PM • 2 Comments •
A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much. I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million. That was an estimate, of course. But what did it really cost?...
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Posted on October 16, 2007 8:06 AM • 8 Comments •
Adding the costs and doing the math.
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Posted on September 6, 2007 12:16 PM • 13 Comments •
If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.) You may be wondering, and rightly so: just what is a...
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Posted on September 5, 2007 10:35 AM • 4 Comments •
"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend." The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value....
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Posted on September 4, 2007 12:42 PM • 11 Comments •
I want my genome sequenced, too! Apparently, it's become a popular thing to get your genome sequenced. Craig Venter was the first. Jim Watson's genome (of Project Jim) was ceremonially released this morning (courtesy of 454), and now George Chuch, Larry King, cosmologist Stephen Hawking, Google co-founder Larry Page, Microsoft co-founder Paul Allen and former junk-bond trader Michael Milken want...
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Posted on May 31, 2007 1:36 PM • 9 Comments •
Is the case for open access truly "open and shut"? Will open access impede science by limiting genetic studies with families? tags: genetics, genetic privacy, bioethics, open access...
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Posted on May 28, 2007 9:10 AM • 2 Comments •
In which we define reads, chromatograms, and shotgun sequencing.
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Posted on January 28, 2007 8:51 PM • 2 Comments •
Some background on the strategies: mapping vs. shotgun
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Posted on January 27, 2007 1:50 PM • 2 Comments •
Ask Dr. Science: yes, I do take requests.
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Posted on January 22, 2007 8:59 AM • 7 Comments •
Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants?...
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Posted on December 22, 2006 8:00 AM • 0 Comments •
A quick guide for the omically challenged.
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Posted on December 1, 2006 1:35 PM • 18 Comments •
Razib inspired me to share some of the story behind why white people are considered derivatives. Reposted from the Classic Digital Bio. No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1)....
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Posted on September 26, 2006 8:58 AM • 3 Comments •
If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3. We also learn something about the people who did the experiment....
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Posted on September 1, 2006 11:37 AM • 0 Comments •
Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest. If we agree that we have a common ancestor, then we can use that idea...
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Posted on August 25, 2006 8:10 AM • 2 Comments •
Have you ever wondered how people actually go about sequencing a genome? If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are Phred, Phrap, and Consed? What is the Golden Path?...
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Posted on August 22, 2006 11:00 AM • 0 Comments •
The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes. We started doing this here, where you can find directions for getting started. And, we've found some interesting things....
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Posted on August 18, 2006 3:43 PM • 2 Comments •
When can a really bad virus be used to do something good? When we can use it to learn. The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide...
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Posted on August 17, 2006 11:59 AM • 2 Comments •
During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra...
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Posted on August 11, 2006 1:14 PM • 5 Comments •
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance shows that the ape with the most similar mitochondrial sequence...
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Posted on August 4, 2006 1:39 PM • 3 Comments •
We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong. We can do much, much more than identifying DNA sequences and obtaining crucial information, like who...
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Posted on July 28, 2006 8:00 AM • 0 Comments •
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ecosystems, isolate DNA, amplify...
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Posted on July 24, 2006 9:20 PM • 0 Comments •
How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes? In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more background, see the post on qualitative measures of DNA quality....
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Posted on July 10, 2006 3:00 PM • 0 Comments •
My colleagues have come up will all kinds of interesting bloggy things to use as an excuse for Friday celebrations. Adventures in Ethics and Science has Friday Sprog Blogging for cute stories about her kids. A Blog Around the Clock considers Friday's the perfect day to write about weird sex. Pharyngula salutes the spineless with Friday Cephalopods. Good Math, Bad...
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Posted on July 7, 2006 9:00 AM • 2 Comments •
What do genetic testing and genealogy have in common? The easy answer is that they're both used by people who are trying to find out who they are, in more ways than one. Another answer is that both tests can involve DNA sequence data. And that leads us to another question. If the sequence of my mitochondrial DNA is only...
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Posted on July 5, 2006 7:00 AM • 2 Comments •
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
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