All posts tagged with genomics

Genomes of straight-tusked elephants

7 minute read

Earlier this month in eLife, Matthias Meyer and colleagues published a cool paper: “Palaeogenomes of Eurasian straight-tusked elephants challenge the current...

Link: Minutes of the mutation rate meeting

less than 1 minute read

Iain Mathieson shares his notes on a recent meeting of scientists investigating mutation rate estimation in humans: “The human mutation rate meeting”.

Variation in cognitive traits and genetics

2 minute read

A new study of more than 50,000 people has identified some of the genetic variations that underlie cognitive variation among middle-aged and older adults (Da...

Link: Personalized medicine going to Congress

less than 1 minute read

The New York Times reports on the new initiative to fund massive research on personalized medicine: “Obama to Request Research Funding for Treatments Tailore...

Link: Ed Yong looks at limb buds

less than 1 minute read

Ed Yong writes about a new paper investigating the evolutionary developmental biology of finger formation: “How Did You Get Five Fingers?”.

Marmoset chimerism

8 minute read

Carl Zimmer has been writing about chimerism in the New York Times: “Having More Than One Set of DNA Carries Legacy of Risk”. As he points out, this conditio...

Sequencing baby Khan

1 minute read

MIT Technology Review has an article this week about Razib Khan’s efforts to sequence his baby son in utero: “For One Baby, Life Begins with Genome Revealed”.

Ghost populations and ancient DNA

2 minute read

The rapidly changing field of ancient DNA has settled into a kind of normal science, as several teams of researchers have coalesced around a set of approache...

TED needs a better curator

5 minute read

As 2013 slipped beneath the waves, The Guardian ran a long excerpt of a TEDGlobal talk by Benjamin Bratton: “We need to talk about TED”. Bratton is a sociolo...

ARG is the word

1 minute read

Adam Siepel has written a very useful explainer about a new preprint he has posted with Matthew Rasmussen on the arXiv preprint server: “Our Paper: Genome-wi...

The fused chromosome 2 was in Denisova

1 minute read

In my post on the new Denisova paper the other day (“Denisova at high coverage”), I forgot to mention one interesting detail in the new paper by Mattias Meye...

Grasping the genomic palantir

3 minute read

Gina Kolata writes in the New York Times about the conundrum faced by research scientists who inadvertently discover the health risks of their research parti...

Into Africa

less than 1 minute read

I have a lot to say about the new study of African genomes by Joseph Lachance and colleagues Lachance:2012, which I think is tremendously exciting, along wit...

Phylo, the genomics game

less than 1 minute read

NOVA describes how some genomics problems are being solved using computer gaming: “Gaming and genomics”.

Sequencing FTL neutrinos

1 minute read

A well-written blog account of a current controversy in human genetics, by Joe Pickrell: “Questioning the evidence for non-canonical RNA editing in humans”.

Finding the scary genes

1 minute read

John Lauerman reports in BusinessWeek on his experience participating in the Personal Genome Project:

He had a sufficiently high opinion of himself"

less than 1 minute read

Gina Kolata profiles Eric Lander, director of Harvard and MIT’s Broad Institute and advisor to President Obama, in the New York Times. It’s a good read for t...

Floating on the data

less than 1 minute read

Technology Review reports on a recent conference trying to spread data mining techniques. The point of departure is the growth of electronic sensor networks ...

A problem of fuzzy mammoths

10 minute read

Paleogenomics is changing the way we study evolution. In a number of cases, it now allows us to study extinct organisms with the same methods as we study liv...

Wolves in coyotes' clothing

1 minute read

Razib’s post on the genetics of canids (“A map of charismatic canid genomic variation”) does a nice summary of a recent paper in Genome Research, by vonHoldt...

Data minding

1 minute read

Dan MacArthur reads the American Medical Association’s letter to the FDA about direct-to-consumer genetics testing, and doesn’t like what he sees (“American ...

Neandertal segments of X chromosomes

15 minute read

Last year, this Neandertal genome came out. No doubt you’ve heard about it. So maybe by now you’re wondering where the new science is that’s being done on th...

Timmer on HGP

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John Timmer tells us “Ten years on: why a complete human genome mattered,” from the perspective first of a bench scientist, then later as a science writer:

Genes and drugs

1 minute read

Nature Reviews Genetics this month has published a panel conversation between five experts on pharmacogenomics Altman:pharmacogenomics:2010. If you’re intere...

Open data genomics

less than 1 minute read

Nature this week carries a story by Ewen Callaway titled, “The rise of the genome bloggers”. The main subject is Dienekes Pontikos, whose “Dodecad Ancestry P...

High school genomics

4 minute read

Ronald Bailey writes in the January Reason about his experiences with personal genomics (“Ill Show You My Genome. Will You Show Me Yours?”). He’s a booster, ...

Copy number variation in 1000 Genomes

5 minute read

When I wrote earlier in the week about the 1000 Genomes Project results, I mentioned that a second paper was being published in Science. That paper, by Peter...

Plague from within

less than 1 minute read

Ewen Callaway describes work probing the biology of a chimpanzee endogenous retrovirus: “Ancient chimp virus ‘brought back to life’”

Ancestry unzipped

1 minute read

One of the incredible benefits of the open source approach to genomics is that non-practitioners have a chance to see how interpretations are built. Sometime...

Genomics by press release

1 minute read

The Spandrel Shop: “When did announcing science become the same as publishing science?”

Personal genomics debacle?

1 minute read

Daniel MacArthur is reporting on today’s big showdown between Congress and genomics testing companies: “A sad day for personal genomics.”

Berkeley DNA tests revisited

2 minute read

I wrote about the UC Berkeley genetic testing of incoming freshmen earlier this spring. The summer is halfway over and the saliva kits have been sent. Now Sc...

Sergey Brin and genetic research

6 minute read

While I was out of town, Wired ran a long article about Google cofounder Sergey Brin and his quest to find the genetic causes of Parkinson’s disease. There i...

UC-Berkeley genetic tests for freshmen

1 minute read

I’m not sure which tags to apply to this story. I’m torn between “colossally-bad-ideas” and “university-auditions-for-big-brother”.

GET smart

1 minute read

Carl Zimmer describes his experience as a master of ceremonies (with Robert Krulwich) at the Genomes, Envrionments, Traits conference (“A day among the genom...

Whole genome action

less than 1 minute read

Daniel MacArthur writes a thoughtful summary of a new study of the DNA of Stephen Quake: “What can you learn from a whole genome sequence?”

Chimp trivia

less than 1 minute read

Courtesy of Jon Cohen in Science (“The Chimpanzee Genome Project’s Seedy Origins”), a detail that I hadn’t heard before:

NIH genetic test registry

4 minute read

The National Institutes of Health directorate this week announced the creation of a new database for tracking and providing public information about commerci...

Genetics and archaeology, 2

8 minute read

I’ve just received the book, Climate Change in Prehistory: The End of the Reign of Chaos, by William Burroughs. I’ll be reading it and reviewing it during th...

This weeks' genomes

1 minute read

Actress Glenn Close joins the ranks of the genomed; Daniel MacArthur discusses the celebrity genomics trend.

Deep versus wide genomes

less than 1 minute read

Remember Genome 10K? Well, here’s a new study by Michel Milinkovitch and colleagues, that points out the deficiencies of comparative data from 1X genomes:

23andMe

less than 1 minute read

From Razib: “Creative destruction in the personal genomics industry?”

SNPs and culture history

less than 1 minute read

Razib lists a taxonomy of culture-gene historical scenarios. Real worked examples for several of these would be worthwhile.

Genes and archaeology

4 minute read

Current Biology has released a special issue titled “Global genetic history of Homo sapiens”. There is much of interest in this issue, with seven papers, mos...

Cancer and personalized drugs

less than 1 minute read

Amy Harmon reappears in the NY Times science page this week, with a series on the clinical trials of a targeted cancer drug (“A Roller Coaster Chase for a Cu...

Genetic lapidaries

2 minute read

Nature News has a short piece on yesterday’s Desmond Tutu and other South African genomes: “Africa yields two full human genomes.”

Drug discovery and GWA

less than 1 minute read

Gene Expression’s p-ter makes an interesting point about weak genome-wide associations and drug development.

Website review: Learn.Genetics

4 minute read

This week’s Science is featuring an essay by the first winners of the “SPORE” competition, the team behind the Learn.Genetics and Teach.Genetics websites. Ev...

Leprosy evolution in humans

4 minute read

Where did leprosy come from as a human pathogen, and how did it spread through the world? Two years ago, this new research would have merited a whole book. N...

Cichlid colors

3 minute read

I really can’t get over how much work went into the cichlid pigmentation paper that’s out in the current Science (Roberts et al. 2009). The paper examines th...

Horse genomics

1 minute read

An interesting passage from the horse genome paper:

Complete genomes

less than 1 minute read

John Timmer gives a great summary of the new paper in Science covering the Complete Genomics sequencing method.

"Filled up with other books"

2 minute read

The 1000 Genomes Project is for people. Now, is it time for 10,000 vertebrate genomes? Erika Check Hayden reports on the idea in Nature news:

Common traits and GWA

2 minute read

Worth reading: Daniel MacArthur comments on 23andMe’s reporting of genome-wide associations coming from their customer surveys of traits. The skinny:

Ardipithecus bloggingheads

1 minute read

Today, Science Saturday on bloggingheads.tv is a conversation between Razib Khan and me. We had a fun conversation about Ardipithecus and the recent study of...

Migraine at 23andMe

1 minute read

23andMe continues its strategy to look for genetic associations of traits that escape most funding for genetic reserach. Latest: migraine:

DNA tech

less than 1 minute read

IBM joins the next-gen sequencing race:

Freeman Dyson and the new Age of Wonder

7 minute read

Last Tuesday, in my review of Chris Anderson’s Free, I mentioned a beneficial side effect of free exchange of information – the creativity that it enables in...

SNPtastic India

6 minute read

The cover story in Nature this week is a paper about the population history of India, from David Reich’s lab. It’s an important contribution to our knowledge...

Is your genome worth guarding?

3 minute read

Katrina Voss wrote in New Scientist a couple of weeks ago: “Your genome isn’t that precious – give it away”. After discussing legislative efforts to provide ...

Enamelin gene loss in toothless mammals

less than 1 minute read

Jerry Coyne describes a new paper on the accumulation of loss-of-function mutations to ENAM in lineages with tooth reductions: “Dead Genes for Tooth Enamel”.

The colors of mice

2 minute read

Science this week features an article by Elizabeth Pennisi about the research of evolutionary biologist Hopi Hoekstra. She studies pigment variations in wild...

Mailbag: Genome fantasy league

1 minute read

Hi John. Here is a variant that I like because the question points at reasons and strategy that the one-genome question does not: If you could pick any o...

Molecular systematics and species trees

3 minute read

I’d like to point readers to a recent essay in Evolution, by Scott V. Edwards, titled, “Is a new and general theory of molecular systematics emerging?”

Mailbag: Race, words and definitions

1 minute read

I believe this problem with the word "race" which biologists have needs to be handled as a communication problem. The way that biologists use the term is, li...

Modern genomics and race

2 minute read

Another little thing from that Anne Wojcicki interview that I linked last week – she fielded a question about race:

Free credit reports and consumer genetics

4 minute read

The Freakonomics blog has a long question-and-answer with Anne Wojcicki, of 23andMe. It’s interesting to see how she takes reader questions – many of the an...

Systems biology and the heritability paradox

1 minute read

Carl Zimmer had an essay in Newsweek a couple of weeks ago that I missed at the time: “The Gene Puzzle”. It starts with a précis of the heritability paradox:...

Data warehousing in genomics interview

1 minute read

Software publisher O’Reilly is running an interview with David Dooling, data chief of the Genome Sequencing Center at Washington University: “Sequencing a ge...

Pbo on Neandertal sequencing

1 minute read

On Edge, Svante Pääbo has a long and interesting narrative about Neandertal genetics, FoxP2 mice, his own biography, and everything else. Nothing new to be h...

Genome data access and funding models

1 minute read

Mike the Mad Biologist checks in with an interesting post on “The Double Standard of Genomic Data Release and the Role of Incentives”. The question: why do l...

To the stars!

1 minute read

Razib pointed me to this really interesting article (by Lee Billings) about the search for planets around Alpha Centauri.

Biohacking

less than 1 minute read

Word of the day: biohacking.

A horse of a different color

4 minute read

I feel like I’ve been transported into the future to see what science will be like fifteen years from now:

Turning ACGT into poetry

5 minute read

The Economist has a “special report” on personalized medicine, focusing on the business of the current set of sequence providers. Generally speaking, Dan Mac...

When genetic drift reduces entropy

11 minute read

This is the third in a series on information theory and tests for recent selection. The first post, “Information theory: a short ...

Conservation by genomics

3 minute read

This week’s Nature has a news article by Emma Marris about bison conservation and genomics. I’ve been very interested in cattle and bison as an example of in...

Surfing and recent selection

5 minute read

Genetic Future and Gene Expression have commented today on the relative roles of selection and demography in shaping the genetic differences between populati...

That which must not be named

10 minute read

Constance Holden was at an October NIH workshop, titled, “Workshop on Ethical, Legal, and Social Issues in Natural Selection Research.”

Population genomics rising

1 minute read

Genetic Future has been on fire lately, with various announcements from and about genomics testing companies. More on that later. Today, he reflects upon the...

An MAPT review

3 minute read

Elizabeth Pennisi writes this week a news focus in Science about the genome region labeled 17q21.31. I’m probably one of the few people who would recognize t...

National Children's Study

2 minute read

Last week, the NY Times printed a short article by Kate Murphy marking the beginning of the National Children’s Study (Official site) this coming January:

Magic indistinguishable from genomics

less than 1 minute read

ThinkGene has a nice critical post reviewing some of deCODE Genetics’ advertising. The main idea is that genetic tests as yet provide almost no information w...

Endogenous retrovirus story

less than 1 minute read

Earlier this week, the Washington Post printed a nice David Brown story about endogenous retroviruses and evolution.

"Wellderly" and "Illderly" study

1 minute read

I meant to point out this news article when it came out earlier this month. It’s a short description of a Scripps-Venter initiative to sequence 2000 healthy ...

Gene Wiki

less than 1 minute read

Larry Moran comments on the Gene Wiki. (If you haven’t read about it, check out this AP article, or the PLoS Biology paper). Larry has written before about t...

Ajit Varki profile

2 minute read

Reporter Bruce Lieberman profiles geneticist Ajit Varki in this week’s Nature. It’s a good summary of Varki’s work in sialic acid evolution, focusing on one ...

How much data in your genome

1 minute read

Daniel Macarthur, of Genetic Future, reviews the amount of information required to store genomic information. Naturally, you’d probably think it was around 1...

Evolution of the monkeyflowers

6 minute read

Spring has finally come to us here in the North, and it's time to start thinking about planting. So, when I went to a seminar yesterday by John Willis, it w...

Probing for the alien within

1 minute read

Laura MacConaill and Matthew Meyerson present a cool short review in Nature Genetics of metagenomics applications in pathogen discovery.

Heritability review

1 minute read

Peter Visscher and colleagues present a long review paper on the concept and use of heritability in the current Nature Reviews Genetics.

The future of genetics is corny

1 minute read

Elizabeth Pennisi's story about maize genomics is a good reminder for why biology will continue to grow in importance toward our understanding of human hist...

Bees R Us

5 minute read

The PNAS Early Edition this week includes a paper by bee genome researchers Amro Zayed and Charles Whitfield. After a short review of honeybee phylogeny, th...

The history of junk DNA explored

1 minute read

T. Ryan Gregory (Genomicron) has been writing a long series of posts looking into the history of junk DNA. He's focusing on what research articles were sayi...

Non-identical identical twins

2 minute read

Identical twins may be genetically different due to somatic variations, and a new study by Bruder and colleagues finds that large deletions contribute to so...

Serial founder effects, again

5 minute read

A flush of papers this week (two today in Nature, one tomorrow in Science) describe new analyses of SNPs across the genome. Two of the papers sample SNPs in...

HIV genetics by the genome

2 minute read

A new whole-genome association study has found more genetic variants protective against HIV. The course of HIV infection is variable, even in the absence of...

Looking for the balances

10 minute read

A nice paper from last August by K. L. Bubb and colleagues went looking for new balanced polymorphisms in the human genome. They didn't find any.

A Neandertal genome exchange

1 minute read

A letter in this week's Science by Thomas Erren and colleagues (2007) questions the whole-genome approach to sequencing Neandertals:

From 100,000 to 25,000, a tale

2 minute read

Larry Moran has summarized a long history of the changing estimates of human gene number over the last fifty years. The post was invoked by the supposed "su...

Alternative splicing

3 minute read

The PNAS early edition includes a paper by Michael Tress and (many) others about the frequency of alternative splicing across the genome. I wrote about alte...

Taking on new functions, protein-wise

4 minute read

I have to note this commentary by Fyodor Kondrashov that I ran across. The commentary discusses this 2004 paper by Amir Aharoni and colleagues:

You and the fugu, part 2

3 minute read

My earlier post introduced the conserved noncoding elements shared by vertebrates. Those elements shared by vertebrates seem to be crucial to regulating dev...

Now I know my ABC's

2 minute read

Reading through a review of risk alleles for cardiovascular disease, I found this section:

You and the fugu

2 minute read

Last year, there was quite a bit of attention to so-called "ultra-conserved elements". These are relatively short stretches of non-coding DNA, which are sha...

When duplicate genes diverge

5 minute read

One of the most important mechanisms of genetic evolution is gene duplication. There are a few well-known gene families, such as the globin gene family, who...

Gene expression in the mouse brain

5 minute read

Last week's Nature included a report on the final draft of the gene expression atlas of the mouse brain. I wish this had come out last semester -- I could h...

How your metagenome makes you fat

4 minute read

This week's Nature is largely about the association of gut biota with body mass in humans, with two papers and a commentary on the subject. Both papers are ...

Neandertal genome FAQ

26 minute read

With the release of the initial two papers describing chromosomal DNA sequences from a Neandertal, I thought I would put together some frequently asked ques...

Neandertal genomics begins

1 minute read

The papers are just being released. I have had copies for a while and have lots of commentary, which I'll be putting up in the next day or so -- the delay i...

An brain atlas to the genes

less than 1 minute read

The news stories are all about how Paul Allen has money to burn, but the brain mapping project is actually really cool:

Patterns Turing spotted

2 minute read

Did you know that Alan Turing tried to solve the problem of biological form? That following D'Arcy Thompson, he laid the groundwork for an important branch ...

DOE genomics

less than 1 minute read

Linked on Evolgen, I found this post from Nobel Intent that gives a quick summary of reasons the U.S. Department of Energy is in the genomics business. It's...

Teaser on Neandertal genomics

1 minute read

There is an article about the nuclear genome work on Neandertals running in Wired, by reporter Annalee Newitz (first on Gene Expression). There's not much t...

Microbiomic metagenomics

1 minute read

At the movies last night I saw a preview for Superman, and now Science tells me that humans are superorganisms!

Primate neurogenomics

7 minute read

James Sikela has a review in PLoS Genetics on genomics as applied to understanding human cognitive evolution (via Brainethics).

HapMap "dumpster diving"

1 minute read

Jennifer Couzin of Science has a conference report about the HapMap, and many of its uses.

Circadian rhythms and noise

3 minute read

One source of noise in human gene expression data may be circadian. A new study (PDF) in Molecular Endocrinology by Lemos, Downs, and Urbanski examines gene...

Genetic structure of the chominids

3 minute read

In view of the previous post on the genetics of the human-chimpanzee divergence, it seems worth going into a bit more detail about the paper by Innan and Wa...

How much are deletions like SNPs?

2 minute read

Hinds et al. (2006) examine the pattern of common deletion polymorphisms in the human genome. These are genetic variants in which the alleles have different...

Canalization

5 minute read

Yesterday I ran across this paper by Thomas Flatt in Quarterly Review of Biology, which is a really thorough review of the concept of canalization from its ...

Genome-wide selection in humans

8 minute read

I spent like a half-hour looking for this paper this morning, which I didn't take notes on when it came out. I don't know if Nature is blocking Google Schol...

Chromosomal inversions in human evolution

2 minute read

A new paper by Lars Feuk et al. in PLoS Genetics is reporting on widespread gene inversions in humans. A press release at ScienceDaily announced the paper, ...

HapMap

2 minute read

This week's Nature has over twenty pages of HapMap coverage. Here's the abstract of the main paper:

Neutrality and selection on gene expression

17 minute read

There is a good case to be made that distinguishing neutrality from selection is now the central problem of molecular evolutionary biology. I don't intend t...

The "dark matter" of the cell

7 minute read

Last week's Nature got most of the media, with its papers on the chimpanzee genome. But last week's Science was actually the more important of the two -- a ...

Chimpanzee genomics

1 minute read

This week's Nature (9/1/05) has a special feature on the chimpanzee genome (subscription required). The introduction is this perspective by Chris Gunter and...

Will anybody pay for genomes?

3 minute read

MSNBC reports this Reuters story about the new microbead technology for gene sequencing. Because it allows such a decrease in cost (down to $2 million per g...

Carroll on evolution and gene regulation

6 minute read

Sean Carroll is a colleague of mine here at UW, author of the recent book, Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the A...

Epistasis and evolution

less than 1 minute read

Razib at Gene Expression has a very informative post referring to the edited volume Epistasis and the Evolutionary Process (Wolf et al. 2000). I'm posting a...

Comparing human and chimpanzee promoters

5 minute read

Current thinking on the nature of differences between humans and chimpanzees (or any other pair of closely related species, for that matter) holds that larg...

A future without men?

2 minute read

H. Allen Orr reviews Brian Sykes' book, Adam's Curse: A Future Without Men in the May 12, 2005 New York Review of Books. This is a great review (with short ...

The probability of parallel evolution

2 minute read

Orr (2005) considers the likelihood of the same mutants being fixed in two populations as a function of parallel selection, compared to drift. The model use...

Mayr on speciation

2 minute read

OK, that headline looks like the title to a dissertation, which this isn't. But in honor of Mayr's recent death, I was looking through some of the things he...

Patents and human chimeras

2 minute read

This article in the Boston Globe (Feb. 13, 2005) summarizes a recent US patent office ruling on whether an application for a human-animal chimera could be a...

How much selection does it take?

13 minute read

I was involved in a discussion this weekend that I think reveals much about the current state of evolutionary genomics. The forum was the "Neanderthals Rev...