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All posts; Tags Include "Genomics"

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  • April 28, 2016
  • 10:45 AM
  • 673 views a new interactive way of visualising and comparing trees

by Christophe Dessimoz in Open Reading Frame

The paper introducing our new tree visualisation tool was just published in MBE.

Yet another tool to display trees, you might say, and indeed, so it is. But for all the tools that have been developed over the years, there are very few that scale to large trees, make it easy to compare trees side-by-side, and simply run in a browser on any computer or mobile device.

To fill this gap, we created

Story behind the paper

The project started as a student summer internshi........ Read more »

  • April 15, 2016
  • 07:31 AM

Size matters: age and telomeres

by sceintists from the Marine group at CEES in Marine Science blog

Growing evidence suggests that the telomeres’ length (a non-coding DNA sequence localized at the end of the chromosomes) is related to individual breeding performances and survival rates in several species.

... Read more »

  • March 6, 2016
  • 01:07 PM

The hand of Code: Developmental transcriptomics in haddock

by scientists from the Marine group at CEES in Marine Science blog

The development of haddock embryos is highly impacted by oil exposure as discussed in a previous post. In a new study Sørhus et al. explored the link between transcriptional changes and developmental processes such as pattern formation and organogenesis. The question is to understand the abnormal development in fish.

... Read more »

  • November 25, 2015
  • 04:41 AM

Data Diving for Genomics Treasure

by Björn Brembs in

This is a post written jointly by Nelson Lau from Brandeis and me, Björn Brembs. In contrast to Nelson’s guest post, which focused on the open data aspect of our collaboration, this one describes the science behind our paper and […] ↓ Read the rest of this entry...... Read more »

Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, & Lau NC. (2015) Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic acids research. PMID: 26578579  

Chirn, G., Rahman, R., Sytnikova, Y., Matts, J., Zeng, M., Gerlach, D., Yu, M., Berger, B., Naramura, M., Kile, B.... (2015) Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. PLOS Genetics, 11(11). DOI: 10.1371/journal.pgen.1005652  

  • June 2, 2013
  • 12:42 PM

The allure of the superficial

by Iddo Friedberg in Byte Size Biology

Paraphrasing Sydney Brenner, we have a ‘high throughput low output problem’. Functional annotations coming from ‘factory science’ carrying low information are taking over what we deem to know about protein function, masking out, by sheer mass, the higher quality annotations. Low information is somewhat worse than no information For bioinformaticians and other biologists doing large scale analyses it is tempting to use these data. But we should beware the allure of the........ Read more »

  • April 3, 2013
  • 04:06 PM

The Most Neglected of the Neglected

by Michael Hsieh in Hsieh Lab Blog

Urogenital infection by Schistosoma haematobium remains an understudied disease, even by neglected tropical disease standards...... Read more »

  • March 20, 2013
  • 10:39 AM

Social Experiences Affect Our Genes and Health

by amikulak in Daily Observations

Prevailing wisdom suggests that our genes remain largely fixed over time. But, an emerging field of research is beginning to prove this intuition wrong. Scientists are uncovering increasing evidence that ... Read more »

  • February 16, 2013
  • 06:00 AM

Waiting For The Human Intestinal Eukaryotome

by Christen Rune Stensvold in Blastocystis Parasite Blog

We address shortcomings of state-of-the-art methodologies used to explore micro-eukaryotic communities and suggest directions for future research.... Read more »

Andersen LO, Vedel Nielsen H, & Stensvold CR. (2013) Waiting for the human intestinal Eukaryotome. The ISME journal. PMID: 23407309  

  • January 22, 2013
  • 03:54 PM

These dudes figured out how to identify supposedly anonymous people whose genomes are publically available

by Sick Papes in Sick Papes

Super nasty genome hacking I CANT BELIEVE IT!!... Read more »

Gymrek M, McGuire AL, Golan D, Halperin E, & Erlich Y. (2013) Identifying personal genomes by surname inference. Science (New York, N.Y.), 339(6117), 321-4. PMID: 23329047  

  • October 3, 2012
  • 09:32 AM

Video Tip of the Week: JBrowse for genome browsing

by Mary in OpenHelix

There are a number of genome browsers out there. Some of them are big and institutional installations and are crucial to research today for a wide range of users. But as we increasingly see that more and more sequence data becomes available on species that have smaller communities, or maybe patient or family sets, or [...]... Read more »

Skinner, M.E., & Holmes, I.H. (2010) Setting up the JBrowse genome browser. Current Protocols in Bioinformatics, 913-913. DOI: 10.1002/0471250953.bi0913s32  

  • September 30, 2012
  • 04:28 AM

Milk, meat and blood: how diet drives natural selection in the Maasai

by aatishb in Empirical Zeal

This post is a little different from the usual fare at this blog, as I am discussing a paper on which I’m a co-author. My collaborators and I just put up a paper in the open-access journal PLOS ONE. We analyzed genetic data … Continue reading →... Read more »

Kshitij Wagh, Aatish Bhatia, Gabriela Alexe, Anupama Reddy, Vijay Ravikumar, Michael Seiler, Michael Boemo, Ming Yao, Lee Cronk, Asad Naqvi, Shridar Ganesan, Arnold J. Levine, Gyan Bhanot. (2012) Lactase Persistence and Lipid Pathway Selection in the Maasai. PLOS ONE, 7(9). info:/10.1371/journal.pone.0044751

  • August 28, 2012
  • 07:32 PM

Sex and the (self-)Pity

by Lee Turnpenny in The Mawk Moth Profligacies

Is the significant link between the rate of disease risk-associated de novo mutation and increased paternal age sufficient argument for young men to consider freeze-storing their sperm?... Read more »

Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A.... (2012) Rate of de novo mutations and the importance of father's age to disease risk. Nature, 488(7412), 471-5. PMID: 22914163  

  • August 1, 2012
  • 08:52 AM

Video Tip of the Week: Microbiome Resources From JGI

by Jennifer in OpenHelix

Just over a month ago an issue of Nature had two articles from the Human Microbiome Project Consortium – you may have seen them, or noticed the Friday SNPets items we had on them. I promised myself that I’d read the articles (which I did), and that I’d visit my old friends the IMG (Integrated [...]... Read more »

Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann.... (2012) IMG/M: the integrated metagenome data management and comparative analysis system. Nucl. Acids Res. . DOI: 10.1093/nar/gkr975  

Victor M. Markowitz1, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams.... (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucl. Acids Res. DOI: 10.1093/nar/gkr1044  

  • June 22, 2012
  • 11:12 AM

More Bits And Pieces On The Microbiome... Or Maybe Mycobiome...

by Christen Rune Stensvold in Blastocystis Parasite Blog

Because the microbiome has been more or less exclusively synonymous with the "bacteriome" it's very refreshing to discover a paper on fungal diversity in the gut. Like Blastocystis, and other single-celled parasites, intestinal fungi are also micro-eukaryotes, and we are continuously searching for the role of micro-eukaryotes in health and disease.
... Read more »

Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, Brown J, Becker CA, Fleshner PR, Dubinsky M.... (2012) Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science (New York, N.Y.), 336(6086), 1314-7. PMID: 22674328  

Holmes E, Kinross J, Gibson GR, Burcelin R, Jia W, Pettersson S, & Nicholson JK. (2012) Therapeutic modulation of microbiota-host metabolic interactions. Science translational medicine, 4(137). PMID: 22674556  

  • June 17, 2012
  • 01:22 AM

The Circular Problem of Blastocystis

by Christen Rune Stensvold in Blastocystis Parasite Blog

The problem with Blastocystis is a circular one: There is currently no single successful treatment, and when people with symptoms Blastocystis cannot get rid of their parasites and thereby get the chance to report on their symptom experience after permanently cleared infection ( /-clinical improvement), it is - to put it mild - extremely challenging to collect information and data that can assist us in drawing conclusions. It doesn't make it any better that we know that a lot of people ha........ Read more »

Christen Rune Stensvold. (2012) Thinking Blastocystis Out Of The Box. Trends in Parasitology. DOI: 10.1016/  

  • June 9, 2012
  • 03:42 AM

On Faecal Bacteriotherapy

by Christen Rune Stensvold in Blastocystis Parasite Blog

For those of you who read my most recent blog post and who went on to read Carl Zimmer's article in The New York Times about gut flora transplantation on a women suffering from chronic Clostridium difficile diarrhoea: The concept of faecal bacteriotherpy is maybe not that new. Allegedly, it dates back to Pliny the Elder and others, who prescribed orally ingested faeces to cure maladies! Stools were, however, incinerated first, and only the ashes ingested.... Read more »

Mueller, K., Ash, C., Pennisi, E., & Smith, O. (2012) The Gut Microbiota. Science, 336(6086), 1245-1245. DOI: 10.1126/science.336.6086.1245  

  • May 15, 2012
  • 03:29 PM

Testing for common ancestry

by Leonardo Martins in bioMCMC

Our commentary on Douglas Theobald's test from Universal Common Ancestry (UCA) just went online. The original idea was to make a user-friendly review of his analysis described in "A formal test of the theory of universal common ancestry", but after a long e-mail exchange between Douglas and us -- actually between him and David, I didn't say much -- we decided to expand the article to include some remaining points of skepticism and spell out the basic problem with his approach.His work His test f........ Read more »

Leonardo de Oliveira Martins, David Posada. (2012) Proving universal common ancestry with similar sequences. Trends in Evolutionary Biology, 14(1). info:/10.4081/eb.2012.e5

  • April 27, 2012
  • 04:46 PM

It’s a smORF world, after all?

by Iddo Friedberg in Byte Size Biology

But throwing away the baby with the bathwater is not a good solution, since short peptides are known to be responsible for many of life’s activities: mating pheromones, small compound transporters, hormones, neurotransmitters and regulation of other proteins’ activities, to name a few. Many of these short peptides are the result of the cleavage of larger proteins, which means that the ORFs encoding for them are originally longer than 300bp. But some may actually have their own ORFs,........ Read more »

  • April 4, 2012
  • 08:35 AM

Paper trail day trip: Genomic systems neuroscience

by Michael Patterson in ...And You Will Know Me By The Trail of Papers

Theoretically, each animal's taste repertoire is determined by the food it eats. For herbivores, the important tastes are sweet and bitter, which lets animals distinguish between calories and poison. For carnivores, they are umami and sour, which help identify whether meat is fresh. Flies, for whatever reason, detect carbonation in water. As omnivores, humans combine the taste repertoires of ... Read more »

Jiang P, Josue J, Li X, Glaser D, Li W, Brand JG, Margolskee RF, Reed DR, & Beauchamp GK. (2012) Major taste loss in carnivorous mammals. Proceedings of the National Academy of Sciences of the United States of America, 109(13), 4956-61. PMID: 22411809  

  • March 14, 2012
  • 09:40 AM

Video Tip of the Week: New Genetic Testing Registry (GTR) Resource

by Jennifer in OpenHelix

For more information, see our blog post at In this movie we compare the new GTR resource from NCBI to other clinical resources that you may already be using, to answer why you may want to use the GTR.... Read more »

Mitchell JA, Fomous C, & Fun J. (2006) Challenges and strategies of the Genetics Home Reference. Journal of the Medical Library Association : JMLA, 94(3), 336-42. PMID: 16888669  

Aymé, S., & Schmidtke, J. (2007) Networking for rare diseases: a necessity for Europe. Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz, 50(12), 1477-1483. DOI: 10.1007/s00103-007-0381-9  

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