The paper introducing our new tree visualisation tool Phylo.io 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 Phylo.io.
Story behind the paper
The project started as a student summer internshi........ Read more »
Robinson, O., Dylus, D., & Dessimoz, C. (2016) Phyla.io: interactive viewing and comparison of large phylogenetic trees on the web . Molecular Biology and Evolution. DOI: 10.1093/molbev/msw080
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 »
Le Vaillant, M., Viblanc, V., Saraux, C., Le Bohec, C., Le Maho, Y., Kato, A., Criscuolo, F., & Ropert-Coudert, Y. (2015) Telomere length reflects individual quality in free-living adult king penguins. Polar Biology, 38(12), 2059-2067. DOI: 10.1007/s00300-015-1766-0
Carney Almroth, B., Skold, M., & Nilsson Skold, H. (2012) Gender differences in health and aging of Atlantic cod subject to size selective fishery. Biology Open, 1(9), 922-928. DOI: 10.1242/bio.20121446
Ovenden, J., Berry, O., Welch, D., Buckworth, R., & Dichmont, C. (2015) Ocean's eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries. Fish and Fisheries, 16(1), 125-159. DOI: 10.1111/faf.12052
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 »
Sørhus, E., Incardona, J., Furmanek, T., Jentoft, S., Meier, S., & Edvardsen, R. (2016) Developmental transcriptomics in Atlantic haddock: Illuminating pattern formation and organogenesis in non-model vertebrates. Developmental Biology, 411(2), 301-313. DOI: 10.1016/j.ydbio.2016.02.012
Sørhus, E., Edvardsen, R., Karlsen, Ø., Nordtug, T., van der Meeren, T., Thorsen, A., Harman, C., Jentoft, S., & Meier, S. (2015) Unexpected Interaction with Dispersed Crude Oil Droplets Drives Severe Toxicity in Atlantic Haddock Embryos. PLOS ONE, 10(4). DOI: 10.1371/journal.pone.0124376
Misund, O., & Olsen, E. (2013) Lofoten-Vesteralen: for cod and cod fisheries, but not for oil?. ICES Journal of Marine Science, 70(4), 722-725. DOI: 10.1093/icesjms/fst086
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
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 »
Schnoes, A., Ream, D., Thorman, A., Babbitt, P., & Friedberg, I. (2013) Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space. PLoS Computational Biology, 9(5). DOI: 10.1371/journal.pcbi.1003063
Urogenital infection by Schistosoma haematobium remains an understudied disease, even by neglected tropical disease standards...... Read more »
Brindley, P., & Hotez, P. (2013) Break Out: Urogenital Schistosomiasis and Schistosoma haematobium Infection in the Post-Genomic Era. PLoS Neglected Tropical Diseases, 7(3). DOI: 10.1371/journal.pntd.0001961
Fu, C., Odegaard, J., Herbert, D., & Hsieh, M. (2012) A Novel Mouse Model of Schistosoma haematobium Egg-Induced Immunopathology. PLoS Pathogens, 8(3). DOI: 10.1371/journal.ppat.1002605
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 »
We address shortcomings of state-of-the-art methodologies used to explore micro-eukaryotic communities and suggest directions for future research.... Read more »
Kittelmann, S., Seedorf, H., Walters, W., Clemente, J., Knight, R., Gordon, J., & Janssen, P. (2013) Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities. PLoS ONE, 8(2). DOI: 10.1371/journal.pone.0047879
Scanlan PD, & Marchesi JR. (2008) Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. The ISME journal, 2(12), 1183-93. PMID: 18670396
Pandey PK, Siddharth J, Verma P, Bavdekar A, Patole MS, & Shouche YS. (2012) Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers. Journal of biosciences, 37(2), 221-6. PMID: 22581327
Hamad, I., Sokhna, C., Raoult, D., & Bittar, F. (2012) Molecular Detection of Eukaryotes in a Single Human Stool Sample from Senegal. PLoS ONE, 7(7). DOI: 10.1371/journal.pone.0040888
Paliy O, & Agans R. (2012) Application of phylogenetic microarrays to interrogation of human microbiota. FEMS microbiology ecology, 79(1), 2-11. PMID: 22092522
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
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 »
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
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
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
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
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 »
Pepper, J., & Rosenfeld, S. (2012) The emerging medical ecology of the human gut microbiome. Trends in Ecology , 27(7), 381-384. DOI: 10.1016/j.tree.2012.03.002
Dethlefsen, L., & Relman, D. (2010) Colloquium Paper: Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences, 108(Supplement_1), 4554-4561. DOI: 10.1073/pnas.1000087107
Stensvold, C., Christiansen, D., Olsen, K., & Nielsen, H. (2011) Blastocystis sp. Subtype 4 is Common in Danish Blastocystis-Positive Patients Presenting with Acute Diarrhea. American Journal of Tropical Medicine and Hygiene, 84(6), 883-885. DOI: 10.4269/ajtmh.2011.11-0005
Domínguez-Márquez, M., Guna, R., Muñoz, C., Gómez-Muñoz, M., & Borrás, R. (2009) High prevalence of subtype 4 among isolates of Blastocystis hominis from symptomatic patients of a health district of Valencia (Spain). Parasitology Research, 105(4), 949-955. DOI: 10.1007/s00436-009-1485-y
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 »
Tvede, M., & Rask-Madsen, J. (1989) BACTERIOTHERAPY FOR CHRONIC RELAPSING CLOSTRIDIUM DIFFICILE DIARRHOEA IN SIX PATIENTS. The Lancet, 333(8648), 1156-1160. DOI: 10.1016/S0140-6736(89)92749-9
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
Theobald, D. (2010) A formal test of the theory of universal common ancestry. Nature, 465(7295), 219-222. DOI: 10.1038/nature09014
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 »
Ladoukakis, E., Pereira, V., Magny, E., Eyre-Walker, A., & Couso, J. (2011) Hundreds of putatively functional small open reading frames in Drosophila. Genome Biology, 12(11). DOI: 10.1186/gb-2011-12-11-r118
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 »
For more information, see our blog post at http://blog.openhelix.eu/?p=11439. 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 »
Pagon RA. (2006) GeneTests: an online genetic information resource for health care providers. Journal of the Medical Library Association : JMLA, 94(3), 343-8. PMID: 16888670
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
Amberger, J., Bocchini, C., & Hamosh, A. (2011) A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Human Mutation, 32(5), 564-567. DOI: 10.1002/humu.21466
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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