Image credit: Thomas ShahanRobber flies (Asilidae family) are not your typical house flies. They are small, predatory insects that feed on a vast array of other arthropods. While they are small in size (10 times smaller than a dragonfly), these guys are serious hunters. For example, Mallophora omboides is known as the “Florida bee killer” for its taste for honey bees. Other robber flies hunt down wasps, dragonflies, spiders, or grasshoppers, just to name a few. Perhaps almost as impressive a........ Read more »
Wardill, T., Fabian, S., Pettigrew, A., Stavenga, D., Nordström, K., & Gonzalez-Bellido, P. (2017) A Novel Interception Strategy in a Miniature Robber Fly with Extreme Visual Acuity. Current Biology, 27(6), 854-859. DOI: 10.1016/j.cub.2017.01.050
ntrinsically disordered proteins are thought to be fully functional, yet do not confirm to a single conformation, thereby identifying their structure via crystallography becomes problematic. Many intrinsically disordered proteins have been studied and analyzed using NMR methods, however the question as to why proteins are intrinsically disordered is still debatable.... Read more »
Basile, W., Sachenkova, O., Light, S., & Elofsson, A. (2017) High GC content causes orphan proteins to be intrinsically disordered. PLOS Computational Biology, 13(3). DOI: 10.1371/journal.pcbi.1005375
Nobody likes strong smells coming from other human beings. It's just that social convention: you are nice, if you smell nice, and you are a monster - like Shakespeare's Caliban - if you smell bad. Caliban, often depicted as a Golumn-like creature, is one of the first cases of fish odor syndrome described in the literature. No amount of soap and water would help him to wash the smell away, as his body is constantly producing a pungent small molecule trimethylamine. ... Read more »
Guo Y, Hwang LD, Li J, Eades J, Yu CW, Mansfield C, Burdick-Will A, Chang X, Chen Y, Duke FF.... (2017) Genetic analysis of impaired trimethylamine metabolism using whole exome sequencing. BMC medical genetics, 18(1), 11. PMID: 28196478
Callewaert C, Lambert J, & Van de Wiele T. (2016) Towards a bacterial treatment for armpit malodour. Experimental dermatology. PMID: 27892611
With increasing computational power (aka GPU) that can be accessed these days, it is no wonder that performing all-atom molecular dynamics simulation for a longer time, with duplicates and/or triplicates, has become easier.... Read more »
Zuo Z, & Liu J. (2016) Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations. Scientific reports, 37584. PMID: 27874072
Marzinek JK, Holdbrook DA, Huber RG, Verma C, & Bond PJ. (2016) Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations. Structure (London, England : 1993), 24(8), 1410-20. PMID: 27396828
Our latest study just came out (Jeffares et al., Nature Comm 2017). In it, we carefully catalogued high-confidence structural variants among all known strains of the fission yeast population, and assessed their impact on spore viability, winemaking and other traits. This post gives a summary and the story behind the paper.
Structural variants (SVs) measure genetic variation beyond single nucleotide changes …
Next generation sequencing is enabling the study of genomic diversity on unprec........ Read more »
Jeffares, D., Jolly, C., Hoti, M., Speed, D., Shaw, L., Rallis, C., Balloux, F., Dessimoz, C., Bähler, J., & Sedlazeck, F. (2017) Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature Communications, 14061. DOI: 10.1038/ncomms14061
Carr AM, MacNeill SA, Hayles J, & Nurse P. (1989) Molecular cloning and sequence analysis of mutant alleles of the fission yeast cdc2 protein kinase gene: implications for cdc2 protein structure and function. Molecular , 218(1), 41-9. PMID: 2674650
Jeffares, D., Rallis, C., Rieux, A., Speed, D., Převorovský, M., Mourier, T., Marsellach, F., Iqbal, Z., Lau, W., Cheng, T.... (2015) The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nature Genetics, 47(3), 235-241. DOI: 10.1038/ng.3215
Benito, A., Jeffares, D., Palomero, F., Calderón, F., Bai, F., Bähler, J., & Benito, S. (2016) Selected Schizosaccharomyces pombe Strains Have Characteristics That Are Beneficial for Winemaking. PLOS ONE, 11(3). DOI: 10.1371/journal.pone.0151102
One central concept in the OMA project and other
work we do to infer relationships between genes is that of Hierarchical
Orthologous Groups, or “HOGs” for the initiated.
We’ve written several papers on aspects pertaining to HOGs—how to infer
how to evaluate them, they being
increasingly adopted by orthology
resources, etc.—but there is
still a great deal of confusion as to what HOGs are and why they matter.
Natasha Glover, talented postdoc in the lab,........ Read more »
Altenhoff, A., Gil, M., Gonnet, G., & Dessimoz, C. (2013) Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs. PLoS ONE, 8(1). DOI: 10.1371/journal.pone.0053786
Boeckmann, B., Robinson-Rechavi, M., Xenarios, I., & Dessimoz, C. (2011) Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings in Bioinformatics, 12(5), 423-435. DOI: 10.1093/bib/bbr034
Sonnhammer, E., Gabaldon, T., Sousa da Silva, A., Martin, M., Robinson-Rechavi, M., Boeckmann, B., Thomas, P., Dessimoz, C., & , . (2014) Big data and other challenges in the quest for orthologs. Bioinformatics, 30(21), 2993-2998. DOI: 10.1093/bioinformatics/btu492
Follicular lymphoma is a B-cell lymphoma that remains incurable with conventional therapies. Ying et al. (2016) present a new study exploring the biological and genetic features of follicular lymphoma and identifying potential new therapeutic targets. The authors identified recurrent mutations in the mTOR regulator RRAGC, a small G-protein, in approximately 10% of follicular lymphoma cases. Mutations in RRAGC localized to one protein surface area surrounding the GTP/GDP–binding sites. In s........ Read more »
Ying ZX, Jin M, Peterson LF, Bernard D, Saiya-Cork K, Yildiz M, Wang S, Kaminski MS, Chang AE, Klionsky DJ.... (2016) Recurrent Mutations in the MTOR Regulator RRAGC in Follicular Lymphoma. Clinical cancer research : an official journal of the American Association for Cancer Research, 22(21), 5383-5393. PMID: 27267853
Long time readers of this blog (hi mom!) know that I am working with many other people in an effort called CAFA: the Critical Assessment of protein Function Annotation. This is a challenge that many research groups participate in, and its goal is to determine how well we can predict a protein function from its amino-acid sequence. The first CAFA challenge (CAFA1) was held in 2010-2011 and published in 2013. We learned several things from CAFA1. First, that the top ranking function prediction pro........ Read more »
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A.... (2016) An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome biology, 17(1), 184. PMID: 27604469
The team at UCSC Genome Browser continues to update their resources and offer new ways to find and visualize features of interest to researchers. One of the newer features is the “multi-region” option. When it was first launched, I did a tip on how to use that, with some of the things that I noticed […]... Read more »
Human skin emits light (albeit the glow is extremely weak) and a wide variety of small molecules that may be sometimes "sniffed" by dogs or even other humans. These chemicals tell a story about our health and wellness, things we eat and drink, touch and breathe. Mosquitoes use such emissions to assess our "attractiveness" from indicators such as Indoles (unpleasantly smelling but healthy "inner soil" biomarker) or carbon dioxide (amount of which correlates with the size of the person........ Read more »
Andreoni G, Standoli CE, & Perego P. (2016) Defining Requirements and Related Methods for Designing Sensorized Garments. Sensors (Basel, Switzerland), 16(6). PMID: 27240361
Gao W, Emaminejad S, Nyein HY, Challa S, Chen K, Peck A, Fahad HM, Ota H, Shiraki H, Kiriya D.... (2016) Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis. Nature, 529(7587), 509-14. PMID: 26819044
Imani S, Bandodkar AJ, Mohan AM, Kumar R, Yu S, Wang J, & Mercier PP. (2016) A wearable chemical-electrophysiological hybrid biosensing system for real-time health and fitness monitoring. Nature communications, 11650. PMID: 27212140
Lee H, Choi TK, Lee YB, Cho HR, Ghaffari R, Wang L, Choi HJ, Chung TD, Lu N, Hyeon T.... (2016) A graphene-based electrochemical device with thermoresponsive microneedles for diabetes monitoring and therapy. Nature nanotechnology, 11(6), 566-72. PMID: 26999482
Panneer Selvam A, Muthukumar S, Kamakoti V, & Prasad S. (2016) A wearable biochemical sensor for monitoring alcohol consumption lifestyle through Ethyl glucuronide (EtG) detection in human sweat. Scientific reports, 23111. PMID: 26996103
by Piter Kehoma Boll In his work “The Hitchhiker’s Guide to the Galaxy”, Douglas Adams defined that the answer to life, the universe and everything is 42. Now a group of scientists measured glucose metabolism in brains in a resting … Continue reading →... Read more »
Stender, J., Mortensen, K., Thibaut, A., Darkner, S., Laureys, S., Gjedde, A., & Kupers, R. (2016) The Minimal Energetic Requirement of Sustained Awareness after Brain Injury. Current Biology. DOI: 10.1016/j.cub.2016.04.024
There are many tools at NCBI, with a huge range of functions. Literature, sequence data, variations, protein structure, chemicals and bioassays, and more. It’s hard to keep track of what’s available. Their video tutorials are helping me to be aware of new tools, and new features within existing tools. For this week’s Tip of the […]... Read more »
Kapustin, Y., Souvorov, A., Tatusova, T., & Lipman, D. (2008) Splign: algorithms for computing spliced alignments with identification of paralogs. Biology Direct, 3(1), 20. DOI: 10.1186/1745-6150-3-20
NCBI staff. (2016) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 44(D1). DOI: 10.1093/nar/gkv1290
For years now we’ve been doing training and outreach on the UCSC Genome Browser. And there’s been a lot of change over the years–so much more data, so many new tools, new species. All that ENCODE information and a portal for that. But the look of the main site was largely the same. Here’s a […]... Read more »
As I mentioned last week, I am watching a lot of farmers on twitter talk about this year’s North American growing season. To get a taste of that yourself, have a look at #Plant16 + wheat as a search. This is where the rubber of tractor tires and plant genomics hits the…well…rows. And just coincidentally […]... Read more »
Philippa Borrill, Ricardo Ramirez-Gonzalez, & Cristobal Uauy. (2016) expVIP: a customisable RNA-seq data analysis and visualisation platform. Plant Physiology, 2172-2186. info:/10.1104/pp.15.01667
Signatures of Mutational Processes Extracted from the Mutational Catalogs of 21 Breast Cancer Genomes. Credit:http://dx.doi.org/10.1016/j.celrep.2012.12.008Cancer is the second leading cause of death worldwide, with approximately 14 million new cases and 8.2 million cancer related deaths each year (Source: WHO). A family history of cancer typically increases a person's risk of developing the disease, yet most cancer cases have no family history at all. This suggests that a combination of both ge........ Read more »
Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL.... (2013) Signatures of mutational processes in human cancer. Nature, 500(7463), 415-21. PMID: 23945592
Alexandrov LB, Nik-Zainal S, Siu HC, Leung SY, & Stratton MR. (2015) A mutational signature in gastric cancer suggests therapeutic strategies. Nature communications, 8683. PMID: 26511885
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
I didn’t expect to do another tip on the paths through experiments or data this week. But there must be something in the water cooler lately, and all of these different tools converged on my part of the bioinformatics ecosphere. As I was perusing my tweetdeck columns, a new tool from the folks who do […]... Read more »
Christian Partl, Samuel Gratzl, Marc Streit, Anne Mai Wassermann, Hanspeter Pfister, Dieter Schmalstieg, & Alexander Lex. (2016) Pathfinder: Visual Analysis of Paths in Graphs. Computer Graphics Forum . info:other/
Recently I highlighted a decision tree tool for experimental design. EDA, or Experimental Design Assistant, helps you to plan your experiment, choose the approrpiate groups and numbers you’ll need. Set some variables, etc. This week’s video also offers decision trees–but these help you to evaluate the data from your studies of interest instead. Branch is a […]... Read more »
Gangavarapu, K., Babji, V., Meißner, T., Su, A., & Good, B. (2016) Branch: an interactive, web-based tool for testing hypotheses and developing predictive models. Bioinformatics. DOI: 10.1093/bioinformatics/btw117
River flooding boosts carbon emissions, six new species of Chinese dragon millipedes discovered, how ancient animals adapted to climate change, maths tell palaeontologists where to find fossils, and the Arctic Ocean was ice-free ten million years ago. Here are five of the latest scientific studies published open-access this week.... Read more »
Stegen, J., Fredrickson, J., Wilkins, M., Konopka, A., Nelson, W., Arntzen, E., Chrisler, W., Chu, R., Danczak, R., Fansler, S.... (2016) Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. Nature Communications, 11237. DOI: 10.1038/ncomms11237
Liu, W., Golovatch, S., & Tian, M. (2016) Six new species of dragon millipedes, genus Desmoxytes Chamberlin, 1923, mostly from caves in China (Diplopoda, Polydesmida, Paradoxosomatidae). ZooKeys, 1-24. DOI: 10.3897/zookeys.577.7825
Botha-Brink, J., Codron, D., Huttenlocker, A., Angielczyk, K., & Ruta, M. (2016) Breeding Young as a Survival Strategy during Earth’s Greatest Mass Extinction. Scientific Reports, 24053. DOI: 10.1038/srep24053
Block, S., Saltré, F., Rodríguez-Rey, M., Fordham, D., Unkel, I., & Bradshaw, C. (2016) Where to Dig for Fossils: Combining Climate-Envelope, Taphonomy and Discovery Models. PLOS ONE, 11(3). DOI: 10.1371/journal.pone.0151090
Stein, R., Fahl, K., Schreck, M., Knorr, G., Niessen, F., Forwick, M., Gebhardt, C., Jensen, L., Kaminski, M., Kopf, A.... (2016) Evidence for ice-free summers in the late Miocene central Arctic Ocean. Nature Communications, 11148. DOI: 10.1038/ncomms11148
Source: PEW Charitable TrustsThe above graphic, from the Antibiotic Resistance Project by the PEW charitable trusts, summarizes how alarming the emergence of drug resistant bacterial strains has gotten over the past few decades. According to data from the Center for Disease Control (CDC), every year 2 million Americans acquire drug-resistant infections , in other words infections that do not respond to treatment with ordinary antibiotics. Not only do drug-resistant infections require muc........ Read more »
Armstrong GL, Conn LA, & Pinner RW. (1999) Trends in infectious disease mortality in the United States during the 20th century. JAMA, 281(1), 61-6. PMID: 9892452
Cherednichenko, G., Zhang, R., Bannister, R., Timofeyev, V., Li, N., Fritsch, E., Feng, W., Barrientos, G., Schebb, N., Hammock, B.... (2012) Triclosan impairs excitation-contraction coupling and Ca2 dynamics in striated muscle. Proceedings of the National Academy of Sciences, 109(35), 14158-14163. DOI: 10.1073/pnas.1211314109
Van Boeckel, T., Brower, C., Gilbert, M., Grenfell, B., Levin, S., Robinson, T., Teillant, A., & Laxminarayan, R. (2015) Global trends in antimicrobial use in food animals. Proceedings of the National Academy of Sciences, 112(18), 5649-5654. DOI: 10.1073/pnas.1503141112
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