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  • April 12, 2017
  • 10:59 AM
  • 309 views

Flyfocals: Vision and Vectors Help Hunting Robber Flies

by Melissa Chernick in Science Storiented

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  

  • April 4, 2017
  • 12:49 AM
  • 248 views

A clue towards understanding intrinsically disordered proteins

by ragothamanyennamalli in Getting to know Structural Bioinformatics

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 »

  • March 31, 2017
  • 12:10 PM
  • 315 views

Giving the underserved the care they deserve

by Aurametrix team in Aurametrix Blog

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  

  • March 3, 2017
  • 11:05 PM
  • 251 views

All-Atom Molecular Dynamics Simulations

by ragothamanyennamalli in Getting to know Structural Bioinformatics

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 »

  • February 8, 2017
  • 05:36 AM
  • 354 views

Sex, alcohol, and structural variants in fission yeast

by Christophe Dessimoz in Open Reading Frame

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  

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  

  • December 8, 2016
  • 09:14 AM
  • 444 views

What are Hierarchical Orthologous Groups (HOGs)?

by Christophe Dessimoz in Open Reading Frame


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
them,
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 »

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  

  • November 18, 2016
  • 07:25 AM
  • 465 views

Mutated mTOR regulator RRAGC proteins decrease interactions with FLCN

by Joana Guedes in BHD Research Blog

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  

  • September 9, 2016
  • 10:00 AM
  • 587 views

Predicting protein function: what’s new?

by Iddo Friedberg in Byte Size Biology

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  

  • June 15, 2016
  • 09:37 AM
  • 623 views

Video Tip of the Week: UCSC Genome Browser Exon-only Mode

by Mary in OpenHelix

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 »

Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A.... (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Research, 44(D1). DOI: 10.1093/nar/gkv1275  

  • June 12, 2016
  • 10:35 PM
  • 920 views

Seeing Through the Skin

by Aurametrix team in Olfactics and Diagnostics

​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 »

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  

Yokota T, Zalar P, Kaltenbrunner M, Jinno H, Matsuhisa N, Kitanosako H, Tachibana Y, Yukita W, Koizumi M, & Someya T. (2016) Ultraflexible organic photonic skin. Science advances, 2(4). PMID: 27152354  

  • May 31, 2016
  • 11:30 PM
  • 836 views

42: the answer to life, the universe and everything (i.e., consciousness)

by Piter Boll in Earthling Nature

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  

  • May 25, 2016
  • 08:31 AM
  • 584 views

Video Tip of the Week: ProSplign in NCBI’s Genome Workbench

by Mary in OpenHelix

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 »

  • May 11, 2016
  • 08:05 AM
  • 524 views

Video Tip of the Week: New UCSC Genome Browser Gateway look

by Mary in OpenHelix

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 »

Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A.... (2015) The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. DOI: 10.1093/nar/gkv1275  

  • May 4, 2016
  • 09:38 AM
  • 686 views

Video Tip of the Week: expVIP, an Expression, Visualization, and Integration Platform

by Mary in OpenHelix

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

  • April 29, 2016
  • 09:38 AM
  • 697 views

Hunting For The Signatures of Cancer

by EE Giorgi in CHIMERAS

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 »

Siegel, R., Miller, K., & Jemal, A. (2015) Cancer statistics, 2015. CA: A Cancer Journal for Clinicians, 65(1), 5-29. DOI: 10.3322/caac.21254  

Alexandrov LB. (2015) Understanding the origins of human cancer. Science (New York, N.Y.), 350(6265), 1175. PMID: 26785464  

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  

  • April 28, 2016
  • 10:45 AM
  • 676 views

Phylo.io a new interactive way of visualising and comparing trees

by Christophe Dessimoz in Open Reading Frame

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 »

  • April 20, 2016
  • 09:36 AM
  • 651 views

Video Tip of the Week: Pathfinder, for exploring paths through data sets

by Mary in OpenHelix

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/

  • April 13, 2016
  • 09:36 AM
  • 599 views

Video Tip of the Week: Branch, a web-based tool offering decision trees for data analysis

by Mary in OpenHelix

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 »

  • April 11, 2016
  • 02:00 AM
  • 921 views

Week 14 In Review: Open-Access Science | 4 to 10 April

by TakFurTheKaffe in Tak Fur The Kaffe

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  

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  

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  

  • April 8, 2016
  • 09:56 AM
  • 762 views

The Antibacterial Resistance Threat: Are We Heading Toward a Post-Antibiotic Era?

by EE Giorgi in CHIMERAS

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 [1], in other words infections that do not respond to treatment with ordinary antibiotics. Not only do drug-resistant infections require muc........ Read more »

Hollis, A., & Ahmed, Z. (2013) Preserving Antibiotics, Rationally. New England Journal of Medicine, 369(26), 2474-2476. DOI: 10.1056/NEJMp1311479  

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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