Prosthetics have come a long way in a relatively short amount of time. With the ongoing wars in the middle east the need for better prosthetics technologies has become more apparent, to this end we now have prosthetics that will allow a person to "feel", we even have motorized prosthetics that will help allow a more fluid walk, but while powered lower limb prosthetics hold promise for improving the mobility of amputees, errors in the technology may also cause some users to stumble or fall. Because of this, new research examines exactly what happens when these technologies fail, with the goal of developing a new generation of more robust powered prostheses.... Read more »
Zhang, F., Liu, M., & Huang, H. (2014) Effects of Locomotion Mode Recognition Errors on Volitional Control of Powered Above-Knee Prostheses. IEEE Transactions on Neural Systems and Rehabilitation Engineering. DOI: 10.1109/TNSRE.2014.2327230
Who can forget the Banana Venn? It was one of the most talked-about visualizations in genomics that I’m aware of. A new concept in data visualization: the Venn/banana diagram. MT @phylogenomics http://t.co/xjitNDNl — Iddo Friedberg (@iddux) July 19, 2012 Banana? RT @phylogenomics: Perhaps the best genomics Venn diagram ever #Bananas #NotSureWhatItMeansButDontCare http://t.co/xMV25GBG — Brian Kent […]... Read more »
D’Hont Angélique, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, & Corinne Da Silva. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488(7410), 213-217. DOI: http://dx.doi.org/10.1038/nature11241
Lex Alexander , Gehlenborg Nils , Strobelt Hendrik , Vuillemot Romain Vuillemot, & Pfister Hanspeter . (2014) UpSet: Visualization of Intersecting Sets. IEEE Transactions on Visualization and Computer Graphics (InfoVis '14). info:other/TBD
Gibbs Richard A., Michael L. Metzker, Donna M. Muzny, Erica J. Sodergren, Steven Scherer, Graham Scott, David Steffen, Kim C. Worley, Paula E. Burch, & Geoffrey Okwuonu. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428(6982), 493-521. DOI: http://dx.doi.org/10.1038/nature02426
Everyone knows a hook when they hear one, but scientists don’t know why. By playing the Hooked on Music game you are exploring the science of songs and helping us to unlock what makes music catchy.
Last weekend the preliminary outcome of the online game was announced in Manchester, UK at the MOSI, answering the question: What is the most instantly recognisable song? Interestingly, numerous media started to report on this. A small media hype?... Read more »
J.A. Burgoyne, D. Bountouridis, J. van Balen, & H. Honing. (2013) Hooked: A Game for Discovering What Makes Music Catchy. Proceedings of the 14th International Society for Music Information Retrieval Conference , 245-250. info:/
Ever think you could have built something better if you had a hand in the design? Sometimes people just have a desire to make, after all the maker movement is huge for a reason. Well geneticists have a new toy tool to play with —dubbed “the telomerator”—that could redefine the limits of synthetic biology and advance how successfully living things can be engineered or constructed in the laboratory based on an organism’s genetic, chemical base-pair structure. How cool is that?!... Read more »
J. Boeke et al. (2014) Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1414399111
To understand the social dynamics of complex software development processes, it is necessary to analyze in which structures the persons involved and how this involvement affected their work. Damian Tamburri has in recent years identified the relevant social structures in a number of publications, analyzed and graded on their effect. He first distinguishes four basic […]... Read more »
Tamburri, D., Lago, P., & Vliet, H. (2013) Organizational social structures for software engineering. ACM Computing Surveys, 46(1), 1-35. DOI: 10.1145/2522968.2522971
We all (of a certain age) remember the Jetsons, a futuristic family with hi-tech gadgets and gizmos. However, nothing said, “the future is here” quite like things hovering. Even in the movie Back to the future, they have hover boards and flying cars. Unfortunately we don’t, which is a shame because according to the 1950’s we are the future, we should have hover-cars and hover boards… well the wait is over. Yep, introducing the first real hover board!... Read more »
Hendo Hover. (2014) Hendo Hoverboards - World's first REAL hoverboard. Kickstarter. info:other/Here
Venus, the place where women are from... supposedly. To say Venus has a harsh climate would be an understatement, this is one of many reasons why we will never (or maybe not soon) see a "long lasting" Venus rover counterpart to our Mars rover missions. Still, the planet (much like all the other plants) can teach us a lot about not just our own origins, but the origins of the universe. Also like all our neighbor planets Venus is hiding something beneath its brilliant shroud of clouds, a mystery that might be soon solved, all thanks to a new re-analysis of twenty-year-old spacecraft data.... Read more »
Harrington, E. et. Al. (2014) The puzzle of radar-bright highlands on venus: a high-spatial resolution study in Ovda regio. Geological Society of America. info:other/136-4
New study uses mobile phone camera to detect light, using shot noise to generate true random numbers which researchers hope could be used for encryption in the future.... Read more »
Sanguinetti, B., Martin, A., Zbinden, H., & Gisin, N. (2014) Quantum Random Number Generation on a Mobile Phone. Physical Review X, 4(3). DOI: 10.1103/PhysRevX.4.031056
When it comes to emails, power makes people spend less time thinking and more time typing. So say German cyber-psychologists Annika Scholl and Kai Sassenberg in a new paper just published: Experienced Social Power Reduces Deliberation During E-Mail Communication In their study, they recruited 49 undergraduate students. Each participant was first randomly assigned to play […]The post Power Makes People Deliberate Less Over Emails appeared first on Neuroskeptic.... Read more »
Scholl A, & Sassenberg K. (2014) "While You Still Think, I Already Type": Experienced Social Power Reduces Deliberation During E-Mail Communication. Cyberpsychology, Behavior and Social Networking. PMID: 25286277
Everything is silicon based, well mainly your computer, your TV, your ipad, and pretty much every piece of electronics in existence. Still the world turns and so does technology; at a similarly fast pace no less. Even as the 2014 Nobel Prize in Physics has enshrined light emitting diodes (LEDs) as the single most significant and disruptive energy-efficient lighting solution of today, scientists around the world continue unabated to search for the even-better-bulbs of tomorrow. In this search we are now ditching silicon for new carbon-based electronics.... Read more »
Sharon Bahena-Garrido, Norihiro Shimoi, Daisuke Abe, Toshimasa Hojo, Yasumitsu Tanaka, & Kazuyuki Tohji. (2014) Plannar light source using a phosphor screen with single-walled carbon nanotubes as field emitters. Review of Scientific Instruments. info:/http://dx.doi.org/10.1063/1.4895913
Solar cells are inefficient, it’s a sad fact. With todays technology they boast about a 10-15% efficiency, compare that to todays gas engine at roughly 20-25% and you can see it’s not quite up to par. Well that could all change very soon thanks to a new method for transferring energy from organic to inorganic semiconductors. This could boost the efficiency of widely used inorganic solar cells to as close as 100% efficiency as they can get.... Read more »
Tabachnyk M, Ehrler B, Gélinas S, Böhm ML, Walker BJ, Musselman KP, Greenham NC, Friend RH, & Rao A. (2014) Resonant energy transfer of triplet excitons from pentacene to PbSe nanocrystals. Nature materials. PMID: 25282509
This post accompanies a recent publication and is part of our
series story behind the paper,
inspired by Jonathan Eisen’s series of the same
One fundamental step in sequence analysis is the identification of homologous
sequences, sequences related through common ancestry. There are many different
ways of identifying homolog but they broadly fall into two categories:
all-against-all comparisons and clustering.
The all-against-all approach aligns every sequence with every other one. This
is straighforward to implement, relatively sensitive, and robust to variations
in sequence lengths. The main downside of all-against-all comparisons is the
quadratic computational cost with respect to the number of sequences.
In contrast, clustering works by using one representative sequence or profile
per homologous family of genes (clusters), thus limiting the number of
required comparisons to one per cluster. Assuming a fixed (or nearly fixed)
number of clusters, the computational cost is (nearly) linear in the number of
input sequences. Clustering methods however tend to miss more homologous
relationships than the all-against-all.
Can the sensitivity of the all-against-all be achieved at the speed of clustering?
The OMA database—developed in our lab—currently
relies upon an all-against-all. With 8,798,758 protein sequences from 1706
genomes in the latest release, this represents 38.7 trillion alignments. We
could probably cope with a few thousands genomes more, but will struggle to
get to the next order of magnitude with the current pipeline.
Furthermore, it is difficult to accept that as we increasingly sample the protein
sequence universe, even though we know more and more about its diversity, the
marginal computational cost of adding sequences goes higher, not lower.
In this project, we thus set out to try to achieve the sensitivity of the
all-against-all at the speed of clustering.
Transitivity of homology
In principle, homology is a transitive relationship: if gene A is homologous
to gene B, and gene B is homologous to gene C, this implies that gene A is
homologous to gene C. Transitive relationships are typically a good fit for
In practice, however, things are more complicated. Homology can be difficult
to ascertain for very divergent sequences. Furthermore, homology is not always
transitive due to insertions, deletions, fusion, fissions, and other events
that may cause inconsistencies in terms of matching residues across multiple
homologs. This figure illustrates these problems and outlines the ideas
we implemented to address them:
Putting together the ideas outlined in the figure above, we were pleasantly
surprised to see that clustering can indeed be both sensitive and fast. We
obtained 4-5x speed-ups across various datasets while recovering ~99.9% of all
homologous relationships identified through all-against-all.
In comparison, general purpose clustering approaches such as
UCLUST—which admittedly have not been
designed to identify distant homologs
~10% of all homologous relationships. They are, however, several orders of
Only the beginning
The results of our proof-of-concept implementation are thus very
encouraging. We have plans to follow up with a long list of refinement ideas,
many of which we discuss in the manuscript. One essential
refinement will be to parallelise the new approach. This is not as
straightforward as with all-against-all compraisons, but we think it can be
Meanwhile, the serial variant is available as part of the OMA
Wittwer, L., Piližota, I., Altenhoff, A., & Dessimoz, C. (2014). Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology PeerJ, 2:e607 DOI: 10.7717/peerj.607
... Read more »
Wittwer, L., Piližota, I., Altenhoff, A., & Dessimoz, C. (2014) Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. PeerJ. DOI: 10.7717/peerj.607
Lupus, Type 1 diabetes, and multiple sclerosis are all diseases brought on by autoimmunity — the bodies inability to tell itself apart from foreign invaders. Finding a cure, or even a suitable treatment has been to put it gently a long, painful road, with little to show for it. On the forefront of the war against the body betrayal is immunosuppressants, which with them carry their own set of side effects and in most cases only off mild to moderate relief of symptoms. But that is all changing and new research on something called immunoproteasomes offer that new hope.... Read more »
Dubiella C, Cui H, Gersch M, Brouwer AJ, Sieber SA, Krüger A, Liskamp RM, & Groll M. (2014) Selective Inhibition of the Immunoproteasome by Ligand-Induced Crosslinking of the Active Site. Angewandte Chemie (International ed. in English). PMID: 25244435
Currently lie detectors (polygraphs) are not admissible in court, this is because (despite what you may read) there is little proof to show that they are much better than a guess — coming in at roughly 50% accuracy. They aren’t really based in science, making them more of a toy. There might just be a new contender in the lie detection department coming soon however, researchers have found that brain activity can be used to tell whether someone recognizes details they encountered in normal, daily life.... Read more »
Meixner JB, & Rosenfeld JP. (2014) Detecting Knowledge of Incidentally Acquired, Real-World Memories Using a P300-Based Concealed-Information Test. Psychological science. PMID: 25231899
Carbon nanotubes, the wave of the future. Our hopes and dreams for the future have been firmly placed in using the unique material for everything from electronics to engineering. Unfortunately the production of carbon nanotubes has been hampered by setbacks, which as it turns out might not be a bad thing. This is because for the first time, scientists have discovered how to produce ultra-thin “diamond nanothreads” that promise extraordinary properties, including strength and stiffness greater than that of today’s strongest nanotubes and polymers.... Read more »
What does lupus, rheumatoid arthritis, type I diabetes, multiple sclerosis, and rheumatic heart disease have in common? All of these (and many other) apparently unrelated disorders are caused by autoimmunity, in which the immune system produces antibodies that attack normal, healthy cells and tissues. Currently considered incurable, these autoimmune diseases can be managed, but to varying degrees and not without serious side effects. Moreover, autoimmune diseases include a wide range of dysfunctional immune responses known as type II, type III, and type IV immune hypersensitivity reactions.... Read more »
Copp JA, Fang RH, Luk BT, Hu CM, Gao W, Zhang K, & Zhang L. (2014) Clearance of pathological antibodies using biomimetic nanoparticles. Proceedings of the National Academy of Sciences of the United States of America, 111(37), 13481-6. PMID: 25197051
Most of our understanding of what genes do comes from computational predictions, rather than actual experiments. For almost any given gene that is sequenced, its function is determined by putting its sequence through one or more function annotation algorithms. Computational annotation is cheaper and more feasible than cloning, translating, and assaying the gene product (typically a protein) to find out exactly what it does. Experiments can be long, expensive and, in many cases, impossible to perform. But, by resorting to computational annotation of the function of proteins, we need to know how well can these algorithms actually perform.... Read more »
Jiang, Y., Clark, W., Friedberg, I., & Radivojac, P. (2014) The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Bioinformatics, 30(17). DOI: 10.1093/bioinformatics/btu472
For most people biofilms conjure up images of slippery stones in a streambed and dirty drains. While there are plenty of "bad" biofilms around – they are even the same stuff that causes pesky dental plaque and a host of other more serious medical problems – a team of researchers sees biofilms as a robust new platform for designer nanomaterials that could clean up polluted rivers, manufacture pharmaceutical products, fabricate new textiles, and more.... Read more »
Peter Q. Nguyen,, Zsofia Botyanszki,, Pei Kun R. Tay,, & Neel S. Joshi. (2014) Programmable biofilm-based materials from engineered curli nanofibres. Nature Communications. info:/10.1038/ncomms5945
When a patient has sepsis Things can go downhill fast. A life-threatening condition in which bacteria or fungi multiply in a patient's blood -- sepsis is often too fast for antibiotics to help. But that's all about to change with the introduction of a new device -- inspired by the human spleen -- that may radically transform the way doctors treat sepsis.... Read more »
Kang JH, Super M, Yung CW, Cooper RM, Domansky K, Graveline AR, Mammoto T, Berthet JB, Tobin H, Cartwright MJ.... (2014) An extracorporeal blood-cleansing device for sepsis therapy. Nature medicine. PMID: 25216635
One of the exciting things in reading philosophy, its history in particular, is experiencing the tension between different schools of thought. This excitement turns to beauty if a clear synthesis emerges to reconcile the conflicting ideas. In the middle to late 18th century, as the Age of Enlightenment was giving way to the Romantic era, […]... Read more »
Post, E.L. (1936) Finite combinatory processes -- formulation 1. Journal of Symbolic Logic, 1(3), 103-105. info:/
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