• May 8, 2017
• 05:45 PM
• 206 views

Let those who never smelled bad cast the first stone

Analysis of our metabolism is crucial to comprehending the responses of our genes and microbes to the stresses of daily life, and to elucidating the causes and consequences of health and disease. And measurement of urinary metabolites - small molecules produced from foods, drinks, drugs, environmental contaminants, bodily waste products and bacterial by-products - is key to the analysis. We applied this approach to an elusive condition that has always evaded diagnosis: s........ Read more »

Bouatra, S., Aziat, F., Mandal, R., Guo, A., Wilson, M., Knox, C., Bjorndahl, T., Krishnamurthy, R., Saleem, F., Liu, P.... (2013) The Human Urine Metabolome. PLoS ONE, 8(9). DOI: 10.1371/journal.pone.0073076

Irene S. Gabashvili. (2017) Raw Data from Clinical Trial NCT02692495. Mendeley Data. info:/DOI: 10.17632/8bk6h6bmkr.1

• April 8, 2016
• 10:29 AM
• 988 views

The Real Cost of Sequencing

The real cost of sequencing is as hard to pin down as a sumo wrestler. Working in a large-scale sequencing laboratory offers an interesting perspective on the duality of the so-called “cost per genome.” On one hand, we see certain equipment manufacturers and many people in the media tossing around claims that sequencing a genome […]... Read more »

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J.... (2016) The real cost of sequencing: scaling computation to keep pace with data generation. Genome biology, 17(1), 53. PMID: 27009100

• February 24, 2016
• 09:42 AM
• 767 views

Video Tip of the Week: ContentMine, with a #Zika example

by Mary in OpenHelix

For quite a while I’ve been watching the development of ContentMine. There have been a number of different ways to text-mine the scientific literature over the years. Most of the efforts I’m familiar with aim at a specific subset of the literature. This could be species-specific mining, topic-specific (such as interaction data, or a field […]... Read more »

• May 8, 2015
• 09:30 AM
• 1,066 views

do memristor chips remember electric sheep?

Humans beware. Our would-be cybernetic overlords made a leap towards hyper-intelligence in the last few months as artificial neural networks can now be trained on specialized chips which use memristors, an electrical component that can remember the flow of electricity through it to help manage the amount of current required in a circuit. Using these specialized chips, robots, supercomputers, and sensors could solve complex real world problems faster, easier, and with far less energy. [...] ...... Read more »

• March 24, 2015
• 07:00 AM
• 1,625 views

A Universal Translator By Any Other Name…

Star Trek wouldn’t have been possible without the universal translator. Who would want to watch a show where characters don’t understand each other – of course, that doesn’t stop people from watching political debates. The technology of a universal translator is easy, we have camera phones that will show you a foreign sign in your own language. It’s the software to decipher a previously unencountered language that’s proving tough to overcome. Are there any uni........ Read more »

Rao, R., Yadav, N., Vahia, M., Joglekar, H., Adhikari, R., & Mahadevan, I. (2009) Entropic Evidence for Linguistic Structure in the Indus Script. Science, 324(5931), 1165-1165. DOI: 10.1126/science.1170391

Snyder, Benjamin, Regina Barzilay and Kevin Knight. (2010) A Statistical Model for Lost Language Decipherment. Proceedings of the 48th Annual Meeting of the Association for Computational Linguistics, ACL 2010. info:/

• March 17, 2015
• 08:00 AM
• 1,831 views

I See, Said The Blind Man

I can’t stand it when I get dust in my eye. Can you imagine having a neural implant in your eye? Star Trek’s Geordi LaForge had implanted electrodes that, along with his visor, let him see. Visual neural prostheses are no longer a thing of science fiction, making the blind see is science fact. The only difference is that he saw in all wavelengths of the electromagnetic spectrum. But there’s no reason we can’t do that as well. ... Read more »

Jung, J., Aloni, D., Yitzhaky, Y., & Peli, E. (2014) Active confocal imaging for visual prostheses. Vision Research. DOI: 10.1016/j.visres.2014.10.023

Nirenberg, S., & Pandarinath, C. (2012) Retinal prosthetic strategy with the capacity to restore normal vision. Proceedings of the National Academy of Sciences, 109(37), 15012-15017. DOI: 10.1073/pnas.1207035109

Stingl, K., Bartz-Schmidt, K., Gekeler, F., Kusnyerik, A., Sachs, H., & Zrenner, E. (2013) Functional Outcome in Subretinal Electronic Implants Depends on Foveal Eccentricity. Investigative Ophthalmology , 54(12), 7658-7665. DOI: 10.1167/iovs.13-12835

• February 17, 2015
• 07:05 AM
• 1,557 views

I'll Beam Right Over

Star Trek’s 50th anniversary is next year. Wouldn’t transporting a person to the ISS be a great way to celebrate? Well, there are a couple of problems to overcome, but we’re on our way. We have recently learned how to transport information and light from one place to another, without it ever existing anywhere in between! And this will help us make quantum computers that will be able to transport all the information contained in every atom of your body.... Read more »

Ma, X., Herbst, T., Scheidl, T., Wang, D., Kropatschek, S., Naylor, W., Wittmann, B., Mech, A., Kofler, J., Anisimova, E.... (2012) Quantum teleportation over 143 kilometres using active feed-forward. Nature, 489(7415), 269-273. DOI: 10.1038/nature11472

Yokoyama, S., Ukai, R., Armstrong, S., Sornphiphatphong, C., Kaji, T., Suzuki, S., Yoshikawa, J., Yonezawa, H., Menicucci, N., & Furusawa, A. (2013) Ultra-large-scale continuous-variable cluster states multiplexed in the time domain. Nature Photonics, 7(12), 982-986. DOI: 10.1038/nphoton.2013.287

• December 3, 2014
• 08:00 AM
• 1,295 views

How Slime Molds Our World

Fungus-like protists have amazing tales to tell. One phylum has been shown to ranch bacteria and hire cowhands to guard them. One phylum has slime mold that can find its way through a maze and is used to model mathematics for video games. Finally, one phylum is responsible for the glut of Irish priests and policeman in late 1800’s America.... Read more »

Goss, E., Tabima, J., Cooke, D., Restrepo, S., Fry, W., Forbes, G., Fieland, V., Cardenas, M., & Grunwald, N. (2014) The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proceedings of the National Academy of Sciences, 111(24), 8791-8796. DOI: 10.1073/pnas.1401884111

Tero, A., Takagi, S., Saigusa, T., Ito, K., Bebber, D., Fricker, M., Yumiki, K., Kobayashi, R., & Nakagaki, T. (2010) Rules for Biologically Inspired Adaptive Network Design. Science, 327(5964), 439-442. DOI: 10.1126/science.1177894

Toshiyuki Nakagaki, Hiroyasu Yamada . (2000) Intelligence: Maze-solving by an amoeboid organism. Nature, 407(470). info:/

Brock, D., Douglas, T., Queller, D., & Strassmann, J. (2011) Primitive agriculture in a social amoeba. Nature, 469(7330), 393-396. DOI: 10.1038/nature09668

• October 20, 2014
• 12:12 PM
• 1,362 views

How a camera and quantum physics could improve phone security

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

• October 7, 2014
• 05:17 AM
• 1,022 views

Story behind our paper on speeding-up all-against-all comparisons for homology inference

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
name.

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........ Read more »

• September 19, 2014
• 06:25 PM
• 1,105 views

Estimating how much we don't know

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 pe........ Read more »

• June 28, 2014
• 11:19 PM
• 1,258 views

Predicting the Flu

Using search engines to predict the future of infectious diseases: computer science meets epidemiology. [Infographic]... Read more »

• June 28, 2014
• 01:57 PM
• 1,421 views

On Luck, Skill and Hard Work - in Soccer and Life

Big data doesn't always get us closer to truth. Especially if there a fair bit of luck involved. And many think this applies to football/soccer games (Sally and Anderson, for example, say that soccer results are 50% luck). Yet data analysis provides valuable, sometimes counter-intuitive insights into this beautiful sport and the science of winning and losing in general.How many measurable elements of a soccer game contribute to the outcome? 2014 FIFA world cup's statistics page displays scores c........ Read more »

Javier López Peña, & Hugo Touchette. (2012) A network theory analysis of football strategies. In C. Clanet (ed.), Sports Physics: Proc. 2012 Euromech Physics of Sports Conference, p. 517-528, \'Editions de l'\'Ecole Polytechnique, Palaiseau, 2013. (ISBN 978-2-7302-1615-9). arXiv: 1206.6904v1

Cotta, C., Mora, A., Merelo, J., & Merelo-Molina, C. (2013) A network analysis of the 2010 FIFA world cup champion team play. Journal of Systems Science and Complexity, 26(1), 21-42. DOI: 10.1007/s11424-013-2291-2

Padulo J, Haddad M, Ardigò LP, Chamari K, & Pizzolato F. (2014) High frequency performance analysis of professional soccer goalkeepers: a pilot study. The Journal of sports medicine and physical fitness. PMID: 24921614

• June 4, 2014
• 06:25 AM
• 999 views

Video Tip of the Week: LineUp, data ranking visualization tool

by Trey in OpenHelix

Caleydo, from the Institute of Computer Graphics and Vision, a suite of genomics and biomolecular visualization tools. As the project developers state, it’s strength is “the visualization of interdependencies between multiple datasets.” The tip of the week this week is a video introducing one of their newest tools: LineUp. LineUp is an open source […]... Read more »

Gratzl S, Lex A, Gehlenborg N, Pfister H, & Streit M. (2013) LineUp: visual analysis of multi-attribute rankings. IEEE transactions on visualization and computer graphics, 19(12), 2277-86. PMID: 24051794

• April 19, 2014
• 04:25 PM
• 1,021 views

Monotonicity of EM Algorithm Proof

Here the monotonicity of the EM algorithm is established. $$f_{o}(Y_{o}|\theta)=f_{o,m}(Y_{o},Y_{m}|\theta)/f_{m|o}(Y_{m}|Y_{o},\theta)$$ $$\log L_{o}(\theta)=\log L_{o,m}(\theta)-\log f_{m|o}(Y_{m}|Y_{o},\theta) \label{eq:loglikelihood}$$ where $$L_{o}(\theta)$$ is the likelihood under the observed data and $$L_{o,m}(\theta)$$ is the likelihood under the complete data. Taking the expectation of the second line with respect to the conditional distribution of \(Y........ Read more »

Ruslan R Salakhutdinov, Sam T Roweis, & Zoubin Ghahramani. (2012) On the Convergence of Bound Optimization Algorithms. arXiv. arXiv: 1212.2490v1

• April 11, 2014
• 12:46 PM
• 1,269 views

Variant Annotation in Coding Regions

The analysis of NGS data comes with many challenges — data management, read alignment, variant calling, etc. — that the bioinformatics community has tackled with some success. Today I want to discuss another critical component of analysis that remains an unsolved problem: annotation of genetic variants. This process, in which we try to predict the […]... Read more »

Davis J McCarthy, Peter Humburg, Alexander Kanapin, Manuel A Rivas, Kyle Gaulton, The WGS500 Consortium, Jean-Baptiste Cazier and Peter Donnelly. (2014) Choice of transcripts and software has a large effect on variant annotation. Genome Medicine, 6(26). info:/doi:10.1186/gm543

• March 12, 2014
• 10:30 AM
• 977 views

Video Tip of the Week: JANE, comparing phylogenies

by Trey in OpenHelix

Unable to display content. Adobe Flash is required. When I was doing my Ph.D. in the ancient days of the Sanger Method sequencing and reading in the results with one hand on the keyboard and reading the GATCs on the read (and going to the lab in the snow uphill both ways), my purpose for […]... Read more »

Conow, C., Fielder, D., Ovadia, Y., & Libeskind-Hadas, R. (2010) Jane: a new tool for the cophylogeny reconstruction problem. Algorithms for Molecular Biology, 5(1), 16. DOI: 10.1186/1748-7188-5-16

• December 19, 2013
• 12:34 PM
• 897 views

When Roughly Is Good Enough: Approximate Computing Saves Energy

Scientists are creating a new type of computers capable of “approximate computing”—performing calculations that are good enough for certain tasks that don’t require perfect accuracy—potentially doubling efficiency and reducing energy consumption.... Read more »

Swagath Venkataramani, Vinay K. Chippa, Srimat T. Chakradhar, Kaushik Roy, & Anand Raghunatha. (2013) Quality programmable vector processors for approximate computing. Proceedings of the 46th Annual IEEE/ACM International Symposium on Microarchitecture, 1-12. info:/10.1145/2540708.2540710

• December 7, 2013
• 10:33 AM
• 1,303 views

That strange behavior of supersymmetry…

I am a careful reader of scientific literature and an avid searcher for already published material in peer reviewed journals. Of course, arxiv is essential to accomplish this task and to satisfy my needs for reading. In these days, I am working on Dyson-Schwinger equations. I have written on this a paper (see here) a […]... Read more »

Marc Bellon, Gustavo S. Lozano, & Fidel A. Schaposnik. (2007) Higher loop renormalization of a supersymmetric field theory. Phys.Lett.B650:293-297,2007. arXiv: hep-th/0703185v1

Markus Q. Huber, & Jens Braun. (2011) Algorithmic derivation of functional renormalization group equations and Dyson-Schwinger equations. Computer Physics Communications, 183(6), 1290-1320. arXiv: 1102.5307v2

Markus Q. Huber, & Mario Mitter. (2011) CrasyDSE: A framework for solving Dyson-Schwinger equations. arXiv. arXiv: 1112.5622v2

• October 27, 2013
• 05:59 AM
• 1,527 views

First, a big thanks to everybody for being engaged in what I thought was just a simple map to visualize relationships …Continue reading »... Read more »

Bouchard-Côté A, Hall D, Griffiths TL, & Klein D. (2013) Automated reconstruction of ancient languages using probabilistic models of sound change. Proceedings of the National Academy of Sciences of the United States of America, 110(11), 4224-9. PMID: 23401532

Atkinson, Q.D. (2013) The descent of words. PNAS, 4159-4160. info:/10.1073/pnas.1300397110