46 posts · 47,101 views
My blog is about systems biology and its applications to drug discovery. The aim is to discuss the latest research in the same area.
Fisheye Perspective
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- August 16, 2010
- 04:42 AM
- 572 views
The misuse of terms ‘homology’ in bioinformatics community
by Abhishek Tiwari in Fisheye Perspective
In a recent letter to the editor of journal Bioinformatics Marabotti and Facchiano have raised the concern over the misuse of term ‘homology’ in peer-reviwed bioinformatics papers. This issues is not new for the scientific community at all, in fact severity of the issue was first recognized in 1987 when a letter to the Editor [...]
... Read more »
Marabotti, A., & Facchiano, A. (2009) When it comes to homology, bad habits die hard. Trends in Biochemical Sciences, 34(3), 98-99. DOI: 10.1016/j.tibs.2008.12.001
Marabotti, A., & Facchiano, A. (2010) The misuse of terms in scientific literature. Bioinformatics. DOI: 10.1093/bioinformatics/btq438
- August 15, 2010
- 12:14 AM
- 647 views
Lancet’s superbug report is another misuse of broken peer review
by Abhishek Tiwari in Fisheye Perspective
First of all I am really disappointed the way most of science and microbiology bloggers avoided to blog this paper. I think this was perfect food for any science blog focused on microbiology and an opportunity to show their zeal for independent science writing but they did not. Although I am neither a microbiologist nor I am [...]
... Read more »
Kumarasamy, K., Toleman, M., Walsh, T., Bagaria, J., Butt, F., Balakrishnan, R., Chaudhary, U., Doumith, M., Giske, C., & Irfan, S. (2010) Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. The Lancet Infectious Diseases. DOI: 10.1016/S1473-3099(10)70143-2
- August 7, 2010
- 07:25 AM
- 580 views
Translational bioinformatics in the cloud
by Abhishek Tiwari in Fisheye Perspective
There is no doubt that large scale on demand computing in cloud can be highly affordable. Right now Bioinformatics and Genomics community is really enjoying this affordability. In a latest article published in Genome Medicine the leading translational bioinformatics researcher Atul J Butte and his group has published a comparative study to evaluate the computational [...]
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Dudley, J., Pouliot, Y., Chen, R., Morgan, A., & Butte, A. (2010) Translational bioinformatics in the cloud: an affordable alternative. Genome Medicine, 2(8), 51. DOI: 10.1186/gm172
- March 31, 2010
- 06:47 AM
- 537 views
Put some breathe life in your papers with clever visualization
by Abhishek Tiwari in Fisheye Perspective
I often screen papers for my reading list based on their illustration appeal. I know this may be bit strange for the people who judge the papers simply based on their abstracts or conclusion section. But trust me it works because I know what I am looking for. I always avoid the sleep inducing papers full of creepy tables and bar graphs, in fact so lacking in interest as to cause mental weariness. When I say illustration appeal, I mean something which can inspire your readers to wake them up, s........ Read more »
Carlson, C., Warren, C., Hauschild, K., Ozers, M., Qadir, N., Bhimsaria, D., Lee, Y., Cerrina, F., & Ansari, A. (2010) Specificity landscapes of DNA binding molecules elucidate biological function. Proceedings of the National Academy of Sciences, 107(10), 4544-4549. DOI: 10.1073/pnas.0914023107
Chen, W., Schoeberl, B., Jasper, P., Niepel, M., Nielsen, U., Lauffenburger, D., & Sorger, P. (2009) Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Molecular Systems Biology. DOI: 10.1038/msb.2008.74
de Souza, N. (2010) The DNA-binding landscape. Nature Methods, 7(4), 254-255. DOI: 10.1038/nmeth0410-254a
- March 6, 2010
- 08:22 PM
- 497 views
Availability decay of Bioinformatics web resources : Yes widgets can change it
by Abhishek Tiwari in Fisheye Perspective
Quality and availability of bioinformatics resources is always a matter of great debate. HTTP 404 not found is quite frequent phenomenon for bioinformatics researchers looking to use some published web accessible database or analysis tool. A 4-year follow-up survey on the lack of persistence of bioinformatics resources was published in year 2008 by Jonathan D. Wren suggests that approximately 20% of URLs published in MEDLINE abstracts are now inaccessible, and the most common types of inaccessi........ Read more »
Bourne, P., Beran, B., Bi, C., Bluhm, W., Dunbrack, R., Prlić, A., Quinn, G., Rose, P., Shah, R., Tao, W.... (2010) Will Widgets and Semantic Tagging Change Computational Biology?. PLoS Computational Biology, 6(2). DOI: 10.1371/journal.pcbi.1000673
Wren, J., & Bateman, A. (2008) Databases, data tombs and dust in the wind. Bioinformatics, 24(19), 2127-2128. DOI: 10.1093/bioinformatics/btn464
Veretnik, S., Fink, J., & Bourne, P. (2008) Computational Biology Resources Lack Persistence and Usability. PLoS Computational Biology, 4(7). DOI: 10.1371/journal.pcbi.1000136
Wren, J. (2008) URL decay in MEDLINE--a 4-year follow-up study. Bioinformatics, 24(11), 1381-1385. DOI: 10.1093/bioinformatics/btn127
- March 6, 2010
- 08:22 PM
- 352 views
Availability decay of Bioinformatics web resources : Yes widgets can change it
by Abhishek Tiwari in Fisheye Perspective
Quality and availability of bioinformatics resources is always a matter of great debate. HTTP 404 not found is quite frequent phenomenon for bioinformatics researchers looking to use some published web accessible database or analysis tool. A 4-year follow-up survey on the lack of persistence of bioinformatics resources was published in year 2008 by Jonathan D. [...]... Read more »
Bourne, P., Beran, B., Bi, C., Bluhm, W., Dunbrack, R., Prlić, A., Quinn, G., Rose, P., Shah, R., Tao, W.... (2010) Will Widgets and Semantic Tagging Change Computational Biology?. PLoS Computational Biology, 6(2). DOI: 10.1371/journal.pcbi.1000673
Wren, J., & Bateman, A. (2008) Databases, data tombs and dust in the wind. Bioinformatics, 24(19), 2127-2128. DOI: 10.1093/bioinformatics/btn464
Veretnik, S., Fink, J., & Bourne, P. (2008) Computational Biology Resources Lack Persistence and Usability. PLoS Computational Biology, 4(7). DOI: 10.1371/journal.pcbi.1000136
Wren, J. (2008) URL decay in MEDLINE--a 4-year follow-up study. Bioinformatics, 24(11), 1381-1385. DOI: 10.1093/bioinformatics/btn127
- March 4, 2010
- 12:13 AM
- 708 views
Bio-ontologies for everyone with new Microsoft Word Add-in
by Abhishek Tiwari in Fisheye Perspective
A latest paper in BMC Bioinformatics describes a Microsoft Word Add-in for ontology recognition. Tool is freely available from Codeplex portal and as prerequisite you will need Microsoft Word 2007. This add-in enables the annotation of scientific documents based on terms that appear in ontologies and controlled vocabularies. I am sure this tool is going to fuel the debate on the article of the future as like everyone else I think that the next generation of scientific articles will be semantic r........ Read more »
Fink, J., Fernicola, P., Chandran, R., Parastitidas, S., Wade, A., Naim, O., Quinn, G., & Bourne, P. (2010) Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinformatics, 11(1), 103. DOI: 10.1186/1471-2105-11-103
- February 8, 2010
- 04:51 AM
- 572 views
MapReduce goes evolutionary
by Abhishek Tiwari in Fisheye Perspective
Scientists from Texas A&M University have developed a new algorithm MrsRF (MapReduce Speeds up Robinson-Foulds) for analyzing large collection of evolutionary trees using MapReduce framework. Matthews et. al, have used their MapReduce algorithm to compute all-to-all Robinson-Foulds (RF) distance matrix on multi-core computing platforms. Calculation of all possible Robinson-Foulds distance pairs is a computationally intensive task. The results show that a significant speedup can be achieved ........ Read more »
Matthews, S., & Williams, T. (2010) MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees. BMC Bioinformatics, 11(Suppl 1). DOI: 10.1186/1471-2105-11-S1-S15
- January 22, 2010
- 12:11 AM
- 746 views
Nothing wrong with synthetic biology, It's just B-I-O-L-O-G-Y and the rest is silence
by Abhishek Tiwari in Fisheye Perspective
Recent issue of Nature magazine has few very interesting articles about synthetic biology and one of them is "Five hard truths for synthetic biology" written by Roberta Kwok. When I first read this article my first reaction was- nothing wrong with synthetic biology, it's just biology gets in the way of the engineering.Nothing to do with their heartsNothing to do with their headsNothing to do with their homesNothing to do with their bedsIt's just B-I-O-L-O-G-YCan't you seeIt's just BiologyBiology........ Read more »
Kwok, R. (2010) Five hard truths for synthetic biology. Nature, 463(7279), 288-290. DOI: 10.1038/463288a
- January 19, 2010
- 01:06 AM
- 473 views
Sherlock Holmes and Proteomics
by Abhishek Tiwari in Fisheye Perspective
By reading the title of the post you may be curious that what remote similarity proteomics can share with Sherlock Holmes? Well not much at this moment except the complexity of storyline. An excerpt from a bit old article, interested readers will find it useful to understand the complexity of proteomeModern proteome analysis is a very complex 'detective story', which might baffle even the most famous investigator, Sherlock Holmes [1]. The reason is that, in any proteome, a few proteins dominate ........ Read more »
Righetti, P., & Boschetti, E. (2007) Sherlock Holmes and the proteome − a detective story. FEBS Journal, 274(4), 897-905. DOI: 10.1111/j.1742-4658.2007.05648.x
- January 14, 2010
- 10:18 PM
- 875 views
Anti-CRO sentiments: Outsourcing any knowledge-based element in drug discovery process can be a risky endeavour?
by Abhishek Tiwari in Fisheye Perspective
In a recent article in Drug Discovery Today Paul Branthwaite writesOutsourcing any knowledge-based element, large or small, on grounds of cost, without fully understanding what that actually means when you hand influence on critical issues over to an outside organization can be a risky endeavour. Drug development strategy, design and decision-making require disease area knowledge, experience, judgement and ‘feel’. When you put that in context of whole development programmes, multiplied by th........ Read more »
Branthwaite, P. (2009) The shrinking of the knowledge base – what is the impact of this on the speed and security of drug development?. Drug Discovery Today. DOI: 10.1016/j.drudis.2009.10.004
- January 14, 2010
- 09:14 PM
- 874 views
Genetic modification of plant cell wall may scale-up biofuel production
by Abhishek Tiwari in Fisheye Perspective
Drive for creating synthetic biofuels is gaining momenta. In fact synthetic biology community is trying to use bacteria and yeast as platform to creat biofuels. To this end microbes can convert the simple fermentable sugar into ethanol or other products. Plants are naturally abundant source of renewable biofuel and as matter of fact most of fossil fuel such as oil and gas have been formed from the anaerobic decomposition of prehistoric plants and animals. Formation of fossil fuel is a very sl........ Read more »
Lionetti, V., Francocci, F., Ferrari, S., Volpi, C., Bellincampi, D., Galletti, R., D'Ovidio, R., De Lorenzo, G., & Cervone, F. (2009) Engineering the cell wall by reducing de-methyl-esterified homogalacturonan improves saccharification of plant tissues for bioconversion. Proceedings of the National Academy of Sciences, 107(2), 616-621. DOI: 10.1073/pnas.0907549107
- December 15, 2009
- 07:45 PM
- 917 views
Steering drug discovery efforts away from the flatland
by Abhishek Tiwari in Fisheye Perspective
Does high-throughput synthetic practices have failed the drug discovery efforts by steering them toward greater unsaturation leading to more flat aromatic compounds those may not be better complement to the target proteins? Yes at least that's what Frank Lovering and others are suggesting. In a recent article published in Journal of Medicinal Chemistry Lovering et. al highlight lack of molecular complexity as key limitation of high-throughput parallel synthesis driven drug discovery efforts. I........ Read more »
Lovering, F., Bikker, J., & Humblet, C. (2009) Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success. Journal of Medicinal Chemistry, 52(21), 6752-6756. DOI: 10.1021/jm901241e
- November 5, 2009
- 09:44 AM
- 605 views
What you call this? Linguistic morphology of chemical names and lost in translation
by Abhishek Tiwari in Fisheye Perspective
Here is a real world example how Linguistic morphology of chemical names may have unwanted secondary effects. For example, English search engines such as Google and Yahoo! are unable to find "chlorobenzene" by searching for "benzene". Interestingly, in other languages such as Chinese, Japanese, or Korean (CJK languages), this is less of a problem, where for example the Japanese "(chlorobenzene) can usually be found by querying for"(benzene).So next time you visit Japan and wish to buy an Aspirin........ Read more »
Sayle, R. (2009) Foreign Language Translation of Chemical Nomenclature by Computer. Journal of Chemical Information and Modeling, 49(3), 519-530. DOI: 10.1021/ci800243w
- November 4, 2009
- 11:02 AM
- 968 views
Lowering Pharma firewalls: Just for Bioinformatics or Chemoinformatics also
by Abhishek Tiwari in Fisheye Perspective
Notion of pre-competitive collaboration has been in under experiment steadily for quite sometime now. Notable examples are the Airbus consortium of European aircraft manufacturers, the Sematech consortium of US semiconductor manufacturers, banks working together to launch Visa and Mastercard, our recent moon lust and many more. But this was never a case for pharmaceutical industry until now which is now lowering industry firewalls to shift funding and focus from early- to late-stage projects by ........ Read more »
Barnes, M., Harland, L., Foord, S., Hall, M., Dix, I., Thomas, S., Williams-Jones, B., & Brouwer, C. (2009) Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery. Nature Reviews Drug Discovery, 8(9), 701-708. DOI: 10.1038/nrd2944
- October 31, 2009
- 12:45 PM
- 722 views
Gladwell states as guidlines for a better omics data management
by Abhishek Tiwari in Fisheye Perspective
Universal application of high throughput omics technologies have enabled scientists to measure tens of thousands of data points in a single experiment. As a result of this scientific world has become deluged with data. This has greater implications the way science will be done in coming years. There is a general accord that science has turned more into a data management problem. Put the technical aspect of scientific data management aside, and ask can we depict useful and practically relevant co........ Read more »
Arita, M. (2009) What can metabolomics learn from genomics and proteomics?. Current Opinion in Biotechnology. DOI: 10.1016/j.copbio.2009.09.011
- October 13, 2009
- 08:28 AM
- 1,169 views
Monkeys exhibit the uncanny valley effect
by Abhishek Tiwari in Fisheye Perspective
Image via WikipediaA recent peer reviewed research published in journal PNAS suggests that monkey visual behavior falls into the uncanny valley. The idea of uncanny valley was introduced by Japanese roboticist Masahiro Mori in 1970. In simple words, as virtual humans approach photorealism or human likeness, they risk making real humans uncomfortable or may evoke negative feelings in human observers. Although uncanny valley is a valid and widely accepted psychological phenomenon in human sup........ Read more »
Steckenfinger, S., & Ghazanfar, A. (2009) Monkey visual behavior falls into the uncanny valley. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0910063106
- October 11, 2009
- 12:28 AM
- 1,189 views
What synthetic biology can learn from programming languages
by Abhishek Tiwari in Fisheye Perspective
What is synthetic biology? In simple words Synthetic biology is nothing but putting engineering into biology. An engineered genetic toggle switch developed by Tim Gardner and Jim Collins is a good example of how engineering principles are driving the boat of synthetic biology. Researchers are now trying to adapt concepts developed in area of programming language development & software engineering for synthetic biology applications. A latest paper in PLoS Computational Biology shows how meth........ Read more »
Cai, Y., Lux, M., Adam, L., & Peccoud, J. (2009) Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars. PLoS Computational Biology, 5(10). DOI: 10.1371/journal.pcbi.1000529
- October 10, 2009
- 10:24 PM
- 1,096 views
BioEngineered personalized human bone grafts created from bone marrow stem cells
by Abhishek Tiwari in Fisheye Perspective
Scale up of engineered bone grafts towards clinical applications is always a central challenge in regenerative medicine. In latest article PNAS Grayson et. al report an approach to develop clinically sized viable bone grafts of human temporomandibular joint (TMJ) condylar or Jaw bone seeded with human bone marrow stem/progenitor cells (hMSCs). This study was carried out by a research group led by Dr Gordana Vunjak-Novakovic at the Columbia University and it appears in the online issue of journ........ Read more »
Grayson, W., Frohlich, M., Yeager, K., Bhumiratana, S., Chan, M., Cannizzaro, C., Wan, L., Liu, X., Guo, X., & Vunjak-Novakovic, G. (2009) Regenerative Medicine Special Feature: Engineering anatomically shaped human bone grafts. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0905439106
- October 9, 2009
- 08:00 AM
- 1,177 views
A Polymer analog of Hilbert's curve at the megabase scale
by Abhishek Tiwari in Fisheye Perspective
Hilbert curve or Hilbert space-filling curve is a continuous fractal space-filling curve that densely fills higher-dimensional space without crossing itself. It was first described by the German mathematician David Hilbert in 1891. In a recent article Aiden et al. describe a new method called as Hi-C for reconstructing the three-dimensional architecture of the human genome which not only reveals folding principles of the human genome but also resembles a polymer analog of Hilbert's curve at th........ Read more »
Lieberman-Aiden, E., van Berkum, N., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B., Sabo, P., Dorschner, M.... (2009) Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science, 326(5950), 289-293. DOI: 10.1126/science.1181369
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