29 posts · 21,645 views
Freelance senior computational biologist from New Zealand. (Job/contract queries welcome.)
Code for life
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- October 13, 2010
- 07:57 PM
- 621 views
Improving screening for gene regulatory sites by using histone-acetylation data
by Grant Jacobs in Code for life
A ‘lite’ review of an attempt to improve motif screening of genomes using additional data. Considering local minima of histone acetylation in a context of high histone acetylation may be one way forward.
A number of years ago at a biotechnology sector after-talk drinks I found myself trying to convince a CEO that often the better [...]... Read more »
Ramsey, S., Knijnenburg, T., Kennedy, K., Zak, D., Gilchrist, M., Gold, E., Johnson, C., Lampano, A., Litvak, V., Navarro, G.... (2010) Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics, 26(17), 2071-2075. DOI: 10.1093/bioinformatics/btq405
- March 27, 2010
- 08:23 PM
- 617 views
Aww, crap.
by Grant Jacobs in Code for life
D’em shrews have shat in me again.
Botanist Dr. Charles Clarke (Monash University, based at Monash’s Selangor campus) has published two research papers showing that the pitchers of mature pitcher plant Nepenthes lowii are opportunistic toilets rather than predatory traps.
Carnivorous pitcher plants typically have waxy interiors and other devices in their pitchers and narrow entrances to [...]... Read more »
Chin, L., Moran, J., & Clarke, C. (2010) Trap geometry in three giant montane pitcher plant species from Borneo is a function of tree shrew body size. New Phytologist, 186(2), 461-470. DOI: 10.1111/j.1469-8137.2009.03166.x
Clarke CM, Bauer U, Lee CC, Tuen AA, Rembold K, & Moran JA. (2009) Tree shrew lavatories: a novel nitrogen sequestration strategy in a tropical pitcher plant. Biology letters, 5(5), 632-5. PMID: 19515656
- October 27, 2009
- 12:00 AM
- 611 views
Autistic children and blood mercury levels
by Grant Jacobs in Code for life
Reviews Hertz-Picciotto et al's study comparing blood mercury autism levels in children with autism or with normal development... Read more »
Hertz-Picciotto I, Green PG, Delwiche L, Hansen R, Walker C, & Pessah IN. (2010) Blood Mercury Concentrations in CHARGE Study Children with and without Autism. Environmental health perspectives, 118(1), 161-6. PMID: 20056569
- January 18, 2011
- 07:49 AM
- 611 views
Fact or fallacy, a survey of immunisation statements in the print media
by Grant Jacobs in Code for life
Most of us know anecdotally that print media on occasion present immunisation information incorrectly, but you can’t put a finger on how often and when without hard numbers.
A recent research article examining New Zealand newspapers puts numbers to the errors.
Helen Petousis-Harris led a team surveying the immunisation statements in articles printed in four national New Zealand newspapers [...]... Read more »
Petousis-Harris, H., Goodyear-Smith, F., Kameshwar, K., & Turner, N. (2010) Fact or fallacy? Immunisation arguments in the New Zealand print media. Australian and New Zealand Journal of Public Health, 34(5), 521-526. DOI: 10.1111/j.1753-6405.2010.00601.x
- September 27, 2010
- 08:08 PM
- 600 views
Choosing an algorithm – benchmarking bioinformatics
by Grant Jacobs in Code for life
You’ve been asked to to run a bioinformatics analysis. How do you choose what algorithm to use?
My first suggestion would be to talk to experienced bioinformatics scientists or computational biologists. It’s a lot quicker, and it’ll save you making mistakes that the research literature assumes you know better not to. You’ll also avoid the trap [...]... Read more »
Aniba, M., Poch, O., & Thompson, J. (2010) Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Research. DOI: 10.1093/nar/gkq625
- September 15, 2010
- 09:13 PM
- 598 views
Autism – looking for parent-of-origin effects
by Grant Jacobs in Code for life
Autism is probably one of the best known neurological disorders, in part due to promotion in Hollywood movies such as Rain Man. It is described in the On-line Mendelian Inheritance in Man (OMIM) database as being
“characterized by a triad of limited or absent verbal communication, a lack of reciprocal social interaction or responsiveness, and restricted, [...]... Read more »
Fradin, D., Cheslack-Postava, K., Ladd-Acosta, C., Newschaffer, C., Chakravarti, A., Arking, D., Feinberg, A., & Fallin, M. (2010) Parent-Of-Origin Effects in Autism Identified through Genome-Wide Linkage Analysis of 16,000 SNPs. PLoS ONE, 5(9). DOI: 10.1371/journal.pone.0012513
- November 24, 2010
- 07:26 AM
- 583 views
Find a home for your research paper, authors, related papers – ask Jane
by Grant Jacobs in Code for life
Jane here is not a woman’s name, but the Journal/Name Author Estimator.*
You take your abstract, plug it into a text field on the Jane web page, and press ‘Find journals’. Alternatively you can find authors or find articles.
Jane will take the words in the abstract and search a database built from Medline to locate the [...]... Read more »
Schuemie, M., & Kors, J. (2008) Jane: suggesting journals, finding experts. Bioinformatics, 24(5), 727-728. DOI: 10.1093/bioinformatics/btn006
- November 7, 2010
- 10:12 PM
- 545 views
Are beached whales and dolphins deaf?
by Grant Jacobs in Code for life
In New Zealand reports of whales stranding on the beaches make headlines, such as the recent stranding of pilot whales at Spirits Bay.[1] They’re mammals like us and New Zealanders have grown up with news stories of whales and their inquisitive cousins, dolphins. It’s pitiful to see these creatures sprawled helpless on the sand.
Frequent readers will know [...]... Read more »
Mann, D., Hill-Cook, M., Manire, C., Greenhow, D., Montie, E., Powell, J., Wells, R., Bauer, G., Cunningham-Smith, P., Lingenfelser, R.... (2010) Hearing Loss in Stranded Odontocete Dolphins and Whales. PLoS ONE, 5(11). DOI: 10.1371/journal.pone.0013824
- November 1, 2011
- 06:20 PM
- 355 views
Teaching bioinformatics at high school
by Grant Jacobs in Code for life
Biology has long been a core subject at high school.
Computer science is now well established too.
Bioinformatics takes computer science and applies it to biological questions. Given that the basic principles are straight-forward and can be allied to basic biology, it seems reasonable that it could be taught at a high school level too.... Read more »
Gallagher, S., Coon, W., Donley, K., Scott, A., & Goldberg, D. (2011) A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms. PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002244
Form, D., & Lewitter, F. (2011) Ten Simple Rules for Teaching Bioinformatics at the High School Level. PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002243
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