All posts; Tags Include "systems biology"
- June 6, 2014
- 01:16 PM
- 109 views
What makes a computational model useful?
by Lily in Quantitative Biology: The Next Generation
A recent commentary argued that computational/mathematical models in biology are "accurate descriptions of our pathetic thinking", and that the best models are simple and specialized. However, recent advances suggest that more detailed, extensive, reusable models may offer interesting benefits as well. ... Read more »
Gunawardena J. (2014) Models in biology: 'accurate descriptions of our pathetic thinking'. BMC biology, 12(1), 29. PMID: 24886484
Bachman, J., & Sorger, P. (2011) New approaches to modeling complex biochemistry. Nature Methods, 8(2), 130-131. DOI: 10.1038/nmeth0211-130
Chelliah V, Laibe C, & Le Novère N. (2013) BioModels Database: a repository of mathematical models of biological processes. Methods in molecular biology (Clifton, N.J.), 189-99. PMID: 23715986
- April 29, 2014
- 04:52 PM
- 161 views
Characterizing Sleep and Wake in the Cat
by Allison in Dormivigilia
The cat is not a new model of sleep. In fact, it is one of the oldest. This study better characterized the electrophysiological output that corresponds with sleep and wake using local field potential recordings and how the sleep states temporally corresponded with neuronal activity in the somatosensory cortex. This is a model of memory consolidation. ... Read more »
Chauvette, S., Seigneur, J., & Timofeev, I. (2012) Sleep Oscillations in the Thalamocortical System Induce Long-Term Neuronal Plasticity. Neuron, 75(6), 1105-1113. DOI: 10.1016/j.neuron.2012.08.034
- April 21, 2014
- 04:27 PM
- 172 views
Daylight Savings is a Public Health Concern. Who is responsible? The circadian system or sleep homeostat?
by Allison in Dormivigilia
A study published in 2013 did a US examination of the risk for heart attack from falling back or springing forward (Daylight Savings). The results mirror those of a landmark study on the subject. But neither study seems to think that disruption of circadian rhythms is responsible, but rather that one hour of precious sleep lost or gained...... Read more »
Jiddou MR, Pica M, Boura J, Qu L, & Franklin BA. (2013) Incidence of myocardial infarction with shifts to and from daylight savings time. The American journal of cardiology, 111(5), 631-5. PMID: 23228926
- April 11, 2014
- 12:46 PM
- 224 views
Variant Annotation in Coding Regions
by Daniel Koboldt in Massgenomics
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 23, 2014
- 05:28 PM
- 195 views
sequencing localized RNA in single cells by FISH
by Gal Haimovich in Green Fluorescent Blog
To celebrate the 2-year anniversary of this blog, lets talk about the new Science paper in which the authors claim to performs in situ single cell, single molecule RNA sequencing. So what’s the big deal? Well, RNA sequencing (RNA-Seq) has become a … Continue reading →... Read more »
Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R.... (2014) Highly multiplexed subcellular RNA sequencing in situ. Science (New York, N.Y.), 343(6177), 1360-3. PMID: 24578530
- March 12, 2014
- 05:46 AM
- 224 views
Optimum-time, Optimum-space, Algorithms for k-mer Analysis of Whole Genome Sequences
by JBCG in JScholar Publishers
The sizable amount of data generated by high throughput cell biology is increasing the demand on traditional computational tools in bioinformatics to handle large input datasets. Large sequence data sets create intractable search spaces that are beyond the scope of many conventional algorithms. One way to address this problem is to transform large sequence data sets to the constituent parts that characterize the features of interest (e.g. transcription factor binding sites, miRNA sites, etc.) of........ Read more »
Sumedha S. Gunewardena. (2014) Optimum-time, Optimum-space, Algorithms for k-mer Analysis of Whole Genome Sequences. JOURNAL OF BIOINFORMATICS AND COMPARATIVE GENOMICS, 1(1), 1-12. info:/JBCG 1: 101
- March 3, 2014
- 09:00 AM
- 211 views
Life (for a mouse) sucks without Bmal1
by Allison in Dormivigilia
Scientists have uncovered a host of pathological consequences in liver- and mitochondrial-pathways in the absence of Bmal1. These studies lend further credence to Bmal1 being important for rhythms of metabolism. These critters are certainly no star athletes. ... Read more »
Peek CB, Affinati AH, Ramsey KM, Kuo HY, Yu W, Sena LA, Ilkayeva O, Marcheva B, Kobayashi Y, Omura C.... (2013) Circadian clock NAD cycle drives mitochondrial oxidative metabolism in mice. Science (New York, N.Y.), 342(6158), 1243417. PMID: 24051248
- February 19, 2014
- 08:05 AM
- 276 views
Who Tastes Best
by Mark Lasbury in As Many Exceptions As Rules
There are links between the function of taste bud receptor cells and solitary chemosensory cells (SCC) that sense nutrients in many animals. New research shows that the evolution of SCC and taste bud receptors were completely independent of one another, even though they share receptors and purinergic signaling systems.... Read more »
Kirino M, Parnes J, Hansen A, Kiyohara S, & Finger TE. (2013) Evolutionary origins of taste buds: phylogenetic analysis of purinergic neurotransmission in epithelial chemosensors. Open biology, 3(3), 130015. PMID: 23466675
Tim Birkhead. (2012) Bird Sense: What It Is Like To Be Bird. Walker Publishing, New York. info:/
- February 14, 2014
- 08:51 AM
- 166 views
New ways to overcome drug resistance for cancer treatment
by ed in Systems Biology Research Note
A tumor often contains several subpopulations or clones. Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. It is possible to quantify and computationally dissect clones from tumors, and then........ Read more »
Wang E, Zou J, Zaman N, Beitel LK, Trifiro M, & Paliouras M. (2013) Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks. Seminars in cancer biology, 23(4), 279-85. PMID: 23791722
Wang E, Zou J, Zaman N, Beitel LK, Trifiro M, & Paliouras M. (2013) Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance. Seminars in cancer biology, 23(4), 286-92. PMID: 23792107
Wang E. (2013) Understanding genomic alterations in cancer genomes using an integrative network approach. Cancer letters, 340(2), 261-9. PMID: 23266571
- February 13, 2014
- 11:00 AM
- 673 views
Neury Thursday: Genotypic Insights on Dopamine, Modafinil, and Sleep
by Allison in Dormivigilia
A recent study in the Journal of Neuroscience uncovers genetic sensitivity to drugs that increase dopamine concentrations and their subsequent effects on sleep in humans. These studies raise important concerns for primary care practitioners when prescribing meds. ... Read more »
Holst SC, Bersagliere A, Bachmann V, Berger W, Achermann P, & Landolt HP. (2014) Dopaminergic role in regulating neurophysiological markers of sleep homeostasis in humans. The Journal of neuroscience : the official journal of the Society for Neuroscience, 34(2), 566-73. PMID: 24403155
- February 7, 2014
- 10:24 AM
- 179 views
Developing a predictive biomarker for PARP inhibition
by Sally Church in Pharma Strategy Blog
Today’s Science Friday post looks at the identification of a potential new biomarker and possible strategies for expanding use of…
... Read more »
Bajrami I, Frankum JR, Konde A, Miller RE, Rehman FL, Brough R, Campbell J, Sims D, Rafiq R, Hooper S.... (2014) Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity. Cancer research, 74(1), 287-97. PMID: 24240700
- January 20, 2014
- 11:07 AM
- 258 views
Gender Influences Sleep Amount and Subsequent Physiology
by Allison in Dormivigilia
Very good friends of mine examined the relationship between actual bed time and underlying physiology in a huge cohort of male versus female college students. Perhaps we should be more sensitive to others' complaints of sleep. ... Read more »
Van Reen E, Sharkey KM, Roane BM, Barker D, Seifer R, Raffray T, Bond TL, & Carskadon MA. (2013) Sex of College Students Moderates Associations among Bedtime, Time in Bed, and Circadian Phase Angle. Journal of biological rhythms, 28(6), 425-31. PMID: 24336420
- January 6, 2014
- 05:00 PM
- 286 views
Synthetic Biology: Engineering Life To Examine It
by Jalees Rehman in The Next Regeneration
Two scientific papers that were published in the journal Nature in the year 2000 marked the beginning of engineering biological circuits in cells. The paper "Construction of a genetic toggle switch in Escherichia coli" by Timothy Gardner, Charles Cantor and James Collins created a genetic toggle switch by simultaneously introducing an artificial DNA plasmid into a bacterial cell. This DNA plasmid contained two promoters (DNA sequences which regulate the expression of genes) and two rep........ Read more »
Daniel R, Rubens JR, Sarpeshkar R, & Lu TK. (2013) Synthetic analog computation in living cells. Nature, 497(7451), 619-23. PMID: 23676681
- December 24, 2013
- 04:25 PM
- 328 views
How not to Write an Original Science Paper
by Allison in Dormivigilia
A recent study in the Journal of Clinical Investigation is a good representative example of bad data organization and presentation. I usually refrain from criticizing studies because I'd like reviewers to give me the same benefit of the doubt, but this is beyond acceptable for such a high-impact journal. ... Read more »
Musiek ES, Lim MM, Yang G, Bauer AQ, Qi L, Lee Y, Roh JH, Ortiz-Gonzalez X, Dearborn JT, Culver JP.... (2013) Circadian clock proteins regulate neuronal redox homeostasis and neurodegeneration. The Journal of clinical investigation, 123(12), 5389-400. PMID: 24270424
- December 6, 2013
- 01:00 PM
- 259 views
Rethinking the Nucleus Accumbens: Regulating Sleep
by Allison in Dormivigilia
The accumbens is historically classified as a reward center. But recent research in animal models shows that it also regulates sleep-This is no surprise, right? Don't you have to hypothetically be awake in order to partake in something pleasurable?... Read more »
Qiu MH, Liu W, Qu WM, Urade Y, Lu J, & Huang ZL. (2012) The role of nucleus accumbens core/shell in sleep-wake regulation and their involvement in modafinil-induced arousal. PloS one, 7(9). PMID: 23029032
- November 13, 2013
- 08:10 AM
- 419 views
Covering All Our Bases
by Mark Lasbury in As Many Exceptions As Rules
We are taught and we teach that DNA codes fro the amino acid sequence of specific proteins. But the truth is that often times, the sequence of the mRNA ends of different than that coded by the DNA. In addition to mRNA processing, there is also RNA editing, which can add, subtract, or change the base sequence in a transcript.
New research is showing just how extensive RNA editing is and the powerful role it plays in cellular expression. A new algorithm has been introduced to better predict R........ Read more »
Paz-Yaacov N, Levanon EY, Nevo E, Kinar Y, Harmelin A, Jacob-Hirsch J, Amariglio N, Eisenberg E, & Rechavi G. (2010) Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates. Proceedings of the National Academy of Sciences of the United States of America, 107(27), 12174-9. PMID: 20566853
Takahashi T, Otsuguro K, Ohta T, & Ito S. (2010) Adenosine and inosine release during hypoxia in the isolated spinal cord of neonatal rats. British journal of pharmacology, 161(8), 1806-16. PMID: 20735412
Lenz H, & Knoop V. (2013) PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation. Bioinformatics and biology insights, 1-19. PMID: 23362369
Poulsen HE, Nadal LL, Broedbaek K, Nielsen PE, & Weimann A. (2013) Detection and interpretation of 8-oxodG and 8-oxoGua in urine, plasma and cerebrospinal fluid. Biochimica et biophysica acta. PMID: 23791936
Wang P, Fisher D, Rao A, & Giese RW. (2012) Nontargeted nucleotide analysis based on benzoylhistamine labeling-MALDI-TOF/TOF-MS: discovery of putative 6-oxo-thymine in DNA. Analytical chemistry, 84(8), 3811-9. PMID: 22409256
- November 3, 2013
- 11:22 AM
- 299 views
Novel Means to Quantify Physiological Sleepiness
by Allison in Dormivigilia
My postdoctoral laboratory has published a methods paper in the recent issue of Sleep that provides a means to determine physiological sleepiness as it occurs, not de facto. They are mice after all, but if these findings were extrapolated to humans, then the scary reality of just a few hours of sleep loss is apparent-a moving body in a brain that is essentially asleep. ... Read more »
Ehlen JC, Jefferson F, Brager AJ, Benveniste M, & Paul KN. (2013) Period-Amplitude Analysis Reveals Wake-Dependent Changes in the Electroencephalogram during Sleep Deprivation. Sleep, 36(11), 1723-35. PMID: 24179307
- October 28, 2013
- 08:00 AM
- 486 views
In Defense of Beavers --Guest Post--
by David Steen in Living Alongside Wildlife
When I lived in Wisconsin's North Woods, my favorite walk was a path that skirted the shore of one of the area's many kettle lakes. I walked it in all kinds of weather, at all times of year, and saw all sorts of interesting things as a result. One of my favorite memories of that lake is the time I got to observe a beaver hard at work doing beaver things: the sound of bubbling and splashing ... Read more »
E. Wohl. (2013) Landscape-scale carbon storage associated with beaver dams . Geophysical Research Letters, 40(14), 3631. DOI: 10.1002/grl.50710
H.A. Cooke, & S. Zack. (2008) Influence of beaver dam density on riparian areas and riparian birds in shrubsteppe of Wyoming. Western North American Naturalist, 68(3), 365-373. DOI: 10.3398/1527-0904(2008)68[365:IOBDDO]2.0.CO;2
C.E. Stevens, C.A. Paszkowski, & A. L. Foote. (2007) Beaver (Castor canadensis) as a surrogate species for conserving anuran amphibians on boreal streams in Alberta, Canada. Biological Conservation, 1-13. DOI: 10.1016/j.biocon.2006.07.017
- October 5, 2013
- 04:30 PM
- 317 views
Revisiting Caffeinated Alcoholic Beverages: Effects on Sleep
by Allison in Dormivigilia
After getting college students hammered via caffeine-infused alcohol (most like Red Bull-vodkas), the researchers surprisingly found that these drinks have little effect on sleep. Their effects on risks for addiction and brain health is a different story...... Read more »
Rohsenow DJ, Howland J, Alvarez L, Nelson K, Langlois B, Verster JC, Sherrard H, & Arnedt JT. (2013) Effects of caffeinated vs. non-caffeinated alcoholic beverage on next-day hangover incidence and severity, perceived sleep quality, and alertness. Addictive behaviors. PMID: 24090620
- October 5, 2013
- 03:30 PM
- 318 views
Neury Thursday: Sleep in Worms Cont'd
by Allison in Dormivigilia
Worms have a sleep-like state known as lethargus in between their molting cycles. Researchers in Germany carefully studied lethargus at behavioral, physiologically, and cellular levels providing convincing evidence that worms and their nervous system works in similar manners to control daily sleep. ... Read more »
Schwarz J, & Bringmann H. (2013) Reduced Sleep-Like Quiescence in Both Hyperactive and Hypoactive Mutants of the Galphaq Gene egl-30 during lethargus in Caenorhabditis elegans. PloS one, 8(9). PMID: 24073282
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