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1.  The water flea Daphnia - a 'new' model system for ecology and evolution? 
Journal of Biology  2010;9(2):21.
Daphnia pulex is the first crustacean to have its genome sequenced. Availability of the genome sequence will have implications for research in aquatic ecology and evolution in particular, as addressed by a series of papers published recently in BMC Evolutionary Biology and BMC Genomics.
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PMCID: PMC2871515  PMID: 20478012
2.  Ecological genomics: steps towards unraveling the genetic basis of inducible defenses in Daphnia 
BMC Biology  2010;8:51.
Little is known about the genetic mechanisms underlying inducible defenses. Recently, the genome of Daphnia pulex, a model organism for defense studies, has been sequenced. Building on the genome information, recent preliminary studies in BMC Developmental Biology and BMC Molecular Biology have assessed gene response profiles in Daphnia under predation pressure. We review the significance of the findings and highlight future research perspectives.
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PMCID: PMC2867779  PMID: 20529235
3.  Genome of a songbird unveiled 
Journal of Biology  2010;9(3):19.
An international collaborative effort has recently uncovered the genome of the zebra finch, a songbird model that has provided unique insights into an array of biological phenomena.
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PMCID: PMC2871510  PMID: 20359317
4.  Coordinated gene expression by post-transcriptional regulons in African trypanosomes 
Journal of Biology  2009;8(11):100.
The regulation of gene expression in trypanosomes is unique. In the absence of transcriptional control at the level of initiation, a subset of Trypanosoma brucei genes form post-transcriptional regulons in which mRNAs are co-regulated in response to differentiation signals.
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PMCID: PMC2804284  PMID: 20017896
5.  SnoPatrol: how many snoRNA genes are there? 
Journal of Biology  2010;9(1):4.
Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA. Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found.
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PMCID: PMC2871523  PMID: 20122292
6.  Toward forward genetic screens in malaria-causing parasites using the piggyBac transposon 
BMC Biology  2011;9:21.
The ability to analyze gene function in malaria-causing Plasmodium parasites has received a boost with a recent paper in BMC Genomics that describes a genome-wide mutagenesis system in the rodent malaria species Plasmodium berghei using the transposon piggyBac. This advance holds promise for identifying and validating new targets for intervention against malaria. But further improvements are still needed for the full power of genome-wide molecular genetic screens to be utilized in this organism.
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PMCID: PMC3068990  PMID: 21453557
7.  Prospects for automated diagnosis of verbal autopsies 
BMC Medicine  2014;12:18.
Verbal autopsy is a method for assessing probable causes of death from lay reporting of signs, symptoms and circumstances by family members or caregivers of a deceased person. Several methods of automated diagnoses of causes of death from standardized verbal autopsy questionnaires have been developed recently (Inter-VA, Tariff, Random Forest and King-Lu). Their performances have been assessed in a series of papers in BMC Medicine. Overall, and despite high specificity, the current strategies of automated computer diagnoses lead to relatively low sensitivity and positive predictive values, even for causes which are expected to be easily assessed by interview. Some methods have even abnormally low sensitivity for selected diseases of public health importance and could probably be improved. Ways to improve the current strategies are proposed: more detailed questionnaires; using more information on disease duration; stratifying for large groups of causes of death by age, sex and main category; using clusters of signs and symptoms rather than quantitative scores or ranking; separating indeterminate causes; imputing unknown cause with appropriate methods.
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PMCID: PMC3912493  PMID: 24495788
Cause of death; Verbal autopsy; Automated diagnosis; Health information system; Evaluation of health programs; Public health
8.  Plastid evolution: gene transfer and the maintenance of 'stolen' organelles 
BMC Biology  2010;8:73.
Many heterotrophic organisms sequester plastids from prey algae and temporarily utilize their photosynthetic capacity. A recent article in BMC Genomics reveals that the dinoflagellate Dinophysis acuminata has acquired photosynthesis-related genes by horizontal gene transfer, which might explain its ability to retain 'stolen' plastids for extended periods of time.
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PMCID: PMC2883544  PMID: 20594287
9.  The global dynamics of RNA stability orchestrates responses to cellular activation 
BMC Biology  2010;8:95.
Transcriptomics is used to quantify changes in accumulated levels of mRNAs following cellular activation. These changes arise from the opposing fluxes of transcription and mRNA decay, both of which affect the functional dynamics of global gene expression. A study published recently in BMC Genomics focuses on the contribution made by mRNA stability in shaping the kinetics of gene responses in mammalian cells.
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PMCID: PMC2900241  PMID: 20619007
10.  No small feat: microRNA responses during vocal communication in songbirds 
BMC Biology  2011;9:35.
Simply hearing the song produced by another bird of the same species triggers the regulation of microRNAs (miRNAs) in high-order auditory parts of the zebra finch brain. Some of the identified miRNAs appear to be unique to birds, possibly to songbirds. These findings, reported in BMC Genomics, highlight the complexities of gene regulation associated with vocal communication and point to possible key regulators of song-triggered gene networks.
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PMCID: PMC3104949  PMID: 21627855
11.  Transcriptomics and disease vector control 
BMC Biology  2010;8:52.
Next-generation sequencing can be used to compare transcriptomes under different conditions. A study in BMC Genomics applies this approach to investigating the effects of exposure to a range of xenobiotics on changes in gene expression in the larvae of Aedes aegypti, the mosquito vector of dengue fever.
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PMCID: PMC2867780  PMID: 20525113
12.  Hidden reach of the micromanagers 
BMC Biology  2010;8:53.
Small interfering RNAs can trigger unintended, microRNA-like off-target effects, but the impact of these effects on functional studies has been controversial. A recent study in BMC Genomics shows that microRNA-like effects can predominate among the 'hits' of functional genomics screens.
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PMCID: PMC2867781  PMID: 20529236
13.  A central role for p38 MAPK in the early transcriptional response to stress 
BMC Biology  2010;8:47.
The mitogen-activated protein kinase p38 (p38 MAPK) is activated by a number of stresses. A recent study in BMC Genomics has uncovered the early transcriptional responses to three types of stress and has demonstrated a central role for p38 MAPK in mediating these responses.
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PMCID: PMC2860348  PMID: 20515460
14.  Unraveling bovin phylogeny: accomplishments and challenges 
BMC Biology  2010;8:50.
The phylogenetic systematics of bovin species forms a common basis for studies at multiple scales, from the level of domestication in populations to major cladogenesis. The main big-picture accomplishments of this productive field, including two recent works, one in BMC Genomics, are reviewed with an eye for some of the limitations and challenges impeding progress. See Research article
PMCID: PMC2861646  PMID: 20525112
15.  Repetitive elements in parasitic protozoa 
BMC Biology  2010;8:64.
A recent paper published in BMC Genomics suggests that retrotransposition may be active in the human gut parasite Entamoeba histolytica. This adds to our knowledge of the various types of repetitive elements in parasitic protists and the potential influence of such elements on pathogenicity.
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PMCID: PMC2875222  PMID: 20529240
16.  The transcriptome of human monocyte subsets begins to emerge 
Journal of Biology  2009;8(11):99.
Human monocytes can be divided into subsets according to their expression or lack of the cell-surface antigen CD16. In papers published recently in the Journal of Proteome Research and in BMC Genomics, two groups publish independent transcriptome analyses of CD16+ and CD16-monocytes, with revealing results.
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PMCID: PMC2804287  PMID: 20067595
17.  A question of scale: Human migrations writ large and small 
BMC Biology  2010;8:98.
Several recent papers illustrate the importance of migration and gene flow in molding the patterns of genetic variation observed in humans today. We place the varied demographic processes covered by these terms into a more general framework, and discuss some of the challenges facing attempts to reconstruct past human mobility and determine its influence on our genetic heritage.
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PMCID: PMC2908064  PMID: 20659353
18.  A new analysis approach of epidermal growth factor receptor pathway activation patterns provides insights into cetuximab resistance mechanisms in head and neck cancer 
BMC Medicine  2012;10:43.
The pathways downstream of the epidermal growth factor receptor (EGFR) have often been implicated to play crucial roles in the development and progression of various cancer types. Different authors have proposed models in cell lines in which they study the modes of pathway activities after perturbation experiments. It is prudent to believe that a better understanding of these pathway activation patterns might lead to novel treatment concepts for cancer patients or at least allow a better stratification of patient collectives into different risk groups or into groups that might respond to different treatments. Traditionally, such analyses focused on the individual players of the pathways. More recently in the field of systems biology, a plethora of approaches that take a more holistic view on the signaling pathways and their downstream transcriptional targets has been developed. Fertig et al. have recently developed a new method to identify patterns and biological process activity from transcriptomics data, and they demonstrate the utility of this methodology to analyze gene expression activity downstream of the EGFR in head and neck squamous cell carcinoma to study cetuximab resistance. Please see related article:
PMCID: PMC3366885  PMID: 22548923
HNSCC; EGFR; cetuximab; drug resistance; matrix factorization; GSEA; pathway signature
19.  Sometimes one just isn't enough: do vertebrates contain an H2A.Z hyper-variant? 
Journal of Biology  2010;9(1):3.
How much functional specialization can one component histone confer on a single nucleosome? The histone variant H2A.Z seems to be an extreme example. Genome-wide distribution maps show non-random (and evolutionarily conserved) patterns, with localized enrichment or depletion giving a tantalizing suggestion of function. Multiple post-translational modifications on the protein indicate further regulation. An additional layer of complexity has now been uncovered: the vertebrate form is actually encoded by two non-allelic genes that differ by expression pattern and three amino acids.
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PMCID: PMC2871525  PMID: 20092611
20.  The small protein floodgates are opening; now the functional analysis begins 
BMC Biology  2014;12(1):96.
Aside from a few serendipitous discoveries, small proteins of less than 50 amino acids in bacteria and 100 amino acids in eukaryotes were largely ignored due to challenges in their genetic and biochemical detection. However, with the ever-increasing availability of completed genome sequences and deep sequencing, which allows analysis of genome-wide ribosome occupancy, hundreds of small proteins are now being identified. This brings to the forefront the challenges and opportunities associated with the characterization of these proteins.
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PMCID: PMC4256750  PMID: 25475548
21.  Biological functions of natural antisense transcripts 
BMC Biology  2013;11:31.
In theory, the human genome is large enough to keep its roughly 20,000 genes well separated. In practice, genes are clustered; even more puzzling, in many cases both DNA strands of a protein coding gene are transcribed. The resulting natural antisense transcripts can be a blessing and curse, as many appreciate, or simply transcriptional trash, as others believe. Widespread evolutionary conservation, as recently demonstrated, is a good indicator for potential biological functions of natural antisense transcripts.
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PMCID: PMC3626547  PMID: 23577602
22.  Genome-wide association studies in Plasmodium species 
BMC Biology  2010;8:90.
Genome-wide association studies (GWAS) look for correlations between traits of interest and genetic markers spread throughout the genome. A recent study in BMC Genetics has found that populations of the malaria parasite Plasmodium vivax should be amenable to GWAS searching for a genetic basis of parasite pathogenicity. Geographical substructure in populations may, however, prove a problem in interpreting the results.
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PMCID: PMC2903549  PMID: 20646263
23.  Expanding networks of RNA virus evolution 
BMC Biology  2012;10:54.
In a recent BMC Evolutionary Biology article, Huiquan Liu and colleagues report two new genomes of double-stranded RNA (dsRNA) viruses from fungi and use these as a springboard to perform an extensive phylogenomic analysis of dsRNA viruses. The results support the old scenario of polyphyletic origin of dsRNA viruses from different groups of positive-strand RNA viruses and additionally reveal extensive horizontal gene transfer between diverse viruses consistent with the network-like rather than tree-like mode of viral evolution. Together with the unexpected discoveries of the first putative archaeal RNA virus and a RNA-DNA virus hybrid, this work shows that RNA viral genomics has major surprises to deliver.
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PMCID: PMC3379944  PMID: 22715894
24.  Tunicates push the limits of animal evo-devo 
BMC Biology  2011;9:3.
The phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated.
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PMCID: PMC3024270  PMID: 21251298
25.  A little bit is better than nothing: the incomplete parthenogenesis of salamanders, frogs and fish 
BMC Biology  2010;8:78.
A re-examination of the mitochondrial genomes of unisexual salamander lineages, published in BMC Evolutionary Biology, shows them to be the oldest unisexual vertebrates known, having been around for 5 million years. This presents a challenge to the prediction that lack of genetic recombination is a fast track to extinction.
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PMCID: PMC2914643  PMID: 20687905

Results 1-25 (734757)