Error bars commonly appear in figures in publications, but experimental biologists are often unsure how they should be used and interpreted. In this article we illustrate some basic features of error bars and explain how they can help communicate…
Biological Sciences
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Choosing good problems is essential for being a good scientist. But what is a good problem, and how do you choose one? The subject is not usually discussed explicitly within our profession. Scientists are expected to be smart enough to figure it out…
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RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a…
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Ten years after the publication of the position paper The hallmarks of cancer (Hanahan and Weinberg Cell 100:5770, 2000), it has become increasingly clear that mutated cells on their way to giving rise to a tumor have also to learn how to thrive in…
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DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection. Over the past three years, massively parallel DNA sequencing platforms have become widely available,…
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We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is…
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We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from…
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Differentiated cells can be reprogrammed to an embryonic-like state by transfer of nuclear contents into oocytes or by fusion with embryonic stem (ES) cells. Little is known about factors that induce this reprogramming. Here, we demonstrate…
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Use of the real-time polymerase chain reaction (PCR) to amplify cDNA products reverse transcribed from mRNA is on the way to becoming a routine tool in molecular biology to study low abundance gene expression. Real-time PCR is easy to perform,…
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Using real-time reverse transcription PCR ten housekeeping genes from different abundance and functional classes in various human tissues were evaluated. The conventional use of a single gene for normalization leads to relatively large errors in a…
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Successful reprogramming of differentiated human somatic cells into a pluripotent state would allow creation of patient- and disease-specific stem cells. We previously reported generation of induced pluripotent stem (iPS) cells, capable of germline…
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The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human…
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MicroRNAs (miRNAs) are endogenous approximately 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs…
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10.1242/jcs.033340
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There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of…
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Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.
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In the last two decades, interest in species distribution models (SDMs) of plants and animals has grown dramatically. Recent advances in SDMs allow us to potentially forecast anthropogenic effects on patterns of biodiversity at different spatial…
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With the rise of new powerful statistical techniques and GIS tools, the development of predictive habitat distribution models has rapidly increased in ecology. Such models are static and probabilistic in nature, since they statistically relate the…
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We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence…
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The surface of nucleosomes is studded with a multiplicity of modifications. At least eight different classes have been characterized to date and many different sites have been identified for each class. Operationally, modifications function either…
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All the texts that should be read by everyone in biological sciences at least once! For everyone adding papers to the collection, it would help a… -
An open group to collect and discuss articles around the future of science, peer review, open access, and science 2.0 / 3.0 ideas. -
A collection on Science 2.0 and new forms of academic publishing.
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Some papers on data analysis methods, statistics. -
This is my own personal selection of recent papers in neuroscience that reflect big/important findings. I try to add articles monthly, and focus on…
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Ph.D. StudentUC Davis -
Post DocCancer Research Institute -
Ph.D. StudentLondon, United Kingdom -
ProfessorBio and Brain Engineering, KAIST -
Researcher (at an Academic Institution)School of Veterinary Medicine, Universidad de San Carlos de Guatemala