Papers

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…

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…

Insights into conducting research and the writing of scientific papers are given by Prof. Whitesides in this short essay. The manuscript and its guidelines has been circulated within the Whitesides' research group since 1989.

This paper describes the process of inducting theory using case studies-from specifying the research questions to reaching closure. Some features of the process, such as problem definition and construct validation, are similar to hypothesis-testing…

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…

We are developing a dual panel breast-dedicated PET system using LSO scintillators coupled to position sensitive avalanche photodiodes (PSAPD). The charge output is amplified and read using NOVA RENA-3 ASICs. This paper shows that the coincidence…

MapReduce is a programming model and an associated implementation for processing and generating large datasets that is amenable to a broad variety of real-world tasks. Users specify the computation in terms of a map and a reduce function, and the…

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…

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…

In this article, we attempt to distinguish between the properties of moderator and mediator variables at a number of levels. First, we seek to make theorists and researchers aware of the importance of not using the terms moderator and mediator…

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,…

Functional magnetic resonance imaging (fMRI) is currently the mainstay of neuroimaging in cognitive neuroscience. Advances in scanner technology, image acquisition protocols, experimental design, and analysis methods promise to push forward fMRI…

In this review, recent developments in the fabrication and understanding of the electronic properties of graphene nanostructures are discussed. After a brief overview of the structure of graphene and the two-dimensional transport properties, the…

In this paper, we present Google, a prototype of a large-scale search engine which makes heavy use of the structure present in hypertext. Google is designed to crawl and index the Web efficiently and produce much more satisfying search results than…

Graphene is a rapidly rising star on the horizon of materials science and condensed-matter physics. This strictly two-dimensional material exhibits exceptionally high crystal and electronic quality, and, despite its short history, has already…

10.1242/jcs.033340

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…

In the course of the routine use of NMR as an aid for organic chemistry, a day-to-day problem is the identifica- tion of signals deriving from common contaminants (water, solvents, stabilizers, oils) in less-than-analyti- cally-pure samples. This…

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…

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…

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…

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…

Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.

This paper describes the process of inducting theory using case studies-from specifying the research questions to reaching closure. Some features of the process, such as problem definition and construct validation, are similar to hypothesis-testing…

Functional magnetic resonance imaging (fMRI) is currently the mainstay of neuroimaging in cognitive neuroscience. Advances in scanner technology, image acquisition protocols, experimental design, and analysis methods promise to push forward fMRI…

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…

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…

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…

Identifying and quantifying planetary boundaries that must not be transgressed could help prevent human activities from causing unacceptable environmental change, argue Johan Rockström and colleagues.

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…

We propose a multivariate approach to the study of geographic species dis- tribution which does not require absence data. Building on Hutchinsons concept of the ecological niche, this factor analysis compares, in the multidimensional space of…

In the course of the routine use of NMR as an aid for organic chemistry, a day-to-day problem is the identifica- tion of signals deriving from common contaminants (water, solvents, stabilizers, oils) in less-than-analyti- cally-pure samples. This…

MapReduce is a programming model and an associated implementation for processing and generating large datasets that is amenable to a broad variety of real-world tasks. Users specify the computation in terms of a map and a reduce function, and the…

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…

In this review, recent developments in the fabrication and understanding of the electronic properties of graphene nanostructures are discussed. After a brief overview of the structure of graphene and the two-dimensional transport properties, the…

The Conjugate Gradient Method is the most prominent iterative method for solving sparse systems of linear equations. Unfortunately, many textbook treatments of the topic are written with neither illustrations nor intuition, and their victims can be…

Generalized gradient approximations (GGA's) for the exchange-correlation energy improve upon the local spin density (LSD) description of atoms, molecules, and solids. We present a simple derivation of a simple GGA, in which all parameters (other…

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,…

The field of self-assembled monolayers (SAMs) has witnessed tremendous growth in synthetic sophisti- cation and depth of characterization over the past 15 years.1 However, it is interesting to comment on the modest beginning and on important…

We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly precipitation and mean, minimum,…