Filter
Associated Lab
- Ahrens Lab (2) Apply Ahrens Lab filter
- Aso Lab (1) Apply Aso Lab filter
- Baker Lab (2) Apply Baker Lab filter
- Betzig Lab (4) Apply Betzig Lab filter
- Bock Lab (2) Apply Bock Lab filter
- Cardona Lab (1) Apply Cardona Lab filter
- Cui Lab (2) Apply Cui Lab filter
- Dickson Lab (1) Apply Dickson Lab filter
- Druckmann Lab (1) Apply Druckmann Lab filter
- Dudman Lab (2) Apply Dudman Lab filter
- Eddy/Rivas Lab (2) Apply Eddy/Rivas Lab filter
- Egnor Lab (1) Apply Egnor Lab filter
- Fetter Lab (3) Apply Fetter Lab filter
- Gonen Lab (9) Apply Gonen Lab filter
- Grigorieff Lab (1) Apply Grigorieff Lab filter
- Harris Lab (3) Apply Harris Lab filter
- Heberlein Lab (1) Apply Heberlein Lab filter
- Hess Lab (2) Apply Hess Lab filter
- Jayaraman Lab (3) Apply Jayaraman Lab filter
- Ji Lab (1) Apply Ji Lab filter
- Karpova Lab (1) Apply Karpova Lab filter
- Keller Lab (9) Apply Keller Lab filter
- Lavis Lab (4) Apply Lavis Lab filter
- Leonardo Lab (3) Apply Leonardo Lab filter
- Looger Lab (10) Apply Looger Lab filter
- Magee Lab (3) Apply Magee Lab filter
- Menon Lab (3) Apply Menon Lab filter
- Reiser Lab (1) Apply Reiser Lab filter
- Riddiford Lab (5) Apply Riddiford Lab filter
- Rubin Lab (5) Apply Rubin Lab filter
- Scheffer Lab (3) Apply Scheffer Lab filter
- Schreiter Lab (5) Apply Schreiter Lab filter
- Spruston Lab (2) Apply Spruston Lab filter
- Stern Lab (5) Apply Stern Lab filter
- Sternson Lab (3) Apply Sternson Lab filter
- Svoboda Lab (10) Apply Svoboda Lab filter
- Tjian Lab (1) Apply Tjian Lab filter
- Truman Lab (3) Apply Truman Lab filter
- Wu Lab (3) Apply Wu Lab filter
- Zlatic Lab (2) Apply Zlatic Lab filter
Associated Project Team
Associated Support Team
Publication Date
- December 2013 (7) Apply December 2013 filter
- November 2013 (10) Apply November 2013 filter
- October 2013 (16) Apply October 2013 filter
- September 2013 (14) Apply September 2013 filter
- August 2013 (11) Apply August 2013 filter
- July 2013 (13) Apply July 2013 filter
- June 2013 (13) Apply June 2013 filter
- May 2013 (5) Apply May 2013 filter
- April 2013 (9) Apply April 2013 filter
- March 2013 (9) Apply March 2013 filter
- February 2013 (9) Apply February 2013 filter
- January 2013 (20) Apply January 2013 filter
- Remove 2013 filter 2013
136 Janelia Publications
Showing 131-136 of 136 resultsThe Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license.
Chemical fluorophores find wide use in biology to detect and visualize different phenomena. A key advantage of small-molecule dyes is the ability to construct compounds where fluorescence is activated by chemical or biochemical processes. Fluorogenic molecules, in which fluorescence is activated by enzymatic activity, light, or environmental changes, enable advanced bioassays and sophisticated imaging experiments. Here, we detail the collection of fluorophores and highlight both general strategies and unique approaches that are employed to control fluorescence using chemistry.
A number of atomic-resolution structures of membrane proteins (better than 3Å resolution) have been determined recently by electron crystallography. While this technique was established more than 40 years ago, it is still in its infancy with regard to the two-dimensional (2D) crystallization, data collection, data analysis, and protein structure determination. In terms of data collection, electron crystallography encompasses both image acquisition and electron diffraction data collection. Other chapters in this volume outline protocols for image collection and analysis. This chapter, however, outlines detailed protocols for data collection by electron diffraction. These include microscope setup, electron diffraction data collection, and troubleshooting.
We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron microscopy image stacks, but for time-series and multi-channel data as well. The system was designed primarily for workloads that build connectomes- neural connectivity maps of the brain-using the parallel execution of computer vision algorithms on high-performance compute clusters. These services and open-science data sets are publicly available at openconnecto.me. The system design inherits much from NoSQL scale-out and data-intensive computing architectures. We distribute data to cluster nodes by partitioning a spatial index. We direct I/O to different systems-reads to parallel disk arrays and writes to solid-state storage-to avoid I/O interference and maximize throughput. All programming interfaces are RESTful Web services, which are simple and stateless, improving scalability and usability. We include a performance evaluation of the production system, highlighting the effec-tiveness of spatial data organization.
The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (\~{}5%) of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of \~{}2,000 copies. We report the high-quality genome assembly of \~{}16,000 complete nanochromosomes (\~{}50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean \~{}3.2 kb) and encode \~{}18,500 genes. Alternative DNA fragmentation processes \~{}10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is \~{}4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.