Jody Clements
A5084167899- Neurobiology and Insect Physiology Research
- Cancer Genomics and Diagnostics
- Insect and Arachnid Ecology and Behavior
- Glioma Diagnosis and Treatment
- Cell Image Analysis Techniques
- Genomics and Phylogenetic Studies
- Neuroinflammation and Neurodegeneration Mechanisms
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- MicroRNA in disease regulation
- Neural dynamics and brain function
- Genetic factors in colorectal cancer
- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- Circular RNAs in diseases
- Lung Cancer Treatments and Mutations
- Advanced Fluorescence Microscopy Techniques
- RNA modifications and cancer
- Genetics, Aging, and Longevity in Model Organisms
- Electron and X-Ray Spectroscopy Techniques
- Neurogenesis and neuroplasticity mechanisms
- Advanced Electron Microscopy Techniques and Applications
- Genomics and Rare Diseases
- Plant and Biological Electrophysiology Studies
- Cancer-related molecular mechanisms research
Janelia Research Campus
2015-2025
Howard Hughes Medical Institute
2016-2025
Helix (United States)
2015-2024
University of British Columbia
2022-2023
Wellcome Sanger Institute
2005-2013
European Bioinformatics Institute
2013
Science for Life Laboratory
2013
Genetic Information Research Institute
2012
Institute for Systems Biology
2012
Wellcome Trust
2004-2008
Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries current release, version 27.0. Since last update article 2 years ago, we have generated 1182 new families maintained sequence coverage UniProt Knowledgebase (UniProtKB) at nearly 80%, despite 50% increase size underlying database. our 2012 describing also undertaken comprehensive review features that...
HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, has mainly been available only as computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted 100-fold speed gain relative to previous versions. It now feasible make efficient profile hidden Markov model (profile HMM) via web. A web server ( http://hmmer.janelia.org ) designed and implemented such that most database...
Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated families as release 26.0. available via servers in the UK (http://pfam.sanger.ac.uk/), USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over last 2 years, generated 1840 new increased coverage UniProt Knowledgebase (UniProtKB) to nearly 80%. Notably, taken step opening up annotation...
The discovery of mutations in cancer genes has advanced our understanding cancer. These results are dispersed across the scientific literature and with availability human genome sequence will continue to accrue. COSMIC (Catalogue Somatic Mutations Cancer) database website have been developed store somatic mutation data a single location display other information related To populate this resource, currently extracted from reports for four genes, BRAF, HRAS, KRAS2 NRAS. At present, holds on 66...
The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in software suite. Since first release of website 2011, repertoire has been expanded include iterative algorithm, jackhmmer. continued growth target sequence databases means that traditional tabular representations significant hits can be overwhelming user. Consequently, additional ways presenting results have developed, allowing them summarised according...
Abstract COSMIC is currently the most comprehensive global resource for information on somatic mutations in human cancer, combining curation of scientific literature with tumor resequencing data from Cancer Genome Project at Sanger Institute, U.K. Almost 4800 genes and 250000 tumors have been examined, resulting over 50000 available investigation. This can be accessed a number ways, convenient being Web‐based system which allows detailed mining, presenting results easily interpretable...
Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database families repetitive DNA elements, in which each family represented by multiple sequence alignment and profile hidden Markov model (HMM). The initial release Dfam, featured the 2013 NAR Database Issue, contained 1143 found humans, was used produce more than 100 Mb additional annotation TE-derived regions human genome, with improved speed. Here, we...
Abstract Protein kinases are frequently mutated in human cancer and inhibitors of mutant protein have proven to be effective anticancer drugs. We screened the coding sequences 518 (∼1.3 Mb DNA per sample) for somatic mutations 26 primary lung neoplasms seven cell lines. One hundred eighty-eight were detected 141 genes. Of these, 35 synonymous (silent) changes. This result indicates that most 188 “passenger” not causally implicated oncogenesis. However, an excess ∼40 nonsynonymous...
Abstract The panel of 60 human cancer cell lines (the NCI-60) assembled by the National Cancer Institute for anticancer drug discovery is a widely used resource. NCI-60 has been characterized pharmacologically and at molecular level more extensively than any other set lines. However, no systematic mutation analysis genes causally implicated in oncogenesis reported. This study reports sequence 24 known an assessment 4 homozygous deletions. One hundred thirty-seven oncogenic mutations were...
Abstract Malignant gliomas have a very poor prognosis. The current standard of care for these cancers consists extended adjuvant treatment with the alkylating agent temozolomide after surgical resection and radiotherapy. Although statistically significant increase in survival has been reported this regimen, nearly all recur become insensitive to further class agents. We sequenced 500 kb genomic DNA corresponding kinase domains 518 protein kinases each nine gliomas. Large numbers somatic...
Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern set sequences. They render information contained sequence alignments or profile hidden Markov models by drawing stack letters for each position, where height corresponds at that and letter within depends on frequency position.We present new tool web server, called Skylign, which provides unified framework creating logos both models. In addition static image files, Skylign...
We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain large fraction DNA, much which is made up remnants transposable elements (TEs). Accurate annotation TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification masking also greatly simplify many downstream genome sequence analysis tasks. The commonly used TE tools RepeatMasker Censor depend homology search such as...
Abstract The neural circuits responsible for behavior remain largely unknown. Previous efforts have reconstructed the complete of small animals, with hundreds neurons, and selected larger animals. Here we (the FlyEM project at Janelia collaborators Google) summarize new methods present circuitry a large fraction brain much more complex animal, fruit fly Drosophila melanogaster . Improved include procedures to prepare, image, align, segment, find synapses, proofread such data sets; that...
Due to advances in electron microscopy and deep learning, it is now practical reconstruct a connectome, description of neurons the chemical synapses between them, for significant volumes neural tissue. Smaller past reconstructions were primarily used by domain experts, could be handled downloading data, performance was not serious problem. But new much larger upend these assumptions. These networks contain tens thousands millions connections, with yet pending, are interest large community...
Precise, repeatable genetic access to specific neurons via GAL4/UAS and related methods is a key advantage of
Abstract Animal behavior is principally expressed through neural control of muscles. Therefore understanding how the brain controls requires mapping neuronal circuits all way to motor neurons. We have previously established technology collect large-volume electron microscopy data sets tissue and fully reconstruct morphology neurons their chemical synaptic connections throughout volume. Using these tools we generated a dense wiring diagram, or connectome, for large portion Drosophila central...
Abstract Background Neuroscience research in Drosophila is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons a brain and their connections. To exploit this knowledge base, researchers relate connectome’s structure neuronal function, often by studying individual neuron cell types. Vast libraries of fly driver lines expressing fluorescent reporter genes sets have been created imaged confocal light (LM), enabling targeting for...
Animal behavior is principally expressed through neural control of muscles. Therefore understanding how the brain controls requires mapping neuronal circuits all way to motor neurons. We have previously established technology collect large-volume electron microscopy data sets tissue and fully reconstruct morphology neurons their chemical synaptic connections throughout volume. Using these tools we generated a dense wiring diagram, or connectome, for large portion Drosophila central brain....
Vision provides animals with detailed information about their surroundings, conveying diverse features such as color, form, and movement across the visual scene. Computing these parallel spatial requires a large network of neurons, that in distant flies humans, regions comprise half brain's volume. These brain often reveal remarkable structure-function relationships, neurons organized along maps shapes directly relate to roles processing. To unravel stunning diversity complex system, careful...
Abstract Vision provides animals with detailed information about their surroundings and conveys diverse features such as colour, form movement across the visual scene. Computing these parallel spatial requires a large network of neurons. Consequently, from flies to humans, regions in brain constitute half its volume. These often have marked structure–function relationships, neurons organized along maps shapes that directly relate roles processing. More than century anatomical studies...