A5007788805- Protein Structure and Dynamics
- Immune Cell Function and Interaction
- Neurobiology and Insect Physiology Research
- Enzyme Structure and Function
- Retinal Development and Disorders
- Genomics and Chromatin Dynamics
- IL-33, ST2, and ILC Pathways
- T-cell and B-cell Immunology
- Bioinformatics and Genomic Networks
- Microbial Natural Products and Biosynthesis
- Plant Molecular Biology Research
- Insect and Arachnid Ecology and Behavior
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Eosinophilic Esophagitis
- Epigenetics and DNA Methylation
- Cancer Immunotherapy and Biomarkers
- Immunotherapy and Immune Responses
- Ferroptosis and cancer prognosis
- Photoreceptor and optogenetics research
- Cytokine Signaling Pathways and Interactions
- RNA Research and Splicing
- Plant and Biological Electrophysiology Studies
- Animal Behavior and Reproduction
Celsius Therapeutics (United States)
2022-2023
Janelia Research Campus
2010-2022
Howard Hughes Medical Institute
2011-2022
National Institute of Arthritis and Musculoskeletal and Skin Diseases
2015-2022
National Institutes of Health
2015-2021
Protein Express (United States)
2017
Helix (United States)
2007-2016
QB3
2005-2008
University of California, San Francisco
2004-2007
University of San Francisco
2007
The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct cell types the Drosophila visual system using genetic lines to access individual types, TAPIN-seq method measure transcriptomes, and a probabilistic interpret these measurements. We used tools build resource high-resolution transcriptomes for 100 driver covering 67 available at...
A significant proportion of colorectal cancer (CRC) patients develop peritoneal metastases (PM) in the course their disease. PMs are associated with a poor quality life, morbidity and dismal disease outcome. To improve care for this patient group, better understanding molecular characteristics CRC-PM is required. Here we present comprehensive characterization cohort 52 patients. This reveals that represent distinct CRC subtype, CMS4, but can be further divided three separate categories, each...
Motivation: In recent years, the Protein Data Bank (PDB) has experienced rapid growth. To maximize utility of high resolution protein–protein interaction data stored in PDB, we have developed PIBASE, a comprehensive relational database structurally defined interfaces between pairs protein domains. It is composed binary extracted from structures PDB and Probable Quaternary Structure server using domain assignments Structural Classification Proteins CATH fold classification systems. Results:...
Rod and cone photoreceptors are highly similar in many respects but they have important functional molecular differences. Here, we investigate genome-wide patterns of DNA methylation chromatin accessibility mouse rods cones correlate differences these features with gene expression, histone marks, transcription factor binding, sequence motifs. Loss NR2E3 shifts their epigenomes to a more cone-like state. The data further reveal wide between retinal brain neurons. Surprisingly, also find...
Many tools are available to analyse genomes but often challenging use in a cell type–specific context. We have developed method similar the isolation of nuclei tagged specific type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple for gene expression chromatin profiling individual types within tissue. Dev. Cell , 18 1030–1040; Steiner,F.A., Talbert,P.B., Kasinathan,S., Deal,R.B. (2012) Cell-type-specific purification from whole animals genome-wide profiling. Genome Res .,...
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence–structure alignment, model building and assessment (http:/salilab.org/modeller). currently contains 5 152 695 reliable domains in 1 593 209 unique sequences; only based statistically significant alignments and/or assessed to have the correct included. also...
Innate lymphoid cells (ILCs) patrol environmental interfaces to defend against infection and protect barrier integrity. Using a genetic tuning model, we demonstrate that the signal-dependent transcription factor (TF) STAT5 is critical for accumulation of all known ILC subsets in mice reveal hierarchy dependency populating nonlymphoid tissues. We apply transcriptome genomic distribution analyses define gene signature natural killer (NK) cells, prototypical subset, provide systems-based...
Pathogens have evolved numerous strategies to infect their hosts, while hosts immune responses and other defenses these foreign challenges. The vast majority of host-pathogen interactions involve protein-protein recognition, yet our current understanding is limited. Here, we present apply a computational whole-genome protocol that generates testable predictions protein interactions. first scans the host pathogen genomes for proteins with similarity known complexes, then assesses putative...
Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during animal development. Despite decades of study, we know little about the dynamics or order events animating TF at cis-regulatory elements in living cells and long-range molecular "dialog" between enhancers promoters. Here, combining genetic, genomic, imaging approaches, characterize complex enhancer cluster governing Krüppel-like 4...
Activated lymphocytes adapt their metabolism to meet the energetic and biosynthetic demands imposed by rapid growth proliferation. Common gamma chain (cγ) family cytokines are central these processes, but role of downstream signal transducer activator transcription 5 (STAT5) signaling, which is engaged all cγ members, poorly understood. Using genome-, transcriptome-, metabolome-wide analyses, we demonstrate that STAT5 a master regulator energy amino acid in CD4 + T helper cells....
The insect mushroom body (MB) is a conserved brain structure that plays key roles in diverse array of behaviors. Drosophila melanogaster MB the primary invertebrate model neural circuits related to memory formation and storage, its development, morphology, wiring, function has been extensively studied. MBs consist intrinsic Kenyon Cells are divided into three major neuron classes (γ, α'/β' α/β) 7 cell subtypes (γd, γm, α'/β'ap, α'/β'm, α/βp, α/βs α/βc) based on their birth order,...
Living in a social environment requires the ability to respond specific stimuli and incorporate information obtained from prior interactions into future ones. One of mechanisms that facilitates interaction is pheromone-based communication. In Drosophila melanogaster, male-specific pheromone cis-vaccenyl acetate (cVA) elicits different responses male female flies, functions modulate behavior context experience-dependent manner. Although it most studied determine complexity response, its...
Efforts to understand nervous system structure and function have received new impetus from the federal Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Comparative analyses can contribute this effort by leading discovery of general principles neural circuit design, information processing, gene-structure-function relationships that are not apparent studies on single species. We here propose extend comparative approach ‘maps' comprising molecular, anatomical,...
Proteins function through interactions with other molecules. Thus, the network of physical among proteins is great interest to both experimental and computational biologists. Here we present structure-based predictions 3387 binary 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 195 proteins, respectively. To generate candidate complexes, comparative models individual were built combined together using known structure as templates. These then assessed a...