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The mission of the Department of Neurobiology is to promote research and teaching that leads to a better understanding of the normal and diseased brain. The Department faculty are committed to training leaders of the next generation of neuroscientists, including graduate and medical students. Candidates for the Ph.D. in Neurobiology are admitted to the graduate Program in Neuroscience. This interdepartmental training program links the Department of Neurobiology with faculty in the Harvard affiliated hospitals and with faculty in other basic science departments. The Program, established in 1981, now includes about 90 investigators who participate in the training of Ph.D. candidates. Approximately fifteen students are accepted each year so that the steady state enrollment is usually about 80-90. This Program in Neuroscience attracts superb students with a broad range of interests from all areas of the globe. The goals of our training are to produce scientists who have explored one area and one level of analysis in great depth, but who are familiar with the full scope of neuroscience. They should be able to move from one level to another in a critical and creative manner. We also try to develop an appreciation for translational research that bears on human brain disease. The Department of Neurobiology, established in 1966 with Stephen W. Kuffler as Chair, was the first of its kind. The intent was to bring together members of traditional departments- physiologists, biochemists, and anatomists- in order to understand the principles governing communication between cells in the nervous system. This interdisciplinary approach was revolutionary at the time, and the interdisciplinary theme has continued to permeate the evolution of the field of neuroscience ever since. The Program in Neuroscience is one of four programs administered by the Division of Medical Sciences (DMS). DMS, located at the medical school, is a division of the Faculty of Arts and Sciences of Harvard University.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A searchable mutant database developed to provide access to relevant mutant information on pyridoxal-5'-phosphate dependent enzymes. All data have been extracted from publications and publicly available databases and organized to enable database searching. The database is a useful tool for planning mutant experiments and for interpretation of information from such experiments. PLPMDB includes mutation information from SWISS-PROT/TrEMBL, several web-based mutation data resources, and data extracted from the literature.

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• SciCrunch
• 16 years ago - by Anonymous

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• SciCrunch
• 16 years ago - by Anonymous

Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs.

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• SciCrunch
• 12 years ago - by Anonymous

Faculty of the Department of Neuroscience participate in the teaching of courses in the Interdisciplinary Program in Neuroscience and the School of Medicine. A Ph.D. in Neuroscience is offered through the Interdisciplinary Program in Neuroscience. Support for graduate training is offered through the Department, the research grants of individual faculty, as well as through three NIH training grants directed by Neuroscience faculty. * Training in Recovery of Function after CNS Injury. Program Director: Barbara S. Bregman, Ph.D. * Training Program in Drug Abuse. Program Director: Barbara S. Bayer, Ph.D. * Training in Neural Injury and Plasticity. Program Director: Jean R. Wrathall, Ph.D. Scientists in the Department of Neuroscience participate in a wide array of research activities with a focus on understanding both the normal and injured nervous system. The theme of neuroplasticity characterizes much of the research in the Department. We study neuroplasticity during normal development and in the adult in response to activity (e.g., learning) or drugs. Our research is also focused on studying the plasticity that ensues after traumatic (such as spinal cord injury) or ischemic damage to the nervous system and over the course of developmental or neurodegenerative diseases (such as Specific Language Impairment, autism, or Parkinson's and Alzheimer's Diseases). The specific research interests of each of the principal investigators falls under four broad subheadings: *CNS disorders ( Faden, Mocchetti, Rebeck, Riesenhuber,Ullman) *Cognitive/Computational (Riesenhuber, Ullman) *Development, Regeneration and recovery of function after injury (Bregman, Faden, Kromer, Ullman, Wrathall) *Neuroimmunology and Drugs of Abuse (Bayer, Faden, Kromer, Mocchetti) Under this common theme, a variety of diverse techniques and models are employed by the faculty. They range from molecular studies of gene function to studies on humans using Event-Related Potentials (ERPs) and functional MRI. Experimental models include cell culture systems, rodent genetic and experimental models of nervous system injury and disorders, as well as the use of computer simulations to understand higher cortical processing.

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• SciCrunch
• 17 years ago - by Anonymous

Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

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• SciCrunch
• 17 years ago - by Anonymous

An ontology that classifies algorithms available for the simulation of models in biology, their characteristics and the parameters required for their use.

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• SciCrunch
• 13 years ago - by Anonymous

A web service for fast microRNA-Seq data analysis in a GPU infrastructure.

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• SciCrunch
• 12 years ago - by Anonymous

Annotated, non-redundant database of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s) (TSS) from various plant species. It contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively (April 2014). This DB presents the published promoter sequences with TSS(s) determined by direct experimental approaches and therefore serves as the most accurate source for development of computational promoter prediction tools.

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• SciCrunch
• 17 years ago - by Anonymous

The Department of Pharmacology & Physiology at the George Washington University provides unique research opportunities at the predoctoral and postdoctoral levels. They also offer courses in Pharmacology and Physiology for Medical and Health Sciences students, as well as a number of graduate-level courses. Our mission is to provide the highest quality of educational opportunities to our community, and to advance scientific knowledge and improve human health through leading-edge research in the biomedical sciences.

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• SciCrunch
• 16 years ago - by Anonymous

A functional network for laboratory mouse based on integration of diverse genetic and genomic data. It allows the users to accurately predict novel functional assignments and network components. MouseNET uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the mouseNET algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. The graph may be explored further. As you move the mouse over genes in the network, interactions involving these genes are highlighted.If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed.

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• SciCrunch
• 17 years ago - by Anonymous

The Cognitive Neuroscience Program provides graduate students with an intense and focused research experience in the areas of perception, attention, and memory, with emphasis on the neural bases of these capacities. The program utilizes diverse research methods such as patient-based testing, neuro-imaging, animal modeling, and psychophysical scaling, and computational modeling. The goal of the program is to train students for careers in academic and research institutions. At the undergraduate level, the program provides both entry level and advanced courses as well as honor seminars in special topics. The program boasts a high faculty / student ratio, reflecting a strong emphasis on close collaboration between faculty and students on joint research projects. The Washington, DC research environment is outstanding, with the National Institutes of Health, Georgetown University, the University of Maryland, Johns Hopkins University, George Mason University, and other research institutions all close by. GWU's other resources for cognitive neuroscience research include a major medical school, a teaching hospital with world-class Neurology, Neurosurgery and Neuroradiology Departments, and an intensive Neuroscience Program. GWU is located in the heart of Washington, DC, a beautiful city with a wide variety of national museums, historical sites, restaurants, and cultural events. The Cognitive Neuroscience program at GW is designed to train students to become independent scientists who do basic research in an academic setting. Please note that ours is not a clinical neuropsychology program -- we provide no training in diagnosing or treating any brain or neurological disorder.

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• SciCrunch
• 17 years ago - by Anonymous

Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. Niftilib currently has C, Java, MATLAB, and Python libraries; we plan to add some MATLAB/mex interfaces to the C library in the not too distant future. Niftilib has been developed by members of the NIFTI DFWG and volunteers in the neuroimaging community and serves as a reference implementation of the nifti-1 file format. In addition to being a reference implementation, we hope it is also a useful i/o library. Niftilib code is released into the public domain, developers are encouraged to incorporate niftilib code into their applications, and, to contribute changes and enhancements to niftilib. Please contact us if you would like to contribute additonal functionality to the i/o library.

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• SciCrunch
• 14 years ago - by Anonymous

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• SciCrunch
• 14 years ago - submitted by Andrea Stagg

An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

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• SciCrunch
• 12 years ago - by Anonymous

A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF.

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• SciCrunch
• 17 years ago - by Anonymous

The Molecular and Systems Pharmacology graduate program at Emory University offers broad training in the biomedical sciences for students interested in learning how the drugs of today work and how the novel therapeutics of tomorrow can be developed. The Program offers a specialization in toxicology. Emory University was recently rated by The Scientist magazine as the number 1 university in the world in terms of impact in pharmacology and toxicology research. Particular strengths within the MSP graduate school program at Emory include neuropharmacology, cancer biology, AIDS research, cardiovascular pharmacology, toxicology, and chemical biology. Ph.D. training in the Emory MSP program provides students with an ideal preparation for successful careers in the biotechnology and pharmaceutical industries as well as in academic research, teaching, government research, patent law and other disciplines that depend upon knowledge of fundamental pharmacological principles.

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• SciCrunch
• 17 years ago - by Anonymous

Faculty members of our Department are actively engaged in delivering outstanding teaching to undergraduate students, graduate students, medical students, and residents. Our Doctor of Philosophy (graduate) students matriculate to Pharmacology through the Biomedical Sciences Graduate Program at the Quillen College of Medicine. Students pursuing Master of Science and Doctor of Philosophy degrees may pursue a focus in Toxicology. Our faculty members are trained in several medical disciplines and our research applies methodological approaches that span molecular biology, cellular biology, systems biology, and human biology and pathology. Through research, our department strives to understand human disease pathology and use this understanding to develop new therapeutic entities (e.g. drugs) for the treatment of major human diseases. The primary foci of department research efforts are cardiovascular and neuropsychiatric diseases, although other areas of interest and activity exist. Our laboratories are funded by the National Institutes of Health, American Heart Association, the American Foundation for Suicide Prevention and a variety of other agencies and sources.

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• SciCrunch
• 17 years ago - by Anonymous

An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied.

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• SciCrunch
• 13 years ago - by Anonymous