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The Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST. Consequently, GST student projects are quite diverse, as indicated by the five themes spelled out below. Themes * Molecular Genetics and Systems Biology * Computational Molecular Biophysics * Structural and Nanoscale Biology * Bioinformatics * Analytical Technologies for Bioenergy and the Environment While some students work on projects that are primarily computational, many other students focus their experimental work at the bench. Increasingly, both types of students are realizing the growing need for work at both the theoretical/computational level and at the practical experimental level. This is the nature of most modern interdisciplinary research. Because individual research groups are generally small, there is much opportunity for interaction between groups employing different experimental or computational strategies. A hallmark of the GST Program is its involvement of faculty from two distinct research environmentsthe University of Tennessee, Knoxville, (UTK) and Oak Ridge National Laboratory (ORNL). The program is enriched by the different research philosophies encountered at a university, emphasizing autonomy, and at a National Lab, emphasizing team effort. Researchers at the two campuses have access to a wide range of research tools and facilities including: * High-field NMR spectroscopy * X-ray crystallography * Mass spectroscopy * Next generation sequencing * Molecular modeling and supercomputing The program is designed to educate PhD-level scientists who are equipped to tackle the complex world of biology using modern technologies. A Master's track is also available for some students. The GST curriculum lays a firm foundation in molecular genetics, biochemistry, and bioinformatics, followed by specialization in the area of the student's dissertation research. GST welcomes students with a solid undergraduate academic background in biological sciences, physical sciences, or computational sciences. New NSF Fellowships Available for Students in Computational Biology.

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• SciCrunch
• 14 years ago - by Anonymous

A multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression. It is our hope that the overall study results will improve the future care of adolescents with depression. This study has been completed. TADS is designed to compare the effectiveness of established treatments for teenagers suffering from major depressive disorder (MDD). The treatments are: psychotherapy (talking therapy); medication; and the combination of psychotherapy and medication. Altogether, 432 teenagers (both males and females) ages 12 to 17, will take part in this study at 12 sites in the United States. The TADS design will provide answers to the following questions: What is the long-term effectiveness of medication treatment of teenagers who have major depression? What is the long-term effectiveness of a specific psychotherapy (talking therapy) in the treatment of teenagers who have major depression? How does medication treatment compare with psychotherapy in terms of effectiveness, tolerability and teenager and family acceptance? And, What is the cost-effectiveness of medication, psychotherapy and combined treatments? The medication being used in this study is called fluoxetine. Fluoxetine is also known as Prozac. Research has shown that medications like Prozac help depression in young persons. Fluoxetine has been approved by the FDA for use in the treatment of child and adolescent (ages 7 to 17 years) depression. The psychotherapy or talking therapy being used in this study is called Cognitive Behavioral Therapy (CBT). CBT is a talking therapy that will teach both the teenager and his or her family member (e.g., parent) new skills to cope better with depression. Specific topics include education about depression and the causes of depression, setting goals, monitoring mood, increasing pleasant activities, social problem-solving, correcting negative thinking, negotiation, compromise and assertiveness. CBT sessions may also help with resolving disagreements as they affect families. For more information see, http://www.clinicaltrials.gov/ct/show/NCT00006286?order=1 and http://www.nimh.nih.gov/trials/practical/tads/index.shtml

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• SciCrunch
• 14 years ago - by Anonymous

Manuals for R created on Debian Linux that can be downloaded as PDF files, EPUB files (for R-devel and R-patched), or directly browsed as HTML. They may differ from the manuals for Mac or Windows on platform-specific pages, but most parts will be identical for all platforms.

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• SciCrunch
• 12 years ago - by Anonymous

A variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools.

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• SciCrunch
• 13 years ago - by Anonymous

Multi-channel data acquisition software.

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• SciCrunch
• 11 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This website contains a database of the mouse SNP. DNA sequencing was performed along with genotyping. There is information on genotyping, mouse strain, and haplotype map.

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• SciCrunch
• 13 years ago - by Anonymous

Software used to characterize the mappability of RNA-Seq reads and create a blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls.

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• SciCrunch
• 12 years ago - by Anonymous

An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

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• SciCrunch
• 11 years ago - by Anonymous

A software package that provides functions to read raw RT-qPCR data of different platforms.

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• SciCrunch
• 11 years ago - by Anonymous

Software Python package for analyzing diffusion data.

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• SciCrunch
• 12 years ago - by Anonymous

A support vector machine for calling variants from next-gen sequencing data. It takes as input a BAM-formatted alignment of sequencing reads, and emits a VCF formatted file describing where all the SNPs (single nucleotide polymorphisms) are.

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• SciCrunch
• 11 years ago - by Anonymous

An online community and information portal that aims to inspire connections, clinical advances and accelerate progress toward multiple sclerosis cures. MSDF updates its site with news and information about topics relevant to multiple sclerosis and hosts discussions about controversial subjects with the goal of spreading information and enabling collaboration between researchers. MSDF provides access to drug development pipelines, tissue repositories, the MS gene, animal models, and clinical trials.

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• SciCrunch
• 12 years ago - by Anonymous

The Epilepsy Foundation of America is the national voluntary agency dedicated solely to the welfare of the almost 3 million people with epilepsy in the U.S. and their families. The organization works to ensure that people with seizures are able to participate in all life experiences; to improve how people with epilepsy are perceived, accepted and valued in society; and to promote research for a cure. :Typical of the Foundations national programs are its Jeanne A. Carpenter Epilepsy Legal Defense Fund, the H.O.P.E. (Helping Other People with Epilepsy) Mentoring Program, a Public Policy Institute, Seniors and Womens Health Initiatives, the Kids Speak Up advocacy program, a school personnel training program, outreach to youth and to the Hispanic community, employment programs and a research grants program. Services commonly provided in local communities are information and referral, counseling, patient and family advocacy, school and community education, support groups and camps for children. Its Web site offers the most comprehensive, medically approved consumer information about epilepsy and seizures on the Internet and is the trusted source for millions of people who seek reliable information about epilepsy. : Each year the Foundation also invites research investigators to apply for grants and fellowships to test new ideas and follow new research leads. The applications, more than a hundred in an average year, are ranked according to merit by a blue ribbon panel of research scientists, and funded according to available resources. Additionally, the Epilepsy Foundation offers a series of training fellowships in basic, clinical and behavioral science to scientists at the start of their careers. These fellowships, awarded to young people at the nation's leading research institutes, have in many cases been the first steps on a lifetime commitment to solving the medical and scientific puzzle of why epilepsy develops and how it can be treated or prevented. Specifically, the Gowers Fellowship is awarded annually to a physician/scientist who is embarking on a career in academic clinical medicine and who wishes to undertake a specific project in epilepsy research. Sponsors: The Epilepsy Foundation is funded primarily through individual donations from the general public and receives restricted grant support from the federal government, foundations and private industry.

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• SciCrunch
• 16 years ago - by Anonymous

Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

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• SciCrunch
• 12 years ago - by Anonymous

An organization which offers services in peptide synthesis, peptide modification, purification and quality analysis, N-terminal protein sequencing by Edman degradation, biomolecular interaction analysis and equilibrium and kinetic measurements.

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• SciCrunch
• 13 years ago - by Anonymous

A haplotype inference program.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 10, 2016. A consortium that created universal descriptors to describe functionally similar gene products and their attributes across all organisms. In 2004, the PAMGO interest group joined the GO consortium to extend the GO to include terms describing various processes related to microbe-host interactions. The organization uses a controlled vocabulary to set a process in place to describe plant associated microbes and their interactions with their plant-hosts. These higher order terms can describe gene products of all types of symbionts (e.g. parasites, commensals, and mutualists), including prokaryotes and eukaryotes that associate with plant or animal hosts. This initiative is a multi-institutional collaborative effort to pool information and research in: the bacteria Dickeya dadantii, Pseudomonas syringae pv tomato and Agrobacterium tumefaciens, the fungus Magnaporthe grisea, the oomycetes Phytophthora sojae and Phytophthora ramorum, and the nematode Meloidogyne hapla.

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• SciCrunch
• 15 years ago - by Anonymous

A collection of podcasts which features experts of the Montreal Neurological Institute and Hospital talking about their research, along with important issues and current events regarding it.

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• SciCrunch
• 15 years ago - by Anonymous

The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project.

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• SciCrunch
• 14 years ago - by Anonymous

Steve Silberman's personal blog highlighting science, culture, politics and neurodiversity. Steve is an investigative reporter for Wired and other national magazines.

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• SciCrunch
• 15 years ago - by Anonymous