Links

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Biomedical Research Tools and Links:


Basic Tools

Enztrez PubMed gateway site

Canadian Bioinformatics Links

Bioinformatics Toolkit--lots of good links

ISI Web of Knowledge

Scopus

NEBCutter 2.0


Genomics web research tools

NGS depth needed for coverage by application (Genohub)

Immunological Genome Project

ENSEMBL genome browser

MGI databank

UC Davis knockout mouse repository (KOMP)

UCSC genome site ("The Golden Path")


Bioinformatics links

Genevestigator

GO Elite

GO Miner (NCI)

PANTHER classification system

Genomic Regions Enrichment of Annotations Tool (GREAT) (Stanford)

DAVID Bioinformatics Resources (NIH/NIAID)

BEDTools

GeneMANIA

iHOP information hyperlinked over proteins

Human Mutation Database (must register)

MEME (SDSC)

The Gibbs Motif Sampler (Brown University)

PipMaker

GSEA: Gene Set Enrichment Analysis

TCGA Tumorscape (Broad Institute)

OncoLnc - quick analysis of TCGA survival data

cBioPortal for Cancer Genomics

Xena Functional Genomics Explorer

Kaplan-Meier Plotter

SEER database

Oncomine (registration required)

BIC (Breast Cancer Information Core, password required)


Expression/developmental web pages

GenePaint

The GTEx Portal

Emouse Atlas


Motif/domain/target site identification pages

Scansite

WebLogo (Berkeley)

NetPhos

Pfam HMM motif seach

ELM Eukaryotic linear motif resource

Superfamily sequence search

CombFunc protein function prediction server

Phyre protein homology/fold prediction

Make a Pictogram

BioVenn

Targetscan


Protein domain/proteomics pages

Protein sequence analysis page at Pasteur (includes PESTfind)

RCSB PDB protein data bank

ExPASy Proteomics Server

UCSF ProteinProspector


Gene regulation pages

TESS (Transcription Element Search System) at U Penn

JASPAR TF binding site profiles

BIOBASE (contains TRANSFAC and PROTEOME, no longer free)

lncRNA database


Ig, TCR, MHC

IMGT Homepage

Immgen database


Sequence alignment

LALIGN server

ClustalW

BOXSHADE

MethPrimer (UCSF)


Database homology searches

BLAST

BLAT


Mouse models

KOMP Repository (UC Davis)

Mouse Models of Human Cancers Consortium

IGTC

Bay Genomics

Jax Mouse Model Database

Taconic Mouse Model Database

Charles River Mouse Models


University of Utah Links

Campus Directory

Pathology Home Page

Cell Biology & Immunology

Pathology R.I.P. + J.C.

Bioscience Calendar

Pathology Event Calendar

Freezer Monitoring (use Firefox)

Canvas

Mission-Based Management

Utah CIS

HSC Core Facilities

Sendit (for file transfers)

Utah Lab Scheduler Version 1

Molecular Biology Graduate Program

MD/PhD Combined Program

University of Utah List Service

Live Shuttle Tracking Map


External Links

ERA Commons

RePORT Expenditures and Results (RePORTER) query tool

Study Section Roster (N.I.H.)

ART - Assisted Referral Tool

Accent Codes for Mac (PSU)

huntsman cancer institute logo

Contact Us

Dean Tantin
Associate Professor
Department of Pathology
University of Utah School of Medicine

Huntsman Cancer Institute
2000 Circle of Hope, Research South
Room 3707 (LL376 for courier service)
Salt Lake City, UT 84112-5550

Lab Phone: 801-587-3802
Office Phone: 801-587-3035
Email Address: dean.tantin [@] path.utah.edu

Lab administrative contact:
Email: Ryan.Tuohy@hci.utah.edu
Phone: 801-213-5767

Lab manager:
Email: zuolian.shen@path.utah.edu
Phone: 801-587-3802