Gene Expression

Biochemistry 118

Sophomore Seminar

FISH

Genomics & Medicine

Doug Brutlag

Gene Expression and Cancer Diagnostics

Lecture Rerources on Gene Expression

Gene Expression Slides

Programs for finding Transcription Factor Binding Sites

Bioprospector

MDScan

CompareProspector

MotifCut

Melina II

WebMotif

Papers on diagnosing Breast Cancer using Gene Expression MicroArrays

Sorlie et al PNAS 2001 PNAS September 11, 2001 vol. 98 page 10871

Lonning et al. Endocrine-Related Cancer (2001) 8 259-263

The ENCODE Project

ENCODE: The human encyclopedia

Nature ENCODE explorer
A series of coordinated scientific reports published in the Nature, Sept. 5, 2012 online issue
NHGRI to host symposium on model organism Encyclopedia of DNA Elements project
June 20-21, 2012
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
PLoS Biology, April 19, 2011
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Nature, June 13, 2007
ENCODE Web Focus
Related articles on ENCODE from Nature, June 2007
Special Issue on ENCODE from Genome Research
June 2007
The ENCODE (ENCylopedia Of DNA Elements) Project. [sciencemag.org] (Full Text)
Science, Vol. 306, Issue 5696, 636-640, 22 October 2004.

ENCODE RFAs Expand Effort to Understand the Genome
October 5, 2011
Funding Now Available for Technology Development to Catalog and Analyze Function of Genomes
May 25, 2011
New user's guide and tutorial helps disease researchers interpret human genome
April 19, 2011

Recent Literature on Gene Expression Profiles and Disease

Web Resources

Affymetrix

Arrayit Corporation

Biocarta Cell Signaling Pathways

miRBASE

miRNA Target Database MicroCom

PathWork Diagnostics

miRBase: http://www.mirbase.org/

MicroCosm: http://www.ebi.ac.uk/enright-srv/microcosm/

miRNAminer: http://groups.csail.mit.edu/pag/mirnaminer

miRviewer: http://people.csail.mit.edu/akiezun/miRviewer

Patrocles: http://www.patrocles.org/

TargetRank: http://hollywood.mit.edu/targetrank

TargetScanS: http://www.targetscan.org

Lectures only available to Stanford Students

Henry Stewart Talks

Accessing and Using ENCODE Data (44 mins) Prof. Peggy Farnham – University of California in Davis, USA

The basal transcription machinery for RNA polymerase II (42 mins) Prof. H. T. Marc Timmers – University of Utrecht, the Netherlands

Genome-wide organization of chromatin and the transcription machinery (48 mins) Prof. Frank Pugh – Pennsylvania State University

The Myc transcription factor network (47 mins) Prof. Robert N. Eisenman – Fred Hutchinson Cancer Research Center, USA

Role of polycomb proteins in gene transcription, stem cell and human diseases Prof. Luciano Di Croce – Center for Genomic Regulation

Heterochromatin, epigenetics and gene expression (51 mins) Prof. Joel C. Eissenberg – Saint Louis University, USA

Histone dynamics, heritability and variants (38 mins) Dr. Genevieve Almouzni – Curie Institute/CNRS, France

Enhancer malfunction in cancer (41 mins) Dr. Ali Shilatifard – Stowers Institute, USA

Genetic variation in gene regulation - Prof. Jonathan Pritchard

Medical Grand Rounds

Roger Kornberg, Professor of Structural Biology, Nobel Laureate - Transcription in Development and Disease

Mark Pegram, Prof. of Medicine – Therapeutic strategies targeting ERBB2

Hanlee Ji, Stanford Oncology – The Genetics of Personalized Cancer Medicine

Ross Levine, Professor of Medicine, Weill Cornell - –Genetics and therapy of Acute Myeloid Leukemia

Steve Coutre, Chief Resident, Stanford Department of Medicine–Chronic Lymphatic Leukemia: Do we have a cure?

Marc Lipman, University of Miami - Will we ever cure Breast Cancer?