Biochemistry 158/258

FISH

Genomics, Bioinformatics & Medicine

Doug Brutlag

Gene Expression and Cancer Diagnostics

Lectures on Gene Expression

Gene Expression Slides

Gene Expression Lecture Video

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

Hanlee, Ji, Lee et al, BMC Medical Genomics 2013, vol 6, 54.

 

Recent Literature on Gene Expression Profiles and Disease

Web Resources

Affymetrix

Arrayit Corporation

Biocarta Cell Signaling Pathways

miRBASE

miRNA Target Database MicroCom

Pat Brown's Lab

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

Medical Grand Rounds

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