Bejerano Lab

Lab Resources

Gill's Presentations

5. " Genomic Regions Enrichment of Annotations Tool", Stanford BioMedical Informatics Talk, May 2010. [watch, slides]

4. "Ultraconservation and the Human Genome regulatory landscape", Stanford BioMedical Informatics Talk, Apr 2009. [watch, slides]

3. "Tales from the Dark Side of Your Genome", Stanford Talks in English Presentation, Oct 2007. [watch, slides]

2. "Deciphering the Human Genome: Computational Insights & Opportunities", NSF advisory meeting, Princeton, Dec. 2006. [watch, slides]

1. "Ultraconservation and Living Fossils: Mysteries of the Human Genome", Google invited talk, Googleplex, Oct 2006. [watch, slides]

Tools & Data

6. Genomic Regions Enrichment of Annotations Tool (ref. #27)

5. LF-SINE co-opted mobile elements (ref. #18)

4. Ultraconserved elements in the human genome (ref. #9)

3. Paralog families of human conserved non-coding DNA (ref. #10)

2. (refs. #12, #19)

1. (refs. #3, #8)

Specialized Resources

Core Stanford Classes
The work in our lab requires skills and knowledge in computer science, biology, and statistics. Lab members follow the core curriculum below. The more of these courses (or equivalent material) you know, the more attractive you will be to our lab, and the more valuable you will find your experience with us.

Computer Science:
CS 106A Programming Methodology / Java  [watch] Aut,Win,Spr,Sum
CS 106B Programming Abstractions / C++  [watch] Win,Spr,Sum
CS 107 Programming Paradigms / C, Python  [watch] Aut,Spr
CS 161 Design and Analysis of Algorithms Aut,Win,Sum
DBIO 201 Development and Disease Mechanisms Aut
GENE 203 Current Genetics Aut
BIO 113 Fundamentals of Molecular Evolution Spr
CS 173 A Computational Tour of the Human Genome Win
CS 262 Computational Genomics Win
GENE 211 Genomics Win
BIOC 218 Computational Molecular Biology [watch] Aut
STATS 200 Intro to Statistical Inference Win,Sum

Note: Many of these courses are cross-listed.

Core Technical Books
These books offer a basic technical introduction to our core skill set.

Basic Biology

  "Genetics for Dummies" by Tara Rodden Robinson

Molecular Evolution

  "Evolution for Dummies" by Greg Krukonis, Tracy Barr

Statistical Hypothesis Testing

  "Statistics for Dummies" by Deborah Rumsey (see Part VI)

Basic Computer Science

  "Programming Methodology" Stanford  CS 106A course [online]

Programming from the Command Line

  "UNIX Shells by Example" by Ellie Quigley [online]

Text Processing Languages (pick either language)

  "Learning Python" by Mark Lutz [online], or
  "Learning Perl" by Randal L. Schwartz, Tom Phoenix, Brian D. Foy [online]

Technical Reviews
A few recent reviews and research articles are there to give you a taste for the type of problems we work on.

General Resources

Popular Science Books
Popular science books are a fun-to-read, gentle introduction to a new field. Some of the many excellent popular science books relevant to our lab are:

The Human Genome

  "Genome: The Autobiography of a Species in 23 Chapters" by Matt Ridley

Genetics and Human Disease

  "When a Gene Makes You Smell Like a Fish:  And Other Amazing Tales about the Genes in Your Body" by Lisa Seachrist Chiu

Evolutionary Developmental Biology

  "Endless Forms Most Beautiful: The New Science of Evo Devo" by Sean Carroll

Human Origins

  "Before the Dawn: Recovering the Lost History of Our Ancestors" by Nicholas Wade

Interdisciplinary Science

  "The Medici effect" by Frans Johansson

Popular Talks
  • HHMI Lectures by Sean Carroll and David Kingsley, 2005 [watch]
  • Sackler Colloquium on Evolution, 2006 [watch]
  • Sackler Colloquium on Animal Development, 2007 [watch]
  • Stanford undergrads DevBio rap, 2009 [watch]

      [last modified 2013/02/07 10:01] Bejerano LabDepartments of Computer Science, Developmental Biology and PediatricsStanford University