The Zebrafish: Genetics, Genomics and Informatics

Professor of Biochemistry and Marine Biology at Northeastern University, promoted 1996. Joined Northeastern faculty in 1987. Previously a faculty member in Dept. of Biochemistry at the University of Mississippi Medical Center, 1983-1987.Principal Investigator in the U.S. Antarctic Program since 1984. Twelve field seasons "on the ice" since 1981. Research conducted at Palmer Station, Antarctica, and McMurdo Station, Antarctica.Research areas: Biochemical, cellular, and physiological adaptation to low and high temperatures. Structure and function of cytoplasmic microtubules and microtubule-dependent motors from cold-adapted Antarctic fishes. Regulation of tubulin and globin gene expression in zebrafish and Antarctic fishes. Role of microtubules in morphogenesis of the zebrafish embryo. Developmental hemapoiesis in zebrafish and Antarctic fishes. UV-induced DNA damage and repair in Antarctic marine organisms.

Part I: Forward and Reverse Genetics

1. Gene Trap Mutagenesis for Generation of Conditional Mutations in Zebrafish – Wenbiao Chen

2. Advances in Tol2 Transposon Mutagenesis – Koichi Kawakami

3. OPEN Zinc Finger Nucleases – Keith Joung and Randy Peterson

4. Retroviral-Mediated Insertional Mutagenesis in Zebrafish – Adam Amsterdam, Nancy Hopkins, and Shawn Burgess

5. Genetic Screens for Maternal-Effects Mutations – Francisco Pelegri and Mary Mullins

6. High-Throughput Target-Selected Gene Inactivation in Zebrafish – Derek Stemple

7. Suppressor Screens in Haploids – Xiaoying Bai

8. Transposons – Stephen Ekker

9. Caged MOs – James Chen

Part II: Transgenesis

1. Advanced Transgenesis with Cre Recombinase – Christian Mosimann

2. Transgenesis with phiC31 Recombinase – James Lister

3. Nuclear Transfer – Jose Cibelli and Dr. Siripattarapravat

Part III: The Zebrafish Genome and Mapping Technologies

1. The Zebrafish Genome Project: Sequence Analysis and Annotation– Derek Stemple

2. Molecular Cytogenetic Methodologies and a Bacterial Artificial Chromosome (BAC) Probe Panel Resource for Genomic Analyses in Zebrafish – Charles Lee and Amanda Smith

3. Automated Analysis of Conserved Syntenies for the Zebrafish Genome – John Postlethwait, Julian Catchen

4. The Zon Laboratory Guide to Positional Cloning in Zebrafish –Yi Zhou and Leonard Zon

Part IV: Informatics and Comparative Genomics

1. Data Warehouse ZFIN – Monte Westerfield and Judy Sprague

2. Epigenetics: Methylation – Brad Cairns

3. Chromatin Structure – Leonard Zon and Yi Zhou

4. ChipSeq – Brad Cairns

5. Micro RNAs – Graham Lieshke and Luke Pase

6. Microarrays – Yi Zhou

7. Sequence-Based Transcriptional Profiling – Shawn Burgess

8. Epigenetic Regulation of Zebrafish Development – Elke Ober and co-author

Part V: Infrastructure

1. Zebrafish Facilities for Small and Large Laboratories – Christian Lawrence

2. Genetic Backgrounds, Standard Lines, and their Husbandry – ZIRC, Zoltan