Jack Chen, Associate Professor

Department of Molecular Biology and Biochemistry
Simon Fraser University

1. Frezal and Felix, 2015. C. elegans outside the petri dish (eLIFE)
2. Koepfli et al., 2015. The Genome 10K Project: A Way Forward. (Annual Review of Animal Biosciences)
3. Gomez et al., 2014. Genetic Variation and Adaptation in Africa: Implications for Human Evolution and Disease. (CSH Perspectives in Biology)
4. Kumar et al., 2012. Toward 959 nematode genomes. (Worm)
5. Dillman et al., 2012. Incorporating Genomics into the Toolkit of Nematology. (The Journal of Nematology)

1. Enard et al., 2014. Genome-wide signals of positive selection in human evolution. (Genome Research)
2. Sabeti et al., 2006. Positive Natural Selection in the Human Lineage. (Science)

1. Carneiro et al., 2014. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. (Science)
2. Lindblad-Toh et al., 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. (Nature)

1. Lu et al., 2015. The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver. (Genome Biology)
2. Zhang et al., 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. (Science)
3. Jarvis et al., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. (Science)
4. Pfenning et al., 2014. Convergent transcriptional specializations in the brains of humans and song-learning birds. (Science)
5. Meredith et al., 2014. Evidence for a single loss of mineralized teeth in the common avian ancestor. (Science)
6. Whitney et al., 2014. Core and region-enriched networks of behaviorally regulated genes and the singing genome. (Science)
7. Zhou et al., 2014. Complex evolutionary trajectories of sex chromosomes across bird taxa. (Science)
8. Cui et al., 2014. Low frequency of paleoviral infiltration across the avian phylogeny. (Genome Biology)
9. Li et al., 2014. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. (GigaScience)
10. Lovell et al., 2014. Conserved syntenic clusters of protein coding genes are missing in birds. (Genome Biology)
11. Shapiro et al., 2013. Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon. (Science)
12. Warren et al., 2010. The genome of a songbird. (Nature)
13. Dalloul et al., 2010. Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis. (PLoS Biology)
14. Hillier et al., 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. (Nature)
15. Wong et al., 2004. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. (Nature)
16. Wallis et al., 2004. A physical map of the chicken genome. (Nature)

1. Song et al., 2015. A genome draft of the legless anguid lizard, Ophisaurus gracilis. (GigaScience)
2. Green et al., 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. (Science)
3. Loire et al., 2013. Population genomics of the endangered giant Galapagos tortoise
4. Shaffer et al., 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. (Genome Biology)
5. Castoe et al., 2013. The Burmese python geno me reveals the molecular basis for extreme adaptation in snakes. (PNAS)
6. Vonk et al., 2013. The king cobra genome rev eals dynamic gene evolution and adaptation in the snake venom system. (PNAS)
7. John et al., 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. (Genome Biology)
8. Alfoldi et al., 2011. The genome of the green anole lizard and a comparative analysis with birds and mammals. (Nature)

1. Harel et al., 2015. A Platform for Rapid Exploration of Aging and Diseases in a Naturally Short-Lived Vertebrate. (Cell)
   Notes: Wang et al., 2015. Fertile waters for aging research. (Cell)
   
2. Wang et al., 2015. The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation. (Nature Genetics)
3. Xu et al., 2014. Genome sequence and genetic diversity of the common carp, Cyprinus carpio. (Nature Genetics)
4. Howe et al., 2013. The zebrafish reference genome sequence and its relationship to the human genome. (Nature)
5. Jones et al., 2012. The genomic basis of adaptive evolution in threespine sticklebacks. (Nature)
6. Star et al., 2011. The genome sequence of Atlantic cod reveals a unique immune system. (Nature)
7. Kasahara et al., 2007. The medaka draft genome and insights into vertebrate genome evolution. (Nature)
8. Jaillon et al., 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. (Nature)
9. Aparicio et al., 2002. Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes. (Science)

1. Sadd et al., 2015. The genomes of two key bumblebee species with primitive eusocial organization. (Genome Biology)
2. Clark et al., 2007. Evolution of genes and genomes on the Drosophila phylogeny. (Nature)

1. Blaxter and Koutsovoulos, 2015. The evolution of parasitism in Nematoda. (Parasitology)
2. Schwarz et al., 2015. The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. (Nature Genetics)
3. Cotton et al., 2014. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. (Genome Biology)
4. Foth et al., 2014. Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. (Nature Genetics)
5. Tang et al., 2014. Genome of the human hookworm Necator americanus. (Nature Genetics)
6. Laing et al., 2013. The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. (Genome Biology)
7. Srinivasan et al., 2013. The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle. (Genetics)
8. Schiffer et al., 2013. The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda. (BMC Genomics)
   Notes: Used OrthoMCL to identify gene clusters that are genome-specific