Recommended Readings: Carlos D. Bustamante, Ph.D., March 18

Friday Lecture Series
Friday, March 18
3:45 p.m., Caspary Auditorium

Carlos D. Bustamante, Ph.D.
Professor of Biomedical Data Science and Genetics,
Founding Director,
Stanford Center for Computational, Evolutionary, and Human Genomics
Director of Informatics,
Stanford Center for Genomics and Personalized Medicine,
Stanford School of Medicine

Population and Medical Genomics in the Personal Genome Era

Recommended Readings

Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., … & Heidari, N. (2015). Genetic control of chromatin states in humans involves local and distal chromosomal interactions. Cell, 162(5), 1051-1065. doi: 10.1016/j.cell.2015.07.048.

Henn, B. M., Botigue, L. R., Peischl, S., Dupanloup, I., Lipatov, M., Maples, B. K., … & Excoffier, L. (2015). Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proceedings of the National Academy of Sciences, 113(4), E440-E449. doi: 10.1073/pnas.1510805112

Shringarpure, S. S., & Bustamante, C. D. (2015). Privacy risks from genomic data-sharing beacons. The American Journal of Human Genetics, 97(5), 631-646. doi: 10.1016/j.ajhg.2015.09.010.

Recommended Readings: Joan Strassmann, Ph.D. & David Queller, Ph.D., January 30

Friday Lecture Series
Friday, January 30, 2015
3:45 p.m., Caspary Auditorium

Joan E. Strassmann, Ph.D.
Charles Rebstock Professor of Biology,
Washington University in St. Louis
David C. Queller, Ph.D.
Spencer T. Olin Professor,
Washington University in St. Louis

Altruism, Cheating, and Mutualism in Social Amoebas: Evolution and Mechanisms

Recommended Readings

Brock, D. a, Read, S., Bozhchenko, A., Queller, D. C., & Strassmann, J. E. (2013). Social amoeba farmers carry defensive symbionts to protect and privatize their crops. Nature Communications, 4, 2385. doi:10.1038/ncomms3385

Kuzdzal-Fick, J., Fox, S., Strassmann, J., & Queller, D. (2011). High relatedness is necessary and sufficient to maintain multicellularity in Dictyostelium. Science, 334(6062), 1548–1552. doi:10.3334/ORNLDAAC/797

Stallforth, P., Brock, D. a, Cantley, A. M., Tian, X., Queller, D. C., Strassmann, J. E., & Clardy, J. (2013). A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the gacA gene. Proceedings of the National Academy of Sciences, 110(36), 14528–14533. doi:10.1073/pnas.1308199110

Strassmann, J. E., & Queller, D. C. (2011). Evolution of cooperation and control of cheating in a social microbe. Proceedings of the National Academy of Sciences, 108 Suppl, 10855–10862. doi:10.1073/pnas.1102451108

Recommended Readings: Neil H. Shubin, Ph.D. December 17

Special Seminar Series
Wednesday, December 17, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Neil H. Shubin, Ph.D.
Robert R. Bensley Distinguished Service Professor,
Senior Advisor to the President,
Department of Organismal Biology and Anatomy,
The University of Chicago

Organogenesis in Deep Time

Recommended Readings

Empirical Papers

Amemiya, C. T., Alföldi, J., Lee, A. P., Fan, S., Philippe, H., Maccallum, I., … Lindblad-Toh, K. (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496(7445), 311–316. doi:10.1038/nature12027

Dahn, R. D., Davis, M. C., Pappano, W. N., & Shubin, N. H. (2007). Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning. Nature, 445(7125), 311–314. doi:10.1038/nature05436

Davis, M. C., Dahn, R. D., & Shubin, N. H. (2007). An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature, 447(7143), 473–476. doi:10.1038/nature05838

Shubin, N. H., Daeschler, E. B., & Jenkins, F. a. (2006). The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature, 440(7085), 764–771. doi:10.1038/nature04637

Review Articles

Schneider, I., & Shubin, N. H. (2013). The origin of the tetrapod limb: from expeditions to enhancers. Trends in Genetics, 29(7), 419–426. doi:10.1016/j.tig.2013.01.012

Shubin, N., Tabin, C., & Carroll, S. (2009). Deep homology and the origins of evolutionary novelty. Nature, 457(7231), 818–823. doi:10.1038/nature07891

Recommended Readings: David Kingsley, Ph.D.

Friday Lecture Series

The Fairfield Osborn Memorial Lecture

Fishing for the Secrets of Vertebrate Evolution

David Kingsley, Ph.D., professor, developmental biology, Stanford University;

investigator, Howard Hughes Medical Institute

April 18, 2014

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

han, Y. F., Marks, M. E., Jones, F. C., Villarreal Jr., G., Shapiro, M. D., Brady, S. D., . . . Kingsley, D. M. (2010). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a pitxl enhancer. Science, 327(5963), 302-305

Haussler, D., O’Brien, S. J., Ryder, O. A., Keith Barker, F., Clamp, M., Crawford, A. J., . . . Turner, S. (2009). Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species. Journal of Heredity, 100(6), 659-674

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., . . . Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55-61

Kingsley, D. M., Zhu, B., Osoegawa, K., De Jong, P. J., Schein, J., Marra, M., . . . Myers, R. (2004). New genomic tools for molecular studies of evolutionary change in threespine sticklebacks. Behaviour, 141(11-12), 1331-1344

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., . . . Haussler, D. (2011). Three periods of regulatory innovation during vertebrate evolution. Science, 333(6045), 1019-1024

Shapiro, M. D., Bell, M. A., & Kingsley, D. M. (2006). Parallel genetic origins of pelvic reduction in vertebrates. Proceedings of the National Academy of Sciences of the United States of America, 103(37), 13753-13758


Recommended Readings: Talking Science, Monday, December 30

Talking Science
Caspary Auditorium
Monday, December 30, 2013
10:30 a.m.-2:30 p.m.

C. David Allis, Ph.D.
Joy and Jack Fishman Professor
Laboratory of Chromatin Biology and Epigenetics
The Rockefeller University

Epigenetics: Inheriting More Than Genes

Recommended Reading:

Epigenetics Basics

Simmons, D. (2008) Epigenetic influence and diseaseNature Education 1(1):6

In-Depth Reading

Feinberg, A. P. (2008). Epigenetics at the epicenter of modern medicine. JAMA : The Journal of the American Medical Association, 299(11), 1345–1350. doi:10.1001/jama.299.11.1345

Goldberg, A. D., Allis, C. D., & Bernstein, E. (2007). Epigenetics: a landscape takes shape. Cell, 128(4), 635–638. doi:10.1016/j.cell.2007.02.006

Recommended Readings: Pardis Sabeti M.D., Ph.D. Friday, Nov 8

Friday, November 8, 2013
3:45 p.m., Caspary Auditorium

Pardis Sabeti M.D., Ph.D.
Senior Associate Member, Broad Institute of MIT and Harvard;
Associate Professor, Center for Systems Biology, Harvard University Department of Organismic and Evolutionary Biology, and Department of Immunology and Infectious Disease at Harvard School of Public Health

Evolutionary Forces in Humans and Pathogens

Recommended Readings:

Empirical Articles

The 100 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061–1073. doi:10.1038/nature09534

The International MapMap Consortium. (2005). A haplotype map of the human genome. Nature, 437(7063), 1299–1320. doi:10.1038/nature04226

Grossman, S. R., Andersen, K. G., Shlyakhter, I., Tabrizi, S., Winnicki, S., Yen, A., … Sabeti, P. C. (2013). Identifying recent adaptations in large-scale genomic data. Cell, 152(4), 703–713. doi:10.1016/j.cell.2013.01.035

Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., … & Lander, E. S. (2002). Detecting recent positive selection in the human genome from haplotype structureNature419(6909), 832-837. doi:10.1038/nature01140

Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., … Gaudet, R. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164), 913–8. doi:10.1038/nature06250

Review Papers

Biswas, S., Akey, J. M. (2006) Genomic insights into positive selection. Trends in Genetics, 22(8), 437-445. doi:10.1016/j.tig.2006.06.005

Kreitman, M. (2000). Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics, 1, 539-559. doi: 10.1146/annurev.genom.1.1.539

Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C., & Clark, A. G. (2007). Recent and ongoing selection in the human genome. Nature Reviews Genetics,8(11), 857-868. doi:10.1038/nrg2187

Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., … & Lander, E. S. (2006). Positive natural selection in the human lineage .Science, 312(5780), 1614-1620. doi:10.1126/science.1124309

Vitti, J. J., Cho, M. K., Tichkoff, S. A., Sabeti, P. C. (2012). Human evolutionary genomics: ethical and interpretive issues. Trends in Genetics, 28(3), 137-145. doi:10.1016/j.tig.2011.12.001

Recommended Readings: Joseph Gleeson, M.D.

Friday Lecture Series

Developing Treatments for Pediatric Brain Diseases through Genomics

Joseph Gleeson, M.D., professor of neurosciences and pediatrics,

University of California, San Diego;

investigator, Howard Hughes Medical Institute

 January 11, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Dixon-Salazar, T. J., J. L. Silhavy, N. Udpa, J. Schroth, S. Bielas, A. E. Schaffer, J. Olvera, et al. 2012. “Exome Sequencing can Improve Diagnosis and Alter Patient Management.” Science Translational Medicine 4 (138)

Novarino, G., N. Akizu, and J. G. Gleeson. 2011. “Modeling Human Disease in Humans: The Ciliopathies.” Cell 147 (1): 70-79

Novarino, G., P. El-Fishawy, H. Kayserili, N. A. Meguid, E. M. Scott, J. Schroth, J. L. Silhavy, et al. 2012. “Mutations in BCKD-Kinase Lead to a Potentially Treatable Form of Autism with Epilepsy.” Science 338 (6105): 394-397

Parisi, M. A., C. L. Bennett, M. L. Eckert, W. B. Dobyns, J. G. Gleeson, D. W. W. Shaw, R. McDonald, A. Eddy, P. F. Chance, and I. A. Glass. 2004. “The NPHP1 Gene Deletion Associated with Juvenile Nephronophthisis is Present in a Subset of Individuals with Joubert Syndrome.” American Journal of Human Genetics 75 (1): 82-91

Yaari, R., I. A. Anselm, I. S. Szer, D. M. Malicki, M. P. Nespeca, and J. G. Gleeson. 2004. “Childhood Primary Angiitis of the Central Nervous System: Two Biopsy-Proven Cases.” Journal of Pediatrics 145 (5): 693-697



Recommended Readings: Gerry Rubin, Ph.D.

Friday Lecture Series

Richard M. Furlaud Distinguished Lecture

A Molecular Geneticist’s Approach to Understanding the Fly Brain

Gerry Rubin, Ph.D., vice president and executive director,

Howard Hughes Medical Institute Janelia Farm Research Campus

October 19, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Aboobaker, A. A., Tomancak, P., Patel, N., Rubin, G. M., & Lai, E. C. (2005). Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proceedings of the National Academy of Sciences of the United States of America, 102(50), 18017-18022

Ashburner, M., Misra, S., Roote, J., Lewis, S. E., Blazej, R., Davis, T., . . . Rubin, G. M. (1999). An exploration of the sequence of a 2.9-mb region of the genome of drosophila melanogaster: The adh region. Genetics, 153(1), 179-219

Bellen, H. J., Levis, R. W., Liao, G., He, Y., Carlson, J. W., Tsang, G., . . . Spradling, A. C. (2004). The BDGP gene disruption project: Single transposon insertions associated with 40% of drosophila genes. Genetics, 167(2), 761-781

Miklos, G. L. G., & Rubin, G. M. (1996). The role of the genome project in determining gene function: Insights from model organisms. Cell, 86(4), 521-529

Pfeiffer, B. D., Jenett, A., Hammonds, A. S., Ngo, T. -. B., Misra, S., Murphy, C., . . . Rubin, G. M. (2008). Tools for neuroanatomy and neurogenetics in drosophila. Proceedings of the National Academy of Sciences of the United States of America, 105(28), 9715-9720

Pfeiffer, B. D., Ngo, T. -. B., Hibbard, K. L., Murphy, C., Jenett, A., Truman, J. W., & Rubin, G. M. (2010). Refinement of tools for targeted gene expression in drosophila. Genetics, 186(2), 735-755


Recommended Readings: Richard Lifton, M.D., Ph.D.

Friday Lecture Series

Rufus Cole Lecture

Genes, Genomes and the Future of Medicine

Richard Lifton, M.D., Ph.D.,director, Yale Center for Human Genetics and

Genomics,chair, department of genetics and Sterling Professor of Genetics and

Internal Medicine, Yale University School of Medicine;

investigator, Howard Hughes Medical Institute

June 1, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium


Recommended Reading

Choi, M., U. I. Scholl, W. Ji, T. Liu, I. R. Tikhonova, P. Zumbo, A. Nayir, et al. 2009. Genetic Diagnosis by Whole Exome Capture and Massively Parallel DNA Sequencing. Proceedings of the National Academy of Sciences of the United States of America 106 (45): 19096-19101

Choi, M., U. I. Scholl, P. Yue, P. Björklund, B. Zhao, C. Nelson-Williams, W. Ji, et al. 2011. K + Channel Mutations in Adrenal Aldosterone-Producing Adenomas and Hereditary Hypertension. Science 331 (6018): 768-772

Ji, W., J. N. Foo, B. J. O’Roak, H. Zhao, M. G. Larson, D. B. Simon, C. Newton-Cheh, M. W. State, D. Levy, and R. P. Lifton. 2008. Rare Independent Mutations in Renal Salt Handling Genes Contribute to Blood Pressure Variation. Nature Genetics 40 (5): 592-599

Lifton, R. P. 2010. Individual Genomes on the Horizon. New England Journal of Medicine 362 (13): 1235-1236

Lo, S. M., M. Choi, J. Liu, D. Jain, R. G. Boot, W. W. Kallemeijn, J. M. F. G. Aerts, et al. 2012. Phenotype Diversity in Type 1 Gaucher Disease: Discovering the Genetic Basis of Gaucher disease/hematologic Malignancy Phenotype by Individual Genome Analysis. Blood 119 (20): 4731-4740

Monette, M. Y., J. Rinehart, R. P. Lifton, and B. Forbush. 2011. Rare Mutations in the Human NA-K-CL Cotransporter (NKCC2) Associated with Lower Blood Pressure Exhibit Impaired Processing and Transport Function. American Journal of Physiology – Renal Physiology 300 (4): 840-847

Scholl, U. I., M. Choi, T. Liu, V. T. Ramaekers, M. G. Häusler, J. Grimmer, S. W. Tobe, A. Farhi, C. Nelson-Williams, and R. P. Lifton. 2009. Seizures, Sensorineural Deafness, Ataxia, Mental Retardation, and Electrolyte Imbalance (SeSAME Syndrome) Caused by Mutations in KCNJ10. Proceedings of the National Academy of Sciences of the United States of America 106 (14): 5842-5847



NATURE Conferences: Genomics of Infectious Diseases in March

The American Society of Human Genetics (ASHG), The Human Genome Organisation (HUGO) and Nature Publishing Group are pleased to announce: Genetics and Genomics of Infectious Diseases March 21-24, 2009, The Ritz Carlton Millenia Hotel, Singapore

Early Bird Registration has been extended to January 30.

Classical and emerging infectious diseases, viral pandemics, and drug-resistant pathogens remain challenges to human health. However, contemporary advances in genetics and genomic technologies provide new approaches to understanding and combating these diseases. The American Society of Human Genetics (ASHG) and the Human Genome Organisation (HUGO) are partnering with Nature Publishing Group (NPG) to organize an international conference to discuss how the genomes, unique biologies, and interactions of both host and pathogen are being revealed using novel genomic technologies, and how this information can and will translate into disease management and therapies. This conference will engage basic and clinical scientists, including human geneticists, genome scientists, computational biologists, and experts in pathogenic microbial agents to chart the effects of genomics on questions in global infectious disease management.