Recommended Readings: Harmit S. Malik, Ph.D.

Friday Lecture Series

Genetic Conflicts: Beyond the Usual Suspects

Harmit S. Malik, Ph.D., principal investigator, basic sciences division,

Fred Hutchinson Cancer Research Center;

early career scientist, Howard Hughes Medical Institute

December 13, 2013

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

Caspary Auditorium

Recommended Readings

Malik, H. S. (2009). Evolution of TRIM antiviral genes in primate genomes. Retrovirology, 6(SUPPL. 2)

Malik, H. S., & Bayes, J. J. (2006). Genetic conflicts during meiosis and the evolutionary origins of centromere complexity. Biochemical Society Transactions, 34(4), 569-573

Malik, H. S., & Henikoff, S. (2002). Conflict begets complexity: The evolution of centromeres. Current Opinion in Genetics and Development, 12(6), 711-718

Moran, J. V., & Malik, H. S. (2009). Diamonds and rust: How transposable elements influence mammalian genomes. conference on mobile elements in mammalian genomes. EMBO Reports, 10(12), 1306-1310

Oliver, P. L., Goodstadt, L., Bayes, J. J., Birtle, Z., Roach, K. C., Phadnis, N., . . . Ponting, C. P. (2009). Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genetics, 5(12)

Vermaak, D., & Malik, H. S. (2009). Multiple roles for heterochromatin protein 1 genes in drosophila. Annual Review of Genetic 43 , pp. 467-492


Recommended Readings: Svante Pääbo, Ph.D.

Friday Lecture Series

Fairfield Osborn Memorial Lecture

A Molecular Perspective on Human Origins

Svante Pääbo, Ph.D., director, department of genetics,

Max Planck Institute for Evolutionary Anthropology

 December 14, 2012

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

Caspary Auditorium

Recommended Readings

Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., . . . Kaessmann, H. (2011). The evolution of gene expression levels in mammalian organs. Nature, 478(7369), 343-348

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., . . . Pääbo, S. (2010). A draft sequence of the neandertal genome. Science, 328(5979), 710-722

Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., . . . Khaitovich, P. (2011). MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genetics, 7(10)

Krause, J., Briggs, A. W., Kircher, M., Maricic, T., Zwyns, N., Derevianko, A., & Pääbo, S. (2010). A complete mtDNA genome of an early modern human from kostenki, russia. Current Biology, 20(3), 231-236

Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern siberia. Nature, 464(7290), 894-897

Xu, A. G., He, L., Li, Z., Xu, Y., Li, M., Fu, X., . . . Khaitovich, P. (2010). Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-seq. PLoS Computational Biology, 6(7), 37


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



Recommended Readings: Sydney Brenner, D.Phil.

Friday Lecture Series

Reading the Human Genome

Sydney Brenner, D.Phil., senior distinguished fellow,

Crick-Jacobs Center Brenner Laboratory, Salk Institute

May 18, 2012

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

Caspary Auditorium


Recommended Readings

Brenner, S. (2010). Sequences and consequences. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1537), 207-212

Brenner, S. (2012). Turing centenary: Life’s code script. Nature, 482(7386), 461

Gilligan, P., Brenner, S., & Venkatesh, B. (2002). Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences. Gene, 294(1-2), 35-44

Gwee, P., Amemiya, C. T., Brenner, S., & Venkatesh, B. (2008). Sequence and organization of coelacanth neurohypophysial hormone genes: Evolutionary history of the vertebrate neurohypophysial hormone gene locus. BMC Evolutionary Biology, 8(1)

Lee, A. P., Yang, Y., Brenner, S., & Venkatesh, B. (2007). TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. BMC Genomics, 8

Ruhe, J. E., Streit, S., Hart, S., Wong, C., Specht, K., Knyazev, P., Ullrich, A. (2007). Genetic alterations in the tyrosine kinase transcriptome of human cancer cell lines. Cancer Research, 67(23), 11368-11376

Venkatesh, B., Kirkness, E. F., Loh, Y., Halpern, A. L., Lee, A. P., Johnson, J., . . . Brenner, S. (2006). Ancient noncoding elements conserved in the human genome. Science, 314(5807), 1892


Erez Lieberman-Aiden Ph.D. Wednesday, April 4, 2012

How the Genome Folds

Erez Aiden  Ph.D.

Fellow, Harvard Society of Fellows

Prinicpal Investigator, Laboratory-at-Large

Harvard University

Visiting Faculty, Google

4:00 Wednesday, April 4, 2012  Refreshments Abby Lounge 3:45

Caspary Auditorium 

Recommended Readings

Zhang Y; McCord RP, Ho YJ; et al.  2012.  Spatial organization of the mouse genome and its role in recurrent chromosomal translocationsCell. 148(5):908-921.  DOI: 10.1016/j.cell.2012.02.002

Sung MH and  GL Hager.  2011.  More to Hi-C than meets the eye.  Nature Genetics.  43(11):1047-1048.  DOI: 10.1038/ng.984

Yaffe E and A Tanay.  2011.  Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nature Genetics.  43(11):1059-U40.  DOI: 10.1038/ng.947

Fudenberg G; Getz G; Meyerson M; et al.  2011.  High order chromatic architecture shapes the landscape of chromosomal alterations in cancer.   Nature Biotechnology. 29(12):1109-U75.  DOI: 10.1038/nbt.2049

Lieberman-Aiden E; van Berkum NL; Williams L; et al.  2009.  Comprehenesive mapping of long-range interactions reveals folding principles of the human genomeScience.  326(5950):289-293.  DOI: 10.1126/science.1181369

Guelen L; Pagie L; Brasset E; et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.   Nature.  453(7197):948-U83.  DOI: 10.1038/nature06947

Rada-Iglesias A; Ameur A; Kapronov P; et al.  2008.  Whole-genome maps opf USA and USF2 binding and histone H3 acetylation reveal new aspects of prmotoer structure and candidate genes for common human disorders.  Genome Research.  18(3):380-392.  DOI: 10.1101/gr.6880908

Xiao G; Wang X; and Ab Khodursky.  2011.  Modeling three-dimensional chromosome structures using gene expression data. Journal of the American Statistical Association.  106(493):61-72.  DOI: 10.1198/jasa.2010/ap09504   Please request copy from Markus Library.