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: Howard C Hang, PhD.

Chemical Reporters for Exploring Posttranslational

Modifications in Innate Immunity

Howard C Hang, Ph.D.

Laboratory of Chemical Biology and Microbial Pathogenesis

The Rockefeller University

4:00 p.m. Monday, June 4, 2012    Refreshments  3:45  Abby Lounge

Caspary Auditorium

Recommended Readings

Yount JS, Charron G, Hang HC.   2012.  Bioorthogonal proteomics of 15-hexadecynyloxyacetic acid chemical reporter reveals preferential targeting of fatty acid modified proteins and biosynthetis enzymes.    Bioorganic & Medicinal Chemistry.  20(2, S1):650-654.  DOI: 0.1016/j.bmc.2011.03.062

Lei YL, Xie K. et al.  2012.  Chemistry-based functional proteomics to identify novel deubiquitylating enzymes involved in viral infection.   Combinatorial Chemistry & High Throughput Screening.  15(4):316-327.   Please request from Markus Library.

Grammel M, Dossa PD, Taylor-Salmon E, et al.  2012.  II-selective labeling of bacterial proteomes with an  orthogonal phenylalanine amino acid reporter.   Chemical Communications.  48(10):1473-1474.  DOI: 10.1039/c1cc14939c

Aguera-Gonzales S, Gross CC, Fernandez-Messina L, et al.  2011.  Palmitoylation of MICA, a ligand for NKG2D, mediates its recruitment to membrane microdomains and promotes its shedding   European Journal of Immunology.  41(12):3667-3676.   DOI: 10.1002/eji.20114165

Hao ZY, Hong SL, Chen X, et al.  2011.  Introducing bioorthogonal functionalities into proteins in living cellsAccounts of Chemical Research   44(9, S1):742-751.   DOI: 10.1021/ar200067r

Hang HC, Linder ME.  2011.  Exploring protein lipidation with chemical biology.  Chemical Reviews.  111(10):6341-6358.   DOI:  10.1021/cr2001977

Yang YY, Hang HC.  2011.  Chemical approaches for the detection and synthesis of acetylated proteins.  Chembiochem.   12(2):314-322.   DOI: 10.1002/cbc.201000558




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


Biologists Produce Malaria Vaccine From Algae

Biologists at the University of California, San Diego have succeeded in engineering algae to produce potential candidates for a vaccine that would prevent transmission of the parasite that causes malaria, an achievement that could pave the way for the development of an inexpensive way to protect billions of people from one of the world’s most prevalent and debilitating diseases. Initial proof-of-principle experiments suggest that such a vaccine could prevent malaria transmission.   Read the report of their research in PLoS ONE. 

Recommended Readings: Yi Rao, Ph.D.

Friday Lecture Series

Molecular Sociophysiology of Sexual Preference

Yi Rao, Ph.D., investigator, National Institute of Biological Sciences;

dean, school of life sciences, Peking University, Beijing

May 11, 2012

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

Caspary Auditorium


Recommended Readings

Liu, Y., Y. -A Jiang, Y. Si, J. -Y Kim, Z. -F Chen, and Y. Rao. 2011. Molecular Regulation of Sexual Preference Revealed by Genetic Studies of 5-HT in the Brains of Male Mice. Nature 472 (7341): 95-100

Park, H. T., J. Wu, and Y. Rao. 2002. Molecular Control of Neuronal Migration. BioEssays 24 (9): 821-827

Park, K. W., C. M. Morrison, L. K. Sorensen, C. A. Jones, Y. Rao, C. -B Chien, J. Y. Wu, L. D. Urness, and D. Y. Li. 2003. Robo4 is a Vascular-Specific Receptor that Inhibits Endothelial Migration. Developmental Biology 261 (1): 251-267

Yuan, W., L. Zhou, J. -H Chen, J. Y. Wu, Y. Rao, and D. M. Ornitz. 1999. The Mouse SLIT Family: Secreted Ligands for ROBO Expressed in Patterns that Suggest a Role in Morphogenesis and Axon Guidance. Developmental Biology 212 (2): 290-306



HHMI News: Janelia Farm’s Newest Addition to HMMER

A few weeks after its release, the Janelia Farm’s Jackhmmer algorithm — an iterative search method in the HMMER package similar to the NCBI’s PSI-BLAST algorithm — is performing as expected.  The new algorithm takes advantage of the sophisticated probabilistic models that underpin profile Hidden Markov Models (HMMs).

Profile HMMs are the most sensitive tools to use, which is why many protein family databases use them. Bench biologists now have a fast method for discovering the likely structure of a sequence which can allow for the creation of functional hypothesis that can guide experiments.