Category Archives: Genomics

Recommended Readings: Jeffrey M. Friedman, M.D., Ph.D. May 20, 2013

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Monday Lecture Series
To Eat or Not To Eat: Studies of a Complex Motivational Behavior
Jeffrey M. Friedman, M.D. , Ph.D.
Marilyn M. Simpson Professor, Laboratory of Molecular Genetics
Investigator, Howard Hughes Medical Institute
Carson Family Auditorium, CRC
4:00 p.m., Refreshments 3:45

Recommended Readings:

L Domingos, Ana I.; Vaynshteyn, Jake; Voss, Henning U.; et al. 2011. Leptin regulates the reward value of nutrient. NATURE NEUROSCIENCE . 14(12):1562-U92 DOI: 10.1038/nn.2977

Scott, Michael M.; Lachey, Jennifer L.; Sternson, Scott M.; et al. 2009. Leptin Targets in the Mouse Brain. JOURNAL OF COMPARATIVE NEUROLOGY. 514(5): 518-532 DOI: 10.1002/cne.22025

Adam, Tanja C.; Epel, Elissa S. 2007. Stress, eating and the reward system. Annual Meeting of the Society-for-the-Study-of-Ingestive-Behavior. Location: Naples, Florida, JUL 18-22, 2006. Society for the Study of Ingestive Behavior. PHYSIOLOGY & BEHAVIOR. 91(4, Sp. Issue SI): 449-458 DOI: 10.1016/j.physbeh.2007.04.011

Heisler, Lora K.; Jobst, Erin E.; Sutton, Gregory M.; et al 2006. Serotonin reciprocally regulates melanocortin neurons to modulate food intake. NEURON. 51(2): 239-249 DOI: 10.1016/j.neuron.2006.06.004

Alon, T; Friedman, JM. 2006. Late-onset leanness in mice with targeted ablation of melanin concentrating hormone neurons. JOURNAL OF NEUROSCIENCE . 26(2): 389-397 DOI: 10.1523/JNEUROSCI.1203-05.2006

Figlewicz, DP; Bennett, J; Evans, SB; et al. 2004. Intraventricular insulin and leptin reverse place preference conditioned with high-fat diet in rats. BEHAVIORAL NEUROSCIENCE . 118(3): 479-487 DOI: 10.1037/0735-7044.118.3.479  REQUEST ARTICLE FROM MARKUS LIBRARY

Pinto, S; Roseberry, AG; Liu, HY; et al. 2004. Rapid rewiring of arcuate nucleus feeding circuits by leptin. SCIENCE . 304(5667): 110-115 DOI: 10.1126/science.

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Recommended Readings: Maurice Swanson, Ph.D.

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Friday Lecture Series

RNA-mediated Pathways to Disease

Maurice Swanson, Ph.D., associate director, Center for NeuroGenetics,

and professor of molecular genetics and microbiology,

University of Florida College of Medicine

 February 15, 2012

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

Caspary Auditorium

Recommended Readings

Daughters, R. S., Tuttle, D. L., Gao, W., Ikeda, Y., Moseley, M. L., Ebner, T. J., . . . Ranum, L. P. W. (2009). RNA gain-of-function in spinocerebellar ataxia type 8. PLoS Genetics, 5(8)

Ho, T. H., Savkur, R. S., Poulos, M. G., Mancini, M. A., Swanson, M. S., & Cooper, T. A. (2005). Colocalization of muscleblind with RNA foci is separable from mis-regulation of alternative splicing in myotonic dystrophy. Journal of Cell Science, 118(13), 2923-2933

Kanadia, R. N., Shin, J., Yuan, Y., Beattie, S. G., Wheeler, T. M., Thornton, C. A., & Swanson, M. S. (2006). Reversal of RNA missplicing and myotonia after muscleblind overexpression in a mouse poly(CUG) model for myotonic dystrophy. Proceedings of the National Academy of Sciences of the United States of America, 103(31), 11748-11753

Osborne, R. J., Lin, X., Welle, S., Sobczak, K., O’Rourke, J. R., Swanson, M. S., & Thornton, C. A. (2009). Transcriptional and post-transcriptional impact of toxic RNA in myotonic dystrophy. Human Molecular Genetics, 18(8), 1471-1481

Shin, J., Charizanis, K., & Swanson, M. S. (2009). Pathogenic RNAs in microsatellite expansion disease. Neuroscience Letters, 466(2), 99-102

Yuan, Y., Compton, S. A., Sobczak, K., Stenberg, M. G., Thornton, C. A., Griffith, J. D., & Swanson, M. S. (2007). Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAs. Nucleic Acids Research, 35(16), 5474-5486

 

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Recommended Readings: Joseph Gleeson, M.D.

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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

 

 

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Recommended Readings: Svante Pääbo, Ph.D.

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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

 

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Recommended Readings: Robert Johnston, Jr. PhD Dec 10, 2012

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Controlling Stochastic Gene Expression in the Drosophila retina

Robert Johnston, Jr.   PhD

Postdoctoral Fellow

Department of Biology, Center for Developmental Genetics

New York University

Monday, December 10,  2012

4 p.m. , Caspary Auditorium.   Refreshments 3:45 p.m.

Recommended Readings:

Sood, P; Johnston, RJ Jr.;Kusssell, E.  2012.  Stochastic de-repression of rhodopsins in single photoreceptors of the fly retina.  PLoS Computational Biology.  8(2):e1002357.  DOI:10.1371/journal.pcbi.1002357

Johnson, RJ, Jr.; Desplan, C.  2010.  Stochastic mechanisms of cell fate specification that yield random or robust outcomes.  Annual Review of Cell and Developmental Biology.  26:689-719.  DOI:10.1146/annurev-cellbio-100109-104113

Jukam, D; Desplan, C.  2010.  Binary date decisions in differentiating neurons.  Current Opinion in Neurobiology.  20(1):6-13.  DOI:10.1016/j.conb.2009.11.002

Wenet, MF; Mazzoni, EO; Ceclik A; et al.  2006.  Stochastic spineless expression creates the retinal mosaic for colour vision.  NATURE.  440(7081):174-180.  DOI:10.1038/nature04615

Bell, ML; Earl, JB; Britt, SG.  2007.  Two types of Drosophila R7 photoreceptor cells are arranged randomly: a model for stochastic cell-fate determination.  Journal of Comparative Neurology. 502(1):75-85.  DOI:10.1002/cne.21298.

Chanas, SA; Collinson, JM; Ramaesh, T; et al.  2009.  Effects of elevated Pax6 expression and genetic background on mouse eye development.  Investigative Ophthalmology and Visual Science.  50(9):4045-4059.  DOI:10-1167/iovs.07-1630

Johnson, RJ Jr.; Desplan, C.  2008.  Stochastic neuronal cell fate choices.  Current Opinion in Neurobiology.  18(1):20-27.  DOI:10.1016/j.conb.2008.04.004

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Recommended Readings: Yanick Crow, PhD September 17, 2012

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Human Type I Interferonopathies

Yanick Crow  PhD

Professor of Genetic Medicine

University of Manchester, UK

Monday, September 17,  2012

4 p.m. , Caspary Auditorium.   Refreshments 3:45 p.m.

Recommended Review:

Banchereau, J; Pascual, V.  2006.  Type I interferon in systemic lupus erythematosus and other autoimmune diseases.   IMMUNITY.   25( 3):383-392.      DOI: 10.1016/j.immuni.2006.08.010

Recommended Readings:

Crow, Y.  2011.  Type I interferonopathies: a novel set of inborn errors of immunity.  Annals of the New York Academy of Sciences   1238: 91-98.     DOI: 10.1111/j.1749-6632.2011.06220.x

Briggs, Tracy A.; Rice, Gillian I.; Daly, Sarah; et al.   2011. Tartrate-resistant acid phosphatase deficiency causes a bone dysplasia with autoimmunity and a type I interferon expression signature. NATURE GENETICS  43(2):127-U71.     DOI: 10.1038/ng.748

 

Alcais, A; Quintana-Murci, L; Thaler, DS.; et al.  2010.  Life-threatening infectious diseases of childhood: single-gene inborn errors of immunity?  Annals of the New York Academy of Sciences    1214:18-33.     DOI: 10.1111/j.1749-6632.2010.05834.x

Crow, Yanick J. 2011. Lupus: How much “complexity” is really (just) genetic heterogeneity?  ARTHRITIS AND RHEUMATISM.   63(12): 3661-3664    DOI: 10.1002/art.30603

 

Crow, Y.; Rehwinkel, J.  2009.  Aicardi-Goutieres syndrome and related phenotypes: linking nucleic acid metabolism with autoimmunity.  HUMAN MOLECULAR GENETICS  18: R130-R136.    DOI: 10.1093/hmg/ddp293

Baechler, EC; Batliwalla, FM; Karypis, G; et al. 2003.  Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus.  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   100( 5):2610-2615.   DOI: 10.1073/pnas.0337679100

 

 

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New Method Improves Accuracy of Whole Genome Sequencing

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July 11, 2012  NATURE has published a research article detailing a new methodology to  dramatically improve the accuracy of whole genome sequencing.  The work was done by a company called Complete Genomics.   The NATURE paper describes the Company’s “Long Fragment Read” technology (LFR) that not only improves the accuracy, but also reduces the amount of DNA needed, for analysis.  This technology is expected to accelerate the clinical adoption of whole genome sequencing.

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

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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

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Recommended Readings: Sydney Brenner, D.Phil.

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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

 

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NIH News: IOM Report on the Complexities of Translating “Omics” Into Treatment

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WASHINGTON — Genomics, proteomics, and other branches of molecular bioscience offer the prospect of greater precision in medical care, but some clinical tests based on “omics” research have proved invalid and highlighted the challenges of dealing with complex data.  To enhance the translation of omics-based discoveries to clinical use, a new report by the Institute of Medicine recommends a detailed process to evaluate whether the data and computational steps underlying such tests are sound and the tests are ready to be used in clinical trials.  The proposed process defines responsibilities and best practices for the investigators, research institutions, funders, regulators, and journals involved in development and dissemination of clinical omics-based technologies.

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