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UPCOMING SPEAKER

Friday, December 3
IBG Room 120 4:00 pm

Philipp Kapranov, Ph.D.

Principal Genomics Scientist
Helicos BioSciences Corporation
Cambridge, Massachusetts

The multifaceted human transcriptome

A large amount of experimental data collected over the last decade has shown that genomic organization is very complex and has highlighted the fact that the current set of gene annotations does not fully capture this complexity. Furthermore, the transcriptome complexity has expanded in several directions. First, there is a significant amount of RNA that can be detected in a cell that originates from outside the exons of annotated genes. This RNA represents a variety of different transcripts from novel exons of annotated genes to stand alone transcripts. In this respect, experiments to empirically annotate exons of protein coding genes have revealed a multiplicity of novel exons of protein coding genes, often shared by multiple genes. Second, exons of annotated and unannotated transcripts separated by large genomic distances can be joined together in chimeric transcripts. Third, individual compartments within the cell differ in the amount of un-annotated transcription with nucleus and polyA- transcriptomes being highly enriched in un-annotated transcripts. Fourth, the short RNA component of the transcriptome is vast and underappreciated. Potential function of some of the novel transcription could be to serve as precursors to functional short RNAs.

These results suggest that the functional space of the human genome is not limited to the annotated exons of protein coding genes and is likely to produce a vast amount of non-coding RNAs. Furthermore, any given base-pair in a genome could be traversed by many protein-coding and non-coding RNAs. Overall, these data support a new model for genome organization that is not co-linear but rather lattice-like and is in part focused on the production of short RNAs. There is evidence to suggest that most of both strands of the human genome might be transcribed, implying extensive overlap of transcriptional units and regulatory elements. These observations imply that genomic architecture is interleaved and modular, and that the same genomic sequences are multifunctional: used as multiple independently regulated transcripts and as regulatory regions. What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states?

Relevant Publications

Studying chromosome-wide transcriptional networks: new insights into disease?

TUF Love for “Junk” DNA

Please join us for refreshments at 3:45 p.m.
University of Colorado, Boulder, East Campus, 303-492-7362

 

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FUTURE SPEAKERS 2010

Friday, January 8, 2010

John C. DeFries, Ph.D

Professor Dept. of Psychology
Institute for Behavioral Genetics
University of Colorado, Boulder

Adventures in Behavioral Genetics

 

Spring 2009

Friday, Jan 9:
HELEN M. KAMENS Ph.D.
"The Involvement of Nicotinic Acetylcholine Receptors in Ethanol Stimulation and Consumption"

 

Friday, Feb 6:
Linda R. Watkins
"Listening" and "talking" to neurons: Clinical implication of glial dysregulation of pain & opioid actions.

Friday, Apr 3:
Ulrike Heberlein
"The unbelievable likeness of beings: Role of Lim-only proteins and their target genes in cocaine-related behaviors in flies and mice"

Friday, May 1:
Karl H. Pfenninger
"Science and Resources in the Intellectual and Developmental Disabilities Research Center"

Fall 2009

Monday, Sept 28:
Justin S. Rhodes Ph.D.
"Genetic basis of motivation for physical activity"

Friday, Nov 13:
Ryan K. Bachtell Ph.D.
"Effects of reversing drug-induced neuroadaptations on drug-related behaviors"

 

 

Spring 2008

February 8
Dr. Allan Collins, Ph.D., Professor, Departments of Psychology and Pharmacology, Department of Psychology; and Faculty Fellow, Institute for Behavioral Genetics, University of Colorado, Boulder
"Teaching in Tanzania"

April 11
Marilyn E. Coors, Ph.D., Assistant Professor of Bioethics and Genetics, Department of Psychiatry and the Center for Bioethics and Humanities, University of Colorado Denver
"The Interface of Bioethics and Psychiatric Genetic Research"

June 6
Henry A. Lester, Ph.D., Bren Professor of Biology, Department of Neuroscience, Division of Biology, California Institute of Technology, Pasadena, California
"Changes in the Brain During Chronic Nicotine"

Fall 2008

Sept 12
Katerina Kechris, PhD
University of Colorado Denver
"Integrating Bioinformatics, Genomics and Genetics"

Friday, October 3
Benjamin F. Voight
Broad Institute of Harvard and MIT & The Center for Human Genetics Research
Massachusetts General Hospital
Cambridge, Massachusetts
"Population-based Homozygosity Mapping using Whole Genome Association Data"

Friday, Nov 14

Isabel Schlaepfer

Doctoral Candidate
Department of Integrative Physiology & Institute for Behavioral Genetics
University of Colorado, Boulder
"Association of Nicotinic CHRNA5/A3/B4 Gene Cluster Variations & Disinhibitory Behaviors"

Friday, Dec 5

Len Hayflick, PhD

Department of Anatomy
University of California at San Francisco.
"Aging, Longevity Determinants and Age Associated Disease."

 

Spring 2007

Min Han  
Ph.D., Investigator and Professor, HHMI and Department of MCD Biology, University of Colorado, Boulder, Colorado. 
“Genetic Redundancy and Tumor Suppressor Functions in C. Elegans”

Kwang-Youn Albert Kim  
Ph.D., Postdoctoral Fellow, Department of Pediatrics, University of Iowa, Iowa City, Iowa.
“Unraveling Complex Diseases by Identifying Gene-Gene Interactions”
(Candidate for Behavioral/Mathematical Genetics Position)

Tiejun Tong  
Ph.D., Postdoctoral Associate Division of Biostatistics, Yale University School of Medicine, New Haven, Connecticut. 
“Minimax Estimation of Means with Applications to Microarray Data Analysis”  (Candidate for Behavioral/Mathematical Genetics Position)

Wei Min Chen  (Ph.D., Postdoctoral Fellow, Center for Statistical Analysis, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan). 
“Efficient Use of Family Data in Genome-Wide Association Scans” 
(Candidate for Behavioral/Mathematical Genetics Position)

Terence P. Thornberry  & Pamela K. Porter
Dr. Thornberry, Director, Problem Behavior Program, Institute of Behavioral Science and Professor, Department of Sociology, University of Colorado, Boulder; and Pamela K. Porter (Research Coordinator, Rochester Youth Development Study, Institute of Behavioral Science, University of Colorado, Boulder).        
“Overview of the Rochester Intergenerational Study”

Laura Jean Bierut  
M.D., Associate Professor, Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri. 
“Genetic Risk Factors for Nicotine Dependence”

Fall 2007

September 7
Allan Jones, Ph.D., Professor, Chief Scientific Officer
Formerly Sr. Director of the Allen Brain Atlas Project—mid 2004-mid 2006 Both with the Allen Institute for Brain Science, Seattle, WA
“The Mouse Transcriptome in 3D:  The Allen Brain Atlas Project”

 September 28
Dr. Stephen A. Petrill, Ph.D., Professor, The Ohio State University, Dept. of Human Development & Family Science, Columbus, Ohio
“Genes, Environments, and Growth in Early Reading Skills”

November 2
Dr. Evan S. Deneris, Ph.D., Professor, Case Western Reserve University, School of Medicine, Department of Neuroscience, Cleveland, Ohio
“Genetic Mechanisms Directing Development of the Brain Serotonin System”

Spring 2006

Brion Maher  
Ph.D., Assistant Professor, Center for Craniofacial and Dental Genetics, Division of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.
Title—ADHD, Endophenotypes and the Dopamine System”  
Co-sponsored by IBG and the Department of Psychology, University of Colorado at Boulder
(Candidate for Behavioral Statistical Genetics Position)

Matthew McQueen
Ph.D., Postdoctoral Fellow, Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts.
Title—“Mapping Genetic Determinants of Bipolar Disorder”
Co-sponsored by IBG and the Department of Psychology, University of Colorado at Boulder  (Candidate for Behavioral Statistical Genetics Position)

Gregory A. Petsko
Gyula and Katica Tauber Professor of Biochemistry and Chemistry; Director, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts. 
Title:  “The Structural Enzymology of Parkinson’s Disease”

Jeesun Jung  
Ph.D., Postdoctoral Associate, Division of Statistical Genetics, Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania. 
Title—Combined Linkage and Linkage Disequilibrium Mapping of Quantitative Trait Loci”  Co-sponsored by IBG and the Department of Psychology, University of Colorado at Boulder  (Candidate for Behavioral Statistical Genetics Position)

Jeesun Jung 
Ph.D., Postdoctoral Associate, Division of Statistical Genetics, Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania. 
“Gene Dropping vs. Empirical Variance Estimation:  A Comparative Study of Standardization Methods for Allele-Sharing Statistics”  
Co-sponsored by IBG and the Department of Applied Math, University of Colorado at Boulder  (Candidate for Behavioral Statistical Genetics Position)

2006 Super Mouse Group Meeting—Sponsored by Beth Bennett.  
The Super Mouse Group Meeting involves researchers giving 15 minute presentations on their current projects (including work mapping ethanol sensitivity genes), with discussion following.

Fall 2006

Ana Maria Cuervo  
M.D., Ph.D., Associate Professor, Department of Anatomy and Structural Biology, and of Medicine, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY.
“Selective Autophagy: Something Else Than Keeping Cells Clean”
           
Gary A. Churchill 
Ph.D., Staff Scientist, The Jackson Laboratory, Bar Harbor, Maine. 
“Co-Adapted Alleles and the Evolution of Complex Traits”

Matthew B. McQueen  
Sc.D., Assistant Professor, Department of Psychology and Faculty Fellow, Institute for Behavioral Genetics, University of Colorado, Boulder.
“Genome-Wide Association: Ready or Not Here it Comes”

Thomas E. Johnson  (ibg.colorado.edu/tj-lab)
Ph.D., Professor of Behavioral Genetics, Department of Integrative Physiology and Faculty Fellow, Institute for Behavioral Genetics, University of Colorado, Boulder. 
“Review of the European Conference on Aging”

 

2005

1/13/2005: Lon Cardon, Ph.D., Professor of Bioinformatics, Principal Research Fellow, Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom "The role of linkage disequilibrium in identifying complex trait genes in humans”
Cosponsored by IBG and MCD Biology

2/4/2005: Marie Banich, Ph.D., Director of the Institute of Cognitive Science and professor of Psychology, University of Colorado at Boulder, Boulder, CO "Neuroimaging of attentional control and its potential linkage to genetics”
Jointly sponsored by IBG and the Center for the Genetics of Antisocial Drug Dependence

3/4/2005: Matthew Stephens, Ph.D., statistical geneticist with the University of Washington in Seattle, develops statistical methods to analyze human genetic data using haplotype mapping and tagging.

4/1/2005: Kaare Christensen, M.D., Ph.D., Dr. Medical Science, Professor of Epidemiology, Institute of Public Health, University of Southern Denmark; and Senior Research Scientist (part time employment) at the Terry Sanford Institute, Duke University, North Carolina, USA "Danish twin studies of aging: Why do we age so differently?"

5/6/2005: Tatiana Foroud, Associate Professor, Departments of Medical & Molecular Genetics and of Psychiatry, Indiana University School of Medicine “Genetics of alcoholism and the COGA study”

9/3/2005: Thomas E. Johnson, Ph.D., Professor of Behavioral Genetics, Department of Integrative Physiology, and Faculty Fellow, Institute for Behavioral Genetics, University of Colorado, Boulder.  (ibg.colorado.edu/tj-lab) “Genes Environment and Chance Interact to Determine Individual Life Span”

10/14/2005: Dr. Robert W. Williams, Department of Anatomy and Neurobiology, Dunavant Chair: Developmental Genetics, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee. “A Systems Genetics Approach to Genes, Brains, and Behavior”

11/4/2005: Dr. David Goldman, Senior Investigator, Laboratory of Neuro- genetics, National Institute on Alcohol Abuse & Alcoholism , National Institutes of Health, Rockville, Maryland. “Addictions: Linkage of functional alleles and haplotypes to intermediate neurobiologies and complex behaviors”

12/3/2005: Dr. Nicholas J. Schork, Professor, Departments of Psychiatry and Biostatistics, Associate Director, University of California, San Diego, Center for Human Genetics and Genomics. “Molecular, Clinical, and Population Profiling via Similarity Matrix Analysis”

2004

01/23/2004: Tatiana Foroud, Ph.D., Associate Professor of Medical & Molecular Genetics and of Psychiatry at Indiana University School of Medicine “Genetics of alcoholism and the COGA study”

02/13/2004: Richard Miller, Ph.D, M.D., Professor of Pathology & Associate Director of Geriatrics Center at University of Michigan, Ann Arbor: “Genetic analysis of aging and disease in mice”

02/27/2004: Michael Miles, Ph.D, M.D., Associate Professor of Pharmacology and Toxicology at Virginia Commonwealth University: “Genetics, drugs and chips: molecular triangulation on CNS plasticity”

04/02/2004: Joe Tsien, Ph.D., Assistant Professor of Molecular Biology at Princeton University: “Inducible protein knockout and ensemble recording for the analysis of memory process in mice”

05/07/2004: Marina Picciotto, Ph.D., Associate Professor of Psychiatry, Pharmacology & Neurobiology at Yale University School of Medicine: “Nicotine effects on signal transduction: possible mechanisms underlying addiction”

09/03/2004: Larry Gold, Chief Science Officer & Chairman of the Board, SomaLogic, Inc., Boulder, Colorado. “Do Serum Protein Concentrations Reflect Behavior?”

10/08/2004: James Sikela, Professor, Department of Pharmacology and Human Genetics Medical Program, University of Colorado Health Sciences Center, Denver, Colorado. “Genome-Wide Identification of Great Ape and Human Lineage-Specific Genes”

11/19/2004: November 19, Al Collins, Professor of Psychology and Pharmacology, Department of Psychology, University of Colorado, Boulder, Colorado. “Unfinished Business

12/16/2004: Leslie Morrow, Professor of Psychiatry and Pharmacology, Associate Director, Bowles Center for Alcohol Studies, University of North Carolina School of Medicine, Chapel Hill, North Carolina. “The role of GABAergic Neuroactive Steroids in Ethanol Action, Tolerance and Drinking Behavior”