Thursday, Dec 11, 2014
3:00 PM
W-257 MSC at University Park; with video to room CG628 at Hershey
Marcia Shu-Wei Su (Penn State)
Maternal Age Effect and Severe Germline Bottleneck in the Inheritance of Human Mitochondrial DNA
Thursday, Nov 13, 2014
3:00 PM
W-257 MSC at University Park; with video to room CG628 at Hershey
Marzia A. Cremona (Politecnico di Milano (Milano, Italy))
Peak shape clustering: an application to GATA-1
In recent years many techniques have been developed to study genetic and epigenetic processes. Among Next Generation Sequencing method, we focus on ChIP-Seq (Chromatin Immuno Precipitation Sequencing), that permits to investigate protein-DNA interactions, e.g. the direct interaction between transcription factors, histones and DNA. At present, in the relevant literature, the analysis of ChIP-Seq data is mainly restricted to the detection of enriched regions (peaks) in the genome, considering only signal intensity. Motivated by the fact that these peaks can show very different shapes, we propose an innovative approach that takes into consideration also the shape of such peaks. We introduce some indices to summarize the shape and we use multivariate clustering techniques in order to detect statistically significant differences in peak shape. We show that an application of this analysis method to ChIP-Seq for the transcription factor GATA-1 reveals novel biological insights. Moreover, we suggest that a functional data analysis approach can lead to even more interesting results, treating peaks directly as curves. Joint work with I. Dellino, A. Parodi, P.G. Pelicci, L. Riva, L.M. Sangalli, P. Secchi and S. Vantini
Friday, Nov 7, 2014
4:30 PM
Life Sciences
Physiology Retreat 2014
This year we have joined forces with the Center for Reproductive Biology and Health (CRBH). The combined Physiology/CRBH retreat consists of a one-and-a-half day meeting featuring keynote speakers, faculty and student talks, and poster presentations. This year we are honored to host Drs. Michael Sturek and Carol Bagnell as keynote speakers. The retreat is open to everyone. Attendance is free, but you must register by November 1, 2014. This year we have joined forces with the Center for Reproductive Biology and Health (CRBH). The combined Physiology/CRBH retreat consists of a one-and-a-half day meeting featuring keynote speakers, faculty and student talks, and poster presentations. This year we are honored to host Drs. Michael Sturek and Carol Bagnell as keynote speakers. The retreat is open to everyone. Attendance is free, but you must register by November 1, 2014.
Thursday, Oct 9, 2014
3:00 PM
W-257 MSC at University Park; with video to room CG628 at Hershey
Marcelo R. S. Briones (Universidade Federal de Sao Paulo)
Evolution of genetic information in pathogenic microorganisms: Implications for diagnostics and epidemiology
Friday, Oct 3, 2014
12:30 PM
307 Wartik
Sarah J. Carnahan Craig (Penn State)
Paternally expressed genes predominate in the placenta (Wang 2013) PNAS
Friday, Sep 19, 2014
12:30 PM
307 Wartik
TBD (Penn State)
N/A
Friday, Sep 12, 2014
4:00 PM
Life Sciences Building, University Park
Bioinformatics and Genomics Retreat
The retreat consists of a one-and-a-half day meeting featuring a keynote speaker, faculty and student talks, data visualization workshop and poster presentations. Dr. Peter J. Park as the keynote speaker.
Thursday, Sep 11, 2014
3:00 PM
W-257 MSC at University Park; with video to room CG628 at Hershey
Sayantani Basu Roy (University of Paris-SUD XI)
Meiotic Crossover Interference – Modeling, Heterogeneity and Inter-Pathway Cross-Talk
Friday, Sep 5, 2014
12:30 PM
307 Wartik
Nicholas Stoler (Penn State)
Hypermutable DNA chronicles the evolution of human colon cancer (Naxerovaa 2014) PNAS
Friday, Jun 6, 2014
11:00 AM
519 Wartik Lab at University Park; with video to room CG623 at Hershey
Dan Mishmar (Ben-Gurion University)
Finally, after 2 billion years, the mitochondrion is part of the general cellular regulation
Billions of years have passed since the fusion event that gave rise to current eukaryotes and their energy producing mitochondria. During that time, the mitochondria, a once free living alpha proteo-bacterium, lost most of its genetic material and became dependent on the cell for its biogenesis. Only 37 genes, which are important for energy metabolism and mitochondrial protein translation, were retained in the current small circular mitochondrial genome. Hence, mitochondrial DNA replication, transcription and post transcriptional regulation are controlled by proteins that are currently encoded by the cell nucleus. It was believed that only a handful of mitochondrial dedicated proteins control mitochondrial function. Hence, one could argue that mitochondria are regulated separately from the rest of the cell. In this talk we will present findings supporting the hypothesis that mitochondria are not only regulated by dedicated factors but are also part of the general cellular regulatory system. We will demonstrate that focusing on mitochondrial DNA transcription and RNA editing. Hence, the long co-existence of the ancient prokaryote within our cells was accompanied by regulatory adaptation.
Friday, May 9, 2014
11:00 AM
Room CG624F at Hershey; with video to 519 Wartik Lab
Laura Carrel (Penn State)
Topological and ncRNA influences on inactive X chromosome gene expression
Friday, Apr 18, 2014
2:00 PM
307 Wartik
Wilfried Guiblet (Penn State)
Selective propagation of functional mitochondrial DNA during oogenesis restricts the transmission of a deleterious mitochondrial variant. Nature Genetics
Friday, Apr 11, 2014
11:00 AM
519 Wartik Lab at University Park; with video to room CG628 at Hershey
Svitlana Tyekucheva (Harvard school of public health)
RNA expression profiling of archival formalin-fixed, paraffin embedded tissues
Friday, Apr 4, 2014
2:00 PM
307 Wartik
Samarth Rangavittal (Penn State)
Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions. Plos Genetics
Tuesday, Mar 25, 2014
8:00 AM
University Conference Center, Penn State Hershey campus
The Fourth Annual Retreat of the Center for Medical Genomics (part of the Huck Institutes of the Life Sciences)
The Fourth Annual Retreat of the Center for Medical Genomics (part of the Huck Institutes of the Life Sciences) will be held Tuesday, March 25, 2014 at the Penn State Hershey, University Conference Center. The keynote speaker for this event will be Dr. Beth A. Tarini, M.D., University of Michigan, C.S. Mott Children s Hospital, Department of Pediatrics and Communicable Diseases. Dr. Tarini is Co-Chair of the American Academy of Pediatrics, Genetics in Primary Care Institute. The retreat also will include short talks by Penn State faculty, a poster session, and networking activities. A goal of this retreat is to provide current genomics information and education to the Penn State University research community, particularly researchers wishing to participate in medical research. All sessions are open to all interested participants.
Friday, Mar 21, 2014
2:00 PM
307 Wartik
Marcia Shu-Wei Su (Penn State)
Andrew H. Moeller, Martine Peeters, Jean-Basco Ndjango, et al. 2013. Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Research Oct;23(10):1715-20
Friday, Feb 21, 2014
2:00 PM
307 Wartik
Boris Rebolledo Jaramillo (Penn State)
Nucleotide variability at its limit? Insights into the number and evolutionary dynamics of the sex-determining specificities of the honey bee Apis mellifera.
Friday, Feb 14, 2014
11:00 AM
519 Wartik Lab at University Park; with video to room CG628 at Hershey
Prabhani Kuruppumullage Don (Penn State)
Model-based block clustering with EM algorithm
The next meeting of the Center for Medical Genomics will take place at 11 am on Feb 14 (Fri). Our speaker will be Prabhani Kuruppumullage Don and she will talk about “Model-based block clustering with EM algorithm”. Prabhani is a statistician, and she has been working on the development of novel and powerful methods for analysis of genomic and medical data. For instance, Prabhani has been working with Francesca Chiaromonte and me on segmenting the human genome into regions differing in mutation rates and patterns, and this work has implications for evaluating disease-causing variants. Prabhani has recently given this talk at Harvard, and it was very well received.
