The Next Generation Sequencing Mini-Symposium held on Thursday, November 29, 2012 was...
The Next Generation Sequencing Mini-Symposium held on Thursday, November 29, 2012 was a huge success with a large turnout and quality presentations focusing on mRNA-seq, sncRNA-seq, and ChIP-seq. The following is a list of presenters with a link to their presentation slides.
1:00 pm Rick Myers (GSI Director) - Introduction and Overview
1:10 pm Rebecca Kusko (Spira Lab) – mRNA sequence analysis
1:35 pm Alexandra Dumitriu (Myers Lab) – mRNA quality control methods
2:05 pm Andi Broka (LinGA System Administrator) - Computational resources (LinGA use)
2:45 pm Elyse Kozlowski (Jones Lab) – Sample and library prep for miRNA
3:10 pm Josh Campbell (Spira Lab) – Analytic strategies for miRNAs
3:35 pm Evan Johnson (Computational Biomed) – Analytic strategies part II
4:00 pm Antonio Luiz (Galagan Lab) - Studying Transcription factors by ChIP-seq
4:30 pm Rick Myers (GSI Director) - Studying Histon marks by ChIP-seq
Standing: Rebecca Kusko, Zachary Hunter, Carly Garrison, Artie Lambert, Anna Lyubetskaya, Joshua CampbellSitting: Kahkeshan Hijazi and Hilo Milo Rasouly Missing: Kristen Ott, Sarah Heerboth, and Ying Shen
At the Genome Science 2012 Research Symposium awards were given to graduate students and post doctoral fellow for oral and poster presentations. The following is a list of winners:
Oral Presentation Winners:
Arthur Lambert (Graduate Student in Molecular Medicine, Thiagalingam Lab) - Periostin signaling regulates breast cancer stem cells
Anna Lyubetskaya (Graduate Student in Bioinformatics, Galagan Lab) - Using ChIP-seq for transcription factor binding sites prediction and validation in M. tuberculosis
Hila Milo Rasouly (Graduate Student in Genetics and Genomics, W. Lu Lab) - Loss of Robo2 improves survival of ILK mutant mice
Kristen Ott (Graduate Student in Genetics and Genomics, Navarro Lab) - Characterizing spindle-E, a protein involved in guarding the genome
Zachary Hunter (Graduate Student in Pathology and Laboratory Medicine, Treon Lab) - Copy number and small variant analysis from whole genome sequencing of 30 patients with Waldenstrom’s Macroglobulinemia
Poster Presentation Winners:
Joshua Campbell (Postdoctoral Fellow, Spira Lab) - Characterizing the small RNA transcriptome associated with COPD and ILD using next generation sequencing
Carly Garrison (Graduate Student in Genetics and Genomics, Spira Lab) - Mir-4423 promoted ciliated cell fate during airway epithelium differentiation
Sarah Heerboth (Undergraduate Student in Biology) - Development of a combination therapy: Allele-specific re-expression of an imprinted tumor suppressor gene ARHI
Kahkeshan Hijazi (Graduate Student in Bioinformatics, Spira Lab) - Nasal epithelial gene expression profiles reflect dyamic biological response to smoking-cessation
Rebecca Kusko (Graduate Student in Genetics and Genomics, Spira Lab) - Comprehensive genomic profiling of the lung transcriptome in emphysema and IPF using RNA-Seq
Ying Shen (Postdoctoral Fellow, Spira Lab) - Adaptive models for predicting pathway activation and drug response in cancer tissues
The 2012 Annual Genome Science Institute Research Symposium held on Monday, October 22 was a resounding sucess with participation from both Boston University campuses and seven technology partners.
The 2012 Seed Grant Recipients were:
Matthew Jones, PhD, Pulmonary
Collaborators: Kenneth H. Albrecht, PhD, Medicine, Genetics and Genomic; Caryn L. Navarro, PhD, Medicine
- To determine whether ZCCHC11 deficiency affects the content level and uridylation of testicular sncRNAs using deep sequencing, mRNA expression using microarrays, and retrotransposon expression using qRT-PCR.
- To how and when ZCCHC11 deficiency causes germ cell loss leading to infertility by analyzing morphology and marker gene expression in Zcchc11 mutant gonads.
Cesar A. Sommer, PhD, Gastroenterology
Collaborator: Gustavo Mostoslavsky, PhD, Gastroenterology
- To interrogate the transcriptome of GIP-expressing K-cells in order to identify genes that define their molecular profile.
- To investigate the ability of K-cell “identity genes” to modulate the production of GIP and the development of K-cells in vitro.
Sam Thiagalingam, PhD, Biomedical Genetics
Collaborator: Maria I. Ramirez, PhD, Pulmonary Center
- To test the effect of SDPR over-expression/knock down in in vitro model systems and screening for SDPR expression in tissue microarrays (TMA)
- In vivo analysis of candidate metastasis suppressor gene, SDPR.
The inaugural meeting of the Next Gen Sequencing working group took place on January 24th. Over 30 individuals attended to discuss the needs of the university for next gen sequencing from library preparation to result analysis.
For the next meeting Andi Broka will present on the LinGA High Performance Compute Cluster and its analytical capabilities and software resources. Additionally, a survey will be prepared to help categorize the university’s needs to help guide the future direction of the working group.
If you are interested in joining the working group, please email firstname.lastname@example.org to be added to the email list for future events and opportunities.
Next Gen Sequencing Working Group
Computational Resources at BU
Speaker: Andi Broka
February 15th, 3pm-4pm
EBRC Rm X714
650 Albany St
The Green High Performance Computing Center (GHPCC): How Will It Impact Research Computing at BUMC ?
On November 30, John Goodhue, Glenn Bresnahan, and Tracy Shroeder came to BUMC to discuss the Massachusetts Green High Performance Computer Center. This new initiative from five universities wil help keep Boston at the cutting edge of computational research.
For those who were not able to attend the meeting in person or online, you can download the slides from the presentation below.
Update: The slides from the meeting have been taken down. If you would like to discuss the GHPCC initiative, please contact email@example.com.
“Scientists, including a Boston University School of Public Health (BUSPH) researcher, have discovered 30 new genes that control the age of sexual maturation in women. Notably, many of these genes also act on body weight regulation or biological pathways related to fat metabolism.
The study, which appears in Nature Genetics, was co-authored by Kathryn Lunetta, a BUSPH professor of biostatistics. The study was a collaborative effort by the international ReproGen consortium, which included 175 scientists from 104 worldwide institutions, including Boston University School of Medicine (BUSM) and BUSPH.” ~From BU School of Public Health: The Insider
For the full article, please visit The Insider’s website.
From Art Jahnke, BU Today~
“The National Research Council has raised concerns in a letter posted on its website yesterday about the methodology used in an ongoing study of the risks associated with the National Emerging Infectious Diseases Laboratories (NEIDL) on the Boston University Medical Campus.
The NRC found that the risk assessment, which is being supervised by the National Institutes of Health and conducted by the consultancy Tetra Tech, had yet to respond to a recommendation for tiered quantitative and qualitative analyses and that its researchers erred when they used expert opinions as a substitute for absence of actual data on 13 pathogens in a modeling process. The NRC committee, whose concerns stem from a scheduled review of a preliminary draft of the risk assessment, urged Tetra Tech to make a “midcourse correction” and use actual data rather than the opinions of experts.”
For the full article, please visit BU Today.
The 2nd Annual GSI Research Symposium has come and gone this October. Hundreds of faculty, staff, and students stopped by the Heibert Lounge to support genetic and genomic research at Boston University.
Dozens of posters lined the walls of the 14th floor of the L-Building on the Medical Campus. Graduate and undergraduate students as well as postdoctoral fellows and faculty were all presenting posters.
Awards were given out to the best student and postdoctoral fellow presenters in multiple categories.
The GSI Symposium Awards Recipients: (top row) Elizabeth Tanner, Badri Vardarajan, Stephanie Correa, Rebecca Kusko, Constantina Christodoulou, Kristen Ott, Stephanie Schneider, Daniel Dworkis; (front row) Catalina Perdomo, Irene Degano, Stephanie van Veen, Cody MacDonald.
Click below to read about Adrienne’s selection as the most recent recipient of the Janet L. Norwood award.