1:00 pm Rick Myers (GSI Director) - Introduction and Overview

MYERS_NGS Symposium mRNA miRNA ChIP-seq – MYERS -INTRO

1:10 pm Rebecca Kusko (Spira Lab) – mRNA sequence analysis

KUSKO_gsi_seq_Nov_2012

1:35 pm Alexandra Dumitriu (Myers Lab) – mRNA quality control methods

DUMITRIU_11.28.2012_GSI_Symposium

2:05 pm Andi Broka (LinGA System Administrator) - Computational resources (LinGA use)

BROKA_Comp. Resources for Next Gen Sequence Analysis

2:45 pm Elyse Kozlowski (Jones Lab) – Sample and library prep for miRNA

KOZLOWSKI_GSI sequencing talk final

3:10 pm Josh Campbell (Spira Lab) – Analytic strategies for miRNAs

CAMPBELL_121129_Joshua_Campbell_GSI_sub

3:35 pm Evan Johnson (Computational Biomed) – Analytic strategies part II

JOHNSON_gsi_2012

4:00 pm Antonio Luiz (Galagan Lab) - Studying Transcription factors by ChIP-seq

GOMES_BUMC_Gomes_nov29

4:30 pm Rick Myers (GSI Director) - Studying Histon marks by ChIP-seq

Click to Enlarge

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

Matthew Jones, PhD, Pulmonary

Collaborators:  Kenneth H. Albrecht, PhD, Medicine, Genetics and Genomic; Caryn L. Navarro, PhD, Medicine

Aims:

• 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

Aims:

• 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

Aims:

• 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.

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.

February 15th, 3pm-4pm

EBRC Rm X714
650 Albany St
Boston, MA

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 gsi@bu.edu.

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.

“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.

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.

http://sph.bu.edu/insider/index.php/Recent-News/busphs-adrienne-cupples-honored-for-achievement-in-statistical-sciences.html?piwik_campaign=insideremail