Category: Uncategorized

RNA-seq data analysis workshop scheduled for April 28th

April 16th, 2014 in Uncategorized

Please click here to go to the workshop webpage.

Registration for the RNA-seq hands-on workshop is closed

December 2nd, 2013 in Uncategorized

Please click here to go to the workshop webpage.

Newly Endowed Chair in Human Genetics

November 26th, 2013 in Uncategorized

Applications are now being accepted for  a new endowed professor position, the Aubrey Milunsky Professor of Human Genetics.  Please click here for more information on how to apply.

GSI Next Generation Sequencing Mini Symposium

December 3rd, 2012 in Uncategorized

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

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

GSI Research Symposium Winners

November 15th, 2012 in Uncategorized

IMG_2346
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

GSI 2012 Research Symposium

November 14th, 2012 in Uncategorized

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.

Seed Grant Recipients for 2012

November 13th, 2012 in Uncategorized

The 2012 Seed Grant Recipients were:

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.

Next Gen Sequencing Working Group

January 26th, 2011 in Uncategorized

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 gsi@bu.edu 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
Boston, MA

The Green High Performance Computing Center (GHPCC): How Will It Impact Research Computing at BUMC ?

November 30th, 2010 in Uncategorized

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 gsi@bu.edu.

BUSM/BUSPH Study Links Genes to Puberty Timing and Body Fat in Women

November 23rd, 2010 in Uncategorized

“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.