Organized by Todd Golub
9:30 am-11:00 am
7 Cambridge Center Monadnock Room (NE30-2040)

NO MEETING

11:30 am-12:30 pm
7 Cambridge Center Monadnock Room (NE30-2040)

"Functional genomic analysis of a human fungal pathogen "
by Malcolm Whiteway (Biotech Research Institute, Montreal, Canada)

Abstract: Candida albicans is an important human pathogen, causing mucosal infections of immunocompetent individuals and potentially fatal systemic infections of immunocompromised patients. Many of the powerful molecular approaches to unravel cellular function pioneered in the yeast Saccharomyces cerevisiae can be applied (with some difficulty) to C. albicans. Molecular analyses can then be coupled with the extensive sequence information available for the ascomycete fungi to compare and contrast how these two fungi with similar genomes but highly divergent lifestyles use transcriptional control to regulate cellular function. In some cases the regulatory circuits have clearly been modified to adapt each organism to a specific ecological niche, while in other cases even fundamentally conserved metabolic processes have dramatic differences in their transcriptional regulation. These studies underscore the great flexibility inherent in the transcriptional regulatory systems of the ascomycetes.

Organized by Chris Newton-Cheh
8:30 am-9:30 am
7 Cambridge Center Monadnock Room (NE30-2040)

"The genetic basis of gene expression"
by Chris Cotsapas with Barbara Stranger (Mass General Hospital and Brigham and Women's Hospital)

Organized by David Altshuler
9:30 am-11:00 am
7 Cambridge Center Monadnock Room (NE30-2040)

"Ancient Admixture in Human Genetic History"
by David Reich, Nick Patterson, and Priya Moorjani (Broad)

Organized by Deb Hung, Bruce Birren, Lisa Cosimi, Pardis Sabeti
9:00 am-10:30 am
7 Cambridge Center Monadnock Room (NE30-2040)

"Human Microbiome Project Update"
by Doyle Ward

Organized by Mike Fitzgerald
10:15 am-11:15 am
320 Charles Street Atlantic Room (NE125-0101)

Abstract: We have adapted the sequence editor Consed and the sequence comparison program Cross_match for use in resequencing projects with large numbers of short reads. Consed now has the capability to read, display, and edit Solexa and 454 reads (and their "traces"), and can handle resequencing assemblies with millions of aligned reads with response times similar to those for small assemblies. Additional features have been added to Consed, such as navigators for variants and high/low depth of coverage regions, and sorting of the reads within a window, making it useful (and not overwhelming) to view such assemblies. Cross_match can now find gapped alignments for a million 36bp Solexa reads against the human genome in about 1.5 hours (about 18 minutes if cross_match is allowed to ignore matches within masked repeats). Consed-ready ace files can be prepared in a fraction more time. Cross_match reports, for resequencing applications, sequence variants & confirmed segments and strength of evidence. It has many options for reporting of hits (including mapping qualities) and can report a histogram of hit scores. It can find local, global (the entire read is aligned), or RNASeq alignments (allowing cDNA to be aligned against genomic DNA with GY-AG splice sites). We have also developed "phaster" which is an order of magnitude or more faster than cross_match, finding alignments of 27 million 76 base reads against the human genome in 64 minutes. I will present evidence that it is faster and more sensitive than Bowtie. We have implemented CALF, a compact file format for both unaligned reads and alignments with the goal of facilitating nimble analysis and visualization of alignments with up to billions of reads. CALF files of unaligned reads are roughly half the size of fastq files with the same data. We have implemented Next_phred for the purpose of calling reads from Illumina image files. I will cover this just briefly.

Speaker David Gordon (and Phil Green), Genome Sciences Dept, Univ of Washington (Seattle)

Organized by Brad Bernstein
9:30 am-11:00 am
7 Cambridge Center Monadnock Room (NE30-2040)

"Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses"
by Ido Amit (Broad Institute)

Abstract: abstract: "Models of mammalian regulatory networks controlling gene expression have been inferred from genomic data, yet have largely not been validated. We present an unbiased strategy to systematically perturb candidate regulators and monitor cellular transcriptional responses. We apply this approach to derive regulatory networks that control the transcriptional response of mouse primary dendritic cells (DCs) to pathogens. Our approach revealed the regulatory functions of 125 transcription factors, chromatin modifiers, and RNA binding proteins and constructed a network model consisting of two dozen core regulators and 76 fine-tuners that help explain how pathogen-sensing pathways achieve specificity. This study establishes a broadly-applicable, comprehensive and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells."


"Large Intergenic Non-coding RNAs : From Discovery to Mechanism "
by John Rinn (Harvard Medical School)

Organized by Kerstin Lindblad-Toh
1:00 pm-2:00 pm
320 Charles Street Caribbean Room (NE125-2250)

"High-lights from the analysis of 29 mammals to annotate the human genome."
by Kerstin Lindblad-Toh (The Broad Institute)

Organized by Todd Golub
9:30 am-11:00 am
7 Cambridge Center Monadnock Room (NE30-2040)

"Medical and Population Genetics in 2009"
by David Altshuler, M.D., Ph.D. (Broad, MGH)


Notes: CANCER PROGRAM SHUTTLE BUS - PICK UP AT 9:00 A.M.: At the Dana Farber Cancer Institute's Main Entrance located at 44 Binney Street and drop off at the main entrance to the Broad (7 Cambridge Center). RETURN PICK UP AT 11:15 a.m.: In front of the Broad (7 Cambridge Center). Will drop off at the Dana Farber Cancer Institute 44 Binney Street entrance.

Organized by Chris Newton-Cheh
8:30 am-9:30 am
7 Cambridge Center Monadnock Room (NE30-2040)

"Copy number variation in the human genome"
by Josh Korn (Broad Institute)

Organized by David Altshuler
9:30 am-11:00 am
7 Cambridge Center Monadnock Room (NE30-2040)

"Comprehensive Phenomes, Personal Stem Cells and Genome Interpretation Software"
by George Church (Harvard Medical School)

Organized by Deb Hung, Bruce Birren, Lisa Cosimi, Pardis Sabeti
9:00 am-10:00 am
7 Cambridge Center Monadnock Room (NE30-2040)

"SPARC BRAINSTORMING SESSION"