February 1, 2011
The Human Genome, written by John Quackenbush, PhD
We are pleased to announce Dr. Quackenbush's recent book, The Human Genome! The book takes the reader on a tour of the history and science behind the Human Genome Project and the technologies that are revolutionizing the practice of medicine today.
You can purchase the book here.
February 9, 2011
Jim Volcker is Dana-Farber's Employee of the Year
Jim Volcker, grants management specialist for our department, won DFCI's Employee of the Year award on February 9, 2011. Said Dr. Quackenbush in his nomination, "Dana-Farber is built on two strong pillars. The first is treating patients using the best available treatments in a compassionate and caring environment. The second is a program of world-leading research into the mechanisms and potential therapies for cancer. In both domains, it is our clinical and research faculty who are often recognized for their contributions, but in truth, we stand on the shoulders of giants who make what we do possible. And there are few 'giants' who stand taller than Jim Volcker."
This summer, the Quackenbush Lab, a subset of the Biostatistics and Computational Biology Department, has provided the opportunity for undergraduate and high school students to explore the world of Computational Biology. These students, under the mentorship of Aedin Culhane, make up the GeneSigDB curation team. GeneSigDB is a database of manually curated gene signatures extracted from published articles (http://www.genesigdb.org).
The team has worked diligently on expanding, and improving GeneSigDB. Individually, they have read through hundreds of publications and have curated a plethora of relevant gene signatures. The team averages over 200 new gene signatures a week. For the fourth release of GeneSigDB, they plan to curate a total of 5,000 gene signatures by the end of the summer. These signatures will include host response to mycobacterium, as well as those pertaining to various cancerous tissues.
Use of Genetic Variance to Identify Potential Therapeutic Targets
June 28, 2012: John Quackenbush chats with ecancer.tv at the Worldwide Innovation Networking 2012 Symposium for Personalized Cancer Medicine in Paris, France.
The Advent of Personalized Genomic Medicine
Watch John Quackenbush's presentation, The Advent of Personalized Genomic Medicine. This Science for the Public lecture took place on May 24, 2012.
New LGRC Press Release
Genomic Data on Chronic Lung Disease Made Readily Available on New Website
The constant focus on customer needs that drives the design of everything from automobiles to personal computers has now been applied to a field traditionally immune to such concepts: the scientific study of disease.
On a new website, the Lung Genomics Research Consortium (LGRC) – an alliance of scientists at five U.S. institutions – makes a broad range of genomic data on chronic lung disease available in a format specifically tailored to investigators’ needs. In contrast to other genomic research websites, which typically upload massive amounts of information without much regard for how the data will be used, the new site, www.lung-genomics.org, was designed entirely with end users in mind.
Continue to read the press release here.
Check out the LGRC website here.
GeneSigDB release 4.0
Announcing release 4.0 of Gene Signature DataBase (GeneSigDB)
GeneSigDB is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized resource of published prognostic, diagnostic, and other gene signatures of cancer and related disease to the community so they can compare the predictive power of gene signatures or use these in gene set enrichment analysis. GeneSigDB 4.0 contains 3,515 gene signatures, which were collected and transcribed from 1,604 published articles largely focused on gene expression in cancer, stem cells, immune cells, development, and lung disease.
In June, Christine Wells of the University of Queensland and her PhD student, Lizzi Mason, visited Dana-Farber to further their collaborative work with John Quackenbush and Jessica Mar. This group has been doing groundbreaking work on the role that variation plays in defining phenotype and in regulating cell-fate transitions and a number of papers describing their work have recently been accepted. Ms. Mason's PhD project will continue this collaborative project, looking at the epiteneitc factors that control transcriptional variation and influence phenotype. In July, Drs. Mar and Quackenbush visited UQ to continue their work with Dr. Wells and her team.
Congratulations to Dr. Jessica Mar on her recent appointment as an Assistant Professor in Systems and Computational Biology at the Albert Einstein College of Medicine. Jess was a PhD student and then postdoctoral fellow working with John Quackenbush and the other members of the Computational Biology and Functional Genomics Laboratory. Her thesis work involved the study of variation in genomic data included the first theoretical and experimental demonstration that gene expression levels in individual cells can be described by Poisson statistics. As a postdoctoral fellow working in collaboration with Quackenbush and Dr. Christine Wells of the University of Queensland, she helped open up new ways of thinking about biological variation and its role in defining phenotype and published a number of landmark papers in this area.
VIZBI Conference, March 16 2011
Jimmy Fund Scooper Bowl, June 9 2011
Enzo Martinelli, a student in our lab, represented the group at this year's Jimmy Fund Scooper Bowl. The Scooper Bowl is an all-out ice cream fest; pay a small amount at the gate and gain unlimited access to as many flavors, brands, and scoops as you wish. The proceeds from this popular event benefit Dana-Farber Cancer Insitute and the Jimmy Fund. Our favorite BU sophomore consumed scoop after scoop of ice cream, creating a leaning tower of Pisa made of little cups and melty dribbles. Stacked 35 cups high, Enzo's tower astonished our lab and livened the child that resides in all of us. An employee with us for 2 years and a Scooper Bowl-er for 5, we are proud to have Enzo on our side!
GeneSigDB Release 3.0
The Gene Signature DataBase is a searchable database of fully traceable,
standardized, annotated gene signatures which have been manually curated
from publications that are indexed in PubMed. GeneSigDB Release 3.0,
contains 2142 gene signatures were manually curated from 973
publications that focus on gene signatures of cancer and viral, lung
disease and stem cell biology.
Introducing the Public Beta of RNASeq-supporting MeV
The MeV team has been working furiously to build a version of MeV that can load and analyze next generation sequencing data. Today we are proud to announce the first public beta version of an RNA-Seq capable MeV.
This project has shown that it is, indeed, feasible to adjust MEV's data model and processing functions to handle this new data; that the memory footprint is not untenable, and that the existing features so important to microarray data analysis can easily be applied to the richer datasets now available.
12/03/2010 - 22:57
John Quackenbush speaks about his work at Dana-Farber
Who Are We?
Genomics has revolutionized biology, but not in the ways that many of us initially envisioned. While the reference genome sequences and the catalogues of genes that genome projects have provided are useful starting points for understanding the basis for development and disease, the tools and technology spawned by the genome project have had a far greater impact. Our group focuses on the application of functional genomics techniques including microarrays, proteomics, metabolomics, and other high-throughput approaches and the development of computational approaches in support of these studies to develop a comprehensive view of human diseases including cancer. Our goal is to develop software, databases, and bioinformatics techniques that will allow the development of new diagnostics and a more complete understanding of the cellular networks that are mechanistically responsible for diseases. Our commitment is to make those tools widely and freely available to the research community to enable research beyond our own.