Brandeis University and NCBI to host Genomics Hackathon in April

Brandeis University is partnering with NCBI to host a Boston-area genomics hackathon April 25-27, 2016. Two previous hackathons held at NCBI successfully integrated scientists from across the country with different skill sets to tackle challenges in RNA-seq and genomics.

The August 2015 NCBI hackathon identified gaps in usability of current RNA-seq analysis tools and in just three days created software that greatly improved ease-of-use.

The August 2015 NCBI hackathon identified gaps in usability of current RNA-seq analysis tools and in just three days created software that greatly improved ease-of-use.

NCBI hackathons identify gaps in the current state-of-the-art analysis pipelines and outline feasible solutions to bring users, especially novices, closer to understanding genomic data and analysis. This hackathon will be highly cooperative: teams of 5-6 individuals will work on non-overlapping projects and share their expertise in a collaborative way. Projects planned for this session include:

  • Network Analysis of Variants
  • Structural Variation
  • RNA-Seq
  • Streaming Data and Metadata
  • Neuroscience/Immunity
  • Command-line user-interface design

The hackathon is an exciting opportunity to meet researchers in similar fields at different institutions, learn new ways of applying your work, and work with a team to contribute original work to the genomics field. Participants are also provided with the opportunity to publish their work in a newly-created F1000 hackathon channel.

Brandeis University and NCBI invite all genomics researchers to apply and visit the NCBI announcement for more information. Participants will need to bring their own laptops to the event and have some knowledge of a scripting language (Python, PERL, Shell, etc).

Please apply by 5:00 PM March 22, 2016.

Tenure-track positions in Biology (application deadline Oct 15)

The Biology Department at Brandeis University invites applications for up to two full-time, tenure-track appointments, beginning Fall 2016, from individuals who are conducting innovative research in the broad areas of molecular and cellular biology. Junior and more senior investigators will be considered, but preference will be given to hiring at the Assistant Professor level. Areas of interest range across molecular genetics, genomics and cell biology, including topics such as RNA biology, cytoskeleton, intracellular transport, development, signal transduction, transcriptional and post-transcriptional regulation, membrane biology, and epigenetics.

The research environment at Brandeis is highly collaborative, and we seek colleagues who will complement and extend existing strengths. Brandeis offers world-class research in the setting of a small liberal-arts university. Brandeis is located 7 miles from Boston, and is part of the vibrant research community of the greater Boston area.

Brandeis recognizes that diversity in its student body, staff and faculty is important to its primary mission of providing a quality education. The search committee is therefore particularly interested in candidates who, through their research, teaching and/or service experiences, will increase Brandeis’ reputation for academic excellence and better prepare its students for a pluralistic society.

To apply, please provide the following: a cover letter, a curriculum vitae, a summary of your research accomplishments to date, including a statement of your goals for future independent research (3-page limit), up to three publications, and at least three letters of reference. Applications will be accepted only through AcademicJobsOnline at

First consideration will be given to applications received by October 15, 2015. Following an initial evaluation by the search committee, finalists will be invited to visit the campus to discuss their research and to meet with faculty and students/postdocs. Additional inquiries may be directed to Leslie Griffith or to Paul Garrity.

Brandeis University is an equal opportunity employer, committed to supporting a culturally diverse intellectual community. Applications are particularly encouraged from applicants of groups underrepresented in the sciences.

TIDAL-Fly: a new database resource of Transposon Landscapes for understanding animal genome dynamics.

We tend to think of our genomes as nicely-ordered encyclopedias,  curated with only useful information that makes up our genes.  In actuality, nature and evolution is extremely sloppy.  All animal genomes, from us humans to the simple fruit fly, are littered with genetic baggage.  This baggage is sizeable, making up at least 11% of the fly genome and more than 45% of our genome.  The scientific term for this baggage is transposable elements (TEs) or transposons, which are mobile entities that must copy themselves to other places of the genome to ensure their survival during animal evolution.

Because there are so many copies of transposons, they can be difficult to analyze by most standard genetic methods. Brandeis postdoctoral fellow Reazur Rahman and a team in Nelson Lau’s lab have formulated a new tool called the Transposon Insertion and Depletion AnaLyzer (TIDAL). TIDAL aims to provide an accurate and user-friendly program to reveal how frequently transposons can move around in animal genomes.  Currently, the TIDAL tool has been applied to over 360 fruit fly genomes that have been sequenced and deposited in the NIH NCBI Sequencing Read Archive.  The outputs from this program are available to the whole genetics community through the TIDAL-FLY database.

tidal fly banner

The TIDAL-Fly database will allow geneticists to pick their favorite fly strain and see if a transposon has landed near to their gene and perhaps affect gene expression. Fruit flies are key model organisms utilized by many researchers, including here at Brandeis, to study human diseases, from infertility to insulin signaling to aging to sleep disorders.  Since these new transposon insertions are not available in the standard genome databases, this tool and website may provide answers to previously puzzling genetic effects not revealed by typical DNA sequencing studies.  It is Reazur’s and the Lau lab’s goal to continue updating the TIDAL-Fly database with more genomes as fly genome re-sequencing becomes easier and easier to perform.

see also: Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res. 2015.

New course on Genomic Health Care

Professor Barbara Lerner will teach a new course, BIOL 235b American Health Policy & Practice and the Delivery of Genomic Health Care, in Spring Semester, 2012. The course is now scheduled for Block X2,  Tuesdays from 6:30 PM–9:20 PM. Enrollment is limited to Genetic Counseling or Health Policy graduate students or with permission of the instructor.

The continuous discovery of genetic markers for common diseases is leading to an increasing demand for genetic services, and for the integration of traditional medical genetics with mainstream medicine and public health care. In addition, the American healthcare system is evolving and huge changes in how care is accessed, financed and delivered can be expected in the coming years. Those providing genetic services will therefore need a strong background in the structure of the American healthcare system and how public policy is influencing the field of medical genetics. This course is specifically designed to meet this objective using a mixture of readings from the literature, writing assignments, lecture, class discussion, guest speakers, and student presentations.

Naegleria Genome

Chan Fulton, Professor Emeritus of Biology at Brandeis, has been for many years a pioneer in using Naegleria gruberi, a single-cell eukaryote, as a research organism. This eukaryote can differentiate from ameobae to swimming flagellates in response to environmental cues.

In a paper published this week in Cell by Chan and his co-workers, the genome sequence of this organism is revealed and analyzed. The sequence information provides new insights into metabolic diversity (aerobic-anaerobic switching) in eukaryote evolution and in the early branching in the development of signalling pathways.

Brandeis users can read the full text on the web.

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