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 https://academicjobsonline.org/ajo/jobs/6064.

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.

Brandeis will host Gene Expression and RNA Seminar (GEARS) meeting this October

Gene Expression and RNA Seminars (GEARS) club is a monthly event that includes scientific talks on the Gene Expression, RNA and Chromatin. Every month it is held at a different institute in the Boston area.

Brandeis University will be hosting the October GEARS meeting on Thursday, October 30 in Rosenstiel 118 from 6:30 – 7.30 PM and will feature three talks from Boston area researchers.  After the talks, there will be a social hour. This event is free and all are welcome to attend.

Speakers List:

“Hijacking an editing enzyme to reveal the targets of RNA-binding proteins”
Aoife McMahon, PhD, Rosbash lab, Brandeis University

“Genome protection against transposons by the piRNA amplifier complex”
Jordi Xiol, PhD, Moazed lab, Harvard Medical School

“Linking cancer metabolism, DNA repair and epigenetics: SIRT6 provides some clues”
Raul Mostoslavsky, PhD, Associate Professor, MGH Cancer Center/Harvard Medical School/Broad Institute

GEARS Club is generously supported with the help of New England Biolabs and Cell Signaling Technology.
This event is also co-sponsored by the Brandeis Biology Office.

For more information please visit: http://www.gearsclub.org/
Facebook: facebook.com/gearsboston
Twitter @gearsclub

Pioneering geneticist Frederick Alt ’71 wins 44th Rosenstiel Award

Geneticist Frederick Alt ’71 will be awarded the 44th Rosenstiel Award for Distinguished Work in Biomedical Science by Brandeis University for his pioneering research exploring the mechanisms of genomic instability and its implications for the immune system and cancer cells. Alt is the second alumnus to win the Rosenstiel Award; the first, Rod McKinnon ’78, won the Rosenstiel in 1999 and went onto win the Nobel Prize in 2003. Learn more on Brandeis Now …

Genetics Training Grant Retreat to be held Friday, 9/26/14

The annual Genetics Training Grant seminar is being held on Friday, September 26th at the Shapiro Campus Center Auditorium at Brandeis University. Four cutting-edge synthetic biologists: Timothy Lu, Ron Weiss, William Shih and Ahmad Khalil will share their research for the Synthetic Biology: Insights and Applications” symposium.
 
Brandeis graduate students and post-docs will have the opportunity to meet the speakers and present their work in a poster session after the talks. We encourage researchers from all departments to contribute. If you are currently, or previously were on the Genetics Training Grant, presentation of a poster is expected. 

Schedule for GTG Retreat

9:30-10:30 Ron Weiss (MIT, Dept. of Biological Engineering)
“Synthetic biology: from parts to modules to therapeutic systems.”
10:30-11:00 Coffee Break
11:00-12:00 Timothy Lu (MIT, Dept. of Biology Engineering)
“Synthetic biology for human health applications.”
12:00-1:30 Break/Lunch
1:30-2:30 William Shih (Wyss Institute)
“DNA nanostructures as building blocks for molecular biophysics and future therapeutics.”
2:30-3:30 Ahmad Khalil (Boston University, Biomedical Engineering)
“Building molecular assemblies to control the flow of biological information.”
3:30-5:00 Poster session
Shapiro Science Center 2nd floor.
All life sciences students are invited to present.

Chromosome Tethering in Yeast

On July 14, 2014, PLOS ONE  published a paper from the Haber and Kondev labs. The paper, Effect of chromosome tethering on nuclear organization in yeast, was authored by Baris Avsaroglu, Gabriel Bronk, Susannah Gordon-Messer, Jungoh Ham, Debra A. Bressan, James E. Haber, and Jane Kondev.

by Baris Avsaroglu

Chromosopone.0102474_350mes are folded into the cell nucleus in a non-random fashion. In yeast cells the Rabl model is used to describe the folded state of interphase chromosomes in terms of tethering interactions of the centromeres and the telomeres with the nuclear periphery. By combining theory and experiments, we assess the importance of chromosome tethering in determining the spatial location of genes within the interphase yeast nucleus. Using a well-established polymer model of yeast chromosomes to compute the spatial distributions of several genetic loci, we demonstrate that telomere tethering strongly affects the positioning of genes within the first 10 kb of the telomere. Further increasing the distance of the gene from the telomere reduces the effect of the attachment at the nuclear envelope exponentially fast with a characteristic distance of 20 kb. We test these predictions experimentally using fluorescently labeled genetic loci on chromosome III in wild type and in two mutant yeast strains with altered tethering interactions. For all the cases examined we find good agreement between theory and experiment. This study provides a quantitative test of the polymer model of yeast chromosomes, which can be used to predict long-ranged interactions between genetic loci relevant in transcription regulation and DNA recombination.

Patching Up Broken Chromosomes

Olga Tsaponina and James Haber’s recent paper “Frequent Interchromosomal Template Switches during Gene Conversion in S. cerevisiae” was published online by Molecular Cell on July 24, 2014.

by James Haber

“The process of copying DNA every time our cells divide is exceptionally accurate, but in copying 6,000,000,000 base pairs of the genome mistakes do occur, including both mutations and the formation of chromosome breaks. These breaks must be repaired to maintain the integrity of our chromosomes.  In our recent paper we have demonstrated that the mechanism of patching up a broken chromosome is associated with a surprisingly high level of alterations of the sequence.  Many of these changes result from “slippage” of the DNA polymerases copying the DNA during the repair process; for example in copying a sequence of 4 Gs, the polymerase occasionally jumps over one, to lose a base from the sequence (a frameshift mutation).

graphical_abstract_350In this paper we focused on more dramatic slippage events in which the copying machinery jumped from one chromosome to a related but divergent sequence on another chromosome and then jumped back, creating a chimeric sequence.  These interchromosomal template switches (ICTS) occur at a low rate when the distant sequence is only 71% identical, but if we make that segment 100% identical we could find such jumps 10,000 times more frequently, in about 1 in 300 events.  This result reveals how unstable the copying machinery in DNA repair is compared to normal DNA replication. This was very surprising and provides an explanation for many complex rearrangements associated with cancers.  In carrying out this work we identified the first protein that is needed to permit these frequent jumps: a chromatin remodeling enzyme known as Rdh54 that previously did not have a well-defined role in DNA repair in somatic cells.

Finally, we learned a new role for the proteins that survey the genome for mismatched bases that arise during replication and found that one of these proteins, Msh6, is required to specify which strand of DNA containing a mismatch is the “good one” that should be used as the template to correct the mismatch.

This work was supported by the National Institutes of Health General Medical Institute”.

How regulatory sequences evolve in fruit flies

An IMP-Brandeis collaboration reveals the evolution of regulatory sequences in Drosophilids

By Yuliya Sytnikova and Nelson Lau

Enhancers are cis-regulatory DNA sequences that influence the promoters of genes, but identifying enhancers is not a straightforward process. Previously, the Stark lab developed a method for genome-wide enhancer detection called STARR-seq, (Arnold, Gerlach et al. 2013), that allowed them to identify thousands of enhancer sequences around the Drosophila melanogaster genome. In the most recent issue of Nature Genetics, a collaboration between the Stark lab of the IMP (Institute of Molecular Pathology) in Vienna, Austria, and the Lau lab at Brandeis University examines this hypothesis by studying the conservation of enhancer regulatory regions during Drosophilid fly evolution.

To ask if enhancers from D. melanogaster enhancers are also conserved in other Drosophila species in their sequences and locations, the Stark lab extended the STARR-Seq approach to D.yakuba and D.ananassae, which are separated from D.melanogaster by 11 and 40 million years ago, respectively (Arnold, Gerlach et al. 2014). Interestingly, this study also revealed hundreds of new sequences that gained enhancer function differentially between D.yakuba, D.ananassae, and D.melanogaster.

However, to test if these new sequences meaningfully direct different gene expression changes, the Lau lab conducted a targeted mRNA profiling experiment in purified endogenous follicle cells from D.yakuba and D.ananassae. The Stark lab had initiated the STARR-Seq analysis in an Ovarian Somatic Cell (OSC) line, which originated from the follicle cells of D.melanogaster, therefore the profiling of endogenous follicle cells from D.yakuba and D.ananassae was critical. The Lau lab achieved this using a methodology they developed for profiling Piwi-interacting RNAs from these cells (Matts, Synikova et al. 2013).

Figure 6: Evolution of enhancer activity in OSCs and gene expression in follicle cells in vivo.

nature_genetic_fig6

Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A. Nat Genet. 2014 Jun 8. doi: 10.1038/ng.3009. [Epub ahead of print] Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution.

Matts JA, Sytnikova Y, Chirn GW, Igloi GL, Lau NC. Methods Mol Biol. 2014;1093:123-36. doi: 10.1007/978-1-62703-694-8_10. Small RNA library construction from minute biological samples.

 

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