ChIP-seq quality control

Aaron Diaz (aad1974 AT gmail DOT com) writes:

“We at UCSF have recently developed a software tool for ChIP-seq quality control and protocol optimization called CHANCE, which appears in the current special issue of Genome Biology.

CHANCE has a graphical interface and doesn’t require any knowledge of programming or statistics. I hope it will be useful and interesting to your readers. The CHANCE program as well as the source code can be downloaded here.”

Take a look and let Aaron know what you think!

Quantitative Imaging: From Cells to Molecules

 Announcing a new course at Cold Spring Harbor Laboratory: “Quantitative Imaging: From Cells to Molecules”.  Applications are due on January 31, 2013.  Apply here.
Course Description:
This course will focus on advanced quantitative fluorescence microscopy techniques used for imaging a range of biological specimens, from cells to single molecules. The course is designed for cell and molecular biologists with little or no microscopy experience, who wish to begin utilizing microscopy in their own research. Students will gain a theoretical understanding of, and hands-on experience with, state-of-the-art equipment used in quantitative fluorescence microscopy, including: laser scanning and spinning disk confocal microscopy, deconvolution methods, total internal fluorescence microscopy (TIRF), super-resolution methods (structured illumination, STORM, and PALM), and digital image processing and analysis. Students will learn how to design and implement a wide range of imaging experiments using these techniques. Students will use the techniques to address specific quantitative questions and then discuss the results as a group, learning to trouble-shoot the common problems that occur in the course of a quantitative imaging experiment. Among the lectures presented are: microscopy basics, CCD cameras, confocal microscopy, multi-photon microscopy, deconvolution, TIRF, single molecule imaging, imaging ratio-metric “biosensors” (including FRET), and super-resolution techniques. Students will also learn specimen preparation for microscopy, including fixation and immunofluorescence in tissue culture cells, choosing fluorescent proteins, working with live samples requiring environmental control, and more.
Organizers/Instructors:  Jennifer Waters (Harvard) and Torsten Wittmann (UCSF)
Instructors:  Max Krummel (UCSF), Bo Huang (UCSF), and Lisa Cameron (DFCI)
More info and online application:

Three UCL Excellence Fellowships, London UK

University College London -UCL Faculty of Maths and Physical Sciences
UCL Reference: 1292831
Salary range: Grade 8 (£39,818 – £46,972 per annum), or Grade 9 (£51,052 – £55,512), depending on experience, inclusive of London Allowance.

UCL is one of the world’s most prestigious, research-led universities, ranked 4th in the world and 2nd in Europe (2012/13 QS World University Rankings). UCL’s Excellence Fellowship Programme seeks to recruit and develop the best early career scientists, supporting them in an environment that fosters academic excellence and creativity to become the leaders of the future.

The current round seeks candidates working in research areas relevant to UCL and the new Francis Crick Institute (, of which UCL is a founding partner. Due to open nearby to UCL in 2015, the Crick promises to be one of the most significant developments in UK biomedical science for a generation.

Fellowships are available within UCL School of Life and Medical Sciences (SLMS) and UCL Faculty of Maths and Physical Sciences (MAPS). Please note that this advertisement is for those based in MAPS. Please search for ‘UCL Excellence Fellowships – SLMS’ to apply for a fellowship based in SLMS.

The posts are funded for 3 years in the first instance.

Applications are welcome from researchers in any area of science involving a physical-biomedical multidisciplinary approach, with a high priority on Computational, Mathematical, Chemical and Biomaterials sciences, although applicants from other fields will also be welcome. Successful candidates will be expected to have (i) a PhD, (ii) a strong publication record in internationally leading journals, (iii) a novel and challenging research agenda which will advance the strategic objective of UCL and its engagement with the Crick Institute, (iv) demonstrable creativity, and v) clear leadership potential.

All UCL Excellence Fellows will be expected to undertake research that aligns with the strategy of both UCL and the Francis Crick Institute, and to promote and participate in collaborative links with the Crick Institute’s other partners – the MRC National Institute for Medical Research, CR-UK London Research Institute, Imperial College London and King’s College London.

Apply here.  Please provide  a full CV and a research proposal to include a statement of research vision and ambition. Enquiries should be directed to .
We particularly welcome female applicants and those from an ethnic minority, as they are under-represented within UCL at this level.

UCL Taking Action for Equality

Closing Date: 7/12/2012

Another spot-on comic from XKCD

Nice to see Randall Munroe return to mathematical snark.

Theory Lunch this week

A programmable DNA origami shuttle to study the dynamics of motor protein ensembles

26 October 2012, 12:00-1.30 pm, Warren Alpert 563 – HMS
Samara Reck-Peterson
Department of Cell Biology
Harvard Medical School

Bi-directional microtubule-based transport in eukaryotic cells drives the movement of intracellular components, allowing cells to move, divide, communicate with neighboring cells, and maintain cellular homeostasis. We built a system composed of both biological and synthetic parts to determine how the opposite-polarity molecular motors dynein and kinesin achieve bi-directional transport of cargo on microtubules. We used three-dimensional DNA origami to build a synthetic cargo structure, to which cytoplasmic dynein and kinesin-1 motors can be linked. The modularity of DNA origami allows us to control cargo size and shape and precisely encode the type, number, density, and spacing of motors. I will discuss our recent empirical studies, which investigate how motor number and type affects cargo movement in vitro.

TL schedule here.

Group leader positions in London


The Cancer Research UK London Research Institute is currently recruiting Junior Group Leaders. The LRI is the largest research institute funded by Cancer Research UK, the largest independent cancer research organisation in Europe. Its research focusses on the analysis of fundamental biological processes involved in cancer. The Institute’s international staff work in 50 research groups at the Institute’s two London laboratory sites at Clare Hall (South Mimms) or Lincoln’s Inn Fields (central London).

In 2015 the LRI will be absorbed into the new Francis Crick Institute, housed in a state-of-the-art laboratory building currently under construction at St Pancras, London. The Crick will use interdisciplinary approaches to investigate the biology of human health and disease, and will work with scientists and research institutions across the UK. In addition to researchers from LRI, the Crick’s research portfolio – some 1500 researchers in over 120 research groups – will be developed from the MRC National Institute for Medical Research, and three London universities: UCL, King’s College London, and Imperial College London.

These positions thus offer a tremendous opportunity for an ambitious young scientist to establish a world-class research programme in an interactive and supportive environment. LRI research groups are extremely well supported: there is no requirement to obtain external grant funding, there are no teaching responsibilities, and we benefit from centrally funded cutting-edge core technology facilities.

LRI is focussed on the broad area of cancer biology, and particularly interested in the following fields:

Tumour Biology: tumour-host interactions, cancer models, human cancer genomics
Genome integrity: Chromosome Biology, DNA damage, Cell Cycle regulation
Computational Biology: Bioinformatics, biological networks, image processing

Applications should be submitted online.

Deadline November 30.

Theory Lunch this week

What cell shape oscillations tell us about cortical actin-microtubule interactions and amoeboid migration

Friday, 19 Oct 2012, 12:00-1:30 pm, Warren Alpert 563, HMS

Kenneth Jacobson
Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill

Many cellular responses to environmental stimuli involve large-scale changes in cell morphology. For example signaling molecules, such as hormones or growth factors, can induce cell differentiation, proliferation, or migration. These global changes in cell shape are highly coordinated and require dynamic regulation of the actin cytoskeleton. Therefore understanding how the actin and microtubule cytoskeleton and associated regulatory proteins function as an integrated system is a central challenge for cell biology. The morphological oscillations that occur during cell spreading are ideally suited for performing a systems-level investigation into the biochemical and biomechanical mechanisms that drive changes in cell shape. In the broader context, these oscillations constitute a mechanochemical prototype of how signaling networks regulate cytoskeletally driven mechanical behavior that in turn feeds back to modulate the signaling network. Importantly, fluorescently labeled cytoskeletal proteins and fluorescent biosensors allow dynamic structural features of the actin-based cortex and spatiotemporal activity of signaling molecules and visualized. I will discuss what we know about the dynamic structural changes in the actin cortex during oscillations, how Rho proteins regulate these oscillations, how this model may be related to amoeboid migration and emerging theoretical models for this phenotype. If time permits, I will also discuss a new paradigm for membrane domains based on pathogen receptors located on the surface of dendritic cells.

TL schedule here.