Debbie Marks wins Overton Prize

April 21, 2016 § Leave a comment

It’s very exciting to announce that our very own Debbie Marks has won the Overton Prize from the International Society for Computational Biology (ICSB).  The Overton Prize recognizes early to mid-career scientists who are emerging leaders in computational biology and bioinformatics, and is offered in memory of G. Christian Overton, a leading bioinformatics researcher and a founding member of the ISCB Board of Directors.  Previous winners include many of our friends, including Uri Alon, Olga Troyanskaya and Aviv Regev.  The prize committee obviously has outstanding taste!


Cell Systems launches Math | Bio article format

October 22, 2015 § 1 Comment

The newest Cell sister journal, Cell Systems, just launched an interesting new format called Math | Bio.  In an editorial announcing the new format, Quincey Justman explains that by creating this new format the editors hope to encourage papers like John Hopfield’s 1974 work on kinetic proofreading — a paper that discussed an idea about how biology could work, without attempting in any way to prove that biology did work that way.   Let’s hope it’s successful! There are many nice things about this format.  What I like most is that it opens a channel between people who have theoretical ideas but no way to test them and people who may have relevant experimental results but are puzzled about how to interpret them. Also, if biology is more theoretical than physics — as Jeremy Gunawardena has argued — we need more and better channels to get the theory out there.

And it’s also nice, of course, that the inaugural Math | Bio paper is from our Department.  In it, Yoni Savir, Ben Tu from UT Southwestern, and Mike Springer describe a possible design for a biological linear rectifier.  A linear rectifier produces an output that is linear relative to input above a threshold, and over a wide range of input values.  Savir et al. argue that such a device could be useful in many settings in biology, including nutrient regulation of growth rate and gene expression; and they show that a relatively simple motif involving competitive inhibition could behave in this way.

So, is anyone out there scratching their head over an output that seems weirdly linear and just won’t saturate?  You could be lucky: it might not be an artefact after all, but the first example of an exciting new form of biological signal processing. Check it out.

Two Assistant Professor positions available

October 19, 2015 § Leave a comment

The Department of Systems Biology at Harvard Medical School invites applications for tenure-track Assistant Professor positions. Two positions are available. We seek creative thinkers who take risks in defining and addressing important problems in biology and medicine, and who use quantitative experimental, computational and/or theoretical approaches in their work. The Department has a diverse faculty with backgrounds in cell biology, biochemistry, physics, mathematics, chemistry, computer science, engineering and medicine, and offers a lively, family-friendly, and supportive environment in which to perform interdisciplinary science.

The successful candidates will become members of Harvard University’s Ph.D. Program in Systems Biology, a cross-campus interdisciplinary program that attracts extraordinary graduate students.

A Ph.D., M.D./Ph.D. or M.D. is required.

The deadline for applications is 15 November, 2015.  For more information, and to apply, please go here.

We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, protected veteran status, or any other characteristic protected by law.

Departmental Fellowships redux

October 19, 2015 § Leave a comment

The deadline for the Departmental Fellow positions I wrote about a few months ago is long past, but if you’re interested in the position we’d still like to hear from you. Here’s the description of the role:

Systems Biology Departmental Fellowships are intended for outstanding recent PhDs with a primary training in the theoretical sciences (theoretical physics, mathematics, engineering, computer sciences and related disciplines). Prior experimental experience is optional; the decision to award a Fellowship will primarily be based on the potential for the Fellow to bring theoretical approaches to bear on biological questions. Candidates should be interested in being embedded in an experimental environment to advance their theoretical work, or to use some of their post-doctoral time to train in experimental biology, or both.

Fellows will join the Department of Systems Biology and make their initial home in a pre-agreed host lab. They will also select a theory mentor who may be external to the department. Fellows are encouraged to interact with multiple labs through conversations or collaborative projects.

If you think you’re a fit, feel free to e-mail me with a CV and a letter explaining how you would use the opportunity to explore biology: becky {at} hms {dot} harvard {dot} edu.

Departmental Fellow positions available!

May 28, 2015 § Leave a comment

Just announced: two Departmental Fellow positions.  These positions are intended to attract researchers with a recent Ph.D. in a theoretical discipline who would benefit from spending a couple of years exploring biological questions, either because they are planning to work on theoretical projects relevant to biology or because they want to gain experimental experience, or both.  Full advertisement here:

Our Department is a very supportive place for theorists exploring the murky realms of biology.  Tell your friends!

ChIP-seq quality control

December 14, 2012 § Leave a comment

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

December 14, 2012 § 1 Comment

 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

November 15, 2012 § 1 Comment

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

November 14, 2012 § 1 Comment

Nice to see Randall Munroe return to mathematical snark.

Theory Lunch this week

October 25, 2012 § Leave a comment

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.