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Cornell University

Eric Siggia Group

Past Projects

My work in biology in retrospect looks like a random walk defined by the experimental groups I was collaborating with.  In rough chronology:

  • Carlos Bustamante 1994-7 DNA elasticity with then postdoc, Rockefeller fellow John Marko, and spin offs towards polymer models of chromosomes. Interactions with the Bensimon-Croquette group at ENS Paris for DNA mechanics and Joe Gall on lampbrush chromosomes were important.
  •  Jennifer Lippincott-Schwartz 1999-2001, Cell biology of protein trafficking, reconstitution of Golgi-Endoplasmic Reticulum through the cell cycle. JLS is a pioneer in live imaging of culture cells and her invention of the photoactivatable GFP enabled Betzig’s super-resolution microscopy. I contributed  physical chemistry ideas to the organelle field and some image processing.
  • Bioinformatics of Gene Regulation 2000-2005, Ulrike Gaul, Carol Gross, David Botstein. When the E.coli and  budding yeast genomes became available, and later Drosophila and related flies, the question arose could one make probabilistic models and infer regulation. A good group of trainees got involved, Hao Li, Harmen Bussemaker, Eldon Emberly, Nicholas Rajewsky, Erik van Nimwegen, Rahul Siddharthan, Saurabh Sinha, Alex Morozov. The most amusing algorithm was Mobydick [LINK], that worked quite well for yeast but dies in metazoans since they are sloppy spellers. Other useful algorithms connected expression data directly with regulatory motifs, and leveraged interspecies comparisons in the search for functional bits of sequence. Our best paper with Gaul, inferring regulation in D.pseudoobscura and testing in D.melanogaster was never published [LINK]. Another useful angle was to build random libraries of binding sites and assay for expression in yeast with labs of Fred Cross and Barak Cohen. I abandoned this area since experimental technologies got to point where the location of any regulatory protein (or RNA) could be found, thus reducing the subject to a cataloguing exercise.
  • Fred Cross 2005-2010 Dynamics of the cell cycle in yeast. This is an exemplary instance of what genetics could accomplish, and the Hartwell papers are an illustration of what biology can do that physics could not imagine. Like a good rock climber, who confronts what appears to be a featureless wall and glides up it. By the time I got involved the subject was considered ‘mature’ or played out. However the dominant technique, derived from the screens was a population phenotype, but budding yeast in particular is very hard to synchronize since it buds asymmetrically. So the physics angle was just to do time lapse imaging on colonies as they grew, and most importantly examine all the mutants that Fred had in his freezer. Working at the intersection of two fields was revelatory, the Start transition which was conceived (with population data) to be a simple feed forward gene cascade was shown to involve feedbacks and bistability. The importance of exploiting the genetics can’t be overstated. Among the games we played was to phase lock the cell cycle to metabolically controlled cyclin pulses.  During this period I evolved a fruitful modus operandi of placing quantitative people in a receptive lab to learn the trade and expand the repertoire of the host lab, Stefano di Talia, Jan Skotheim, Gilles Charvin, and Lu Bai took the plunge.
  • It's a matter of almost religious conviction among biologists that evolution is contingent, redo the process and the outcomes will be different. Contingency is highly plausible as regards to the exact amino acid sequence of a protein, but what the dynamical process that during axial growth will lay down a series of genes that serve to define axial position, or the periodic array of somites that are now known to arise from a clock and wavefront mechanism. A decade + ago Paul Francois and I wrote code to do Darwinian evolution on gene networks, subject to boundary conditions and optimizing a fitness function that favored the pattern of interest. The results were uniformly interesting. Among applications was looking for the last common ancestor of flies and mosquitos, that define their AP pattern with homologous genes.  The expression domains of the posterior gap genes have moved while their targets, the pair-rule genes appear invariant.  How did evolution move the regulators around but preserve the targets? More tangibly with Prof A. Tomasz at Rockefeller, we traced the evolution of a S.aureus infection in a single patient undergoing Vancomycin therapy.  A handful of point mutations resulted in jumps in resistance, and the patient died after 2 months from the infection.
  • Ali Brivanlou and I collaborated for about a decade with a talented group of postdocs and students from the physical sciences (Sorre, Warmflash, Etoc, Metzger, Yoney, Martyn, Phan-Everson, and Valet).  We used human embryonic stem cells to recreate aspects of embryonic development in defined geometries. Starting with cells, it’s easy to use CRISPR to knock out or tag genes. With these tools a great deal was learned about the cascade of morphogens kicked off by BMP, and how they together with their secreted inhibitors generate spatial patterns. The cell biology of apical-basal polarized epithelia is intimately involved in the patterning process.