Marinka Zitnik

Fusing bits and DNA

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Marinka Zitnik

@University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research (Part III)

So what have I been up to in recent weeks here at Toronto? Highlights include my first ride with famous American yellow school bus to a reception at ICSB12 conference, some sightseeing in Toronto city and a trip to Niagara Falls.

Besides, I have finished with data analysis of real-time yeast S. cerevisiae microscopy screens, an idea about it can be captured here. I am now starting with time series analysis and will probably have time to work on integration of phenomics data with genetic interaction and protein interaction data.

Recently a quantum optics research group here at UofT demonstrated a violation of Heisenberg's uncertainty principle and I was really excited about their work. "The quantum world is still full of uncertainty, but at least our attempts to look at it don't have to add as much uncertainty as we used to think!" ... and an easy reading to motivate you to learn more.

I have also come upon a nice real-world (I do not like this term) implementation of an argument based machine learning offered through classification module in CellProfiler Analyst package, participated in a discussion about Gaussian processes (intro, notes) at ccbr-stats meeting and much more. The Lab organized a farewell lunch for summer students only two weeks after my arrival to Toronto, as here and in US classes have already begun (after the Labour Day), I considered it as a welcome event :)

Below are images of Toronto CN Tower, Niagara Falls as seen from Skylon Tower and squirrels at UofT campus (Yes, one cannot miss numerous squirrels playing in parks at campus. A careful look should reveal four of them.), respectively.


Stanford News Story on How Species Evolve Ways to Backup Life's Machinery

Spotlight on our study of versatile and robust molecular machinery and evolution of protein interactomes in Stanford Engineering News.


Proceedings of the National Academy of Sciences: Evolution of Molecular Networks

Our paper on evolution of resilience in protein interactomes is published inĀ Proceedings of the National Academy of Sciences (PNAS).

Using protein-protein interaction data that have only recently become available, we composed and analyzed interactome networks from 1,840 species across the tree of life, expanding the number of species from about 5 in previous studies to 1,840. This unique dataset allowed us to conduct the largest ever study of protein interactomes and quantify the resilience of interactomes--a critical property as the breakdown of proteins may lead to cell death or disease.

Our study reveals that evolution leads to more resilient interactomes, providing evidence for a longstanding hypothesis that interactomes evolve favoring robustness against protein failures. We show that a highly resilient interactome has an astonishingly beneficial impact on the organism to survive in complex, variable, and competitive habitats, a finding that draws attention to a previously unknown critical role of evolution in mediating the effects of the interactome on the ability of a species to thrive in specific habitats.


@University of Toronto, The 13th International Conference on Systems Biology (Part II)

The 13th international conference on systems biology was held in Toronto, 19th--23rd August 2012. Here is a list of talks from platform sessions which I found especially interesting:

  • Modeling the regulatory diversity of human cancers (S. Nelander)
  • Tissue specific modeling of functional genomics data: from networks to understanding human disease (O. Troyanskaya)
  • An evaluation of methods for the modeling of transcription factor sequence specificity (M. T. Weirauch)
  • SEEK and find: data management for systems biology projects (O. Krebs)
  • Excerbt: next-generation knowledge extraction and hypothesis generation from massive amounts of biomedical literature (B. Wachinger)
  • Combining multiple biological domains using patient network fusion (B. Wang)
  • Combining many interaction networks to predict gene function and analyze gene lists (Q. Morris)
  • Assembling global maps of cellular function through integrative analysis of physical and genetic networks (R. K. Srivas)
  • iCAVE: immersive 3d visualization of biomolecular interaction network (Z. Gumus)
  • Systems-level insights from the global yeast genetic interaction network (C. Myers)
  • Monopoly systems edition: advance to GO collect $200 (T. Idekar) (*actually about NeXO, a network extracted ontology and functional enrichment)
  • Genome-scale metabolic models: a bridge between bioinformatics and systems biology (J. Nielsen)

The organizers came up with a nice social program, parts of it is depicted on images below. At opening ceremony Tanja Tagaq, an Inuit woman, performed a unique style of traditional throat singing, Amanda and Rasmus from Sweden made performance at first poster session, Serena Ryder entertained us at conference reception dinner. Shonen Knife, a Japanese punk band that opened Nirvana, played at second poster session at Hart House.

I attended workshops on Designing experiments using state of the art Bayesian global parameter search methodology (M. Goldstein), Introduction to the statistical inference or regulatory networks (F. Emmert-Streib), Imaging flow cytometry: a new view on systems biology (R. DeMarco). In addition to parallel sessions I also enjoyed special lectures and plenary sessions. A few of them are: Reading and writing omes (G. Church), Towards unification of genetic and hierarchy models of tumor heterogeneity (J. Dick), Interactome networks and human disease (M. Vidal), The genetics of individuals (B. Lehner), Synthetic genetic interaction analysis by high-throughput imaging to map cellular networks, Unraveling principles of gene regulation using thousands of designed promotor sequences (E. Segal), Systems biology applications of imaging flow cytometry (T. Galitski).


@University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research (Part I)

In the past few days I have settled in Toronto, Canada, where I will stay until October this year. As a graduate student I will be working at the University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research in the Charlie Boone's Lab.

My work will be mostly data analysis of S. cerevisiae screens by employing various statistical and machine learning methods to gain new knowledge about identification of yeast mutant strains with non-WT phenotype. Possibly I will also work on time-series analysis of actin patches in yeast cells to differentiate them. First impressions are great, I have already met some great people and am looking forward to meet some at the International Conference on Systems Biology (ICSB12), which is held in Toronto in the next week and have a fortunate opportunity to attend.


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