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Computational Modeling of Gene Expression and its Evolution
From Tuesday 13 October 2015
To Friday 16 October 2015

 

 

tamir workshop plus sponsors 

 

 

 

 

 

Organizers

Registration and Call for Abstracts

Workshop Description

Invited Speakers

Program

Visas and Local Information

Transportation

Accommodation

Venue

Weather

Funding

Contact


Organizers

Tamir Tuller, Tel Aviv University, Israel (tamirtul@post.tau.ac.il)
Michal Linial, The Hebrew University, Israel (michall@cc.huji.ac.il)
Claus Wilke, The University of Texas at Austin, USA (wilke@austin.utexas.edu)
Mans Ehrenberg, Uppsala University, Sweden (ehrenberg@xray.bmc.uu.se)

 


The place of the workshop 

The lectures will take place at Rosenblatt Auditorium of the Engineering Faculty. Signs will be put up to guide you to the Auditorium from gate 4 (if you reside in Einstein) and gate 17 (if you reside in Broshim).

 

 


Workshop Description

Gene expression is the fundamental process by which information encoded in the DNA (genotype) is used to produce proteins (phenotype). The process includes several stages and sub-stages (e.g. transcription, RNA processing, translation, transport, mRNA and protein degradation, etc), and as it is partially encoded in the transcript it affects and relates to its evolution. The increasing rate by which experimental data related to gene expression is generated, and the knowledge related to gene expression gained in recent years enables: 1) Developing/tailoring multivariate machine learning and biophysical models of this process. 2) Developing/tailoring computational models that connect gene expression to molecular evolution of transcripts.   

The aim of the workshop will be to deal with computational modeling (or mathematical formalizations enabling computational modeling) and analysis of all aspects of gene expression biophysics and evolution. Specifically, we aim to bring together leading researchers (e.g. systems/computational biologists, evolutionary biologists, mathematical biologists, and biophysicists) that employ computational tools to study gene expression evolution and/or gene expression biophysics. Since many stages of genes expression interact/overlap with each other, and since models of various gene expression stages share various similarities, we will promote presentations related to all aspects/stages of gene expression. 

Some specific (overlapping) topics will include: 1) Mathematical formalization of various aspects/stages of gene expression that enables computational study. 2) Computational simulation of gene expression. 3) Mathematical/computational models that connect gene expression and evolution. 3) Computational prediction/analyzing of various aspects of gene expression based on large scale genomic data. 4) Gene expression engineering base on rational algorithms. 5) Computational handling of noise and stochasticity in gene expression processing and data. 6) Employing computational biophysical approaches to understand molecular evolution.

 

Some relevant papers:

* Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection.
Johansson M, Zhang J, Ehrenberg M. Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):131-6.

* Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets. Amar D, Hait T, Izraeli S, Shamir R.
Nucleic Acids Res. 2015 Sep 18;43(16):7779-89.

* ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.
Schöneberg J, Noé F. PLoS One. 2013 Sep 11;8(9):e74261.

* One third of dynamic protein expression profiles can be predicted by a simple rate equation.
Tchourine K, Poultney CS, Wang L, Silva GM, Manohar S, Mueller CL, Bonneau R, Vogel C.
Mol Biosyst. 2014 Nov;10(11):2850-62.

* Dissecting the expression landscape of RNA-binding proteins in human cancers.
Kechavarzi B, Janga SC. Genome Biol. 2014 Jan 10;15(1):R14.

* An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, Zaborske J, Pan T, Dahan O, Furman I, Pilpel Y. Cell. 2010 Apr 16;141(2):344-54.

* Slow fitness recovery in a codon-modified viral genome. Bull JJ, Molineux IJ, Wilke CO. Mol Biol Evol. 2012 Oct;29(10):2997-3004. 

* Ribosome flow model with positive feedback. Margaliot M, Tuller T. J R Soc Interface. 2013 May 29;10(85):20130267.

* Facilitated diffusion buffers noise in gene expression. Schoech AP, Zabet NR. Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Sep;90(3):032701.

* Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Frenkel-Morgenstern M, Danon T, Christian T, Igarashi T, Cohen L, Hou YM, Jensen LJ. Mol Syst Biol. 2012 Feb 28;8:572.

*Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA.
Gorgoni B, Marshall E, McFarland MR, Romano MC, Stansfield I. Biochem Soc Trans. 2014 Feb;42(1):160-5. 

*Ribosome recycling induces optimal translation rate at low ribosomal availability.
Marshall E, Stansfield I, Romano MC. J R Soc Interface. 2014 Sep 6;11(98):20140589.

* Observation of dually decoded regions of the human genome using ribosome profiling data. Michel AM, Choudhury KR, Firth AE, Ingolia NT, Atkins JF, Baranov PV. Genome Res. 2012;22(11):2219-29.

* Inferring gene function from evolutionary change in signatures of translation efficiency.
Krisko A, Copic T, Gabaldón T, Lehner B, Supek F. Genome Biol. 2014 Mar 3;15(3):R44. 

* Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site. Panecka J, Šponer J, Trylska J. Biochimie. 2015 May;112:96-110.

* Genome-wide organization of eukaryotic preinitiation complex is influenced by nonconsensus protein-DNA binding. Afek A, Lukatsky DB. Biophys J. 2013 Mar 5;104(5):1107-15.

* Automated design of synthetic ribosome binding sites to control protein expression. Salis HM, Mirsky EA, Voigt CA. Nat Biotechnol. 2009 Oct;27(10):946-50.

* Effect of ribosome shielding on mRNA stability. Deneke C, Lipowsky R, Valleriani A. 
Phys Biol. 2013 Aug;10(4):046008. 

* Speed controls in translating secretory proteins in eukaryotes--an evolutionary perspective. Mahlab S, Linial M. PLoS Comput Biol. 2014 Jan;10(1):e1003294.

* A Model of Protein Translation Including Codon Usage Bias, Nonsense Errors, and Ribosome Recycling. Gilchrist, M.A. and A. Wagner. 2006. Journal of Theoretical Biology 239: 417-434.

* The ribosome as an optimal decoder: a lesson in molecular recognition. Savir Y, Tlusty T. Cell. 2013, 11;153(2):471-9.

* Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates. O'Brien EP, Vendruscolo M, Dobson CM. Nat Commun. 2014;5:2988.

* Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. Sanchez-Freire V, Ebert AD, Kalisky T, Quake SR, Wu JC. Nat Protoc. 2012 Apr 5;7(5):829-38.

* Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation. Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Barte DP. bioRxiv, 021501.


Invited Speakers 

List of Invited Speakers and Talks (Sorted Alphabetically):

* Pavel Baranov, University College Cork, Ireland  
"Untangling Protein Synthesis with Ribosome Profiling"

* Mans Ehrenberg, Uppsala University, Sweden
"
Accuracy of Genetic Code Translation by Transfer RNAs"

* Milana Frenkel-Morgenstern, Bar Ilan University, Israel
"
Non-Optimal Codon Usage Creates Cell-Cycle-Dependent Oscillations in Protein Levels"

 * Michael Gilchrist, University of Tennessee, USA  

"Decoupling the Effects of Selection, Mutation and Drift on the Evolution of CUB: A Genomic Approach"

Sarath Chandra Janga, Indiana University-Purdue University Indinnapolis, USA
"Dissecting the Post-Transcriptional Networks of RNA-Binding Proteins in the Human Genome Using Genomic and Systems Approaches"

* Tomer Kalisky, Bar Ilan University, Israel
"Single Cell Genomics in Regenerating Tissues and Tumors"

* Michal Linial, The Hebrew University, Israel
"Design Principles in Translating the Secretory Proteome"

* David Lukatsky, Ben Gurion University, Israel
"Protein-DNA Binding in the Absence of Specific Base-Pair Recognition"

 * Michael Margaliot, Tel Aviv University, Israel

"The Ribosome Flow Model: Theory and Applications"

* Frank Noé, Freie University of Berlin, Germany
"Interacting-Particle Reaction-Diffusion (iPRD) Simulations : Towards Realistic in Silico Models of Cellular Signal Transduction"

 * Edward O'BrienPenn State University, USA
"Codon Positions that Strongly Influence Cotranslational Folding are Far from Equilibrium: A Method for Controlling Nascent-Protein Folding"

* Yizhak Pilpel, Weizmann Institute of Science, Israel
"How to Make More (Protein) for Less (of Cell's Resources): Lessons Learned from Lab Evolution"

* Shlomi Reuveni, Harvard Medical School, USA
"Sculpted by Auto-Replication"

* M. Carmen Romano, University of Aberdeen, UK
"Reduce, Reuse, Recycle: Modelling of Ribosome Recycling in S. Cerevisiae"

* Howard Salis, Pennsylvania State University, USA
"Biophysical Models of Translation Initiation and Regulation: Predicting Function from Sequence"

* Yonatan Savir, Harvard Medical School, USA
"Yeast Response to Multiple Carbon Sources: A Case study of Combinatorial Signal Integration"

* Premal Shah, University of Pennsylvania, USA
"Opportunities and Pitfalls in Modeling Protein Translation Using Ribosome-Profiling Data"

* Ron Shamir, Tel Aviv University, Israel
"Using Gene Expression to Understand and Distinguish Diseases"

 * Ian Stansfield, University of Aberdeen, UK

 "Genome-Wide Simulation of Translation Correctly Identifies the Gene Targets of tRNA Regulation "

* Fran Supek, Centre for Genomic Regulation, Spain
"Patterns of Evolutionary Change in Gene Expression Levels Predict Biological Roles of Genes"

* Joanna Trylska, University of Warsaw, Poland
"Functional Dynamics of Ribosomal RNA"

* Tamir Tuller, Tel Aviv University, Israel
"Deciphering the Gene Expression Code with Synthetic Reporter Gene Libraries"

* Angelo Valleriani, Max Planck Institute of Colloids and Interfaces, Germany
"Signals of Premature Ribosomal Drop-Off in E. Coli Riboseq Data"

* Christine Vogel, New York University, USA
"Deciphering the Ups and Downs of Protein Expression Regulation"

* Claus Wilke, The University of Texas at Austin, USA
"Attenuating Bacteriophage T7 through Systematic Codon De-Optimization"

* Nicolae Radu Zabet, University of Essex, UK
"Diffusion of Transcription Factors Displays Complex Effects on the Noise in Gene Expression"

 

Participants (in alphabetical order)

* Zohara Alfandary, Tel Aviv University, Israel

* Amit Alon, Tel Aviv University, Israel

* David Amar, Tel Aviv University, Israel

* Fábio Tadeu Arrojo Martins, Tel Aviv University, Israel

* Shimshi Atar, Tel Aviv University, Israel
 
* Tali Bar-Lev, Bar-Ilan University, Israel
 
* Reut Bar Yaacov, Ben-Gurion University, Israel
 
Rachel Elizabeth Bell, Tel Aviv University, Israel
 
* Nissim Ben-Haim, Tel Aviv University, Israel

* Itamar Borukhov, Compugen Ltd, Israel
 
* Avital Brodt, Tel Aviv University, Israel
 
* Lauren Bushnell, Tel Aviv University, Israel
 
* Liran Carmel, Hebrew University of Jerusalem, Israel

* Ruthie Caspi, Tel Aviv University, Israel

* Catherine Charneski, MRC CSC & Imperial College, UK
 
* Jun Cheng, University of Munich, Germany
 
* Eyal Cohen, Tel Aviv University, Israel
 
* Emiliano Cohen, Hebrew University of Jerusalem, Israel
 
* Tal Cohen, Ben-Gurion University, Israel

* Natalie Day, Tel Aviv University, Israel

Alon Diament, Tel Aviv University, Israel
 
* Roi Dor, Tel Aviv University, Israel

* Iris Dror, Technion - Israel Institute of Technology, Israel

* Benjamin Dubreuil, Weizmann Institute of Science, Israel
 
* Hila Dvir, Tel Aviv University, Israel

* Anna Feldman, Tel Aviv University, Israel

* Simon Fishilevich, Weizmann Institute of Science, Israel
 
* Tamar Friedlander, IST, Austria

* Idan Frumkin, Weizmann Institute of Science, Israel

* Maya Galili, Tel Aviv University, Israel
 
* Tal Galili, Tel Aviv University, Israel
 
* Yehonatan Glick, Bar-Ilan University, Israel
 
* Uri Gophna, Tel Aviv University, Israel

* Eli Goz, Tel Aviv University, Israel
 
* Ruth Hershberg, Technion - Israel Institute of Technology, Israel

* Etai Jacob, Compugen Ltd, Israel

Maciej Jasiński, University of Warsaw, Poland
 
* Sivan KaminskiWeizmann Institute of Science, Israel
 
 * Itamar Kanter, Bar-Ilan University, Israel

Yossef Kliger, Compugen Ltd, Israel
 
* Michael Korostishevsky, Tel Aviv University, Israel
 
* Hillel Kugler, Bar-Ilan University, Israel 

* Marta Kulik, University of Warsaw, Poland
 
* Efrat Leopold, Tel Aviv University, Israel
 
* Roei Levy, Tel Aviv University, Israel

* Kiril Lomakin, Tel Aviv University, Israel

* Shelly Mahlab Aviv, Hebrew University of Jerusalem, Israel
 
* Aharon Nachshon, Tel Aviv University, Israel
 
* Sarit Oriel, Ben-Gurion University, Israel
 
* Nir Pillar, Tel Aviv University, Israel
 
* Eyal Privman, University of Haifa, Israel

* Renana Sabi, Tel Aviv University, Israel
 
* Naor Sagy, Tel Aviv University, Israel
 
* Avital Sarusi, Bar-Ilan University, Israel
 
* Dvir Schirman, Weizmann Institute of Science, Israel
 
* Regev Schweiger, Tel Aviv University, Israel
 
* Gilad Shaham, Tel Aviv University, Israel
 
* Shula Shazman, The Open University of Israel, Israel
 
* Yuval Tabach, Hebrew University of Jerusalem, Israel

* Lior Trieman, Tel Aviv University, Israel

* Florian Uhlitz, Charité - Universitätsmedizin Berlin, Germany

* Iddo Weiner, Tel Aviv University, Israel
 
* Daphna Weissglas, Tel Aviv University, Israel
 
* Eitan Winter, Hebrew University of Jerusalem, Israel
 
* Liron Yoffe, Tel Aviv University, Israel
 
* Evgeny Yurkovsky, Tel Aviv University, Israel

* Zohar Zafrir, Tel Aviv University, Israel

* Yoram Zarai, Tel Aviv University, Israel

* Hadas Zur, Tel Aviv University, Israel


 

Program

The workshop program can be found in:

http://www.cecam.org/workshop-2-1190.html

 


 


Visas and Local Information

Information regarding visa requirements and other local information can be found on the webpages of the Ministry of Tourism and the Ministry of Foreign Affairs of Israel.


Transportation

From the airport: Once you exit the terminal at Ben-Gurion airport, you will find a good (and relatively affordable) taxi service named Hadar-Lod that can take you to your hotel. More information regarding this and other transportation routes to and from the airport (and a lot of other relevant information) can be found on the webpage of the Ministry of Tourism.


Accommodation

A. Tel Aviv University (TAU) Guest Houses (http://meonot-shik.co.il/guest-apartments)

Einstein Office: 63 Haim Levanon Street, Tel Aviv 6997804, Israel. 
Phone: +972-3-6408333
FAX: +972-3-6413671
e-mail: office@meonot-shik.co.il

 

We have a limited number of rooms available for our workshop guests at TAU's guest houses, which are in walking distance from the workshop's venue (Einstein guest house on 63 Haim Levanon Street and Broshim guest house on 20 George Wise Street). Rooms will be reserved on a first-register first-served basis.

Each room includes:

  • Linens and towels.
  • A fully operational kitchen including: pots and pans, cutlery, ceramic stove, microwave, kettle and refrigerator.
  • LCD 32'' television + expanded cable package.
  • Air conditioning/heating.
  • Free Wi-Fi access.
  • Basic coffee and tea set.

Please note that there is no breakfast service in the guest houses.

Price: we have reserved several rooms at different rates, with prices ranging between 175 and 291 NIS per night including VAT (see http://meonot-shik.co.il/guest-apartments). These prices may somewhat vary as we approach the workshops dates. Please verify the final price upon reservation.

Reservations: for further details and reservations, please contact Mrs. Jacqueline Gorsky (cecam@tau.ac.il).

 

B. TEL AVIV HOTELS

Tel Aviv University (TAU) has signed agreements with several hotels in the Tel Aviv area to provide attractive prices for TAU affiliates. As participants of a CECAM activity @ TAU you are entitled to book these hotels at a reduced price. We recommend our participants to choose one of the following hotels, where we will reserve several rooms. For each hotel the reservation will be valid until a different date (detailed below), after which rooms can still be booked at the reduced price based on hotel availability. Room bookings should be made directly by you to the hotel of your choice.

 

1. LEONARDO BASEL HOTEL (http://www.fattal-hotels-israel.com/tel-aviv-hotels/leonardo-basel-tel-aviv)

Leonardo 156 Hayarkon Street, Tel Aviv 63451, Israel. 
Phone: +972-3-5207711
FAX: +972-3-5270005
e-mail:  info@fattal.co.il

 

The Leonardo Basel hotel is located near the beach and in the center of Tel Aviv, offering you a variety of dining and entertainment choices at your doorstep. Every room has a comfortable work table and free Internet wireless access, a private bathroom with shower, WC and hair dryer. Room amenities include cable LCD TV, mini-fridge, coffee and tea maker, safe and telephone. Some rooms can be booked by smokers, but should be reserved in advance. The hotel offers various types of rooms:

Comfort Room (not overlooking the sea): Price for: single occupancy: 690 NIS; double occupancy: 790 NIS.

Comfort Sea View Room: Price for: single occupancy: 730 NIS ; double occupancy: 830 NIS.

The hotel price includes: Breakfast, free WiFi in all rooms and public areas, coffee/tea kit in each room, business lounge (open from 7am till 10pm) with copier, fax and printer, light buffet and soft/hot drinks.

PRICES DO NOT INCLUDE VAT (18% to be paid only by Israeli passport holders). Rates are subject to the Dollar/Shekel or Euro/Shekel exchange rates and may vary as we approach the workshops dates.

 

2. ALEXANDER HOTEL (http://www.alexander.co.il)

Alexander 3 Havakuk Street, Tel Aviv 63505, Israel. 
Phone: +972-3-5452228
FAX:  +972-3-5469346
e-mail: hotel@alexander.co.il , tali.pessach@alexander.co.il

 

The Alexander is a boutique hotel located on the beach, near the center of Tel Aviv, offering you a variety of dining and entertainment choices at your doorstep. An AM-PM branch is nearby and open 24/7. The hotel offers various types of rooms:

Junior Suites (45 m2) with 1 double bedroom, living room, kitchenette, full bathroom, interactive cable LCD TV Price for: single occupancy: 660 NIS;  double occupancy: 790 NIS; triple occupancy: 910 NIS. 

Luxury Suites (55 m2) with 1 double bedroom, large living room, fully equipped kitchen, walk-in closet, full bathroom, working desk, interactive cable LCD TV. Price for: single occupancy: 740 NIS; double occupancy: 860 NIS. For each additional person you will need to add 120 NIS (maximum 4 persons per room).

The hotel rate includes: full Israeli buffet breakfast, complimentary wireless internet throughout the hotel, and complimentary entrance to the business lounge and modern fitness room.

PRICES DO NOT INCLUDE VAT (18% to be paid only by Israeli passport holders). Rates are subject to the Dollar/Shekel or Euro/Shekel exchange rates and may vary as we approach the workshops dates.

 

3. MAXIM HOTEL (http://www.maxim-htl-ta.co.il/

Maxim 86 Hayarkon Street, Tel Aviv 63903, Israel. 
Phone: +972-3-5173721
FAX: +972-3-5173726
e-mail:  info@maxim-htl-ta.co.il

 

The Maxim Hotel is located near the beach and in the center of Tel Aviv, offering you a variety of dining and entertainment choices on our doorstep.  This hotel is smaller and more intimate than the other ones offered and was fully refurbished in 2012. The rooms are small but comfortable and economical. The price includes free WiFi, tea and coffee making facilities, and a fridge. Guests are welcome to take advantage of the hotel's complimentary afternoon "Coffee & Cake".

Room prices:

Single room with single bed:                 360 NIS.

Double room with single occupancy:   470 NIS.

Double room with double occupancy:  570 NIS.

PRICES DO NOT INCLUDE VAT (18% to be paid only by Israeli passport holders). Rates are subject to the Dollar/Shekel or Euro/Shekel exchange rates and may vary as we approach the workshops dates.


Venue

The workshop venue will be anounced soon.

An interactive map of TAU campus can be found at:

http://www2.tau.ac.il/map/unimaple1.asp 


Weather

The weather in Tel-Aviv in October is usually very pleasant during the day and can be somewhat chilly during the evenings. Average temperatures for the dates of the workshop are 15C(low)-25C(high) (http://www.wunderground.com/). Average water temperature for these dates is 26C (http://www.israelweather.co.il/page3.asp?topic_id=76&topic2_id=73&page_id=62). Nevertheless, since it is autumn, the fluctuations can be large. Therefore, we recommend that you check the weather forecast close to your departure date.


Funding

Funding for the workshop was generously provided by the following organizations:

  • CECAM-ISR Node @ TAU.
  • Edmond J. Safra Bioinformatics Center.
  • Sagol School of Neuroscience.
  • Radbiomed, Technology incubator.
  • SGI
  • Evogene
  • Danyel Biotech
  • TransAlgea
  • Tel Aviv University

Contact

Jacqueline Gorsky (cecam@tau.ac.il)

Located in Lausanne, Switzerland, CECAM is a well established (since 1969) European organization devoted to the promotion of fundamental research on advanced computational methods and to their application to important problems in frontier areas of science and technology. CECAM's fields of interest include computational chemistry, materials science, physics, and biology.