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Today's Topics:
1. AlCoB 2014: 2nd call for papers (GRLMC)
2. New exchange platform for Graph Theory (Reinhard Diestel)
3. PhD Scholarship and Postdoc position on Theory of
Evolutionary Computation (Dirk Sudholt)
4. PhD study at the London School of Economics in Management
Science (Operations Research / Algorithms, Combinatorics, and
Optimization) (Gregory Sorkin)
5. Algebra and Mathematical Logic: Theory and Applications,
Kazan, June 2-6, 2014 - preliminary announcement (S Barry Cooper)
----------------------------------------------------------------------
Message: 1
Date: Mon, 11 Nov 2013 11:50:29 +0100
From: "GRLMC" <grlmc@urv.cat>
To: <dmanet@zpr.uni-koeln.de>
Subject: [DMANET] AlCoB 2014: 2nd call for papers
Message-ID: <FD77C4D44D884C13B7E2DD8F8E29236E@Carlos1>
Content-Type: text/plain; charset="iso-8859-1"
*********************************************************************
1st INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY
AlCoB 2014
Tarragona, Spain
July 1-3, 2014
Organized by:
Research Group on Mathematical Linguistics (GRLMC)
Rovira i Virgili University
http://grammars.grlmc.com/alcob2014/
*********************************************************************
AIMS:
AlCoB aims at promoting and displaying excellent research using string and
graph algorithms and combinatorial optimization to deal with problems in
biological sequence analysis, genome rearrangement, evolutionary trees, and
structure prediction.
The conference will address several of the current challenges in
computational biology by investigating algorithms aimed at: 1) assembling
sequence reads into a complete genome, 2) identifying gene structures in the
genome, 3) recognizing regulatory motifs, 4) aligning nucleotides and
comparing genomes, 5) reconstructing regulatory networks of genes, and 6)
inferring the evolutionary phylogeny of species.
Particular focus will be put on methodology and significant room will be
reserved to young scholars at the beginning of their career.
VENUE:
AlCoB 2014 will take place in Tarragona, located 90 kms. to the south of
Barcelona. The venue will be the Catalunya Campus.
SCOPE:
Topics of either theoretical or applied interest include, but are not
limited to:
Exact sequence analysis
Approximate sequence analysis
Pairwise sequence alignment
Multiple sequence alignment
Sequence assembly
Genome rearrangement
Regulatory motif finding
Phylogeny reconstruction
Phylogeny comparison
Structure prediction
Compressive genomics
Proteomics: molecular pathways, interaction networks ...
Transcriptomics: splicing variants, isoform inference and quantification,
differential analysis ?
Next-generation sequencing: population genomics, metagenomics,
metatranscriptomics ...
Microbiome analysis
Systems biology
STRUCTURE:
AlCoB 2014 will consist of:
invited talks
invited tutorials
peer-reviewed contributions
INVITED SPEAKERS:
Michael Galperin (National Center for Biotechnology Information, Bethesda),
Comparative Genomics Approaches to Identifying Functionally Related Genes
Uwe Ohler (Max-Delbr?ck Centre for Molecular Medicine, Berlin), Decoding
Non-coding Regulatory Regions in DNA and RNA (tutorial)
Jason Papin (University of Virginia, Charlottesville), Network Analysis of
Microbial Pathogens
PROGRAMME COMMITTEE:
Tatsuya Akutsu (Kyoto, JP)
Amihood Amir (Ramat-Gan, IL)
Alberto Apostolico (Atlanta, US)
Joel Bader (Baltimore, US)
Pierre Baldi (Irvine, US)
Serafim Batzoglou (Stanford, US)
Bonnie Berger (Cambridge, US)
Francis Y.L. Chin (Hong Kong, HK)
Benny Chor (Tel Aviv, IL)
Keith A. Crandall (Washington, US)
Bhaskar DasGupta (Chicago, US)
Joaqu?n Dopazo (Valencia, ES)
Liliana Florea (Baltimore, US)
Olivier Gascuel (Montpellier, FR)
David Gilbert (Uxbridge, UK)
Gaston H. Gonnet (Zurich, CH)
Roderic Guig? (Barcelona, ES)
Dan Gusfield (Davis, US)
Vasant Honavar (University College, US)
Sorin Istrail (Providence, US)
Tao Jiang (Riverside, US)
Inge Jonassen (Bergen, NO)
Anders Krogh (Copenhagen, DK)
Giovanni Manzini (Alessandria, IT)
Carlos Mart?n-Vide (Tarragona, ES, chair)
Satoru Miyano (Tokyo, JP)
Burkhard Morgenstern (G?ttingen, DE)
Shinichi Morishita (Tokyo, JP)
C?dric Notredame (Barcelona, ES)
Graziano Pesole (Bari, IT)
Mark Ragan (Brisbane, AU)
Timothy Ravasi (Thuwal, SA)
Allen G. Rodrigo (Durham, US)
Steven Salzberg (Baltimore, US)
David Sankoff (Ottawa, CA)
Thomas Schiex (Toulouse, FR)
Jo?o C. Setubal (S?o Paulo, BR)
Steven Skiena (Stony Brook, US)
Peter F. Stadler (Leipzig, DE)
Wing-Kin Sung (Singapore, SG)
Alfonso Valencia (Madrid, ES)
Jacques van Helden (Marseille, FR)
Arndt von Haeseler (Vienna, AT)
Lusheng Wang (Hong Kong, HK)
Limsoon Wong (Singapore, SG)
Xiaohui Xie (Irvine, US)
Dong Xu (Columbia, US)
Zohar Yakhini (Santa Clara, US)
Alex Zelikovsky (Atlanta, US)
Michael Q. Zhang (Dallas, US)
ORGANIZING COMMITTEE:
Adrian Horia Dediu (Tarragona)
Carlos Mart?n-Vide (Tarragona, chair)
Bianca Truthe (Magdeburg)
Florentina Lilica Voicu (Tarragona)
SUBMISSIONS:
Authors are invited to submit non-anonymized papers in English presenting
original and unpublished research. Papers should not exceed 12 single-spaced
pages (including eventual appendices) and should be formatted according to
the standard format for Springer Verlag's LNCS series (see
http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0).
Submissions have to be uploaded to:
https://www.easychair.org/conferences/?conf=alcob2014
PUBLICATIONS:
A volume of proceedings published by Springer in the LNCS/LNBI series will
be available by the time of the conference.
A special issue of a major journal will be later published containing
peer-reviewed extended versions of some of the papers contributed to the
conference. Submissions to it will be by invitation.
REGISTRATION:
The period for registration is open from September 21, 2013 to July 1, 2014.
The registration form can be found at:
http://grammars.grlmc.com/alcob2014/Registration.php
DEADLINES:
Paper submission: February 4, 2014 (23:59 CET)
Notification of paper acceptance or rejection: March 15, 2014
Final version of the paper for the LNCS/LNBI proceedings: March 22, 2014
Early registration: March 29, 2014
Late registration: June 17, 2014
Starting of the conference: July 1, 2014
End of the conference: July 3, 2014
Submission to the post-conference journal special issue: October 3, 2014
QUESTIONS AND FURTHER INFORMATION:
florentinalilica.voicu@urv.cat
POSTAL ADDRESS:
AlCoB 2014
Research Group on Mathematical Linguistics (GRLMC)
Rovira i Virgili University
Av. Catalunya, 35
43002 Tarragona, Spain
Phone: +34 977 559543
Fax: +34 977 558386
ACKNOWLEDGEMENTS:
Departament d?Economia i Coneixement, Generalitat de Catalunya
Universitat Rovira i Virgili
------------------------------
Message: 2
Date: Mon, 11 Nov 2013 13:11:10 +0100
From: Reinhard Diestel <R.Diestel@math.uni-hamburg.de>
To: DMANET@zpr.uni-koeln.de
Subject: [DMANET] New exchange platform for Graph Theory
Message-ID: <EFF5720D-BDAD-42E5-8A82-871CB4A55DD5@math.uni-hamburg.de>
Content-Type: text/plain; charset=us-ascii
The free Web edition of my book has migrated to a new platform hosted by "Flooved". It now offers - in addition to the main text - an exchange forum for discussions, questions/answers and so on. Please change your bookmarks to
http://diestel-graph-theory.com/basic.html
for the relevant links, which I'll try to keep up-to-date even when the Flooved URLs change.
Please encourage your students to try it out. I'm planning to monitor the posts loosely and occasionally reply too, especially should there be passages that readers mark as difficult to understand.
If you have lecture notes of your own which you'd like to post there, just get in touch with the Flooved people directly; they're very friendly and eager to make their forum a success. They also offer to set up user groups where students of a particular course can post to each other, just within that course.
Reinhard Diestel
------------------------------
Message: 3
Date: Mon, 11 Nov 2013 13:24:54 +0000
From: Dirk Sudholt <d.sudholt@sheffield.ac.uk>
To: dmanet@zpr.uni-koeln.de
Subject: [DMANET] PhD Scholarship and Postdoc position on Theory of
Evolutionary Computation
Message-ID: <5280DAA6.7080709@sheffield.ac.uk>
Content-Type: text/plain; charset=UTF-8; format=flowed
The Department of Computer Science at the University of Sheffield is
looking for outstanding candidates for a PhD studentship and a Postdoc
position on the Theory of Evolutionary Computation and other
Bio-Inspired Algorithms, with close links to Population Genetics.
*******************************************************************************
PHD STUDENTSHIP ON THEORY OF BIO-INSPIRED COMPUTATION
The Department of Computer Science at the University of Sheffield is
offering a fully funded 3 year PhD studentship on theoretical
foundations of Bio-Inspired Computation.
Bio-inspired algorithms include general-purpose metaheuristics like
evolutionary algorithms, ant colony optimisation and particle swarm
optimisation. The idea is to mimic powerful mechanisms from nature, such
as the natural evolution of species or the collective intelligence of a
swarm of animals, and to apply these mechanisms for solving complex
optimisation problems. Bio-inspired algorithms have been applied to a
broad range of problems in various disciplines with remarkable success.
They are particularly useful in settings where no knowledge on the
problem is available (black-box optimisation) and evaluating candidate
solutions is the only means of learning about the problem in hand.
However, the reasons behind their success are often elusive: their
performance often depends crucially, and unpredictably, on design
choices and parameters. This lack of understanding represents a major
obstacle for the uptake and usage of bio-inspired algorithms and for
developing more effective variants thereof.
In recent years theoretical analyses have emerged that provide such an
understanding through studying the performance of bio-inspired
algorithms. They rigorously estimate the expected time until such an
algorithm finds a satisfactory solution for various optimisation
problems; a vital stepping stone towards designing more efficient
bio-inspired algorithms. Analyses use mathematical techniques from the
analysis of randomised algorithms, probability theory and computational
complexity. The results allow for insights into the working principles
of bio-inspired metaheuristics, enable the assessment of parameter
choices and design aspects, and contribute to the design of more
powerful algorithms.
This studentship offers a valuable opportunity to work within this very
active, challenging, and exciting field at the intersection of
computational complexity and bio-inspired computation. In addition,
candidates may contribute to the upcoming SAGE project (Speed of
Adaptation in Population Genetics and Evolutionary Computation,
http://www.project-sage.eu), an ambitious interdisciplinary project
funded by the EU's Future and Emerging Technologies scheme. SAGE aims at
bringing together Population Genetics and Evolutionary Computation to
develop a unified theory describing the speed of adaptation in both
biological and artificial evolution.
Applicants should have, or expect to achieve, a minimum of an
upper-second-class Honours degree (2.1 or above) or a Master?s degree in
Computer Science, Mathematics, or related disciplines (or equivalent).
The project is mathematically challenging. Expertise with computational
complexity, probability theory and bio-inspired computation is
desirable. Good analytical thinking and an interest in these areas are
essential.
The award covers UK/EU tuition fees and a stipend at the standard UK
research rate of ?13,726 per annum.
UK applicants and EU applicants are eligible for a full scholarship
award. International non-EU applicants cannot be funded and are not
eligible to apply.
Applicants need to apply before December 15, 2013 using the online
application form at:
http://www.shef.ac.uk/postgraduate/research/apply
Please send informal enquiries to Dirk Sudholt, d.sudholt@sheffield.ac.uk
******************************************************************************
RESEARCH ASSOCIATE IN EVOLUTIONARY COMPUTATION AND POPULATION GENETICS
A Research Associate position is available to work on a unified
quantitative theory of evolution that describes the efficiency of
evolution in both natural systems and evolutionary algorithms. The
position is part of SAGE (Speed of Adaptation in Population Genetics and
Evolutionary Algorithms, see http://www.project-sage.eu/ ), a new
European project in the Future and Emerging Technologies scheme. It is
based in the Computational Biology Group in the Department of Computer
Science, and reports to Dr Dirk Sudholt.
SAGE is a joint effort between four European research institutions -
University of Nottingham, University of Sheffield, Friedrich Schiller
University Jena, and IST Austria - to develop world-leading research at
the interface between Population Genetics and Computer Science.
Specifically, SAGE aims at bringing together these two research fields
to develop a unified quantitative theory that describes how quickly
populations adapt to evolve high-fitness individuals in both natural and
artificial evolution. Our goal is to reveal how this efficiency is
fundamentally determined by evolutionary and environmental parameters,
and how these parameters can be tuned to use evolution most effectively
in applications ranging from evolutionary algorithms to experimental
evolution and synthetic biology. The post involves close collaboration
with colleagues from different disciplines, in particular computer
scientists in Sheffield, Nottingham, and Jena, and theoretical
population biologists in the Barton group at IST Austria.
Applications are invited from highly skilled researchers in Computer
Science, Mathematics, Physics, Theoretical Biology or related areas (at
the interface between computer science and biology). A good
understanding of evolutionary computation and/or population genetics
will be an advantage. In addition, strong mathematical and analytical
skills are essential. The applicants must have (or be very close to
completing) a PhD in Computer Science, Biology, Mathematics, Physics or
related disciplines.
The post offers a salary in the range of ?28,685 - ?36,298 per annum. It
is available from January 2014, for a period of 36 months.
Further details and an online application form are available from
http://www.dcs.shef.ac.uk/~dirk/sage-ad.html
Applicants need to apply through the above online system before November
28, 2013.
Please send informal enquiries to Dirk Sudholt, d.sudholt@sheffield.ac.uk
------------------------------
Message: 4
Date: Mon, 11 Nov 2013 14:00:10 +0000
From: Gregory Sorkin <G.B.Sorkin@lse.ac.uk>
To: dmanet@zpr.uni-koeln.de
Subject: [DMANET] PhD study at the London School of Economics in
Management Science (Operations Research / Algorithms, Combinatorics,
and Optimization)
Message-ID: <5280E2EA.3000600@lse.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
The Management Science Group at the London School of Economics has
openings for PhD students. Applicants will automatically be considered
for funding covering fees and paying ?18,000/year (approximately 21,500
Euro or $28,800) for 4 years. The award of these scholarships is
competitive across LSE based on academic performance (typically in an
MSc or equivalent) and suitability of the proposed research.
Specifically, Gregory Sorkin, Richard Steinberg, Laszlo Vegh, and
Giacomo Zambelli are seeking PhD students with a strong mathematical
background and interest in algorithms, combinatorics, discrete
optimization, auctions and mechanism design, and related areas. For
further information about us please see
http://www.lse.ac.uk/management/people/academic-staff/ms.aspx
Prospective applicants are encouraged to contact Prof. Sorkin at
g.b.sorkin@lse.ac.uk by early December 2013 to discuss their
qualifications and research interests before submitting a formal
application. Application procedures may be found at
http://www.lse.ac.uk/study/graduate/enquirer/howToApply/home.aspx Note
that GRE or GMAT results are required.
Ideally, the full application should be submitted by December 13, 2013
to allow time for full consideration by LSE's first funding deadline.
Please access the attached hyperlink for an important electronic communications disclaimer: http://lse.ac.uk/emailDisclaimer
------------------------------
Message: 5
Date: Mon, 11 Nov 2013 17:03:49 +0000 (GMT)
From: S Barry Cooper <pmt6sbc@maths.leeds.ac.uk>
To: dmanet@zpr.uni-koeln.de
Subject: [DMANET] Algebra and Mathematical Logic: Theory and
Applications, Kazan, June 2-6, 2014 - preliminary announcement
Message-ID: <alpine.GSO.1.10.1311111702280.23490@amsta>
Content-Type: TEXT/PLAIN; charset=US-ASCII
International Conference
<<Algebra and Mathematical Logic: Theory and Applications>>,
Kazan, June 2-6, 2014
INFORMATION LETTER No.1
Kazan Federal University and Tatarstan Republic Academy of Science
organize an International Conference "Algebra and Mathematical Logic:
Theory and Applications" dedicated to 80-th anniversary of Department
of Algebra of Kazan University and to 70-th anniversary of Professor
M.M. Arslanov.
The meeting will be held in Kazan (Russia), June 2-6, 2014. The main
topics of the conference include (but are not limited to) Lie
Algebras, Group Theory, Ring Theory, Algebraic Geometry, Universal
Algebra, Model Theory, Mathematical Logic, Computability Theory,
Algebraic and Logic Methods in Computer Science.
The Program Committee of the conference consists of academician Yu. L.
Ershov - Chairman, I.Sh. Kalimullin (Kazan) - Vice-chairman, Chairman
of the Organizing ?ommittee, A.N. Frolov (Kazan) - Secretary of the
conference, Yu.A. Alpin (Kazan), K. Ambos-Spies (Heidelberg, Germany),
M.M. Arslanov (Kazan), V.A. Artamonov (Moscow), S.B. Cooper (Leeds,
UK), S.S. Goncharov (Novosibirsk), C. Jockusch (Urbana-Champaign,
USA), N.G. Khisamiev (Ust-Kamenogorsk, Kazakhstan), B. Khoussainov
(Auckland, New Zealand), J. Knight (South Bend, USA), M.I. Kuznetsov
(Nizhny Novgorod), V.N. Latyshev (Moscow), S. Lempp (Madison, USA),
V.M. Levchuk (Krasnojarsk), A.A. Makhnev (Ekaterinburg), V.D. Mazurov
(Novosibirsk), A. Montalban (Berkeley, USA), R.Sh. Omanadze (Tbilisi,
Georgia), R.A. Shore (Ithaca, USA), S.M. Skryabin (Kazan), R.I. Soare
(Chicago, USA), S.N. Tronin (Kazan), S.V. Vostokov (St. Petersburg),
Y. Yang (Singapore, Singapore).
Invited speakers (on October 20, 2013, the list is updating): K.
Ambos-Spies (Heidelberg University, Germany), V.A. Artamonov (Moscow
State University), S.B. Cooper (Leeds Universtity, UK), Yu.L. Ershov
(Sobolev Institute of Mathematics), A.N. Frolov (Kazan Federal
University), S.S. Goncharov (Sobolev Institute of Mathematics), I.Sh.
Kalimullin (Kazan Federal University), N.G. Khisamiev (East Kazakhstan
Technical State University, Kazakhstan),
B. Khoussainov (University of Auckland, New Zealand), J. Knight
(University of Notre Dame, USA), V.N. Latyshev (Moscow State
University, S. Lempp (University of Wisconsin, USA), R.Sh. Omanadze
(Tbilisi State University, Georgia), Y. Yang (National University of
Singapore, Singapore).
The scientific program of the conference includes invited plenary
lectures and contributed talks.
The official webpage of the conference: http://www.algmathlog14.kpfu.ru
English version: http://www.kpfu.ru/main_page?p_sub=25931
All necessary information can be found at this webpage.
To participate at the conference you need proceed the registration
(see "Registration" at the webpage).
All your questions you may address to the secretary of the conference
e-mail: algmathlog14@kpfu.ru - Secretary of the conference Frolov Andrey
phone: (843) 233-70-39.
Important dates:
Deadline for submissions of abstracts: March 1, 2014
Notification to authors: March 10, 2014
Conference: June 2 - 6, 2014
After the conference (on June 7) an excursion to the ancient city
Bolghar (Volga Bulgaria) will be organized.
The Organizing Committee
------------------------------
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