I quite to pursue my academic dream, because I failed to obtain a permanent academic job in 7 years after my Ph.D.

I found an engineering job, in a small company which develops power electronic related products. I need to recall my knowledge of undergraduate to fit the work.

Bye, with a little bit regrets, my academic dream.

Good luck to those post-doc who are still fighting for a permanent job.

Our paper on biological clock was cited, more precisely mentioned, by a Nature article: A synchronized quorum of genetic clocks. It appeared in the modeling part of Supplementary information:

There has been much work on modeling asynchronous, oscillating cells coming into synchrony in the context of synthetic biology (McMillen et al. (2002); Garcia-Ojalvo et al. (2004)), though less attention has been focused on gene networks that do not oscillate in individual cells but oscillate collectively (Ma and Yoshikawa (2009)).

Spatiotemporal pattern in somitogenesis: A non-Turing scenario with wave propagation

Phys. Rev. E 80, 021906 (2009) [7 pages]

Hiroki Nagahara, Yue Ma, Yoshiko Takenaka, Ryoichiro Kageyama, and Kenichi Yoshikawa

ABSTRACT

Living organisms maintain their lives under far-from-equilibrium conditions by creating a rich variety of spatiotemporal structures in a self-organized manner, such as temporal rhythms, switching phenomena, and development of the body. In this paper, we focus on the dynamical process of morphogens in somitogenesis in mice where propagation of the gene expression level plays an essential role in creating the spatially periodic patterns of the vertebral columns. We present a simple discrete reaction-diffusion model which includes neighboring interaction through an activator, but not diffusion of an inhibitor. We can produce stationary periodic patterns by introducing the effect of spatial discreteness to the field. Based on the present model, we discuss the underlying physical principles that are independent of the details of biomolecular reactions. We also discuss the framework of spatial discreteness based on the reaction-diffusion model in relation to a cellular array, by comparison with an actual experimental observation.

Get the PDF file

Finally, my first paper at Kyoto got published, online. I made a related site for supplying animations.

Phys. Rev. E 79, 046217 (2009) [11 pages]

Self-sustained collective oscillation generated in an array of nonoscillatory cells

Yue Ma and Kenichi Yoshikawa

Spatio-Temporal Order Project, ICORP, Japan Science and Technology Agency (JST), Tokyo 102–0075, Japan
and Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan

Oscillations are ubiquitous phenomena in biological systems. Conventional models of biological periodic oscillations usually invoke interconnecting transcriptional feedback loops. Some specific proteins function as transcription factors, which in turn negatively regulate the expression of the genes that encode these “clock proteins.” These loops may lead to rhythmic changes in gene expression in a cell. In the case of multicellular tissue, collective oscillation is often due to the synchronization of these cells, which manifest themselves as autonomous oscillators. In contrast, we propose here a different scenario for the occurrence of collective oscillation in a group of nonoscillatory cells. Neither periodic external stimulation nor pacemaker cells with intrinsically oscillator are included in the present system. By adopting a spatially inhomogeneous active factor, we observe and analyze a coupling-induced oscillation, inherent to the phenomenon of wave propagation due to intracellular communication.

Nonlinearity 21 (2008) T131–T147
doi:10.1088/0951-7715/21/8/T03

OPEN PROBLEM : Some nonlinear challenges in biology

Francesco Mosconi, Thomas Julou, Nicolas Desprat, Deepak Kumar
Sinha, Jean-Franc¸ ois Allemand, Vincent Croquette and David Bensimon

ABSTRACT

Driven by a deluge of data, biology is undergoing a transition to a more quantitative science. Making sense of the data, building new models, asking the right questions and designing smart experiments to answer them are becoming ever more relevant. In this endeavour, nonlinear approaches can play a fundamental role. The biochemical reactions that underlie life are very often nonlinear. The functional features exhibited by biological systems at all levels (from the activity of an enzyme to the organization of a colony of ants, via the development of an organism or a functional module like the one responsible for chemotaxis in bacteria) are dynamically robust. They are often unaffected by
order of magnitude variations in the dynamical parameters, in the number or concentrations of actors (molecules, cells, organisms) or external inputs (food, temperature, pH, etc). This type of structural robustness is also a common feature of nonlinear systems, exemplified by the fundamental role played by dynamical fixed points and attractors and by the use of generic equations (logistic map, Fisher–Kolmogorov equation, the Stefan problem, etc.) in the study of a plethora of nonlinear phenomena. However, biological systems differ from these examples in two important ways: the intrinsic stochasticity arising from the often very small number of actors and the role played by evolution. On an evolutionary time scale, nothing in biology is frozen. The systems observed today have evolved from solutions adopted in the past and they will have to adapt in response to future conditions. The evolvability of biological system uniquely characterizes them and is central to biology. As the great biologist T Dobzhansky once wrote: ‘nothing in biology makes sense except in the light of evolution’.

Ten Simple Rules for Getting Published
Philip E. Bourne

Citation: Bourne PE (2005) Ten Simple Rules for Getting Published . PLoS Comput Biol 1(5): e57 doi:10.1371/journal.pcbi.0010057

Published: October 28, 2005

Copyright: © 2005 Philip E. Bourne. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

Philip E. Bourne is Editor-in-Chief of PLoS Computational Biology. E-mail: bourne@sdsc.edu

The student council (http://www.iscbsc.org/) of the International Society for Computational Biology asked me to present my thoughts on getting published in the field of computational biology at the Intelligent Systems in Molecular Biology conference held in Detroit in late June of 2005. Close to 200 bright young souls (and a few not so young) crammed into a small room for what proved to be a wonderful interchange among a group of whom approximately one-half had yet to publish their first paper. The advice I gave that day I have modified and present as ten rules for getting published.

Rule 1: Read many papers, and learn from both the good and the bad work of others.
It is never too early to become a critic. Journal clubs, where you critique a paper as a group, are excellent for having this kind of dialogue. Reading at least two papers a day in detail (not just in your area of research) and thinking about their quality will also help. Being well read has another potential major benefit—it facilitates a more objective view of one’s own work. It is too easy after many late nights spent in front of a computer screen and/or laboratory bench to convince yourself that your work is the best invention since sliced bread. More than likely it is not, and your mentor is prone to falling into the same trap, hence rule 2.

Rule 2: The more objective you can be about your work, the better that work will ultimately become.
Alas, some scientists will never be objective about their own work, and will never make the best scientists—learn objectivity early, the editors and reviewers have.

Rule 3: Good editors and reviewers will be objective about your work.
The quality of the editorial board is an early indicator of the review process. Look at the masthead of the journal in which you plan to publish. Outstanding editors demand and get outstanding reviews. Put your energy into improving the quality of the manuscript before submission. Ideally, the reviews will improve your paper. But they will not get to imparting that advice if there are fundamental flaws.

Rule 4: If you do not write well in the English language, take lessons early; it will be invaluable later.
This is not just about grammar, but more importantly comprehension. The best papers are those in which complex ideas are expressed in a way that those who are less than immersed in the field can understand. Have you noticed that the most renowned scientists often give the most logical and simply stated yet stimulating lectures? This extends to their written work as well. Note that writing clearly is valuable, even if your ultimate career does not hinge on producing good scientific papers in English language journals. Submitted papers that are not clearly written in good English, unless the science is truly outstanding, are often rejected or at best slow to publish since they require extensive copyediting.

Rule 5: Learn to live with rejection.
A failure to be objective can make rejection harder to take, and you will be rejected. Scientific careers are full of rejection, even for the best scientists. The correct response to a paper being rejected or requiring major revision is to listen to the reviewers and respond in an objective, not subjective, manner. Reviews reflect how your paper is being judged—learn to live with it. If reviewers are unanimous about the poor quality of the paper, move on—in virtually all cases, they are right. If they request a major revision, do it and address every point they raise both in your cover letter and through obvious revisions to the text. Multiple rounds of revision are painful for all those concerned and slow the publishing process.

Rule 6: The ingredients of good science are obvious—novelty of research topic, comprehensive coverage of the relevant literature, good data, good analysis including strong statistical support, and a thought-provoking discussion. The ingredients of good science reporting are obvious—good organization, the appropriate use of tables and figures, the right length, writing to the intended audience—do not ignore the obvious.
Be objective about these ingredients when you review the first draft, and do not rely on your mentor. Get a candid opinion by having the paper read by colleagues without a vested interest in the work, including those not directly involved in the topic area.

Rule 7: Start writing the paper the day you have the idea of what questions to pursue.
Some would argue that this places too much emphasis on publishing, but it could also be argued that it helps define scope and facilitates hypothesis-driven science. The temptation of novice authors is to try to include everything they know in a paper. Your thesis is/was your kitchen sink. Your papers should be concise, and impart as much information as possible in the least number of words. Be familiar with the guide to authors and follow it, the editors and reviewers do. Maintain a good bibliographic database as you go, and read the papers in it.

Rule 8: Become a reviewer early in your career.
Reviewing other papers will help you write better papers. To start, work with your mentors; have them give you papers they are reviewing and do the first cut at the review (most mentors will be happy to do this). Then, go through the final review that gets sent in by your mentor, and where allowed, as is true of this journal, look at the reviews others have written. This will provide an important perspective on the quality of your reviews and, hopefully, allow you to see your own work in a more objective way. You will also come to understand the review process and the quality of reviews, which is an important ingredient in deciding where to send your paper.

Rule 9: Decide early on where to try to publish your paper.
This will define the form and level of detail and assumed novelty of the work you are doing. Many journals have a presubmission enquiry system available—use it. Even before the paper is written, get a sense of the novelty of the work, and whether a specific journal will be interested.

Rule 10: Quality is everything.
It is better to publish one paper in a quality journal than multiple papers in lesser journals. Increasingly, it is harder to hide the impact of your papers; tools like Google Scholar and the ISI Web of Science are being used by tenure committees and employers to define metrics for the quality of your work. It used to be that just the journal name was used as a metric. In the digital world, everyone knows if a paper has little impact. Try to publish in journals that have high impact factors; chances are your paper will have high impact, too, if accepted.

When you are long gone, your scientific legacy is, in large part, the literature you left behind and the impact it represents. I hope these ten simple rules can help you leave behind something future generations of scientists will admire.

– From Nature News in Brief — Nature 449, 271 (20 September 2007)

Japan has selected its five World Premier International Research Centers (WPIs), a group of institutes that will share US$70 million per year for up to ten years (see Nature 447, 362–363; 2007).

A central goal of the WPI initiative is to create world-leading research organizations by attracting foreign scientists and collaborating with foreign institutions. For instance, the National Institute for Materials Science in Tsukuba, named as a WPI, aims to make materials for sustainable development through a new technology called nanoarchitectonics. It already has collaborators lined up in the United States, South Korea, China and the Czech Republic.

But there were few surprises among the chosen five, or in the fact that Japan’s most prestigious national universities — Tokyo, Kyoto, Osaka and Tohoku — each has one designated WPI.

NEWS OF THE WEEK at Science 7 September 2007, Vol. 317. no. 5843, p. 1307

by Dennis Normile

New programs to lure foreign scientists and more funding for young researchers highlight next year’s budget proposal from Japan’s Ministry of Education. The 2008 request from the ministry, which funds the bulk of Japanese academic science, fleshes out the “Innovation 25″ strategy announced last year by Prime Minister Shinzo Abe to grow the economy through increased spending on science and technology (Science, 13 April, p. 186).

Despite recent efforts, Japan’s scientific institutions have attracted only limited interest from abroad and few non-Japanese researchers. But this month, the ministry expects to announce the winners of a new initiative that it hopes will address both problems. The five World Premier International Research Centers will each receive between $40 million and $170 million over the next decade in return for conducting their business in English and recruiting 30% of their research staff, and up to 20% of their principal investigators, from overseas. The ministry is seeking $80 million next year to launch the centers, which Hiroshi Ikukawa, director of strategic programs for the ministry, hopes will build reputations within their field to rival the likes of the U.K.’s Laboratory of Molecular Biology in Cambridge and MIT’s Media Lab.

The government’s Innovation 25 plan also aims to increase research opportunities for young scientists. Accordingly, the ministry’s budget request includes a 40% increase, to $351 million, for peer-reviewed grants to those in the first decade of their career. It also contains a 45% jump in funding, to $106 million, for a clutch of programs to promote international cooperation by sending young Japanese scientists abroad, bringing foreign scientists of all levels to Japan as visiting scholars, and strengthening ties with Asia and Africa. The ministry’s overall portfolio of competitively reviewed grants would grow by 22%, to $3.9 billion.

Big-ticket international projects would also benefit if the ministry’s request is approved. Japan’s contribution to the International Thermonuclear Experimental Reactor, under construction in Cadarache, France, would double, to $106 million. Spending on ocean drilling would increase 60%, to $159 million. And Japan’s contribution to the Atacama Large Millimeter/Submillimeter Array (ALMA), a joint Japanese, European, and U.S. radio astronomy facility in the Chilean Andes, would jump 27%, to $37 million. Shoken Miyama, director general of the National Astronomical Observatory of Japan, says the additional funding will help Japan complete work on its 16 antennas in time for the scheduled start of ALMA observations in 2012.

The 2008 request will be reviewed by the Council for Science and Technology Policy, which Miyama says “understands the value of basic research.” The final hurdle, the Ministry of Finance, will likely pose a bigger challenge, says Miyama. “We don’t know if the ministry will approve these requests or not.”
If recent history is any guide, overall prospects are not good. Last year, the ministry initially sought a 20% increase for science and ended up with a tiny 0.4% boost, although several individual initiatives were spared. This year’s requested increase for science, says Kazuo Todani, the education ministry’s budget chief, would add more than 20% to this year’s $20.1 billion in spending. The budget will be finalized by the end of the year and take effect on 1 April 2008.

The IWCSN2007 — International Workshop on Complex Systems and Networks 2007 — will be held in Guilin, one of China’s most picturesque cities, between July 19 to 21, 2007.

The 2007 International Conference of Systems Biology and Bioengineering (ICSBB 2007)

2-4 July, 2007, London, U.K.

http://www.iaeng.org/WCE2007/ICSBB2007.html

The conference ICSBB’07 is held under the World Congress on Engineering
2007. The WCE 2007 is organized by the International Association of
Engineers (IAENG), a non-profit international association for the
engineers and the computer scientists. Our congress committees have
been formed with over two hundred and eighty committee members who are
mainly research center heads, faculty deans, department heads,
professors, and research scientists from different universities like
Cambridge, MIT and Oxford etc.

The conference proceedings will be published by IAENG (ISBN:
978-988-98671-5-7) in hardcopy. The full-text congress proceeding will
be indexed in major database indexes so that it can be assessed easily.
The Technology Research Databases (TRD) of CSA (Cambridge Scientific
Abstracts), DBLP and Computer Science Bibliographies have promised to
index the print proceeding in advance of its publication. And after the
publication of the proceeding, print copies will also be sent to
databases like IEE INSPEC, Engineering Index (EI) and ISI Thomson
Scientific for indexing. The accepted papers will also be considered
for publication in the special issues of the journal Engineering
Letters. Some participants may also be invited to submit extended
version of their conference papers for considering as book chapters
(soon after the conference).

The topics include, but not limited to, the following:

Microarray
Pathways and Networks
Computational Biology
Computational Neurobiology
Computational Ecology
Drug Discovery
Proteomics
Development Theory
Metabolism
Cellular Signalling
Evolution
Phylogenetics
Sequence Motifs
Sequence Alignments
Genetics Structure and Regulation
Functional Genomics
Regulatory Modelling
Genetic Variations

Mathematical Biology
Combinators
Data Mining
Data Visualization
Stochastic Modelling
Hidden Markov Model
Ontologies
Sequencing Algorithms
Biocomputing
Bioinformatics
Bioinformatics Projects
Linguistic Methods
Medical Imaging
Image Processing
Signal Processing
Medical Devices
Medical Instrumentation
Health Care Technology
Molecular Bioengineering