New address:(26.06.2013 ~)
Nagasaki Lab
8F #West, IDAC Research Building
Tohoku University
Seiryo-machi 4-1, Aoba-ku, Sendai, Miyagi, JAPAN 980-8575

The 31st In Silico Megabank Research Seminar will be held on Monday, June 10.
This Time, we will be welcoming Dr. Toshitaka Odamaki, Food Science & Technology Institute, Morinaga Milk Industry Co., Ltd. as our lecturer, and he will be speaking on “The Anti-allergic Action by Bifidobacterium Administration.”

・Date/Time: June 10(Mon.) 16:00‐17:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: The Anti-allergic Action by Bifidobacterium Administration
・Lecturer: Toshitaka Odamaki (Food Science & Technology Institute, Morinaga Milk Industry Co., Ltd.)

・Abstract: Bifidobacterium is a kind of dominant bacterial species in the intestine, and various physiologies of it have been reported as “probiotics” as well as lactic acid bacterium. In the seminar, we will share the basic knowledge of bifidobacterium and introduce this focusing on two clinical tests that were confirmed with the anti-allergic action, namely, “Symptom relieving action of cedar pollen allergy for adults” and “Preventative action on the development of infant allergy by administration of bifidobacterium to pregnant women/infants” along with the analysis of the intestinal flora.

・Organizer: Masao Nagasaki

「ChopSticks: High-resolution analysis of homozygous deletions by
exploiting concordant read pairs」
Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki and Satoru Miyano

Detail here

The 30th In Silico Megabank Research Seminar will be held on Friday, May 24. This Time, we will be welcoming Dr. Naoki Osada, National Institute of Genetics as our lecturer, and he will be speaking on “The role of natural selection and genetic drift in the evolution of human genome.”

・Date/Time: May 24(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: The role of natural selection and genetic drift in the evolution of human genome
・Lecturer: Naoki Osada (National Institute of Genetics )

・Abstract: It was the medical importance of deciphering the human genome that served as a great motivator for it. It is considered that study on human genome and its diversity would realize the development of a new therapeutic agent and individualized preventative health-care. On the other hand, human genome is a product of 3.5 billion years of evolution and therefore it would be impossible to understand human genome without discussing evolution. Then, what is it that makes human genome significantly different from other creatures? Based on the population genetics and molecular phylogeny that have been developing so far, it is known that the effect of genetic drift plays a big role in genome evolution in addition to natural selection. In particular, in a group such as the human group that has a long generation time and has experienced a bottle neck in the past, the effect of genetic drift has become strong while the effect of natural selection has become relatively weak. As a result, it can be considered that harmful variations have widespread not only in the group but also throughout the whole groups due to genetic drift. These variations could be a cause of a lot of human diseases. This lecture would discuss the evolution of human genome and its direction, sharing the lecture’s study regarding human or non-human primate genome.

・Organizer: Masao Nagasaki

The Graduate School of Information Sciences has announced the special selective admission upon recommendation for the year 2013.

The admission by recommendation system is introduced for the courses in the first two years of Doctor’s Program. The aim of this system is to proactively accept individuals who are seeking for studies appropriate for our school from among those who are expected to graduate from an advanced course of university or technical college other than Tohoku University in order to promote the mobilization of students among universities and activate the postgraduate education.

【Application qualification and requirements for recommendation】
The applicant must have outstanding academic records as well as personality and be recommended by the academic dean of the applicant’s university or the principal of the applicant’s technical college. In addition, the applicant must affirm that he or she will surely enter our university when they pass the examination, and must fall under either of the following conditions.

・The applicants must be 1) students who are expected to graduate from other university by March 31, 2014, or 2) those who are enrolled in the two years of study in the advanced course at technical college and expected to receive a Bachelor’s degree by March 31, 2014.

【Selection method】
Acceptance to the graduate school is determined in a comprehensive manner by a short essay, an oral examination and application documents.

【Number to be admitted】 10 persons

【Examination Schedule】
*Period of Application: May 27 –May 31, 2013
* Date of the Entrance Examinations: July 1, 2013
*Announcement of successful applicants: July 5, 2013

The 29th In Silico Megabank Research Seminar will be held on Friday, May 17.

This Time, we will be welcoming Mr. Yosuke Hatanaka, i3Systems, Inc. as our lecturer, and he will be speaking on “Medicine3.0: Future of Medicine to be Opened Up by Mobile Computing That Took Mr. Masayoshi Son by Surprise.”

・Date/Time: May 17(Fri.) 16:30‐18:00
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Medicine3.0: Future of Medicine to be Opened Up by Mobile Computing That Took Mr. Masayoshi Son by Surprise.
・Lecturer: Yosuke Hatanaka (i3Systems, Inc.)

・Abstract: Six years have passed since iPhone was born. Smart phones and tablets which were born to utilize cloud computing, that is, the natural supercomputing have become used not only for private or business purposes but also in the various medical welfare fields such as emergency care, home care and disaster medical care and have caused many people change of the irreversible information contact and information experience.
The lecturer joined into Apple after studying genome at The Institute of Medical Sciences, University of Tokyo and was soon promoted as the Director of Japan Market Development. He is now 31 years old and has rich experience of leading the social change of the smart phone. While he was working for Apple, he developed a sense of crisis that Japan did not work on any fundamental problem solving in the face of the super-aged society and that the local government, academia, and media were likely to lose sight of their identity in solving fundamental problems and only claiming for the ad hoc, aimless law development and wasteful budget. Then he started to advocate the next-generation vision of “Medicine 3.0”, in which the medical front itself was to promote the reconstruction of the medical model for medical practice while using the next-generation IT technology that was entrusted for him at that time with iPhone at the center of it.
“Team Medicine 3.0” that was struck by his vision consists of medical professionals such as doctors, nurses, and pharmacists and making significant changes in the various fields such as emergency medical care, home medical care, disaster medical care, and dispensing pharmacy, with the impact of the information revolution such as smart phones and cloud behind them. He continues to spread the know-hows of changes gained from the front lines and insights learned from the members of Team Medicine 3.0 through the dialogue with Masayoshi Son, the president of Soft Bank, and various lectures and writing activities.  When the lecturer intuitively got to know the paradigm shift of the information age, he moved to i3-systems, a venture company in Fukuoka, from Apple in order to start up a new information venture from within Japan. He is also at the helm of the company. His company is working on the promotion to gain sympathy for the vision of “Medicine 3.0” by building “relief goods management system to support smooth supply of relief goods to the victims” jointly with Soft Bank and Sales Force within a few days right after the earthquake using the mobile phone and the cloud, and the company is offering the system for free. In this lecture, he introduces the vision and activity of “Medicine 3.0” and the future of personal computing seen beyond it.

・Organizer: Masao Nagasaki

The 28th In Silico Megabank Research Seminar will be held on Friday, May 10.
This Time, we will be welcoming Mr. Yuji Yoshida, Nara Institute of Science and Technology as our lecturer, and he will be speaking on “Kinase Estimation for Neurite Elongation .”

・Date/Time: May 10(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization       http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Kinase Estimation for Neurite Elongation
・Lecturer: Yuji Yoshida (Nara Institute of Science and Technology)

・Abstract: Kinases and their interactions play important roles in elongating a neurite of a developing neuron. If we can identify the kinases inhibiting neurite elongation, application to regenerative medicine is expected. Currently, it is possible to measure averaged neurite elongation for each of various patterns of kinase inhibition by existing kinase inhibitors. However, data mining is necessary for these measurements to identify the kinases which should be inhibited. It is also unknown which data mining technique is appropriate.

In this study, firstly we applied four standard regression algorithms such as least squares, partial least squares, support vector machines, and random forest, to experimental measurements. We found that random forest regression shows the best performance than the others. Using random forest algorithm, we estimated the kinases which should be inhibited for neurite elongation. As a result, three candidate kinases could be extracted.

・Organizer: Masao Nagasaki

The 27th In Silico Megabank Research Seminar will be held on Friday, April 26.
This Time, we will be welcoming Mr. Katsumi Takahashi, NTT Secure Platform Laboratories as our lecturer, and he will be speaking on “Trend of Privacy Protection Data Mining Technology and its Application to Medical Statistics.”

Privacy Protection Data Mining is a secret calculation technology that conducts data analysis keeping data secret. When analyzing highly confidential data, the analysis can be done without revealing data. NTT Secure Platform Laboratories has demonstrated the secret calculation technology developed with an aim to safely and securely utilize data that need to be handled under strictly controlled conditions including clinical research data for the first time in the world in collaboration with Japan Adult Leukemia Study Group (JALSG). This accomplishment has enabled the statistical analysis with research data being coded, and the performance of which achieved a speed that meets the demand for the practical application.

・Date/Time: April 26(Fri.) 17:00‐19:00
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Trend of Privacy Protection Data Mining Technology and its Application to Medical Statistics
・Lecturer: Katsumi Takahashi (NTT Secure Platform Laboratories)

・Abstract: In this study we will overview the technology to conduct information processing of sensitive data as well as Privacy Protection Data Mining (PPDM) and introduce a research under study in NTT currently. Processing technology taking care of privacy of data is required when utilizing sensitive data. PPDM is the generic name for all these technologies, chief among of them being anonymization and coding. We will give an explanation of these trends and illustrate the applications into medical statistics (secret calculation) that are conducted as a collaborative study by NTT Laboratories.

・Organizer: Soichi Ogishima

The 26th In Silico Megabank Research Seminar will be held on Friday, April 19.
This Time, we will be welcoming Mr. George Chalkidis, Insititute of Medical Science, The University of Tokyo as our lecturer, and he will be speaking on “Information Theoretic Analysis of Long non-coding RNA as a gene expression
control mechanism.”

・Date/Time: April 19(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization
http://www.megabank.tohoku.ac.jp/english/info/access.html

・Title: Information Theoretic Analysis of Long non-coding RNA as a gene expression
control mechanism

・Lecturer: George Chalkidis (Institute of Medical Science, The University of Tokyo)

・Abstract:
An emerging theme from multiple model systems is that lncRNAs form
extensive networks of regulatory mechanisms that control the higher-order
organization of the transcriptome. The importance of these modes of
regulation is underscored by the newly recognized roles of long non-coding
RNAs for proper gene control across all kingdoms of life.
The means by which such lncRNAs regulate transcription are speculated to
encompass a diversity of mechanisms and the identification and
characterization of these mechanisms is an active area of research.
There will be 30-50 RNA-seq and TSS-seq data samples from human cultured
cells from various cell lines and various conditions. The objective will be
to discover potential control mechanisms and model them from small, noisy
samples. The Minimum Description Length Principle (MDL) together with the
maximal information coefficient (MIC) are particularly suited for that
task, because MDL shows excellent non- asymptotical performance in terms of
learning the statistics of finite size context sources from finite length
training data and thus enables the de-noising and correct model
identification even from small sample sizes. Furthermore, MIC is a powerful
novel dependency measure for two-variable relationships of the class of
maximal information-based nonparametric exploration statistics that
captures a wide range of associations both functional and non-functional
and provides a score close to 1 for functional and non-functional
relationships and score close to 0 for statistically independent random variables.

・Organizer: Masao Nagasaki

The 25th In Silico Megabank Research Seminar will be held on Friday, March 15.

This Time, we will be welcoming Dr. Makalowski Wojciech Rafal, Univ. Muenster as our lecturer, and he will be speaking on “Natural history of vertebrate globins.”

・Date/Time: March 15(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2^ndFloor), Tohoku Medical Megabank Organization   http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Natural history of vertebrate globins
・Lecturer: Prof. Wojciech Makalowski
(Institute of Bioinformatics, University of Muenster)

・Abstract: Globins are small heme proteins that bind various external ligands, such as oxygen or nitric oxide, and they are found in all kingdoms of life. Vertebrate genomes harbor seven different globin types, including prominent hemoglobin (Hb) and myoglobin (Mb). Tetrameric Hb is present in erythrocytes and transports oxygen via blood to the inner tissues. The monomeric, muscle-specific myoglobin, on the other hand, stores oxygen, enhances the oxygen diffusion to the muscle cells and detoxifies nitric oxide. Five recent additions to vertebrate globin repertoire are cytoglobin (Cygb), neuroglobin (Ngb), globin X (GbX), globin E (GbE) and globin Y (GbY). It has been suggested that the GbE and Mb genes, as well as the GbY and proto-Hb genes, are the paralogous products of tandem gene duplications that occurred early in the evolution of vertebrates. In contrast, Ngb and GbX derive from independent duplication events that occurred before the split of Deuterostomia and Protostomia. To date little is known regarding the functions of the novel globin proteins. I will focus on our recent evolutionary studies of Ngb and GbX in which we demonstrated ancestry of these two globins reaching dating back to origins of metazoans.

・Organizer: Yumi Yamaguchi, Masao Nagasaki