The 42nd In Silico Megabank Research Seminar will be held on Friday, December 13.

This Time, we will be welcoming Dr. Masafumi Nozawa, National Institute of Genetics as our lecturer, and he will be speaking on “A novel approach based on interspecies comparison to trace the evolution of dosage compensation.”

・Date/Time: December 13(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization
・Title: A novel approach based on interspecies comparison to trace the evolution of dosage compensation
・Lecturer: Masafumi Nozawa（Center for Information Biology, National Institute of Genetics）

＊This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: Evolution of sex chromosomes is normally initiated by assembling of sex-determining genes and sexually antagonistic genes into a pair of autosomes. Recombination between proto-X and proto-Y chromosomes derived from this pair is then suppressed, because these genes must be tightly linked to maintain sexes. This promotes the divergence of these chromosomes and makes the authentic X and Y chromosomes. At the same time, the Y chromosome is gradually degenerated due to the accumulation of mutations and transposable elements. When Y-linked genes are inactivated or deleted due to the inefficacy of natural selection, their orthologous X-linked genes become monoallelic (or hemizygous) in males, which results in dosage imbalance between sexes as well as between chromosomes in males. Since this imbalance could potentially be deleterious in the evolution of heteromorphic sex chromosomes, it has been thought that there must be some mechanisms to compensate the imbalance. In this context, the concept of dosage compensation was proposed. Indeed, this concept has widely been accepted in many organisms, such as humans and nematodes. Yet, most of these conclusions are based on the results that gene expression levels are similar between sexes and/or between chromosomes and it remains to be elusive how dosage compensation has evolved. To trace the evolutionary process of dosage compensation, I have compared the gene expression on the so-called neo-X chromosome in Drosophila pseudoobscura with that on the orthologous autosomes in other species. In this presentation, I would like to discuss about the results obtained so far and introduce my future plans.

・Organizer : Yukuto Sato, Masao Nagasaki

Access : http://www.megabank.tohoku.ac.jp/english/info/access.html

The 41st In Silico Megabank Research Seminar will be held on Tuesday, December 10.

This Time, we will be welcoming Dr. Yu Nishiyama, The Institute of Statistical Mathematics as our lecturer, and he will be speaking on “Topic of Bayesian Inference Using Positive Definite Kernel as the Most Recent Kernel Method.”

・Date/Time: December 10 (Tue.) 17:00‐18:30
・Venue: Middle Conference Room (2nd Floor), Building #1, Tohoku University School of Medicine
・Title: Topic of Bayesian Inference Using Positive Definite Kernel as the Most Recent Kernel Method
・Lecturer: Yu Nishiyama ( The Institute of Statistical Mathematics)

＊This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: In recent studies regarding Kernel Method, Bayesian inference using positive definite Kernel (Kernel Bayes’ Rule) is examined. This methodology reasons with a kernel mean setting forth a consistency rate instead of probability distribution. The kernel mean is defined with an average in the feature space rather than regular average of probability distribution.  In this study, we will introduce kernelized version of both “Sum rule” used for marginalization and “Bayes’ rule” producing Bayesian Posterior Distribution known as “Kernel Sum Rule” and “Kernel Bayes’ Rules.” Combination of these two rules results in filtering of state special model and reinforcement learning algorithm. Kernel Bayes’ Rule which is the combined form of probability models performed by the presenters recently is also introduced.

・Organizer : Kaname Kojima, Masao Nagasaki

The 40th In Silico Megabank Research Seminar will be held on Friday, December 6.

This Time, we will be welcoming Dr. Osamu Komori, The Institute of Statistical Mathematics as our lecturer, and he will be speaking on “Discussion of Asymptotic Properties of Generalized t-statistics and Its Application to Actual Data Analysis .”

・Date/Time: December 6(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization

・Title:Discussion of Asymptotic Properties of Generalized t-statistics and Its Application to Actual Data Analysis
・Lecturer: Osamu Komori ( The Institute of Statistical Mathematics)

＊This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: In recent years, search for variable quantities (makers) that are valid for high-dimensional data analysis used at settings such as clinical medicine or various diagnosis of illness has become more and more important. For analysis on high-dimensional continues variable such as data of gene expression levels, often t statistics and c statistics (AUC) are used at the phase narrowing down the variables. In this research, we focus on the t statistics, one of test statistics, and consider the application of t statistics to classification problems while taking account of multivariate linear combination instead of univariate. By considering U Function, a generating function to t statistics, we can discuss generalization of various t statistics. This research revealed close relation among t statistics, c statistics (AUC), Fisher Linear Discriminant, and Kullback-Libler divergence. In addition, the result suggests Lasso type method which L1 penalty is added to generalized t statistics as an example of application of this method to actual data analysis. One feature of this method is that selection of other variables is possible after fixing variables that are recognized as valid beforehand (such as variables that strong relation to risk of development). Its usability is to be examined with simulation and actual data analysis. In addition, we would like to consider applicable statistical method on discrete data such as SNP in the future.

・Organizer: Gen Tamiya, Masao Nagasaki

Access : http://www.megabank.tohoku.ac.jp/english/info/access.html

The 39th In Silico Megabank Research Seminar will be held on Friday, November 15. This Time, we will be welcoming Dr. Jun Ohashi, University of Tsukuba as our lecturer, and he will be speaking on “The specificity of the HLA gene region and HLA-related analysis”.

・Date/Time: November 15(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization
・Title: The specificity of the HLA gene region and HLA-related analysis
・Lecturer: Jun Ohashi（University of Tsukuba）

＊This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: The major function of HLA (Human Leukocyte Antigen) is to present autologus and non-autologus antigen (pathogen) to T cells. Classical HLA molecules have class I molecules and class II molecules, and the HLA gene cluster encoding those HLA molecules is located in short arm region, 6p21.3, of the sixth chromosome.  Characteristics of the HLA gene region include the presentation of the most sophisticated polymorphism in human genome, actual observation of high in linkage disequilibrium for several Mbs, difference in the number of genes by Haplotypes, and existence of polymorphism related to sensitivity toward disorders. In this presentation, the roles of natural selection, which is the key to understand the linkage disequilibrium of HLA gene region, is explained using an example of recent action of positive selection on DPB1*04:01 allyl in Japanese group. Also, we would like to introduce HLA gene-related studies on patients with Plasmodium Falciparum Malaria.

・Organizer: Gen Tamiya, Masao Nagasaki

Access : http://www.megabank.tohoku.ac.jp/english/info/access.html

The 38th In Silico Megabank Research Seminar will be held on Friday, November 8.

This Time, we will be welcoming Dr. Minae Kawashima, JST as our lecturer, and she will be speaking on “NBDC Human Database: Human Data Sharing Guideline and Provision of Private Data. Report on the User Application”.

・Date/Time: November 8(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization
・Title: NBDC Human Database: Human Data Sharing Guideline and Provision of Private Data. Report on the User Application
・Lecturer: Minae Kawashima (Japan Science and Technology Agency (JST))

・Abstract: Life science data, properties of human, such as Next Generation Sequencer and image has become large in volume in accordance with the advancement of analysis techniques. Rules and systems are necessary to arrange and store such data of Next Generation Sequencer and utilize them effectively for the advancement of life science.  Japan Science and Technology Agency (JST) and National Bioscience Database Center (NBDC) created the Platform “NBDC Human Database” for sharing various database regarding human database and have promoted for disclosure of human data with cooperation of and National Institute of Genetics and DNA Data Bank of Japan (DDBJ) in order to share human data and promote its usage while considering the protection of personal information. They have also created and released the “NBDC Human Data Sharing Guideline” and “Security Guideline for handling NBDC Human Data” as operative rules (http://humandbs.biosciencedbc.jp/guidelines). In this article, we introduce the points to share data while complying with Human Data Sharing Guideline and concretely show how to submit application for data provision and data usage as well as required documents for the application.

・Organizer: Gen Tamiya、Masao Nagasaki

Access : http://www.megabank.tohoku.ac.jp/english/info/access.html

The 36th In Silico Megabank Research Seminar will be held on Friday, October 18.
This Time, we will be welcoming Dr. Kana Shimizu, The National Institute of Advanced Industrial Science and Technology as our lecturer, and she will be speaking on “Database Search with Secret （private）Computation” .

・Date/Time: October 18(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: Database Search with Secret （private）Computation – Aim for its Application to Genome Database –
・Lecturer: Kana Shimizu（The National Institute of Advanced Industrial Science and Technology (AIST)）

・Abstract: In recent years the cost of DNA sequencing drastically fell, which enabled acquisition of genome data at individual level. However, the extreme difficulty still lies in the realization of both protecting privacy of genome including personal information and analyzing information with high flexibility. Although extraordinary amount of cost and effort has generated this rich store of data, such balance issue does not allow full utilization of the data at the present state. On the other hand, in the area of the Computer Science, data itself is coded, and secret computation technology is being developed where coded information is analyzed while contents of individual data are not revealed. By this lecture, we would like to introduce database search technology by the secret computation that we have developed and argue about its application to genome database.

・Organizer: Soichi Ogishima

The 35th In Silico Megabank Research Seminar will be held on Wednesday, October 16.
This Time, we will be welcoming Mr. Satoshi Hirata, Criminal Investigation Laboratory, Miyagi Prefectural Police Headquarters as our lecturer, and he will be speaking on “Duties of Criminal Investigation Laboratory: On DNA Identification”.

・Date/Time: October 16, 2013(Wed.) 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: Duties of Criminal Investigation Laboratory: On DNA Identification
・Lecturer: Satoshi Hirata (Criminal Investigation Laboratory, Miyagi Prefectural Police Headquarters )

・Abstract: In recent years, the role of objective evidence utilizing scientific technique such as DNA identification is becoming important because it is getting harder to obtain information from the witness due to the increase of crimes of high anonymity and the collapse of the local communities and because the need for objective evidence is increasing more than before in criminal trials due to the introduction of the citizen judge system. There are quite a few cases, including retrials, in which credibility and probative value of scientific evidence become controversial. Above all, the role of such evidence is particularly important in the serious cases for which the citizen judge system might be considered. The following functions are in charge of criminal investigation: National Research Institute of Police Science set up in the National Police Agency, Criminal Investigation Laboratory and Criminal Identification Department in the Tokyo Metropolitan Police Department and the Prefectural Police Headquarters, and Identification Section in each police station. These organizations are working on the investigation of objective evidence working closely with detectives engaged in the criminal investigation or according to the request by them. Based on these circumstances, I would like to outline the duties of the criminal investigation laboratory, especially about the principles and methods of DNA identification. Finally, I would like to talk about the police measures such as body identification associated with the East Japan great earthquake disaster.

・Organizer: Yukuto Sato, Masao Nagasaki

Prof. Nagasaki will be delivering a lecture at ” Fukuoka International Symposium on Genomics & Epigenomics 2013 – Kyusyu University” (September 10, 2013)

・Date/Time: September 10(Tues.) 10: 05‐10:40
・Venue: Biomedical Research Station 1F Seminar Room 105 and Science Cafe Hospital Campus, Kyushu University
・Title: Towards thousands Japanese whole genome project and its data management and bioinformatics

The 34h Silico Megabank Research Seminar will be held on Friday, August 2.
This Time, we will be welcoming Dr. Yosuke Kawai, Maebashi Institute of Technology as our lecturer, and he will be speaking on “Molecular Evolution of Natural Denatured Protein.”

・Date/Time: August 2(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: Molecular Evolution of Natural Denatured Protein
・Lecturer: Yosuke Kawai (Maebashi Institute of Technology)

・Abstract: There are some proteins that include an irregular region which does not form a fixed structure under a physiological condition. They are called natural denatured proteins. It is predicted that 30% or more of human proteins are natural denatured protein, and many of which are located in a nucleus and associated with transcription control and signal transduction. Some irregular region forms a fixed structure when forming a complex with other proteins, which is considered because the polypeptide chain in an irregular state recognizes the target molecule and both binding and folding occur in a conjugated manner. The molecular recognition mechanism of this natural denatured protein has been attracting attention in recent years as the different paradigm from the molecular recognition mechanism of proteins with a structure. Natural denatured protein is hardly present in a prokaryotic organism, and the molecular recognition through the irregular region is thought to be inherent to a eukaryotic organism. In addition, the amino acid sequence in the irregular region has poor keeping quality and seems to undergo molecular evolution close to neutrally. However, it is not understood as to why such a site came to play an important role in the protein-protein interaction. This presentation will especially focus on the interaction involving the irregular region and introduce findings regarding the relationship between the structure, function, and evolutionary rate of the natural denatured protein that have not been clarified so far.

・Organizer: Masao Nagasaki

The 33rd In Silico Megabank Research Seminar will be held on Friday, July 26.
This Time, we will be welcoming Dr. Kryukov Kirill, National Institute of Genetics as our lecturer, and he will be speaking on “A tool for genomic multiple sequence alignment.”

・Date/Time: July 26(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: MISHIMA – a tool for genomic multiple sequence alignment
・Lecturer: Kryukov Kirill (National Institute of Genetics )
・Abstract: MISHIMA is a multiple DNA sequence alignment method that uses heuristics for quickly finding regions of high similarity between sequences. MISHIMA operates by locating rare DNA fragments shared by multiple sequences and using them as alignment anchors. This technique allows aligning multiple bacterial genomes in short time. Here we present the improved version 2 of MISHIMA aligner. Sensitivity of the aligner has been improved by using only certain positions within the analyzed DNA words. Another improvement concerns the choice of the word length. In the original MISHIMA a fixed user-specified word length was used. Now it is chosen dynamically and automatically during the alignment process. Also MISHIMA can now better handle circular DNA sequences. The improved MISHIMA aligner has been tested on a range of bacterial and fungal genomes.

・Organizer: Masao Nagasaki